------------------------------------------------------------------------ r4756 | pemsley | 2013-09-10 15:31:40 +0100 (Tue, 10 Sep 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Force -O usage for guile compilation. ------------------------------------------------------------------------ r4755 | b.lohkamp | 2013-09-10 13:59:43 +0100 (Tue, 10 Sep 2013) | 1 line Changed paths: M /trunk/build-it-win New python build order for Windows build. ------------------------------------------------------------------------ r4754 | pemsley | 2013-09-10 13:04:41 +0100 (Tue, 10 Sep 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple LD_LIBRARY_PATH changes/fixup. ------------------------------------------------------------------------ r4753 | pemsley | 2013-09-06 13:20:58 +0100 (Fri, 06 Sep 2013) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Better test for gnomecanvas. Remove old command line args for coot configure. ------------------------------------------------------------------------ r4752 | pemsley | 2013-09-06 05:47:49 +0100 (Fri, 06 Sep 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update gmp version (so that the right ABI is built on CentOS 5). ------------------------------------------------------------------------ r4751 | b.lohkamp | 2013-09-05 12:02:25 +0100 (Thu, 05 Sep 2013) | 1 line Changed paths: M /trunk/build-it-win Fix windows ssm install. ------------------------------------------------------------------------ r4749 | b.lohkamp | 2013-09-04 15:20:56 +0100 (Wed, 04 Sep 2013) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/WinCoot_install_masta.nsi M /trunk/windows/wincoot-autobuild-all Update windows build script. Allow rebuld from scratch. ------------------------------------------------------------------------ r4748 | pemsley | 2013-09-03 02:20:34 +0100 (Tue, 03 Sep 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Protection from null pointer for atom spec constructor. ------------------------------------------------------------------------ r4747 | b.lohkamp | 2013-08-26 09:21:04 +0100 (Mon, 26 Aug 2013) | 4 lines Changed paths: M /trunk/build-it-gtk2-simple Allow autobuilding without guile and specific building directory. Bug fixes for autobuild script. ------------------------------------------------------------------------ r4746 | pemsley | 2013-08-25 04:31:27 +0100 (Sun, 25 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo Add server check args to publish. ------------------------------------------------------------------------ r4745 | pemsley | 2013-08-24 12:24:03 +0100 (Sat, 24 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debug merge. ------------------------------------------------------------------------ r4744 | pemsley | 2013-08-22 13:22:53 +0100 (Thu, 22 Aug 2013) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Fix publish syntax. Update libcurl version. ------------------------------------------------------------------------ r4743 | pemsley | 2013-08-21 12:25:31 +0100 (Wed, 21 Aug 2013) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/ligand/ideal-rna.cc M /trunk/macros/mmdb-ssm.m4 M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/coot-align.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Update ssm configure test. Should now fail when ssm include files not found. RNA sequence alignment. ------------------------------------------------------------------------ r4742 | b.lohkamp | 2013-08-20 05:52:28 +0100 (Tue, 20 Aug 2013) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win Update windows build. ssm-1.3, mmdb, dictionary. ------------------------------------------------------------------------ r4741 | b.lohkamp | 2013-08-20 05:49:23 +0100 (Tue, 20 Aug 2013) | 1 line Changed paths: M /trunk/python-tests/04_cootaneer.py Fix pythonic cootaneer test for new standard-residues.pdb. ------------------------------------------------------------------------ r4740 | pemsley | 2013-08-19 11:42:29 +0100 (Mon, 19 Aug 2013) | 2 lines Changed paths: A /trunk/analysis/test-cablam.cc Add missing test-cablam.cc. ------------------------------------------------------------------------ r4739 | pemsley | 2013-08-18 11:08:39 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update mmdb tar server spec. ------------------------------------------------------------------------ r4738 | pemsley | 2013-08-18 11:01:54 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use ssm-1.3. ------------------------------------------------------------------------ r4737 | pemsley | 2013-08-18 10:36:48 +0100 (Sun, 18 Aug 2013) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/nsv.cc M /trunk/src/nsv.hh Allow setting of canvas_pixel limit for the NSV. I don't know why on some hardware/OSs the limit seems different. ------------------------------------------------------------------------ r4736 | pemsley | 2013-08-18 09:54:03 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk M /trunk/macros/mmdb-ssm.m4 M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc Apply r4731 ssm-1.3 interface update from branch release-0.7.x. ------------------------------------------------------------------------ r4735 | pemsley | 2013-08-18 09:34:02 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4734 | pemsley | 2013-08-18 09:33:46 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/analysis/Makefile.am A /trunk/analysis/cablam.cc A /trunk/analysis/cablam.hh Initial implementation of cablam analysis (needs work). ------------------------------------------------------------------------ r4733 | pemsley | 2013-08-18 09:32:35 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh SSE string representation. ------------------------------------------------------------------------ r4732 | pemsley | 2013-08-18 09:31:26 +0100 (Sun, 18 Aug 2013) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Trivial format change. ------------------------------------------------------------------------ r4730 | pemsley | 2013-08-17 10:40:18 +0100 (Sat, 17 Aug 2013) | 5 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/greg-tests/04-cootaneer.scm M /trunk/skeleton/BuildCas.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/standard-residues.pdb Remove MyCMMDBManager (at last), so use GetTMatrix() from the CMMDBManager, not the CMMDBCryst. No longer use MMDBF_IgnoreDuplSeqNum. So standard-residues.pdb needs a fix, as does the cootaneer test pdb file. ------------------------------------------------------------------------ r4729 | pemsley | 2013-08-17 10:36:11 +0100 (Sat, 17 Aug 2013) | 2 lines Changed paths: M /trunk/configure.in Remove gtk2 configure command line arg. ------------------------------------------------------------------------ r4728 | pemsley | 2013-08-17 10:33:23 +0100 (Sat, 17 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add publish (a means to transfer files to web server). ------------------------------------------------------------------------ r4727 | pemsley | 2013-08-13 05:51:03 +0100 (Tue, 13 Aug 2013) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm More info in bug report. ------------------------------------------------------------------------ r4726 | pemsley | 2013-08-12 17:43:17 +0100 (Mon, 12 Aug 2013) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Fix typo in make_environment_bonds_box(). ------------------------------------------------------------------------ r4725 | pemsley | 2013-08-12 16:45:21 +0100 (Mon, 12 Aug 2013) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Protection for atom index in make_symmetry_environment_bonds_box(). ------------------------------------------------------------------------ r4724 | pemsley | 2013-08-12 15:46:18 +0100 (Mon, 12 Aug 2013) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb.cc Add Null model protection. ------------------------------------------------------------------------ r4723 | pemsley | 2013-08-11 05:48:29 +0100 (Sun, 11 Aug 2013) | 2 lines Changed paths: M /trunk/configure.in Add back libpng test to configure. ------------------------------------------------------------------------ r4722 | pemsley | 2013-08-11 05:47:08 +0100 (Sun, 11 Aug 2013) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi apply-lsq-matches doc fix. ------------------------------------------------------------------------ r4721 | pemsley | 2013-08-11 05:46:18 +0100 (Sun, 11 Aug 2013) | 2 lines Changed paths: M /trunk/scheme/coot-lsq.scm Fix typo in fix-match-element. ------------------------------------------------------------------------ r4720 | pemsley | 2013-08-09 13:44:16 +0100 (Fri, 09 Aug 2013) | 2 lines Changed paths: M /trunk/doc/Makefile.am M /trunk/doc/tutorial.tex Small fixes to tutorial (thanks Andrea). ------------------------------------------------------------------------ r4719 | pemsley | 2013-08-09 13:43:18 +0100 (Fri, 09 Aug 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Trivial comment fix. ------------------------------------------------------------------------ r4718 | pemsley | 2013-08-09 13:41:59 +0100 (Fri, 09 Aug 2013) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Add LMB button for crash log. ------------------------------------------------------------------------ r4717 | pemsley | 2013-08-07 16:56:03 +0100 (Wed, 07 Aug 2013) | 2 lines Changed paths: M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix pre/post coordinate transformation when applying local morph shifts. ------------------------------------------------------------------------ r4716 | pemsley | 2013-08-07 16:54:28 +0100 (Wed, 07 Aug 2013) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Stars for unbonded CAs in CA mode. ------------------------------------------------------------------------ r4715 | b.lohkamp | 2013-08-07 16:13:49 +0100 (Wed, 07 Aug 2013) | 4 lines Changed paths: M /trunk/python/extensions.py M /trunk/python/user_define_restraints.py Pythonic menu item for chain morph. Add more pythonic prosmart (external restraints) tools. ------------------------------------------------------------------------ r4714 | pemsley | 2013-08-06 14:07:18 +0100 (Tue, 06 Aug 2013) | 2 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/mini-mol/atom-quads.hh M /trunk/mini-mol/mini-mol.cc M /trunk/src/molecule-class-info-maps.cc Fix bug in minimol-generation used in fit_to_map_by_random_jiggle(). ------------------------------------------------------------------------ r4711 | pemsley | 2013-08-06 11:11:07 +0100 (Tue, 06 Aug 2013) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.7.2.png Add new splashscreen. ------------------------------------------------------------------------ r4710 | pemsley | 2013-08-05 15:41:27 +0100 (Mon, 05 Aug 2013) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Handle upper-case nucleotides also in mutate-nucleotide-range. ------------------------------------------------------------------------ r4709 | pemsley | 2013-08-01 06:17:30 +0100 (Thu, 01 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update extras_place. ------------------------------------------------------------------------ r4708 | pemsley | 2013-08-01 06:16:09 +0100 (Thu, 01 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple More updates to dist_name and dist_ver. ------------------------------------------------------------------------ r4707 | pemsley | 2013-08-01 06:01:40 +0100 (Thu, 01 Aug 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjustments in setting dist_name and dist_ver (needed for RHEL 6 (and others?)). ------------------------------------------------------------------------ r4706 | pemsley | 2013-07-31 22:12:49 +0100 (Wed, 31 Jul 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2 Adjustments in setting dist_name and dist_ver (needed for RHEL 6 (and others?)). ------------------------------------------------------------------------ r4705 | pemsley | 2013-07-30 15:11:41 +0100 (Tue, 30 Jul 2013) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/coot.in Add function to allow scripting of "Find Ligand Here". ------------------------------------------------------------------------ r4704 | pemsley | 2013-07-30 15:08:56 +0100 (Tue, 30 Jul 2013) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm update email address - not used yet. ------------------------------------------------------------------------ r4703 | pemsley | 2013-07-30 15:08:26 +0100 (Tue, 30 Jul 2013) | 2 lines Changed paths: M /trunk/ligand/ligand.cc M /trunk/ligand/wiggly-ligand.cc Trivial formatting. ------------------------------------------------------------------------ r4702 | pemsley | 2013-07-30 15:07:28 +0100 (Tue, 30 Jul 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Shelx AFIT and negative U handling improvements. ------------------------------------------------------------------------ r4701 | pemsley | 2013-07-30 15:06:51 +0100 (Tue, 30 Jul 2013) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Remove plane manipulation debugging. ------------------------------------------------------------------------ r4700 | pemsley | 2013-07-22 04:57:27 +0100 (Mon, 22 Jul 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Refmac dictionary version 5.41. ------------------------------------------------------------------------ r4699 | pemsley | 2013-07-22 03:04:45 +0100 (Mon, 22 Jul 2013) | 2 lines Changed paths: M /trunk/src/graphics-info-render.cc ppmutil.h is in ccp4mg-utils. ------------------------------------------------------------------------ r4698 | pemsley | 2013-07-22 02:30:26 +0100 (Mon, 22 Jul 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Make extras_place=http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies. ------------------------------------------------------------------------ r4697 | pemsley | 2013-07-16 16:32:24 +0100 (Tue, 16 Jul 2013) | 2 lines Changed paths: M /trunk/analysis/Makefile.am Add missing kolmogorov.hh (for make dist). ------------------------------------------------------------------------ r4696 | pemsley | 2013-07-16 16:16:36 +0100 (Tue, 16 Jul 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Move source server to personal/pemsley. ------------------------------------------------------------------------ r4695 | pemsley | 2013-07-16 16:14:28 +0100 (Tue, 16 Jul 2013) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Menu item for chain morph. ------------------------------------------------------------------------ r4694 | pemsley | 2013-07-16 16:14:10 +0100 (Tue, 16 Jul 2013) | 2 lines Changed paths: M /trunk/src/graphics-info-pick.cc Add graphics_draw() after symm chain shift function. ------------------------------------------------------------------------ r4693 | pemsley | 2013-07-16 15:10:13 +0100 (Tue, 16 Jul 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/src/molecule-class-info-refine.cc Use more robust statistics for averaging the rtops when morphing. ------------------------------------------------------------------------ r4692 | b.lohkamp | 2013-07-11 15:25:51 +0100 (Thu, 11 Jul 2013) | 1 line Changed paths: M /trunk/python/redefine_functions.py M /trunk/src/c-interface-ligands-swig.hh M /trunk/src/c-interface-ligands.cc Add pythonic kolmogorov_smirnov and kullback_liebler tests. ------------------------------------------------------------------------ r4691 | pemsley | 2013-07-11 13:07:21 +0100 (Thu, 11 Jul 2013) | 2 lines Changed paths: M /trunk/analysis/Makefile.am A /trunk/analysis/kolmogorov.cc A /trunk/analysis/kolmogorov.hh M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-ligands-swig.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/cc-interface.hh Add kolmogorov_smirnov and kullback_liebler tests. ------------------------------------------------------------------------ r4690 | pemsley | 2013-07-11 12:53:04 +0100 (Thu, 11 Jul 2013) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps-2.cc Add scaling and border for export_map_fragment_with_origin_shift(). ------------------------------------------------------------------------ r4689 | b.lohkamp | 2013-07-11 09:15:26 +0100 (Thu, 11 Jul 2013) | 1 line Changed paths: M /trunk/windows/wincoot-autobuild-all Copy windows build logs after each build attempt. ------------------------------------------------------------------------ r4688 | pemsley | 2013-07-10 19:04:04 +0100 (Wed, 10 Jul 2013) | 4 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/read-sm-cif.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-maps.cc M /trunk/src/c-interface.h A /trunk/src/molecule-class-info-maps-2.cc M /trunk/src/molecule-class-info.h export_map_fragment_with_origin_shift() function added. Rework calc_atom_map internals (more robust now?) const a few exception catches. ------------------------------------------------------------------------ r4687 | pemsley | 2013-07-10 19:00:34 +0100 (Wed, 10 Jul 2013) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.8-pre.png remove transparent pixels. ------------------------------------------------------------------------ r4686 | pemsley | 2013-07-09 08:13:01 +0100 (Tue, 09 Jul 2013) | 2 lines Changed paths: M /trunk/scheme/user-define-restraints.scm Add more prosmart (external restraints) tools. ------------------------------------------------------------------------ r4685 | b.lohkamp | 2013-07-08 15:18:47 +0100 (Mon, 08 Jul 2013) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/wincoot-autobuild-all Update windows build scripts to allow stable release build. ------------------------------------------------------------------------ r4684 | pemsley | 2013-07-07 18:42:11 +0100 (Sun, 07 Jul 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjustment to build-stable logic. ------------------------------------------------------------------------ r4683 | b.lohkamp | 2013-07-07 14:10:09 +0100 (Sun, 07 Jul 2013) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/jligand_gui.py M /trunk/python/refmac.py M /trunk/python/user_define_restraints.py User define bond restraint can stay open for multiple restraints (python). Add Modelling home for symm shift for python Extensions. Start rework on associating sequence gui. Fix bug in views panel (only show one "Play Views"). ------------------------------------------------------------------------ r4682 | b.lohkamp | 2013-07-07 14:07:07 +0100 (Sun, 07 Jul 2013) | 1 line Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Introduce functions to test for protein and nucleotide chain. ------------------------------------------------------------------------ r4681 | b.lohkamp | 2013-07-06 17:50:14 +0100 (Sat, 06 Jul 2013) | 1 line Changed paths: M /trunk/ligand/rotamer.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/molecule-class-info-build.cc Fix include file usage for windows. ------------------------------------------------------------------------ r4680 | pemsley | 2013-07-06 01:33:58 +0100 (Sat, 06 Jul 2013) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/graphics-info-pick.cc Add a Extensions->Modelling home for symm shift. ------------------------------------------------------------------------ r4679 | pemsley | 2013-07-05 18:22:42 +0100 (Fri, 05 Jul 2013) | 2 lines Changed paths: M /trunk/analysis/Makefile.am M /trunk/analysis/bfkurt.cc M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/angles/Makefile.am M /trunk/build/CalphaBuild.hh M /trunk/build/Makefile.am M /trunk/ccp4mg-utils/Makefile.am M /trunk/compat/Makefile.am M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/Makefile.am M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/coot-surface/Makefile.am M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/bonded-pairs.hh M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-h-bonds.hh M /trunk/coot-utils/coot-hole.hh M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-rama.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-tree-extras.cc M /trunk/coot-utils/elastic.cc M /trunk/coot-utils/helix-analysis.hh M /trunk/coot-utils/hole.cc M /trunk/coot-utils/read-sm-cif.cc M /trunk/coot-utils/test-h-bonds.cc M /trunk/coot-utils/test-shelx-reader.cc M /trunk/coot-utils/test-spherical.cc M /trunk/coot-utils/test-utils.cc M /trunk/db-main/Makefile.am M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/density-contour/CIsoSurface.h M /trunk/density-contour/Makefile.am M /trunk/geometry/Makefile.am M /trunk/geometry/chem_mods.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/goograph/Makefile.am M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/high-res/Makefile.am M /trunk/high-res/coot-atom-graph.hh M /trunk/high-res/high-res.cc M /trunk/high-res/high-res.hh M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/ideal/Makefile.am M /trunk/ideal/chirals.cc M /trunk/ideal/coot-compare-residues.cc M /trunk/ideal/mini-rsr.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/regularize-minimol.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/torsion-bonds.cc M /trunk/ideal/with-geometry.cc M /trunk/lbg/Makefile.am M /trunk/lbg/flev-annotations.cc M /trunk/lbg/flev-annotations.hh M /trunk/lbg/lbg.hh M /trunk/lbg/qed-interface.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/cod-types.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/lidia-core/test-cod-atom-types.cc M /trunk/ligand/Makefile.am M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh M /trunk/ligand/base-pairing.cc M /trunk/ligand/base-pairing.hh M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/ligand/dunbrack.cc M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/primitive-chi-angles.cc M /trunk/ligand/primitive-chi-angles.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/torsion-general.hh M /trunk/ligand/wiggly-ligand.cc M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol.cc M /trunk/protein_db/Makefile.am M /trunk/rel-todo M /trunk/sequence-view/Makefile.am M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/BuildCas.h M /trunk/skeleton/Makefile.am M /trunk/skeleton/graphical_skel.cc M /trunk/skeleton/graphical_skel.h M /trunk/src/Makefile.am M /trunk/src/align.cc M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface-maps.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mogul-scripting.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface-sfs.cc M /trunk/src/c-interface-test.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters-gui.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface-mogul.hh M /trunk/src/cc-interface.hh M /trunk/src/cmtz-interface.cc M /trunk/src/command-arg.hh M /trunk/src/command-line.cc M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/coot-hydrogens.cc M /trunk/src/coot-nomenclature.cc M /trunk/src/coot-nomenclature.hh M /trunk/src/coot-render.hh M /trunk/src/coot.i M /trunk/src/density-score-by-residue-src.cc M /trunk/src/dots-representation.hh M /trunk/src/fix-nomenclature.cc M /trunk/src/flev.cc M /trunk/src/generic-display-object.hh M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/get-residue.hh M /trunk/src/gl-matrix.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-network.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc M /trunk/src/graphics-ligand-view.hh M /trunk/src/gtk-manual.cc M /trunk/src/gtk-widget-conversion-utils.cc M /trunk/src/lbg-callbacks-outer.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-kdc.cc M /trunk/src/molecule-class-info-kk.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/nsv.cc M /trunk/src/nsv.hh M /trunk/src/pick.cc M /trunk/src/pick.h M /trunk/src/probe-clash-score.cc M /trunk/src/probe-clash-score.hh M /trunk/src/protein_db-interface.cc M /trunk/src/protein_db-interface.hh M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/restraints-editor.cc M /trunk/src/sdf-internal.hh M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/src/user-mods.cc M /trunk/tw/Makefile.am M /trunk/utils/Makefile.am M /trunk/utils/coot-utils.cc Rearrange include file usage. ------------------------------------------------------------------------ r4678 | pemsley | 2013-07-05 13:35:35 +0100 (Fri, 05 Jul 2013) | 2 lines Changed paths: M /trunk/rel-todo Reset rel-todo for new release. ------------------------------------------------------------------------ r4677 | pemsley | 2013-07-05 13:34:44 +0100 (Fri, 05 Jul 2013) | 3 lines Changed paths: M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/test-spherical.cc M /trunk/dnotes M /trunk/ideal/extra-restraints.cc M /trunk/ligand/helix-placement.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h move_reference_chain_to_symm_chain_position() function added for Randy. Needs a gui. ------------------------------------------------------------------------ r4676 | pemsley | 2013-07-03 16:13:59 +0100 (Wed, 03 Jul 2013) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Check return status of fopen() in cns_file_has_phases_p(). Fixes crash on no read permission mtz file(!). ------------------------------------------------------------------------ r4675 | pemsley | 2013-07-02 15:48:06 +0100 (Tue, 02 Jul 2013) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.8-pre.png Add splash screen png file. ------------------------------------------------------------------------ r4674 | pemsley | 2013-07-02 15:44:03 +0100 (Tue, 02 Jul 2013) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/pixmaps/Makefile.am M /trunk/src/gtk2-interface.c New splash screen for 0.8-pre (thanks Phil). ------------------------------------------------------------------------ r4673 | pemsley | 2013-07-02 12:17:42 +0100 (Tue, 02 Jul 2013) | 2 lines Changed paths: M /trunk/configure.in M /trunk/coot-utils/coot-map-utils.cc Move to 0.8-pre ------------------------------------------------------------------------ r4672 | pemsley | 2013-06-28 15:23:59 +0100 (Fri, 28 Jun 2013) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h Add morph-by-chain. ------------------------------------------------------------------------ r4671 | pemsley | 2013-06-28 15:04:17 +0100 (Fri, 28 Jun 2013) | 3 lines Changed paths: M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Weight rtops for morphing by distance to central residue. Factor out residue selection from morphing function. ------------------------------------------------------------------------ r4670 | pemsley | 2013-06-28 13:05:52 +0100 (Fri, 28 Jun 2013) | 3 lines Changed paths: M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h In morphing, replace residue shifts by quaternion-based RTop averaging of local shifts. ------------------------------------------------------------------------ r4669 | pemsley | 2013-06-27 14:49:56 +0100 (Thu, 27 Jun 2013) | 2 lines Changed paths: M /trunk/src/molecule-class-info-refine.cc Morphing transformation of neighbouring residues now at unity weight. ------------------------------------------------------------------------ r4668 | pemsley | 2013-06-27 14:49:20 +0100 (Thu, 27 Jun 2013) | 2 lines Changed paths: M /trunk/src/c-interface-nucleotides.cc Centre nucleic acid molecule after creation. ------------------------------------------------------------------------ r4667 | pemsley | 2013-06-27 09:04:14 +0100 (Thu, 27 Jun 2013) | 2 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/src/c-interface-build.cc Tweak helix placement by adding an explicit upper limit for density fitting. ------------------------------------------------------------------------ r4666 | pemsley | 2013-06-26 13:39:50 +0100 (Wed, 26 Jun 2013) | 3 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/src/c-interface-build.cc Use helix fudge factor fit fitting strands. Change tube orientation sampling to 5 degrees. ------------------------------------------------------------------------ r4665 | pemsley | 2013-06-26 09:06:12 +0100 (Wed, 26 Jun 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h First bash at morph-all tool. ------------------------------------------------------------------------ r4664 | pemsley | 2013-06-24 10:48:38 +0100 (Mon, 24 Jun 2013) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/doc/tutorial.tex M /trunk/ligand/helix-placement.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add function for jiggle-fitting a molecule. Works mediocrely - room for improvement. ------------------------------------------------------------------------ r4663 | b.lohkamp | 2013-06-22 15:13:42 +0100 (Sat, 22 Jun 2013) | 1 line Changed paths: M /trunk/src/molecule-class-info.h Fix guessing of residue type and element for place_typed_atom_at_pointer. ------------------------------------------------------------------------ r4662 | b.lohkamp | 2013-06-18 16:37:41 +0100 (Tue, 18 Jun 2013) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win Tinker to get correct release version for Windows as well. ------------------------------------------------------------------------ r4661 | pemsley | 2013-06-14 17:09:15 +0100 (Fri, 14 Jun 2013) | 5 lines Changed paths: M /trunk/TODO M /trunk/doc/coot-user-manual.texi M /trunk/ligand/helix-placement.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mogul-scripting.cc M /trunk/src/c-interface-mogul.hh M /trunk/src/c-interface-sequence.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-gui.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h M /trunk/src/positioned-widgets.h NCS related chain code updates (still not ready at user level). Update doc for merge-molecules. mogul_results_process_many() for updating sigmas and z values. Transient and position for difference map peaks dialog. ------------------------------------------------------------------------ r4659 | pemsley | 2013-06-12 13:43:31 +0100 (Wed, 12 Jun 2013) | 3 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/lidia-core/rdkit-interface.cc M /trunk/mini-mol/mini-mol.cc M /trunk/pixmaps/Makefile.am M /trunk/python/extensions.py M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c Release 0.7.1. No news or updates. ------------------------------------------------------------------------ r4658 | pemsley | 2013-06-12 13:41:05 +0100 (Wed, 12 Jun 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple More awk tinkering to get the correct version for release from the server. ------------------------------------------------------------------------ r4657 | pemsley | 2013-06-11 08:10:12 +0100 (Tue, 11 Jun 2013) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.7.1.png Icon for 0.7.1 ------------------------------------------------------------------------ r4656 | b.lohkamp | 2013-06-07 22:13:29 +0100 (Fri, 07 Jun 2013) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/WinCoot_install_masta.nsi M /trunk/windows/wincoot-autobuild-all Update windows build system (e.g. include tests properly, fix installer). ------------------------------------------------------------------------ r4655 | b.lohkamp | 2013-06-06 22:49:31 +0100 (Thu, 06 Jun 2013) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win Change MRC server details for windows buiild. ------------------------------------------------------------------------ r4654 | pemsley | 2013-06-05 19:45:54 +0100 (Wed, 05 Jun 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix the position of the reporting of ending of rsync. ------------------------------------------------------------------------ r4653 | pemsley | 2013-06-05 17:17:19 +0100 (Wed, 05 Jun 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Change python default logic, MRC server details, remove ssh to biop. ------------------------------------------------------------------------ r4652 | pemsley | 2013-06-04 12:10:19 +0100 (Tue, 04 Jun 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Use --includes argument for python-config. ------------------------------------------------------------------------ r4651 | b.lohkamp | 2013-05-23 16:01:58 +0100 (Thu, 23 May 2013) | 1 line Changed paths: M /trunk/python/refmac.py Fix use of swap_map_colours_post_refmac in pythonic run_refmac_by_filename. ------------------------------------------------------------------------ r4650 | pemsley | 2013-05-23 15:46:53 +0100 (Thu, 23 May 2013) | 3 lines Changed paths: M /trunk/src/coot.in Use "$@" for arguments exit with $status. ------------------------------------------------------------------------ r4649 | pemsley | 2013-05-22 13:48:46 +0100 (Wed, 22 May 2013) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Don't accumulate stats for correlation where the calc map is nan. ------------------------------------------------------------------------ r4648 | pemsley | 2013-05-21 12:33:36 +0100 (Tue, 21 May 2013) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/graphics-info-modelling.cc Remove refinement debugging from output. ------------------------------------------------------------------------ r4647 | b.lohkamp | 2013-05-21 09:46:34 +0100 (Tue, 21 May 2013) | 1 line Changed paths: M /trunk/scheme/refmac.scm After refmac pick up new map as refinement map (scheme). ------------------------------------------------------------------------ r4646 | pemsley | 2013-05-17 18:23:11 +0100 (Fri, 17 May 2013) | 2 lines Changed paths: M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lig-build.hh Add delete_bond_between() function. ------------------------------------------------------------------------ r4645 | pemsley | 2013-05-17 15:38:28 +0100 (Fri, 17 May 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Fix $ typo for PYTHON_CONFIG. ------------------------------------------------------------------------ r4644 | pemsley | 2013-05-17 14:57:19 +0100 (Fri, 17 May 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Allow the user to set PYTHON_CONFIG at configure-time. ------------------------------------------------------------------------ r4643 | pemsley | 2013-05-17 12:42:55 +0100 (Fri, 17 May 2013) | 4 lines Changed paths: M /trunk/Makefile.am M /trunk/auxil/sec-str/sec-str-dist-check.hh M /trunk/auxil/vectors/diff-vec.cc M /trunk/configure.in M /trunk/dnotes M /trunk/doc/validation-tutorial.tex A /trunk/pixmaps/Makefile.am Add a Makefile.am for pixmaps so that the files get installed (and more importantly, uninstalled) in a canonical manner. Add mmdb to include file for auxil files (low importance). ------------------------------------------------------------------------ r4642 | pemsley | 2013-05-17 12:21:20 +0100 (Fri, 17 May 2013) | 3 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm M /trunk/scheme/refmac.scm Add some debugging for refmac extra params. Now NOLIGAND seems to work with refmac on pdbe cif downloads. ------------------------------------------------------------------------ r4641 | b.lohkamp | 2013-05-16 08:42:09 +0100 (Thu, 16 May 2013) | 1 line Changed paths: M /trunk/build-it-win Fix glob inclusion in Windows build system. ------------------------------------------------------------------------ r4640 | b.lohkamp | 2013-05-14 15:08:41 +0100 (Tue, 14 May 2013) | 1 line Changed paths: M /trunk/build-it-win Windows build clean install_top_dir before stable build. ------------------------------------------------------------------------ r4639 | b.lohkamp | 2013-05-14 14:42:24 +0100 (Tue, 14 May 2013) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python-tests/01_pdb_mtz.py Add pythonic test for placing typed atoms. Add COOT_BUILD_INFO_STRING for Windows. ------------------------------------------------------------------------ r4638 | pemsley | 2013-05-14 09:51:30 +0100 (Tue, 14 May 2013) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test for placing typed atoms (Harry Greenblatt bug). ------------------------------------------------------------------------ r4637 | pemsley | 2013-05-14 09:44:17 +0100 (Tue, 14 May 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add COOT_BUILD_INFO_STRING. ------------------------------------------------------------------------ r4636 | pemsley | 2013-05-14 09:43:02 +0100 (Tue, 14 May 2013) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/command-line.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Make unused_chain_id() robust (using erase()). Call chain_only_of_type() with the correct argument in add_typed_pointer_atom(). Fixes crash. Don't output builder info if was not set. ------------------------------------------------------------------------ r4635 | pemsley | 2013-05-13 12:35:42 +0100 (Mon, 13 May 2013) | 2 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc Add get_max_z_badness() and stream output operator. ------------------------------------------------------------------------ r4634 | pemsley | 2013-05-13 11:19:22 +0100 (Mon, 13 May 2013) | 3 lines Changed paths: M /trunk/configure.in M /trunk/src/Makefile.am M /trunk/src/command-line.cc Add the ability to set builder info with COOT_BUILD_INFO_STRING. Displayed (if set) by --version-full. ------------------------------------------------------------------------ r4633 | pemsley | 2013-05-03 11:56:37 +0100 (Fri, 03 May 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove SWIG version test (now it is not needed to build source). ------------------------------------------------------------------------ r4632 | pemsley | 2013-05-02 19:10:08 +0100 (Thu, 02 May 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Better diagnostics for goocanvas compile. ------------------------------------------------------------------------ r4631 | b.lohkamp | 2013-05-02 16:54:30 +0100 (Thu, 02 May 2013) | 1 line Changed paths: M /trunk/analysis/Makefile.am M /trunk/bldnotes M /trunk/configure.in M /trunk/coot-utils/Makefile.am M /trunk/db-main/Makefile.am M /trunk/geometry/Makefile.am M /trunk/ideal/Makefile.am M /trunk/lbg/Makefile.am M /trunk/ligand/Makefile.am A /trunk/macros/windows_glob.m4 M /trunk/macros/with-python.m4 M /trunk/src/Makefile.am M /trunk/utils/Makefile.am Fixes for Windows globbing. ------------------------------------------------------------------------ r4630 | pemsley | 2013-05-02 16:43:57 +0100 (Thu, 02 May 2013) | 2 lines Changed paths: M /trunk/src/post-process-coot-wrap-python.sh Add #include to post-processed python wrap code. ------------------------------------------------------------------------ r4629 | b.lohkamp | 2013-05-02 16:09:55 +0100 (Thu, 02 May 2013) | 3 lines Changed paths: M /trunk/python/get_ebi.py New server for file downloading pdb files from the EBI. Add own function to retrieve url content. ------------------------------------------------------------------------ r4628 | b.lohkamp | 2013-05-02 11:04:01 +0100 (Thu, 02 May 2013) | 6 lines Changed paths: M /trunk/python/clear_backup.py M /trunk/python/ncs.py M /trunk/python/prodrg_import.py M /trunk/python/redefine_functions.py Python updates: Fix typo in clear_backups. Works now. Add function update_ncs_ghosts_by_local_sphere. Sbase to ccp4srs rename. ------------------------------------------------------------------------ r4627 | b.lohkamp | 2013-05-02 10:52:16 +0100 (Thu, 02 May 2013) | 1 line Changed paths: M /trunk/src/c-interface-refine.cc Windows jiggery for CAtom. ------------------------------------------------------------------------ r4626 | b.lohkamp | 2013-05-02 10:51:31 +0100 (Thu, 02 May 2013) | 1 line Changed paths: M /trunk/build-it-win Update Windows build to download all from Cambridge. ------------------------------------------------------------------------ r4625 | pemsley | 2013-05-01 12:27:39 +0100 (Wed, 01 May 2013) | 2 lines Changed paths: M /trunk/scheme/ncs.scm Add function update-ncs-ghosts-by-local-sphere. ------------------------------------------------------------------------ r4624 | pemsley | 2013-05-01 12:21:40 +0100 (Wed, 01 May 2013) | 2 lines Changed paths: M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Add glob_files() function. ------------------------------------------------------------------------ r4623 | pemsley | 2013-04-29 15:41:26 +0100 (Mon, 29 Apr 2013) | 2 lines Changed paths: M /trunk/geometry/Makefile.am Fix typo in previous - srs-interface.hh ------------------------------------------------------------------------ r4622 | pemsley | 2013-04-29 15:38:36 +0100 (Mon, 29 Apr 2013) | 2 lines Changed paths: M /trunk/geometry/Makefile.am Add srs-geometry.hh to include_HEADERS. ------------------------------------------------------------------------ r4621 | pemsley | 2013-04-29 15:23:09 +0100 (Mon, 29 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple mmdb version bump 1.25.2 ------------------------------------------------------------------------ r4620 | pemsley | 2013-04-27 17:33:06 +0100 (Sat, 27 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple CXX testing updates (for ubuntu). ------------------------------------------------------------------------ r4619 | pemsley | 2013-04-27 16:23:04 +0100 (Sat, 27 Apr 2013) | 3 lines Changed paths: M /trunk/src/Makefile.am Add to EXTRA_DIST the swig wrap pre files (the intension is that swig is not needed for build clients). ------------------------------------------------------------------------ r4618 | pemsley | 2013-04-26 04:00:36 +0100 (Fri, 26 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple SWIG 1.3.29 is broken no matter what architecture. ------------------------------------------------------------------------ r4617 | pemsley | 2013-04-24 16:21:32 +0100 (Wed, 24 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove ssh copying. ------------------------------------------------------------------------ r4616 | pemsley | 2013-04-24 14:29:27 +0100 (Wed, 24 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Rework (fix typo) for python include directory slimming. ------------------------------------------------------------------------ r4615 | pemsley | 2013-04-22 23:10:49 +0100 (Mon, 22 Apr 2013) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-build.cc Fix up the rotation vector for screen residue rotation. Remove debugging. ------------------------------------------------------------------------ r4614 | pemsley | 2013-04-22 14:19:40 +0100 (Mon, 22 Apr 2013) | 2 lines Changed paths: M /trunk/scheme/get-ebi.scm Add a "." to the extension of Fetched pdb file names. ------------------------------------------------------------------------ r4613 | pemsley | 2013-04-20 02:02:44 +0100 (Sat, 20 Apr 2013) | 2 lines Changed paths: M /trunk/src/Makefile.am Add c-interface-refine.hh to Makefile.am ------------------------------------------------------------------------ r4612 | pemsley | 2013-04-20 01:58:43 +0100 (Sat, 20 Apr 2013) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/rel-todo M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h rotate-residue function added. flip-peptide fall-back (when no next N, CA) shifts backbone O to the other side. ------------------------------------------------------------------------ r4611 | pemsley | 2013-04-20 01:57:05 +0100 (Sat, 20 Apr 2013) | 2 lines Changed paths: M /trunk/scheme/jligand-gui.scm M /trunk/scheme/jligand.scm start jligand with jligand on the command line, don't mess with java stuff. ------------------------------------------------------------------------ r4610 | pemsley | 2013-04-17 20:57:03 +0100 (Wed, 17 Apr 2013) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/gtk2-interface.c Difference map peaks results dialog wider. ------------------------------------------------------------------------ r4609 | pemsley | 2013-04-17 20:52:23 +0100 (Wed, 17 Apr 2013) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4608 | pemsley | 2013-04-17 15:45:20 +0100 (Wed, 17 Apr 2013) | 4 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/src/c-interface-maps.cc M /trunk/src/cmtz-interface.cc M /trunk/src/drag-and-drop.cc M /trunk/src/drag-and-drop.hh M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.cc M /trunk/src/read-cif.c Comp-id for iodine is IOD. drag and drop strings from qtrview. scrollable maps after try_read_cif(). ------------------------------------------------------------------------ r4604 | pemsley | 2013-04-13 18:12:16 +0100 (Sat, 13 Apr 2013) | 3 lines Changed paths: M /trunk/TODO M /trunk/ideal/Makefile.am A /trunk/ideal/mini-rsr.cc (from /trunk/ideal/with-map.cc:4600) D /trunk/ideal/with-map.cc M /trunk/src/c-interface.h Add mini-rsr into the main build. Extend the interface to mini-rsr to allow residues-near-residues. ------------------------------------------------------------------------ r4603 | pemsley | 2013-04-12 14:47:37 +0100 (Fri, 12 Apr 2013) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Build interface, updates to blobs window and symmetry dialogs. ------------------------------------------------------------------------ r4602 | pemsley | 2013-04-12 13:51:49 +0100 (Fri, 12 Apr 2013) | 5 lines Changed paths: M /trunk/configure.in M /trunk/lbg/lbg-search.cc M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-mutate.cc A /trunk/src/c-interface-sequence.cc A /trunk/src/c-interface-sequence.hh M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/coot.i M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/utils/coot-fasta.cc M /trunk/utils/coot-fasta.hh Updates for fasta file reading and sequence assignment. assign_sequences_to_best_matching_chain_from_fasta() function added. Enable CCP4 SRS configuration option. Allow setting of title of main window from the command line. ------------------------------------------------------------------------ r4601 | pemsley | 2013-04-12 13:45:20 +0100 (Fri, 12 Apr 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update python version to 2.7.3 ------------------------------------------------------------------------ r4600 | pemsley | 2013-04-03 15:16:16 +0100 (Wed, 03 Apr 2013) | 4 lines Changed paths: M /trunk/autogen.sh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/torsion-bonds.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-refine.cc A /trunk/src/c-interface-refine.hh M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/probe-clash-score.cc Updates for adding number of trials to add_linked_residue() and multi_residue_torsion_fit() interface. add_regularize_residues() and initial_position_restraints() functions added. ------------------------------------------------------------------------ r4598 | pemsley | 2013-03-25 14:19:59 +0000 (Mon, 25 Mar 2013) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Remove test-rotamer-tables-sql from check targets. ------------------------------------------------------------------------ r4597 | pemsley | 2013-03-25 14:17:43 +0000 (Mon, 25 Mar 2013) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Make the unmodelled blobs results dialog longer (needs a code build). ------------------------------------------------------------------------ r4596 | pemsley | 2013-03-22 17:39:42 +0000 (Fri, 22 Mar 2013) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add a function to set the main window title. ------------------------------------------------------------------------ r4595 | pemsley | 2013-03-16 01:14:59 +0000 (Sat, 16 Mar 2013) | 2 lines Changed paths: M /trunk/ideal/chirals.cc Remove chiral hydrogen debugging. ------------------------------------------------------------------------ r4594 | pemsley | 2013-03-16 01:13:26 +0000 (Sat, 16 Mar 2013) | 3 lines Changed paths: M /trunk/ideal/torsion-bonds.cc In the rand-angle conformer generating code for multi_residue_fit, disfavour trans/gauche switches later on in the trial set. ------------------------------------------------------------------------ r4593 | pemsley | 2013-03-15 17:50:48 +0000 (Fri, 15 Mar 2013) | 3 lines Changed paths: M /trunk/ideal/torsion-bonds.cc Fix multi_residue_torsion_fit_map() by calling set_dihedral_multi with a vector of atom_tree_t::tree_dihedral_quad_info_t. ------------------------------------------------------------------------ r4592 | pemsley | 2013-03-15 16:25:40 +0000 (Fri, 15 Mar 2013) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Remove strict_parsing from function line (fixes prefix mistaken fix). ------------------------------------------------------------------------ r4591 | pemsley | 2013-03-15 14:25:26 +0000 (Fri, 15 Mar 2013) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Use the saved widgets map for the toggle buttons. ------------------------------------------------------------------------ r4590 | pemsley | 2013-03-15 13:08:49 +0000 (Fri, 15 Mar 2013) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/rel-todo Updates for SMILES handling (now text and dialog have consistent usage). Scale an RDKit mol on conversion to widgeted_molecule_t. ------------------------------------------------------------------------ r4589 | pemsley | 2013-03-15 12:02:14 +0000 (Fri, 15 Mar 2013) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes Initial patch for adding accelerators to Lidia. ------------------------------------------------------------------------ r4588 | pemsley | 2013-03-13 16:17:04 +0000 (Wed, 13 Mar 2013) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.hh M /trunk/goograph/goograph.cc M /trunk/ligand/Makefile.am M /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.hh A /trunk/ligand/test-rotamer-tables-sql.cc M /trunk/src/c-interface-mogul.cc Add sql test for rotamers - not complete and now commented out of Makefile.am Remove (mogul results) debugging. ------------------------------------------------------------------------ r4587 | b.lohkamp | 2013-03-11 21:59:46 +0000 (Mon, 11 Mar 2013) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/geometry/protein-geometry.cc M /trunk/ideal/coot-compare-residues.cc M /trunk/lbg/lbg.cc Several Windows updates and fixes. Improve path handling for monomers (may fix bug on windows 7/8). Update to mmdb 1.25.0. Fix the way coot pre-release version is extracted on Windows. Fix for older rdkit on windows (for now). GetAtomName jiggery is jigging too much it seems in coot-compare-residues. ------------------------------------------------------------------------ r4586 | pemsley | 2013-03-10 17:47:55 +0000 (Sun, 10 Mar 2013) | 2 lines Changed paths: A /trunk/geometry/srs-interface.hh Add srs-interface.hh ------------------------------------------------------------------------ r4585 | pemsley | 2013-03-10 17:45:19 +0000 (Sun, 10 Mar 2013) | 2 lines Changed paths: A /trunk/macros/ccp4srs.m4 Add ccp4srs macros. ------------------------------------------------------------------------ r4584 | pemsley | 2013-03-10 14:23:41 +0000 (Sun, 10 Mar 2013) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/rel-todo Better positioning of the key (bigger goocanvas needed). ------------------------------------------------------------------------ r4583 | pemsley | 2013-03-10 13:49:36 +0000 (Sun, 10 Mar 2013) | 2 lines Changed paths: M /trunk/python/get_ebi.py M /trunk/rel-todo M /trunk/scheme/get-ebi.scm New server path file downloading pdb files from the EBI. ------------------------------------------------------------------------ r4582 | pemsley | 2013-03-10 13:08:20 +0000 (Sun, 10 Mar 2013) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Remove debuging writing of rdkit.mol. ------------------------------------------------------------------------ r4581 | pemsley | 2013-03-09 19:19:54 +0000 (Sat, 09 Mar 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple change the setup script for ccp4 on x86_64-centos-5. ------------------------------------------------------------------------ r4580 | pemsley | 2013-03-09 14:13:25 +0000 (Sat, 09 Mar 2013) | 8 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-crystal.h M /trunk/doc/coot-user-manual.texi M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.cc Better output of symmetry info (translations). Updated doc. Add function to show and display idle function flev bonds. Remove some flev debugging. Protection added in undo and ramachandran plots (fixed Jade Li crash). Linux specific code in build-it-gt2-simple. Fix up wedges when converting from restraints/CRresidue (there is order-dependence). ------------------------------------------------------------------------ r4579 | pemsley | 2013-03-08 15:19:44 +0000 (Fri, 08 Mar 2013) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc Fixups for conditional SRS includes. ------------------------------------------------------------------------ r4578 | pemsley | 2013-03-08 14:48:16 +0000 (Fri, 08 Mar 2013) | 4 lines Changed paths: M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/python/prodrg_import.py M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/lbg-interface.cc M /trunk/src/main.cc M /trunk/src/testing.cc M /trunk/src/testing.hh SBase -> CCP4SRS conversion - but not used due to unresolved runtime crash when compiling with CCP4SRS lib. lbg now contains a protein geometry. ------------------------------------------------------------------------ r4577 | pemsley | 2013-02-28 00:50:47 +0000 (Thu, 28 Feb 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple New mmdb version - 1.25.0. ------------------------------------------------------------------------ r4576 | pemsley | 2013-02-27 20:53:51 +0000 (Wed, 27 Feb 2013) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo Hack in rdkit mol 3d state (typically false) when reading from a 2d mdl file. Rework rdkit_mol_post_read_handling. Make import_rdkit_mol() more robust. Rework bond->canvas line scaling. ------------------------------------------------------------------------ r4575 | pemsley | 2013-02-25 16:54:03 +0000 (Mon, 25 Feb 2013) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc In wrapped_create_accept_reject_refinement_dialog(), use graphics_info_t::accept_reject_dialog if it is set already (hopefully it is only set when it is shown). ------------------------------------------------------------------------ r4574 | pemsley | 2013-02-25 16:52:27 +0000 (Mon, 25 Feb 2013) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/src/molecule-class-info.cc Bond orders for ligands in CA mode. ------------------------------------------------------------------------ r4573 | pemsley | 2013-02-25 15:25:28 +0000 (Mon, 25 Feb 2013) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r4572 | pemsley | 2013-02-25 15:24:40 +0000 (Mon, 25 Feb 2013) | 6 lines Changed paths: M /trunk/analysis/mogul.cc M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo constification and referencing of exceptions. When writing an mdl file - apply values for charge. mogulification of nitro groups. undelocalization of nitro groups. More diagnostics when parsing mogul output file. ------------------------------------------------------------------------ r4571 | pemsley | 2013-02-25 12:50:03 +0000 (Mon, 25 Feb 2013) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/rel-todo M /trunk/src/graphics-info-defines.cc Add bonds to HOHs with hydrogens. Update environment distances after delete residue. ------------------------------------------------------------------------ r4570 | pemsley | 2013-02-22 15:54:05 +0000 (Fri, 22 Feb 2013) | 4 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/rel-todo M /trunk/src/c-interface-sfs.cc M /trunk/src/lbg-interface.cc M /trunk/src/molecule-class-info.cc Improve use of ring centre info in the highlighted bond info when drawing new rings. Remove debugging. ------------------------------------------------------------------------ r4569 | pemsley | 2013-02-21 16:08:52 +0000 (Thu, 21 Feb 2013) | 3 lines Changed paths: M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/lidia-core/test-cod-atom-types.cc charge_undelocalized_guanidinos() (and do not charge them for mogul mdl). undelocalize_aminos() now looks for N-C-O bonds, not N-C-x. ------------------------------------------------------------------------ r4568 | pemsley | 2013-02-18 15:58:13 +0000 (Mon, 18 Feb 2013) | 5 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/lidia-core/test-cod-atom-types.cc M /trunk/src/sdf-interface.cc M /trunk/src/sdf-interface.hh More mogul-related updates. Make the test-cod-atom-types more readable for different types of input. Now use mdl file for input to mogul. Calls mogulify function (does nothing yet). ------------------------------------------------------------------------ r4567 | b.lohkamp | 2013-02-18 14:39:23 +0000 (Mon, 18 Feb 2013) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/get_recent_pdbe.py M /trunk/python/parse_pisa_xml.py M /trunk/python/redefine_functions.py Omit pisa.cfg in pythonic pisa interface. Pythonic residue spec to individual conversion takes 3 and 4 args now. Python pdbe recent downloader uses 14 threads now. ------------------------------------------------------------------------ r4566 | pemsley | 2013-02-16 17:22:42 +0000 (Sat, 16 Feb 2013) | 4 lines Changed paths: M /trunk/analysis/mogul.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/rel-todo M /trunk/scheme/get-ebi.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/main.cc M /trunk/src/sdf-interface.cc M /trunk/src/sdf-interface.hh residue-to-sdf-file has an extra argument for kekulized bonds in file. Hide search button in lidia window. Some changes for key press event in lbg. Detected now, but not handled. ------------------------------------------------------------------------ r4565 | pemsley | 2013-02-15 15:05:43 +0000 (Fri, 15 Feb 2013) | 3 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface-mogul.hh M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Fix up mogul colours for items. Add set_mogul_max_badness() function. Remove torsions for the moment. ------------------------------------------------------------------------ r4564 | pemsley | 2013-02-15 15:03:29 +0000 (Fri, 15 Feb 2013) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix typo in set-colour-map-rotation-for-map. ------------------------------------------------------------------------ r4563 | pemsley | 2013-02-15 11:52:17 +0000 (Fri, 15 Feb 2013) | 10 lines Changed paths: M /trunk/ideal/chirals.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/qed-interface.cc M /trunk/lbg/wmolecule.cc M /trunk/rel-todo M /trunk/src/graphics-info.cc Newcastle fixes: Remove debugging for QED. Convert rdkit_mol to widgeted_molecule_t directly (rather than going through molfile_molecule_t, which was ugly). Increase steps per frame for idealization even further. Increase tolerance in refinement to 0.15 (testing). Add a function call to check_through_ring_bonds() not activated yet because calling this function "early" in refinement would be a mistake - it needs to be called late on somehow - not sure how yet. ------------------------------------------------------------------------ r4562 | pemsley | 2013-02-09 10:54:31 +0000 (Sat, 09 Feb 2013) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am Add cod-types.hh ------------------------------------------------------------------------ r4561 | pemsley | 2013-02-08 14:53:47 +0000 (Fri, 08 Feb 2013) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Remove debugging. ------------------------------------------------------------------------ r4560 | pemsley | 2013-02-07 17:19:57 +0000 (Thu, 07 Feb 2013) | 5 lines Changed paths: M /trunk/analysis/mogul.cc M /trunk/dnotes M /trunk/doc/tutorial.tex M /trunk/doc/validation-tutorial.tex M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lidia-core/cod-types.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/lidia-core/test-cod-atom-types.cc M /trunk/lidia-core/test-fei-vs-mine.py Generate restraints for all entries (with exceptions). Add a method debug_rdkit_molecule() which writes out the atoms and bonds. Add charge_metals() function to undelocalise(). Update documentation. ------------------------------------------------------------------------ r4559 | b.lohkamp | 2013-02-06 11:37:27 +0000 (Wed, 06 Feb 2013) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win Update windows build script to use refmac dictionary 5.39 and href to get pre-release file name ------------------------------------------------------------------------ r4558 | b.lohkamp | 2013-01-31 12:49:54 +0000 (Thu, 31 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/cod-types.cc Make cod types code (and test) work on Windows. ------------------------------------------------------------------------ r4557 | b.lohkamp | 2013-01-31 12:48:44 +0000 (Thu, 31 Jan 2013) | 2 lines Changed paths: M /trunk/src/Makefile.am Swig interface for pythonic enterprise commands. ------------------------------------------------------------------------ r4554 | pemsley | 2013-01-28 10:17:38 +0000 (Mon, 28 Jan 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Refmac dictionary to 5.39 ------------------------------------------------------------------------ r4553 | pemsley | 2013-01-27 17:15:40 +0000 (Sun, 27 Jan 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Remove debugging. ------------------------------------------------------------------------ r4552 | pemsley | 2013-01-27 16:15:37 +0000 (Sun, 27 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am Add cod types code into build. ------------------------------------------------------------------------ r4551 | pemsley | 2013-01-27 16:08:40 +0000 (Sun, 27 Jan 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Fix up PYTHON_LIBS patch, using test not (substituted) [. ------------------------------------------------------------------------ r4550 | pemsley | 2013-01-27 15:56:59 +0000 (Sun, 27 Jan 2013) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Change PYTHON_LIBS so that they have -ldl after -lpython2.x. ------------------------------------------------------------------------ r4549 | pemsley | 2013-01-26 11:45:45 +0000 (Sat, 26 Jan 2013) | 2 lines Changed paths: M /trunk/analysis/Makefile.am Add lidia-core to includes. ------------------------------------------------------------------------ r4548 | pemsley | 2013-01-25 16:32:56 +0000 (Fri, 25 Jan 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use the href to get the file names of pre-release tars. ------------------------------------------------------------------------ r4547 | pemsley | 2013-01-25 12:42:52 +0000 (Fri, 25 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am Remove cod code for the moment. ------------------------------------------------------------------------ r4546 | b.lohkamp | 2013-01-24 11:57:21 +0000 (Thu, 24 Jan 2013) | 2 lines Changed paths: M /trunk/build-it-win Windows builds use Cambridge server too. ------------------------------------------------------------------------ r4545 | pemsley | 2013-01-23 22:49:05 +0000 (Wed, 23 Jan 2013) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Move pre-releases and releases server to Cambridge. ------------------------------------------------------------------------ r4544 | pemsley | 2013-01-22 21:58:26 +0000 (Tue, 22 Jan 2013) | 4 lines Changed paths: M /trunk/lidia-core/cod-types.cc M /trunk/lidia-core/cod-types.hh M /trunk/lidia-core/test-cod-atom-types.cc M /trunk/lidia-core/test-fei-vs-mine.py Reference for 0xx are new from Fei. Add trace_path() methods to find all rings for atoms that are in fused rings. Remove debugging. ------------------------------------------------------------------------ r4543 | pemsley | 2013-01-19 23:03:57 +0000 (Sat, 19 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/test-fei-vs-mine.py Better formating of results. ------------------------------------------------------------------------ r4542 | b.lohkamp | 2013-01-19 16:49:16 +0000 (Sat, 19 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/test-cod-atom-types.cc Fix typo. ------------------------------------------------------------------------ r4541 | b.lohkamp | 2013-01-19 16:48:36 +0000 (Sat, 19 Jan 2013) | 2 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py Better error messaging for pythonic pdbe cif dictionary download. ------------------------------------------------------------------------ r4540 | pemsley | 2013-01-19 12:49:13 +0000 (Sat, 19 Jan 2013) | 2 lines Changed paths: A /trunk/lidia-core/test-fei-vs-mine.py Add python test. ------------------------------------------------------------------------ r4539 | pemsley | 2013-01-19 12:45:12 +0000 (Sat, 19 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am A /trunk/lidia-core/cod-types.cc A /trunk/lidia-core/cod-types.hh A /trunk/lidia-core/test-cod-atom-types.cc Add first bash at cod types, including test. ------------------------------------------------------------------------ r4538 | pemsley | 2013-01-19 12:44:38 +0000 (Sat, 19 Jan 2013) | 3 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh Add a method to charge Borons of degree 4. Clear up debugging. ------------------------------------------------------------------------ r4537 | b.lohkamp | 2013-01-17 16:56:55 +0000 (Thu, 17 Jan 2013) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/src/drag-and-drop.cc Update notes. Deal properly with finishing up drag'n'drop signals. ------------------------------------------------------------------------ r4536 | pemsley | 2013-01-17 14:07:07 +0000 (Thu, 17 Jan 2013) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Give better error message when dictionary cif is not available or fails to download. ------------------------------------------------------------------------ r4535 | pemsley | 2013-01-16 16:59:09 +0000 (Wed, 16 Jan 2013) | 2 lines Changed paths: M /trunk/src/c-interface-mogul.cc Add goograph protection for mogul dialog. ------------------------------------------------------------------------ r4534 | b.lohkamp | 2013-01-16 14:08:45 +0000 (Wed, 16 Jan 2013) | 5 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py Turn off backup for pythonic fit_protein_fit_function. Do not replace fragment in prodrg_ify. Fix pythonic get_SMILES_for_comp_id_from_pdbe. Add function to fetch PDBe ligand description in python extensions. ------------------------------------------------------------------------ r4533 | b.lohkamp | 2013-01-16 13:38:31 +0000 (Wed, 16 Jan 2013) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc M /trunk/windows/runwincoot.bat Give python specific hint for make_map_from_cif_sigmaa. DOS format for windows bat file. ------------------------------------------------------------------------ r4532 | pemsley | 2013-01-15 15:06:56 +0000 (Tue, 15 Jan 2013) | 3 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/nsv.cc M /trunk/src/nsv.hh Better layout of seqeunce view. Update notes. ------------------------------------------------------------------------ r4531 | pemsley | 2013-01-15 15:05:37 +0000 (Tue, 15 Jan 2013) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove debugging. ------------------------------------------------------------------------ r4530 | pemsley | 2013-01-15 15:05:20 +0000 (Tue, 15 Jan 2013) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Menu item for PDBe minimal description of ligand (for bond by dictionary). ------------------------------------------------------------------------ r4529 | b.lohkamp | 2013-01-13 16:05:55 +0000 (Sun, 13 Jan 2013) | 3 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/coot-fileselections.h M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/restraints-editor.cc Add ccp4 directories and file filter buttons to filechoosers. ------------------------------------------------------------------------ r4528 | b.lohkamp | 2013-01-13 13:55:21 +0000 (Sun, 13 Jan 2013) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/graphics-ligand-view.cc Protect rdkit_mol_post_read_handling in enterprise. ------------------------------------------------------------------------ r4527 | b.lohkamp | 2013-01-13 13:53:22 +0000 (Sun, 13 Jan 2013) | 3 lines Changed paths: M /trunk/autogen.sh Make sure we can autogen for pre-release and systems without $HOST. ------------------------------------------------------------------------ r4526 | pemsley | 2013-01-12 13:04:49 +0000 (Sat, 12 Jan 2013) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc Tweak map sharpening and increase scale limit on slider. Thanks Chang Liu. ------------------------------------------------------------------------ r4525 | pemsley | 2013-01-11 22:07:51 +0000 (Fri, 11 Jan 2013) | 2 lines Changed paths: A /trunk/src/testing-data.hh Add missing testing-data.hh ------------------------------------------------------------------------ r4524 | pemsley | 2013-01-11 22:07:19 +0000 (Fri, 11 Jan 2013) | 2 lines Changed paths: A /trunk/src/testing-2.cc Add missing testing-2.cc ------------------------------------------------------------------------ r4523 | pemsley | 2013-01-11 21:52:58 +0000 (Fri, 11 Jan 2013) | 5 lines Changed paths: M /trunk/TODO M /trunk/autogen.sh M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/geometry/Makefile.am A /trunk/geometry/dreiding.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/lbg-search.cc M /trunk/rel-todo M /trunk/scheme/get-recent-pdbe.scm M /trunk/src/Makefile.am M /trunk/src/generic-objects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Add dreiding torsion terms (needs more work). On generating bonds, factor out add_bond_by_dictionary_maybe(), allowing bond-by-dictionary for colour-by-chain Add a construtor which takes the dictionary as the only argument. ------------------------------------------------------------------------ r4522 | pemsley | 2013-01-11 18:37:34 +0000 (Fri, 11 Jan 2013) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Save Symmetry coords dialog now resizable. ------------------------------------------------------------------------ r4521 | pemsley | 2013-01-11 18:28:52 +0000 (Fri, 11 Jan 2013) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lig-build.hh Factor out rdkit_mol_post_read_handling() function. near point test for new atom addtion in molecule_t reduced to tolerance of 0.2. Widden lidia window. ------------------------------------------------------------------------ r4520 | pemsley | 2013-01-10 16:37:18 +0000 (Thu, 10 Jan 2013) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh Add deloc of carboxylates. ------------------------------------------------------------------------ r4519 | pemsley | 2013-01-08 16:08:32 +0000 (Tue, 08 Jan 2013) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r4518 | pemsley | 2013-01-08 15:56:14 +0000 (Tue, 08 Jan 2013) | 5 lines Changed paths: M /trunk/analysis/Makefile.am M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/analysis/test-mogul.cc M /trunk/coot-gtk2.glade M /trunk/goograph/goograph.cc M /trunk/lbg/lidia-main.cc M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface-mogul.hh M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Mogul goographs get hidden now, not created and destroyed. mogul_geometry_dialog renamed to mogul_geometry_results_table_dialog. Update rel-todo for 0.7.1. Add some work on torsion modelling - not completed/successful. ------------------------------------------------------------------------ r4517 | pemsley | 2013-01-07 22:52:56 +0000 (Mon, 07 Jan 2013) | 3 lines Changed paths: M /trunk/python/generic_objects.py Return a True status from reduce_on_pdb_file() no matter the return status of reduce. ------------------------------------------------------------------------ r4516 | pemsley | 2013-01-07 22:03:36 +0000 (Mon, 07 Jan 2013) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Add non-function protection for buttons in keybindings dialog. ------------------------------------------------------------------------ r4515 | pemsley | 2013-01-07 21:34:49 +0000 (Mon, 07 Jan 2013) | 2 lines Changed paths: M /trunk/python/coot_utils.py Fixup for get_drug_via_wikipedia(). ------------------------------------------------------------------------ r4514 | pemsley | 2013-01-07 17:37:50 +0000 (Mon, 07 Jan 2013) | 2 lines Changed paths: M /trunk/src/cmtz-interface.cc M /trunk/src/positioned-widgets.h Add setting of transient for MTZ column selector. ------------------------------------------------------------------------ r4513 | pemsley | 2013-01-07 17:24:57 +0000 (Mon, 07 Jan 2013) | 2 lines Changed paths: M /trunk/python/coot_utils.py add global user_defined_alert_smarts. ------------------------------------------------------------------------ r4512 | pemsley | 2013-01-07 17:18:11 +0000 (Mon, 07 Jan 2013) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Fix typo with USE_GUILE #ifdef in get_drug_mdl_via_wikipedia_and_drugbank(). ------------------------------------------------------------------------ r4511 | pemsley | 2013-01-07 17:08:46 +0000 (Mon, 07 Jan 2013) | 5 lines Changed paths: M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-network.cc M /trunk/src/c-interface.cc No longer call py_clean_internal() in safe_python_command_with_return(). No longer Py_XDECREF() the result of Py_RunString(). get_drug_mdl_via_wikipedia_and_drugbank no longer throws an exception. Add use_graphics_interface_flag protection for screen_vectors_py(). ------------------------------------------------------------------------ r4508 | pemsley | 2013-01-06 12:00:09 +0000 (Sun, 06 Jan 2013) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Allow navigation to residues by specification of a sequence triple. ------------------------------------------------------------------------ r4507 | pemsley | 2013-01-06 11:29:45 +0000 (Sun, 06 Jan 2013) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r4506 | b.lohkamp | 2012-12-09 13:08:03 +0000 (Sun, 09 Dec 2012) | 4 lines Changed paths: M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Create atom_index_full to deal with alt confs. Use in refine_auto_range. ------------------------------------------------------------------------ r4505 | b.lohkamp | 2012-12-09 13:07:02 +0000 (Sun, 09 Dec 2012) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/fitting.py In python interruptable fit function turn off backup properly. ------------------------------------------------------------------------ r4504 | b.lohkamp | 2012-12-05 22:28:52 +0000 (Wed, 05 Dec 2012) | 1 line Changed paths: M /trunk/src/c-interface-ligands-swig.hh M /trunk/src/probe-clash-score.cc Some python include fixups. ------------------------------------------------------------------------ r4503 | b.lohkamp | 2012-12-04 16:40:54 +0000 (Tue, 04 Dec 2012) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/ideal/coot-compare-residues.cc M /trunk/lidia-core/Makefile.am M /trunk/macros/clipper.m4 Some windows fixups. AddAtom in coot-compare-residues.cc include coot-utils in lidia-core ------------------------------------------------------------------------ r4502 | b.lohkamp | 2012-12-04 08:44:09 +0000 (Tue, 04 Dec 2012) | 1 line Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/probe-clash-score.cc M /trunk/src/probe-clash-score.hh Add probe_clash_score_py and protect scm function. ------------------------------------------------------------------------ r4501 | b.lohkamp | 2012-12-04 08:42:57 +0000 (Tue, 04 Dec 2012) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/python/refmac.py Fix typo to include the correct refmac extra param file. ------------------------------------------------------------------------ r4500 | b.lohkamp | 2012-12-04 08:35:17 +0000 (Tue, 04 Dec 2012) | 1 line Changed paths: M /trunk/cootilus/cootilus-build.cpp Cootilus NA are proper 'U' now. ------------------------------------------------------------------------ r4499 | b.lohkamp | 2012-12-04 08:33:43 +0000 (Tue, 04 Dec 2012) | 1 line Changed paths: M /trunk/doc/crib-sheet.tex M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex M /trunk/doc/validation-tutorial.tex Fix some typos and update tutorials. ------------------------------------------------------------------------ r4498 | pemsley | 2012-12-03 11:30:15 +0000 (Mon, 03 Dec 2012) | 2 lines Changed paths: M /trunk/src/c-interface-mogul.cc M /trunk/src/cc-interface-mogul.hh Fix up missing declaration of mogul histogram close button callback. ------------------------------------------------------------------------ r4497 | pemsley | 2012-12-03 08:50:55 +0000 (Mon, 03 Dec 2012) | 3 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/scheme/get-recent-pdbe.scm M /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface.h M /trunk/src/generic-display-object.hh M /trunk/src/generic-objects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Rework input parser to handle csv mogul output. Add mogul torsions and counts. ------------------------------------------------------------------------ r4496 | pemsley | 2012-12-03 08:48:08 +0000 (Mon, 03 Dec 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Correct charge on deloc phosphate. ------------------------------------------------------------------------ r4495 | b.lohkamp | 2012-12-02 15:56:03 +0000 (Sun, 02 Dec 2012) | 1 line Changed paths: M /trunk/src/molecule-class-info-other.cc Make reworked merge_molecule to return status and list of added chains. ------------------------------------------------------------------------ r4494 | pemsley | 2012-11-28 11:35:44 +0000 (Wed, 28 Nov 2012) | 3 lines Changed paths: M /trunk/src/c-interface-mogul.cc Reduce number of decimal places for mogul items by making the records be strings rather than floats (except z). ------------------------------------------------------------------------ r4493 | pemsley | 2012-11-28 11:12:07 +0000 (Wed, 28 Nov 2012) | 3 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/goograph/Makefile.am M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/cc-interface-mogul.hh Add mogul result histograms on changing the item line. Function added to get mogul items given indices. ------------------------------------------------------------------------ r4492 | pemsley | 2012-11-26 19:40:46 +0000 (Mon, 26 Nov 2012) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.hh M /trunk/src/c-interface-mogul.cc M /trunk/src/cc-interface-mogul.hh M /trunk/src/gtk2-interface.c Fill mogul results tables. Move to the right place on change. Add keypress test code in lbg. ------------------------------------------------------------------------ r4491 | pemsley | 2012-11-21 15:44:09 +0000 (Wed, 21 Nov 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh M /trunk/src/probe-clash-score.hh Add link info information to scripting layer. ------------------------------------------------------------------------ r4490 | pemsley | 2012-11-20 10:30:14 +0000 (Tue, 20 Nov 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/ideal/Makefile.am A /trunk/ideal/coot-compare-residues.cc A /trunk/ideal/coot-compare-residues.hh Add compare residue by torsions function. ------------------------------------------------------------------------ r4489 | pemsley | 2012-11-19 20:45:04 +0000 (Mon, 19 Nov 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Use Extended HM symbols when converting from clipper symmetry to mmdb symmetry. ------------------------------------------------------------------------ r4488 | pemsley | 2012-11-16 14:11:27 +0000 (Fri, 16 Nov 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am Remove coot_gtk1.py from EXTRA_DIST. ------------------------------------------------------------------------ r4487 | pemsley | 2012-11-16 11:16:51 +0000 (Fri, 16 Nov 2012) | 2 lines Changed paths: M /trunk/src/generic-objects.cc Don't close the probe dots FILE * if it is null. ------------------------------------------------------------------------ r4486 | pemsley | 2012-11-16 10:02:55 +0000 (Fri, 16 Nov 2012) | 6 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ideal/Makefile.am M /trunk/lidia-core/lig-build.hh M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/scheme/libcheck.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands-swig.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface-mogul.hh M /trunk/src/cc-interface.hh M /trunk/src/generic-objects.cc M /trunk/src/graphics-info.cc M /trunk/src/probe-clash-score.hh Add infrastructure for filtering ligand fitting solutions by torsion (not filled yet). rename function mogul_markup(). Fill the bond results in show_mogul_geometry_dialog(). Fix up cc-interface.hh documentation markup so that make coot.html passes. ------------------------------------------------------------------------ r4485 | pemsley | 2012-11-15 13:54:40 +0000 (Thu, 15 Nov 2012) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-waters-gui.cc M /trunk/src/coot.i M /trunk/src/probe-clash-score.cc M /trunk/src/probe-clash-score.hh Rework the probe dots parser. Update notes. ------------------------------------------------------------------------ r4484 | pemsley | 2012-11-12 14:26:08 +0000 (Mon, 12 Nov 2012) | 2 lines Changed paths: M /trunk/scheme/jligand.scm Use JLigand.jar as the default file name. ------------------------------------------------------------------------ r4483 | pemsley | 2012-11-09 13:32:59 +0000 (Fri, 09 Nov 2012) | 2 lines Changed paths: A /trunk/src/c-interface-mogul-scripting.cc A /trunk/src/c-interface-mogul.hh A /trunk/src/probe-clash-score.cc A /trunk/src/probe-clash-score.hh Add missing files from previous. ------------------------------------------------------------------------ r4482 | pemsley | 2012-11-09 13:19:07 +0000 (Fri, 09 Nov 2012) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mogul.cc M /trunk/src/cc-interface-mogul.hh M /trunk/src/coot.i Mogul results interface partial implementation. Adding functions to scripting layer. ------------------------------------------------------------------------ r4481 | pemsley | 2012-11-09 13:14:17 +0000 (Fri, 09 Nov 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Remove debugging of the maps used for correlation. ------------------------------------------------------------------------ r4480 | pemsley | 2012-11-09 13:10:42 +0000 (Fri, 09 Nov 2012) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add LIQUORICE as a representation type. Needs some more fixing up. ------------------------------------------------------------------------ r4479 | pemsley | 2012-11-09 13:09:44 +0000 (Fri, 09 Nov 2012) | 2 lines Changed paths: M /trunk/configure.in AC_PROG_LIBTOOL added... ------------------------------------------------------------------------ r4478 | pemsley | 2012-11-09 13:05:18 +0000 (Fri, 09 Nov 2012) | 2 lines Changed paths: M /trunk/config.guess M /trunk/config.sub More recent config.sub and config.guess ------------------------------------------------------------------------ r4477 | pemsley | 2012-11-07 18:43:22 +0000 (Wed, 07 Nov 2012) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c Add tranisent for file chooser for save coords. Remove gtk1 code. ------------------------------------------------------------------------ r4476 | pemsley | 2012-10-21 16:35:36 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am A /trunk/src/c-interface-ligands-swig.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/coot.i scripting function for creating a new molecule sans ligand. ------------------------------------------------------------------------ r4475 | pemsley | 2012-10-21 16:31:50 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-recent-pdbe.scm residue spec handling for lists with 4 args. ------------------------------------------------------------------------ r4474 | pemsley | 2012-10-21 16:31:07 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r4473 | pemsley | 2012-10-21 16:26:44 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add function to return biggest hetgroup. ------------------------------------------------------------------------ r4472 | pemsley | 2012-10-21 16:25:53 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/src/graphics-ligand-view.cc Allow superscripting in ligand view text. ------------------------------------------------------------------------ r4471 | pemsley | 2012-10-21 16:24:35 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Remove debugging. ------------------------------------------------------------------------ r4470 | pemsley | 2012-10-21 16:24:02 +0100 (Sun, 21 Oct 2012) | 2 lines Changed paths: M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh Better handling of sulphates and phosphates. ------------------------------------------------------------------------ r4469 | pemsley | 2012-10-21 16:23:22 +0100 (Sun, 21 Oct 2012) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove debugging Add end-caps for deloc. ------------------------------------------------------------------------ r4468 | pemsley | 2012-10-14 16:42:25 +0100 (Sun, 14 Oct 2012) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Version 0.7.1-pre Restore ligand fitting result presentation. ------------------------------------------------------------------------ r4467 | pemsley | 2012-10-10 16:04:50 +0100 (Wed, 10 Oct 2012) | 3 lines Changed paths: M /trunk/ligand/find-ligand.cc Allow --blobs command line argument to findligand, allows searching for blobs, not ligands. A blob table is written. ------------------------------------------------------------------------ r4466 | pemsley | 2012-10-09 15:10:15 +0100 (Tue, 09 Oct 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc remove debugging. ------------------------------------------------------------------------ r4465 | pemsley | 2012-10-09 15:09:45 +0100 (Tue, 09 Oct 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc remove debugging. ------------------------------------------------------------------------ r4464 | pemsley | 2012-10-09 15:08:37 +0100 (Tue, 09 Oct 2012) | 2 lines Changed paths: M /trunk/src/graphics-ligand-view.cc remove debugging. ------------------------------------------------------------------------ r4463 | pemsley | 2012-10-09 15:08:09 +0100 (Tue, 09 Oct 2012) | 2 lines Changed paths: M /trunk/src/flev.cc remove debugging. ------------------------------------------------------------------------ r4462 | pemsley | 2012-10-09 13:48:31 +0100 (Tue, 09 Oct 2012) | 2 lines Changed paths: M /trunk/configure.in Change to version 0.8-pre-1. ------------------------------------------------------------------------ r4461 | b.lohkamp | 2012-10-07 15:57:36 +0100 (Sun, 07 Oct 2012) | 1 line Changed paths: M /trunk/build-it-win Update windows build script slightly. ------------------------------------------------------------------------ r4460 | pemsley | 2012-09-28 17:56:41 +0100 (Fri, 28 Sep 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use --enable-shared for mmdb build (now that we use CCP4 tar). ------------------------------------------------------------------------ r4459 | b.lohkamp | 2012-09-28 14:01:10 +0100 (Fri, 28 Sep 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py No old_coot for python. Hope gets into releasesvn status -qsvn status -q ------------------------------------------------------------------------ r4458 | pemsley | 2012-09-28 13:11:38 +0100 (Fri, 28 Sep 2012) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes A /trunk/pixmaps/coot-0.7.png M /trunk/scheme/coot-gui.scm M /trunk/src/gtk2-interface.c Release 0.7. ------------------------------------------------------------------------ r4457 | pemsley | 2012-09-28 13:11:19 +0100 (Fri, 28 Sep 2012) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Lighting change protection (see previous). ------------------------------------------------------------------------ r4456 | pemsley | 2012-09-28 13:10:04 +0100 (Fri, 28 Sep 2012) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc Don't change the lighting if there are no display list objects. ------------------------------------------------------------------------ r4455 | KevKeating | 2012-09-27 21:08:22 +0100 (Thu, 27 Sep 2012) | 1 line Changed paths: M /trunk/rcrane/Makefile.am add new RCrane files to Makefile ------------------------------------------------------------------------ r4454 | pemsley | 2012-09-27 19:10:28 +0100 (Thu, 27 Sep 2012) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/lbg/lbg.cc M /trunk/rel-todo M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c Change button label on residue info dialog. update attributes after lbg 2d cleanup. ------------------------------------------------------------------------ r4453 | b.lohkamp | 2012-09-27 17:46:53 +0100 (Thu, 27 Sep 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/parse_pisa_xml.py Update pythonic pisa interface to work with v1.13 (only currently). ------------------------------------------------------------------------ r4452 | pemsley | 2012-09-27 15:59:25 +0100 (Thu, 27 Sep 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm target-auto-weighting-value set to 1.0 ------------------------------------------------------------------------ r4451 | b.lohkamp | 2012-09-27 15:38:56 +0100 (Thu, 27 Sep 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/fitting.py In pythonic fit protein function accept the regularizement. ------------------------------------------------------------------------ r4450 | KevKeating | 2012-09-27 00:53:56 +0100 (Thu, 27 Sep 2012) | 1 line Changed paths: M /trunk/rcrane/CHANGELOG.txt M /trunk/rcrane/revisionNum.py update RCrane changelog ------------------------------------------------------------------------ r4449 | KevKeating | 2012-09-27 00:43:51 +0100 (Thu, 27 Sep 2012) | 1 line Changed paths: M /trunk/python/rcrane_loader.py M /trunk/rcrane/README.txt M /trunk/rcrane/__init__.py M /trunk/rcrane/about.py M /trunk/rcrane/buildPhosOxy.py M /trunk/rcrane/calcCoords.py A /trunk/rcrane/extendChain.py M /trunk/rcrane/menu.py M /trunk/rcrane/pseudoMolecule.py A /trunk/rcrane/reportInputErrors.py M /trunk/rcrane/reviewSuitesGui.py M /trunk/rcrane/revisionNum.py M /trunk/rcrane/rotamerize.py M /trunk/rcrane/traceGui.py update RCrane to 1.1 ------------------------------------------------------------------------ r4448 | pemsley | 2012-09-26 21:13:35 +0100 (Wed, 26 Sep 2012) | 8 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/python/fitting.py M /trunk/src/globjects.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc M /trunk/src/graphics-ligand-view.hh M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h graphics ligand view works with alt confs now. Improve hydrogen sprouting on alt-confed residues. split up function for easier reading. rdkit_mol() now takes an alt conf argument. No non-bonded contacts for hydrogens in the same residue (not sure if this is a good thing). delete_alt_confs_except() function added. ------------------------------------------------------------------------ r4447 | pemsley | 2012-09-26 19:31:04 +0100 (Wed, 26 Sep 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Remove debugging. ------------------------------------------------------------------------ r4446 | pemsley | 2012-09-26 17:56:13 +0100 (Wed, 26 Sep 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/src/molecule-class-info-maps.cc Report map rmsd, not map sigma. ------------------------------------------------------------------------ r4445 | pemsley | 2012-09-24 14:28:43 +0100 (Mon, 24 Sep 2012) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-build.cc Fix-up PISA interface (no longer use pisa-config). Clean up goosh status handling. Remove debugging in new_molecule_by_symmetry_matrix_from_molecule(). ------------------------------------------------------------------------ r4444 | pemsley | 2012-09-24 13:25:07 +0100 (Mon, 24 Sep 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc No longer hack the formal charge of P in rdkit_mol(). ------------------------------------------------------------------------ r4443 | pemsley | 2012-09-24 12:31:47 +0100 (Mon, 24 Sep 2012) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/src/callbacks.c Toggling the "apply all" checkbutton for occupancies in the residue info dialog should not set the occupancy widget insensitve if the alt conf checkbutton is active. ------------------------------------------------------------------------ r4442 | b.lohkamp | 2012-09-23 22:39:05 +0100 (Sun, 23 Sep 2012) | 1 line Changed paths: M /trunk/src/c-interface.cc Decref Py_None in run_python_command. ------------------------------------------------------------------------ r4441 | b.lohkamp | 2012-09-23 22:33:36 +0100 (Sun, 23 Sep 2012) | 1 line Changed paths: M /trunk/macros/with-python.m4 Use python-config to fix -ldl linking issues. ------------------------------------------------------------------------ r4440 | b.lohkamp | 2012-09-23 16:38:47 +0100 (Sun, 23 Sep 2012) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py Pythonic test for bas mutation to handle C7 correctly. Add a pythonic test for merge molecules. Pythonic shelx test for fcf reading uses new small molecule cif data reader function. ------------------------------------------------------------------------ r4439 | b.lohkamp | 2012-09-23 16:32:52 +0100 (Sun, 23 Sep 2012) | 6 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/prodrg_import.py M /trunk/python/shelx.py Use new data cif reader fof fcf file reading in python too. Factor out ligand overlay in pythonic prodrg import. Add pythonic get_SMILES_for_comp_id_from_pdbe. (not tested - no data). Reorder pythonic addable solvent molecules. ------------------------------------------------------------------------ r4438 | b.lohkamp | 2012-09-23 15:59:50 +0100 (Sun, 23 Sep 2012) | 1 line Changed paths: M /trunk/build-it-win Update Windows build to mmdb version 1.24.2 ------------------------------------------------------------------------ r4437 | pemsley | 2012-09-23 15:19:03 +0100 (Sun, 23 Sep 2012) | 3 lines Changed paths: M /trunk/coot-utils/read-sm-cif.cc M /trunk/greg-tests/02-shelx.scm M /trunk/scheme/shelx.scm M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/read-cif.c Fix up the interface for cif data reading and the test (we should not use the internal function). ------------------------------------------------------------------------ r4436 | pemsley | 2012-09-22 18:18:06 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Fix merging of single residues (by consolidation). ------------------------------------------------------------------------ r4435 | pemsley | 2012-09-22 18:16:10 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Use GdkEventConfigure * for event handling. ------------------------------------------------------------------------ r4434 | pemsley | 2012-09-22 16:51:07 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Add some protection for udd failing in add_bonds(). ------------------------------------------------------------------------ r4433 | pemsley | 2012-09-22 16:18:40 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/lbg/lbg.glade M /trunk/rel-todo M /trunk/src/gtk2-interface.c Rework gui a bit: lbg opens bigger, File menu reordered. ------------------------------------------------------------------------ r4432 | pemsley | 2012-09-22 16:17:55 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Use the new data cif reader to read fcf data by scripting. ------------------------------------------------------------------------ r4431 | pemsley | 2012-09-22 15:52:23 +0100 (Sat, 22 Sep 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/rel-todo M /trunk/skeleton/graphical_skel.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc All bonds can now have end-caps. Double bonds do have end-caps. ------------------------------------------------------------------------ r4430 | pemsley | 2012-09-21 21:44:48 +0100 (Fri, 21 Sep 2012) | 3 lines Changed paths: M /trunk/ideal/torsion-bonds.cc M /trunk/rel-todo Add torsions from dictionary link torsions to torsionable_link_bonds() (not just torsions from link bonds). ------------------------------------------------------------------------ r4429 | pemsley | 2012-09-21 17:12:37 +0100 (Fri, 21 Sep 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Fix typo in avoid_ring_centres() so that now we get good ring radius, improves substitution contour. ------------------------------------------------------------------------ r4428 | pemsley | 2012-09-21 14:38:45 +0100 (Fri, 21 Sep 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo Update mmdb to version 1.24.2 ------------------------------------------------------------------------ r4427 | pemsley | 2012-09-20 13:44:41 +0100 (Thu, 20 Sep 2012) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc Cancel on an add-alt-conf now deletes (undoes) the addition of the alt-conf. ------------------------------------------------------------------------ r4426 | pemsley | 2012-09-19 15:48:05 +0100 (Wed, 19 Sep 2012) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc Better initial positions for some transient dialogs: delete item, rotamer and distances. ------------------------------------------------------------------------ r4425 | pemsley | 2012-09-19 15:26:14 +0100 (Wed, 19 Sep 2012) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/density-score-by-residue-src.cc mutate_base reworked to handle C7 atoms from std_base Td. Add a test. base_to_base() function removed (it was not called by anything). ------------------------------------------------------------------------ r4424 | pemsley | 2012-09-18 18:18:21 +0100 (Tue, 18 Sep 2012) | 5 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Rework merge-molecules to do a better job at putting het-groups into the same chain as other het-groups (of the same type). Add suggest_new_chain_id() function. Add a test. ------------------------------------------------------------------------ r4423 | pemsley | 2012-09-18 17:50:52 +0100 (Tue, 18 Sep 2012) | 3 lines Changed paths: M /trunk/macros/with-python.m4 Fix extra_dl_lib to include Fed 14 (gcc 4.5.1 > 4.4) now that lidia includes python. ------------------------------------------------------------------------ r4422 | pemsley | 2012-09-18 14:07:15 +0100 (Tue, 18 Sep 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc Adding a single residue adds to an existing chain if that chain consists of residues of the same residue type as is being added. ------------------------------------------------------------------------ r4421 | pemsley | 2012-09-18 08:21:09 +0100 (Tue, 18 Sep 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo Split up undelocalize() function into parts. ------------------------------------------------------------------------ r4420 | pemsley | 2012-09-18 08:05:49 +0100 (Tue, 18 Sep 2012) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/ideal/torsion-bonds.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/gtk2-interface.c Clear up multi-residue torsion setting on cancel. Add protection in torsionable_link_bonds() for being called with null molecule. ------------------------------------------------------------------------ r4419 | pemsley | 2012-09-18 07:34:50 +0100 (Tue, 18 Sep 2012) | 2 lines Changed paths: A /trunk/lbg/05_Hotel_Icon_Hair_Salon.svg Add hair-solon (tidy up) icon. ------------------------------------------------------------------------ r4418 | pemsley | 2012-09-18 02:17:15 +0100 (Tue, 18 Sep 2012) | 5 lines Changed paths: M /trunk/dnotes M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/ligand/Makefile.am M /trunk/ligand/ligand.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc Undelocalize phosphates. Clean up 2d representations. OpenMP flags in ligand Makefile. Add username_password map holder. ------------------------------------------------------------------------ r4417 | pemsley | 2012-09-17 23:01:31 +0100 (Mon, 17 Sep 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc Add protection for bad/unset atom indices in rotate_about(). ------------------------------------------------------------------------ r4416 | b.lohkamp | 2012-09-17 16:51:51 +0100 (Mon, 17 Sep 2012) | 1 line Changed paths: M /trunk/windows/wincoot-autobuild-all Fix the new Windows clean build option. ------------------------------------------------------------------------ r4415 | b.lohkamp | 2012-09-17 08:35:08 +0100 (Mon, 17 Sep 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/windows/wincoot-autobuild-all For Windows build add option to make clean one. ------------------------------------------------------------------------ r4414 | pemsley | 2012-09-16 09:02:52 +0100 (Sun, 16 Sep 2012) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Put user-defined solvents at top, expand comp-id name if possible. ------------------------------------------------------------------------ r4413 | pemsley | 2012-09-15 00:02:17 +0100 (Sat, 15 Sep 2012) | 2 lines Changed paths: M /trunk/lbg/Makefile.am Not the way to to it. Revert 4412. ------------------------------------------------------------------------ r4412 | b.lohkamp | 2012-09-14 21:43:03 +0100 (Fri, 14 Sep 2012) | 1 line Changed paths: M /trunk/lbg/Makefile.am Add -ldl when linking lidia. Needed at least by FC14. ------------------------------------------------------------------------ r4411 | pemsley | 2012-09-14 11:20:09 +0100 (Fri, 14 Sep 2012) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Remove debugging. ------------------------------------------------------------------------ r4410 | pemsley | 2012-09-14 08:21:43 +0100 (Fri, 14 Sep 2012) | 7 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/rel-todo M /trunk/scheme/with-jligand.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/lbg-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/testing.cc M /trunk/utils/coot-utils.cc Add multiple ligand solutions per cluster (default is off). Add set_find_ligand_multi_solutions_per_cluster() to enable it. clean up (refactor) ligand.cc fit_ligands_to_cluster(). Add functon delete_molecule_from_from_display_manager() to handle the closing of molecules without atoms. clean-up-2d button added to lidia - no callback yet. ------------------------------------------------------------------------ r4409 | pemsley | 2012-09-14 02:07:38 +0100 (Fri, 14 Sep 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Correct the residue name of atoms placed at pointer. ------------------------------------------------------------------------ r4408 | pemsley | 2012-09-12 14:20:24 +0100 (Wed, 12 Sep 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info.cc 3D annotations (draw_generic_text()) use font_colour. ------------------------------------------------------------------------ r4407 | pemsley | 2012-09-11 11:47:11 +0100 (Tue, 11 Sep 2012) | 3 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Catch const reference. Minor debug-related changes. ------------------------------------------------------------------------ r4406 | pemsley | 2012-09-11 11:45:24 +0100 (Tue, 11 Sep 2012) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Don't expand occupancy frame in add alt conf dialog. ------------------------------------------------------------------------ r4405 | pemsley | 2012-09-11 11:44:27 +0100 (Tue, 11 Sep 2012) | 2 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/scheme/prodrg-import.scm Factor out ligand overlaying from input of prodrg output. ------------------------------------------------------------------------ r4404 | pemsley | 2012-09-11 03:16:02 +0100 (Tue, 11 Sep 2012) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/molecule-class-info-other.cc Hydrogen ball radius follows radius scaling whenn colour is HYDROGEN_GREY_BOND in make_ball_and_stick(). ------------------------------------------------------------------------ r4403 | pemsley | 2012-09-11 03:11:11 +0100 (Tue, 11 Sep 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Add exception protection for get_smiles_for_mol(). ------------------------------------------------------------------------ r4402 | pemsley | 2012-09-09 00:14:18 +0100 (Sun, 09 Sep 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-residues.cc Don't show a ligand view if the molecule for the ligand is not displayed. ------------------------------------------------------------------------ r4401 | pemsley | 2012-09-08 22:54:54 +0100 (Sat, 08 Sep 2012) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lidia-core/lig-build.hh render_from_molecule() should not consider closed bonds. lbg_info_t::rdkit_mol() conformer size on the number of atoms of input mol (excluding closed ones). ------------------------------------------------------------------------ r4400 | pemsley | 2012-09-08 16:25:09 +0100 (Sat, 08 Sep 2012) | 5 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc Extend atoms_match_dictionary() so that we can also apply a bond distance check (all bonds must be < sqrt(10) to pass). The flag is set when bonding, but unset when refining. More to-do items for release. ------------------------------------------------------------------------ r4399 | pemsley | 2012-09-08 16:19:09 +0100 (Sat, 08 Sep 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/qed-interface.cc Clear up bond rotation problem due to missing button release signal (due to the alert circle being deleted before emitting the signal). ------------------------------------------------------------------------ r4398 | pemsley | 2012-09-07 14:01:08 +0100 (Fri, 07 Sep 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Lower the alert_group (parent is root) not individual alerts (parent is alert_group). ------------------------------------------------------------------------ r4397 | pemsley | 2012-09-07 13:59:55 +0100 (Fri, 07 Sep 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove some debugging. ------------------------------------------------------------------------ r4396 | pemsley | 2012-09-07 12:51:51 +0100 (Fri, 07 Sep 2012) | 2 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh File -> New in lbg makes a new window (not clear). ------------------------------------------------------------------------ r4395 | pemsley | 2012-09-07 11:25:33 +0100 (Fri, 07 Sep 2012) | 2 lines Changed paths: M /trunk/lbg/Makefile.am M /trunk/lbg/lidia-main.cc Initialize python and use export-dynamic when linking lidia. ------------------------------------------------------------------------ r4394 | pemsley | 2012-09-06 19:04:28 +0100 (Thu, 06 Sep 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/test_lbg_functions.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc scale and centre calculator for widgeted molecule. split and join rdkit molecules. ------------------------------------------------------------------------ r4393 | pemsley | 2012-09-05 18:44:44 +0100 (Wed, 05 Sep 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/globjects.cc Change the way the mouse changes the clipping planes. ------------------------------------------------------------------------ r4389 | pemsley | 2012-09-04 22:22:03 +0100 (Tue, 04 Sep 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/python/redefine_functions.py M /trunk/rel-todo M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-maps.cc M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc Add map correlations with masking out grid points that have contributions from atoms of neighbouring residues. ------------------------------------------------------------------------ r4388 | pemsley | 2012-09-04 19:00:44 +0100 (Tue, 04 Sep 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc Remove Py_XDECREF() call in run_python_command(). ------------------------------------------------------------------------ r4387 | pemsley | 2012-09-04 18:59:01 +0100 (Tue, 04 Sep 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/python/coot_utils.py Trivial clean-ups. ------------------------------------------------------------------------ r4386 | pemsley | 2012-09-03 17:19:13 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. Now empty. ------------------------------------------------------------------------ r4385 | pemsley | 2012-09-03 17:18:47 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add get-SMILES-for-comp-id-from-pdbe function. ------------------------------------------------------------------------ r4384 | pemsley | 2012-09-03 12:29:13 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-maps.cc Don't complain about dark map when background is not dark. ------------------------------------------------------------------------ r4383 | pemsley | 2012-09-03 10:10:36 +0100 (Mon, 03 Sep 2012) | 7 lines Changed paths: M /trunk/src/graphics-info.cc Previously (r4209) I had noted that glEnable(GL_COLOR_MATERIAL) needed for correct tube colours. But this creates problems when displaying chemical features (they become solid yellow (with nvidia drivers?)). I currently don't understand what problems result if we do not enable GL_COLOR_MATERIAL here. (Mogul output markup seems OK?). So comment out. ------------------------------------------------------------------------ r4382 | pemsley | 2012-09-03 09:56:14 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Trivial change to ligand fitting debuggging. ------------------------------------------------------------------------ r4381 | pemsley | 2012-09-03 09:53:13 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Another go at fixing the python rotamer name test. ------------------------------------------------------------------------ r4380 | pemsley | 2012-09-03 09:12:51 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am Add named-rotamer-score.hh to Makefile.am ------------------------------------------------------------------------ r4379 | pemsley | 2012-09-03 01:26:17 +0100 (Mon, 03 Sep 2012) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python-tests/01_pdb_mtz.py Update tests now that set-residue-to-rotamer-number has an alt-conf arg. ------------------------------------------------------------------------ r4378 | pemsley | 2012-09-02 18:13:17 +0100 (Sun, 02 Sep 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/src/c-interface-maps.cc M /trunk/src/cc-interface.hh Add an extra param to map_to_model_correlation() specifying useful atom selections. ------------------------------------------------------------------------ r4377 | pemsley | 2012-09-02 16:08:49 +0100 (Sun, 02 Sep 2012) | 2 lines Changed paths: A /trunk/src/named-rotamer-score.hh Add missing header. ------------------------------------------------------------------------ r4376 | pemsley | 2012-09-02 15:38:42 +0100 (Sun, 02 Sep 2012) | 2 lines Changed paths: M /trunk/python/redefine_functions.py M /trunk/src/c-interface-residues.cc M /trunk/src/cc-interface.hh Add a python wrapper for score_rotamers(). ------------------------------------------------------------------------ r4375 | pemsley | 2012-09-02 15:00:53 +0100 (Sun, 02 Sep 2012) | 7 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/dnotes M /trunk/ligand/ligand.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/rel-todo M /trunk/scheme/redefine-functions.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc A /trunk/src/c-interface-residues.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h set_residue_to_rotamer_name() function added. score_rotamers() function added. Has SCM wrapper. Add an output stream function for a residue_probability_info_t. GetResidue(name) function for rotamer class set_dihedrals() abstraction in rotamer class. score_atoms() added for a map and a minimol residue. ------------------------------------------------------------------------ r4374 | b.lohkamp | 2012-09-01 21:11:20 +0100 (Sat, 01 Sep 2012) | 1 line Changed paths: M /trunk/src/rama_plot.cc Update rama zoom from rama resize. ------------------------------------------------------------------------ r4373 | pemsley | 2012-08-31 18:49:31 +0100 (Fri, 31 Aug 2012) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-modelling.cc Add are_all_one_atom_residues for residue vector refinement to handle HOH on HOH case (doesn't handle single HOH). ------------------------------------------------------------------------ r4372 | pemsley | 2012-08-31 18:45:13 +0100 (Fri, 31 Aug 2012) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi Add documentation for fill-partial-residue. ------------------------------------------------------------------------ r4371 | pemsley | 2012-08-31 18:40:29 +0100 (Fri, 31 Aug 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Add use-graphics-interface protection for update_descriptor_attributes() and flip/rotate widgets. ------------------------------------------------------------------------ r4370 | pemsley | 2012-08-30 13:15:39 +0100 (Thu, 30 Aug 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Add ifdef protection for handle_bond_picking_maybe(). ------------------------------------------------------------------------ r4369 | pemsley | 2012-08-30 13:06:57 +0100 (Thu, 30 Aug 2012) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/coot-user-manual.texi M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc Update coot ref in manual(!) Call close_yourself() for molecules in coot_real_exit(). Update notes. ------------------------------------------------------------------------ r4368 | pemsley | 2012-08-29 23:18:49 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/auxil/strand-analysis/Makefile.am M /trunk/auxil/vectors/Makefile.am Clean up (for automake) recent changes for make check. ------------------------------------------------------------------------ r4367 | pemsley | 2012-08-29 23:08:02 +0100 (Wed, 29 Aug 2012) | 3 lines Changed paths: M /trunk/configure.in guile-gui depends on a guile-gtk gui interface being present. If it is, force check for guile-gui too. ------------------------------------------------------------------------ r4366 | pemsley | 2012-08-29 22:38:32 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/auxil/sec-str/Makefile.am M /trunk/auxil/strand-analysis/Makefile.am M /trunk/auxil/vectors/Makefile.am M /trunk/lbg/alerts.cc M /trunk/lbg/graphics-c-interface-functions-blanks.cc M /trunk/lbg/lbg.hh M /trunk/lbg/test_lbg_functions.cc Small fix-ups so that make check works. ------------------------------------------------------------------------ r4365 | pemsley | 2012-08-29 20:06:14 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Remove some debugging. ------------------------------------------------------------------------ r4363 | pemsley | 2012-08-29 18:07:14 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add new targets, Ubuntu 10.04 and Debian Wheezy. ------------------------------------------------------------------------ r4362 | pemsley | 2012-08-29 17:18:04 +0100 (Wed, 29 Aug 2012) | 4 lines Changed paths: M /trunk/lbg/alerts.cc M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh No_python fixups. Add a bond pick handler. rotate/translate button press callbacks added (placeholders for action). ------------------------------------------------------------------------ r4361 | pemsley | 2012-08-29 17:16:19 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/python/extensions.py Trivial comment edit. ------------------------------------------------------------------------ r4360 | pemsley | 2012-08-29 12:16:10 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Re-add "Prune & Colour" (now simply "prune" because colouring no longer works). ------------------------------------------------------------------------ r4359 | pemsley | 2012-08-29 12:13:31 +0100 (Wed, 29 Aug 2012) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh Use "svn info" to get revision number. ------------------------------------------------------------------------ r4358 | b.lohkamp | 2012-08-29 11:53:06 +0100 (Wed, 29 Aug 2012) | 1 line Changed paths: M /trunk/ligand/find-waters.cc M /trunk/src/c-interface-network.cc Add timeout for curl functions - 10s to start with. ------------------------------------------------------------------------ r4357 | pemsley | 2012-08-28 15:10:44 +0100 (Tue, 28 Aug 2012) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/python/extensions.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface.h M /trunk/src/graphics-info-residues.cc Don't have a ligand view for a residue of less than 2 atoms. Dotted surfaces are now single-colour grey. ------------------------------------------------------------------------ r4356 | pemsley | 2012-08-28 14:01:36 +0100 (Tue, 28 Aug 2012) | 2 lines Changed paths: M /trunk/src/graphics-ligand-view.cc Trivial changes (for debugging). ------------------------------------------------------------------------ r4355 | pemsley | 2012-08-28 13:56:00 +0100 (Tue, 28 Aug 2012) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Use the Extension menu item to load tutorial data. ------------------------------------------------------------------------ r4354 | pemsley | 2012-08-28 13:55:01 +0100 (Tue, 28 Aug 2012) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Tweak the merge molecules scrollwindow size. ------------------------------------------------------------------------ r4353 | pemsley | 2012-08-28 13:54:11 +0100 (Tue, 28 Aug 2012) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Use NO_SIGNAL because this is used in a parallel thread. ------------------------------------------------------------------------ r4352 | pemsley | 2012-08-28 13:52:58 +0100 (Tue, 28 Aug 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Rework atom and bond addition so that non-bonded atoms are not added. ------------------------------------------------------------------------ r4351 | b.lohkamp | 2012-08-27 08:08:02 +0100 (Mon, 27 Aug 2012) | 4 lines Changed paths: M /trunk/build-it-win Update libcurl version for Windows build. On Windows build clean stable release. ------------------------------------------------------------------------ r4350 | b.lohkamp | 2012-08-26 14:30:16 +0100 (Sun, 26 Aug 2012) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/get_recent_pdbe.py Remove debug statements in get_recent_pdbe.py. Add a pythonic PDBe extensions submenu. ------------------------------------------------------------------------ r4349 | pemsley | 2012-08-26 12:42:02 +0100 (Sun, 26 Aug 2012) | 2 lines Changed paths: M /trunk/libgtkgraph/Makefile.am as-needed maths library addtion. ------------------------------------------------------------------------ r4348 | pemsley | 2012-08-26 12:31:40 +0100 (Sun, 26 Aug 2012) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple Update libcurl version. Update notes. ------------------------------------------------------------------------ r4347 | pemsley | 2012-08-26 12:30:48 +0100 (Sun, 26 Aug 2012) | 3 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/scheme/get-recent-pdbe.scm Yet more conservative limit when throwing image requests at server. PDBe functions in PDBe menu. ------------------------------------------------------------------------ r4346 | pemsley | 2012-08-24 18:12:13 +0100 (Fri, 24 Aug 2012) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Tweak size params for text entry in mutate sequence (fit loop) dialog. Addesses Abhinav Kumar's problem? ------------------------------------------------------------------------ r4345 | pemsley | 2012-08-24 16:32:44 +0100 (Fri, 24 Aug 2012) | 3 lines Changed paths: M /trunk/python/extensions.py M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh Add PISA menu items - including interfaces. Enable quick-save with USE_PYTHON. ------------------------------------------------------------------------ r4344 | pemsley | 2012-08-24 16:24:11 +0100 (Fri, 24 Aug 2012) | 2 lines Changed paths: M /trunk/README M /trunk/ccp4mg-utils/cartesian.cc M /trunk/ccp4mg-utils/cartesian.h M /trunk/ccp4mg-utils/mmut/mman_base.cc M /trunk/ccp4mg-utils/mmut/mman_base.h M /trunk/ccp4mg-utils/mmut/mman_manager.cc M /trunk/ccp4mg-utils/mmut/mman_manager.h M /trunk/ccp4mg-utils/mmut/mmut_bonds.cc M /trunk/ccp4mg-utils/mmut/mmut_bonds.h M /trunk/ccp4mg-utils/mmut/mmut_colour.cc M /trunk/ccp4mg-utils/mmut/mmut_colour.h M /trunk/ccp4mg-utils/mmut/mmut_connectivity.cc M /trunk/ccp4mg-utils/mmut/mmut_connectivity.h M /trunk/ccp4mg-utils/mmut/mmut_contact.cc M /trunk/ccp4mg-utils/mmut/mmut_contact.h M /trunk/ccp4mg-utils/mmut/mmut_hbond.cc M /trunk/ccp4mg-utils/mmut/mmut_hbond.h M /trunk/ccp4mg-utils/mmut/mmut_lipids.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.h M /trunk/ccp4mg-utils/mmut/mmut_morph.cc M /trunk/ccp4mg-utils/mmut/mmut_sasarea.cc M /trunk/ccp4mg-utils/mmut/mmut_sasarea.h M /trunk/ccp4mg-utils/mmut/mmut_sbase.cc M /trunk/ccp4mg-utils/mmut/mmut_sbase.h M /trunk/ccp4mg-utils/mmut/mmut_secstr.cc M /trunk/ccp4mg-utils/mmut/mmut_secstr.h M /trunk/ccp4mg-utils/mmut/mmut_spline.cc M /trunk/ccp4mg-utils/mmut/mmut_util.cc M /trunk/ccp4mg-utils/mmut/mmut_util.h M /trunk/ccp4mg-utils/mmut/splineinfo.h M /trunk/ccp4mg-utils/pygl/atom_util.cc M /trunk/ccp4mg-utils/pygl/atom_util.h M /trunk/ccp4mg-utils/pygl/billboard.cc M /trunk/ccp4mg-utils/pygl/build_tree_primitives.cc M /trunk/ccp4mg-utils/pygl/catmull.cc M /trunk/ccp4mg-utils/pygl/catmull.h M /trunk/ccp4mg-utils/pygl/cbuild.h M /trunk/ccp4mg-utils/pygl/cdisplayobject.cc M /trunk/ccp4mg-utils/pygl/cdisplayobject.h M /trunk/ccp4mg-utils/pygl/cprimitive.cc M /trunk/ccp4mg-utils/pygl/cprimitive.h M /trunk/ccp4mg-utils/pygl/font_info.cc M /trunk/ccp4mg-utils/pygl/font_info.h M /trunk/ccp4mg-utils/pygl/font_util.cc M /trunk/ccp4mg-utils/pygl/font_util.h M /trunk/ccp4mg-utils/pygl/freetype_dl.h M /trunk/ccp4mg-utils/pygl/freetype_font.cc M /trunk/ccp4mg-utils/pygl/freetype_font.h M /trunk/ccp4mg-utils/pygl/help.cc M /trunk/ccp4mg-utils/pygl/help.h M /trunk/ccp4mg-utils/pygl/lincrv.cc M /trunk/ccp4mg-utils/pygl/lincrv.h M /trunk/ccp4mg-utils/pygl/psutil.cc M /trunk/ccp4mg-utils/pygl/psutil.h M /trunk/ccp4mg-utils/pygl/qt-text.cc M /trunk/ccp4mg-utils/pygl/rgbreps.cc M /trunk/ccp4mg-utils/pygl/rgbreps.h M /trunk/ccp4mg-utils/pygl/sphere.cc M /trunk/ccp4mg-utils/pygl/sphere.h M /trunk/ccp4mg-utils/pygl/sphere_0.h M /trunk/ccp4mg-utils/pygl/sphere_4.h M /trunk/ccp4mg-utils/pygl/sphere_arrays.h M /trunk/ccp4mg-utils/pygl/splineset.cc M /trunk/ccp4mg-utils/pygl/subdivide.cc M /trunk/ccp4mg-utils/pygl/subdivide.h M /trunk/ccp4mg-utils/pygl/symmetry.cc M /trunk/ccp4mg-utils/pygl/symmetry.h M /trunk/ccp4mg-utils/pygl/text.cc M /trunk/ccp4mg-utils/pygl/texture.cc M /trunk/ccp4mg-utils/pygl/texture.h M /trunk/ccp4mg-utils/pygl/win_font.cc M /trunk/ccp4mg-utils/pygl/win_font.h M /trunk/ccp4mg-utils/pygl/x11_font.cc M /trunk/ccp4mg-utils/pygl/x11_font.h M /trunk/ccp4mg-utils/pygl/zsortps.cc M /trunk/ccp4mg-utils/util/cartesian.cc M /trunk/ccp4mg-utils/util/cartesian.h M /trunk/ccp4mg-utils/util/connect.cc M /trunk/ccp4mg-utils/util/connect.h M /trunk/ccp4mg-utils/util/geomutil.cc M /trunk/ccp4mg-utils/util/geomutil.h M /trunk/ccp4mg-utils/util/matrix.cc M /trunk/ccp4mg-utils/util/matrix.h M /trunk/ccp4mg-utils/util/mgtree.cc M /trunk/ccp4mg-utils/util/mgtree.h M /trunk/ccp4mg-utils/util/mgutil.cc M /trunk/ccp4mg-utils/util/mgutil.h M /trunk/ccp4mg-utils/util/plane.cc M /trunk/ccp4mg-utils/util/plane.h M /trunk/ccp4mg-utils/util/quat.cc M /trunk/ccp4mg-utils/util/quat.h M /trunk/ccp4mg-utils/util/redirect.cc M /trunk/ccp4mg-utils/util/redirect.h M /trunk/ccp4mg-utils/util/volume.cc M /trunk/ccp4mg-utils/util/volume.h M /trunk/coot-surface/rgbreps.cc M /trunk/coot-surface/rgbreps.h M /trunk/dnotes M /trunk/rel-todo M /trunk/src/coot_pythonmodule.cc M /trunk/surface/CXXChargeTable.cpp M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCoord.h M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXFFTSolventMap.h M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h M /trunk/surface/CXXNode.cpp M /trunk/surface/CXXNode.h M /trunk/surface/CXXQADSurface.cpp M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXSurfaceVertex.cpp M /trunk/surface/CXXSurfaceVertex.h M /trunk/surface/CXXTorusElement.cpp M /trunk/surface/CXXTorusElement.h M /trunk/surface/CXXTorusNode.cpp M /trunk/surface/CXXTorusNode.h M /trunk/surface/CXXTorusTriangle.cpp M /trunk/surface/CXXTorusTriangle.h M /trunk/surface/CXXTorusTriangle.h.h M /trunk/surface/CXXTriangle.cpp M /trunk/surface/CXXTriangle.h M /trunk/surface/TokenIterator.h M /trunk/surface/surface.cpp M /trunk/surface/surface.h Remove executable type on source code files. ------------------------------------------------------------------------ r4343 | pemsley | 2012-08-24 16:07:04 +0100 (Fri, 24 Aug 2012) | 2 lines Changed paths: M /trunk/python/parse_pisa_xml.py Restore generic pisa command. ------------------------------------------------------------------------ r4342 | b.lohkamp | 2012-08-24 15:23:09 +0100 (Fri, 24 Aug 2012) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/redefine_functions.py M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/graphics-info.h Complete pythonic version of map_to_model correlation and het_group_residues. Add pythonic residue_spec2residue_name. make_residue_spec() handles Python objects of length 4. Add shelx coordinate file extensions to command line args (without specifier). Add .pda files to know shelx coordinate files. Update notes. ------------------------------------------------------------------------ r4341 | pemsley | 2012-08-24 10:08:58 +0100 (Fri, 24 Aug 2012) | 4 lines Changed paths: M /trunk/macros/glut.m4 If glut is specified on the command line, it is going to be installed in $glut_prefix/lib, not $glut_prefix/$acl_libdirstem, I think. System libs use $acl_libdirstem though. ------------------------------------------------------------------------ r4340 | pemsley | 2012-08-23 23:36:18 +0100 (Thu, 23 Aug 2012) | 12 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/cycle-page-builder.scm M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/lbg.cc M /trunk/ligand/helix-placement.cc M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-maps.cc D /trunk/src/c-interface-network.hh M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/utils/coot-utils.cc calc_atom_map() has clipper exception protection added. map_to_model correlation function added. add scripting interface. n_non_hydrogen_atoms(comp_id) function added to dictionary. Helix placement function tweaked - density scoring function improved? cylinder radius increased. het_group_residues() function added to scripting. fle_view_set_water_dist_max() function added. fle_view_set_h_bond_dist_max() function added. make_residue_spec() handles SCM objects of length 4. residue-spec->residue-name scheme function added. ------------------------------------------------------------------------ r4339 | pemsley | 2012-08-23 19:16:59 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/macros/glut.m4 Use libdirstem for GLUT libraries for x86_64-unknown-linux-gnu. ------------------------------------------------------------------------ r4338 | pemsley | 2012-08-23 16:13:38 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-defines.cc check_if_in_save_symmetry_define(): tweak auto-generated symmetry filenames. ------------------------------------------------------------------------ r4337 | pemsley | 2012-08-23 16:03:25 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Fix up atom clicking stored values for distances to symmetry-related molecules. ------------------------------------------------------------------------ r4336 | pemsley | 2012-08-23 14:33:29 +0100 (Thu, 23 Aug 2012) | 3 lines Changed paths: M /trunk/ligand/ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/src/molecule-class-info-other.cc Add null protection for lack of model (null pointer) in minimol's setup(). Fixes Steffen Schmidt's bug. ------------------------------------------------------------------------ r4335 | pemsley | 2012-08-23 14:19:01 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r4334 | pemsley | 2012-08-23 14:18:28 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc Change the rock timeout interval. ------------------------------------------------------------------------ r4333 | pemsley | 2012-08-23 14:16:04 +0100 (Thu, 23 Aug 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/qed-interface.cc Add top-left correction for residue circles. Some debugging for QED strangeness. ------------------------------------------------------------------------ r4332 | pemsley | 2012-08-23 14:13:40 +0100 (Thu, 23 Aug 2012) | 2 lines Changed paths: M /trunk/macros/glut.m4 Add libdirstem usage for x86_64-*-linux-gnu. ------------------------------------------------------------------------ r4331 | pemsley | 2012-08-21 12:49:12 +0100 (Tue, 21 Aug 2012) | 2 lines Changed paths: M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4330 | pemsley | 2012-08-21 12:48:41 +0100 (Tue, 21 Aug 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in warning for ccp4 setup file missing. ------------------------------------------------------------------------ r4329 | pemsley | 2012-08-21 12:47:48 +0100 (Tue, 21 Aug 2012) | 2 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Improvements to parsing of PISA XML output for interfaces. ------------------------------------------------------------------------ r4328 | pemsley | 2012-08-21 12:46:19 +0100 (Tue, 21 Aug 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Remove debugging. ------------------------------------------------------------------------ r4327 | pemsley | 2012-08-21 12:45:49 +0100 (Tue, 21 Aug 2012) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Update to handle Tim's server. ------------------------------------------------------------------------ r4326 | b.lohkamp | 2012-08-20 17:08:47 +0100 (Mon, 20 Aug 2012) | 1 line Changed paths: M /trunk/src/globjects.cc Add green flash bond for keyboard chi editing. ------------------------------------------------------------------------ r4325 | pemsley | 2012-08-20 11:32:12 +0100 (Mon, 20 Aug 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debian /etc/issue handling for wheezy. ------------------------------------------------------------------------ r4324 | b.lohkamp | 2012-08-16 15:10:21 +0100 (Thu, 16 Aug 2012) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/pixmaps/glyco-structures.svg M /trunk/python/refmac.py M /trunk/src/molecule-class-info-residues.cc split_waters halves occupancy of water. Fix windows font for glyco-structures.svg. Fix read_refmac_log for newer refmac. ------------------------------------------------------------------------ r4323 | b.lohkamp | 2012-08-14 21:30:34 +0100 (Tue, 14 Aug 2012) | 4 lines Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/main.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Fix char, string conversion for version in title. Add simple ramachandran resize function. ------------------------------------------------------------------------ r4322 | b.lohkamp | 2012-08-14 12:32:18 +0100 (Tue, 14 Aug 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/src/main.cc Show Coot version in window title. ------------------------------------------------------------------------ r4321 | b.lohkamp | 2012-08-12 16:10:46 +0100 (Sun, 12 Aug 2012) | 3 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Fix all_molecule_ramachandran functions. ------------------------------------------------------------------------ r4320 | pemsley | 2012-08-10 16:23:57 +0100 (Fri, 10 Aug 2012) | 3 lines Changed paths: M /trunk/scheme/fitting.scm Fix up typo in fit-protein-fit-function so that refinement is run after auto-fit-best-rotamer. ------------------------------------------------------------------------ r4319 | pemsley | 2012-08-10 14:27:01 +0100 (Fri, 10 Aug 2012) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add function n_symops() for a given molecule number. ------------------------------------------------------------------------ r4318 | KevKeating | 2012-08-09 22:57:55 +0100 (Thu, 09 Aug 2012) | 1 line Changed paths: M /trunk/rcrane/CHANGELOG.txt M /trunk/rcrane/README.txt M /trunk/rcrane/about.py M /trunk/rcrane/pseudoMolecule.py M /trunk/rcrane/reviewSuitesGui.py M /trunk/rcrane/revisionNum.py M /trunk/rcrane/rotamerize.py Update RCrane to 1.0.2 (r444) ------------------------------------------------------------------------ r4317 | pemsley | 2012-08-08 18:08:34 +0100 (Wed, 08 Aug 2012) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Allow generic single entry (e.g. for SMILES) to expand. ------------------------------------------------------------------------ r4316 | pemsley | 2012-08-08 17:56:51 +0100 (Wed, 08 Aug 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update to handle version of debian in /etc/issue. ------------------------------------------------------------------------ r4315 | pemsley | 2012-08-07 20:07:14 +0100 (Tue, 07 Aug 2012) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add a link to google source list. ------------------------------------------------------------------------ r4314 | pemsley | 2012-08-07 18:23:48 +0100 (Tue, 07 Aug 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-h-bonds.cc M /trunk/coot-utils/coot-h-bonds.hh M /trunk/lbg/residue-circles.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Export hydrogen bond length for FLEV to graphics-info member data. Test for hydrogens fixed up, not used yet. ------------------------------------------------------------------------ r4313 | pemsley | 2012-08-07 15:01:22 +0100 (Tue, 07 Aug 2012) | 3 lines Changed paths: M /trunk/src/coot.in Fix long-standing problem with the crash catcher (it was not being executed because COOT_USE_GUILE was incorrectly quoted/substituted). ------------------------------------------------------------------------ r4312 | pemsley | 2012-08-07 01:43:15 +0100 (Tue, 07 Aug 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add a fix to loop over alt confs when drawing aromatic rings. ------------------------------------------------------------------------ r4311 | pemsley | 2012-08-07 00:04:14 +0100 (Tue, 07 Aug 2012) | 2 lines Changed paths: M /trunk/src/c-interface-test.cc Use the right network include file. ------------------------------------------------------------------------ r4310 | pemsley | 2012-08-06 17:37:01 +0100 (Mon, 06 Aug 2012) | 3 lines Changed paths: M /trunk/src/rama_plot.hh Add a type for the rama plot types enum - so that get_all_molecule_rama_score()'s use of make_pair() works. ------------------------------------------------------------------------ r4309 | b.lohkamp | 2012-08-05 16:39:53 +0100 (Sun, 05 Aug 2012) | 5 lines Changed paths: M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/redefine_functions.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.hh Add a split water button to toolbuttons. Add a function to retrive Ramachandran outliers (not working yet - as all_molecule_ramachandran_score - results in wrong probabilities). ------------------------------------------------------------------------ r4308 | pemsley | 2012-08-04 20:04:27 +0100 (Sat, 04 Aug 2012) | 16 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/read-sm-cif.cc M /trunk/coot-utils/read-sm-cif.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/torsion-bonds.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-network.cc M /trunk/src/c-interface-network.hh M /trunk/src/c-interface-test.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface-network.hh M /trunk/src/cmtz-interface.cc M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h ACA updates: Small molecule cif data reader - creating sigmaa maps (now fcf maps use this interface). Add interface to calculate atom map (not tested). Add debugging for torsion bonds (carbohydrate fitting debugging). Add --comp-id/comp_id command line argument. Add split water interface (which fits to map by jiggle). Rework residue info dialog to allow edits for alt confs. Add residue name to residue info dialog. Ctrl-i works now by active atom. Add flip and rotate buttons to lbg - non-active currently. on_canvas_button_press_new renamed to on_canvas_button_press. on_canvas_button_release_new renamed to on_canvas_release_new. Add fix up for ligand view of an alt confed residue. Add curl_make_a_post() - needs debugging/server. ------------------------------------------------------------------------ r4307 | b.lohkamp | 2012-07-29 21:48:38 +0100 (Sun, 29 Jul 2012) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info-navigation.cc Keyboard short cut update environment distances, labels etc. Update notes. ------------------------------------------------------------------------ r4306 | b.lohkamp | 2012-07-29 21:46:10 +0100 (Sun, 29 Jul 2012) | 4 lines Changed paths: M /trunk/python/fitting.py M /trunk/python/prodrg_import.py Fill properly pythonic get_sbase_monomer_and_overlay. Add pythonic version for add_extra_start_pos_restraints. ------------------------------------------------------------------------ r4305 | b.lohkamp | 2012-07-29 17:46:00 +0100 (Sun, 29 Jul 2012) | 6 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/user_define_restraints.py M /trunk/src/molecule-class-info.cc Fix molecule_name_stub for windows file names. Add simple python ProSmart gui. Add pythonic pubchem interface too (for chemical/drug lookups). Various other pythonic restraint manipulations. ------------------------------------------------------------------------ r4304 | b.lohkamp | 2012-07-29 16:00:16 +0100 (Sun, 29 Jul 2012) | 1 line Changed paths: M /trunk/python/Makefile.am A /trunk/python/user_define_restraints.py (from /trunk/python/user_defined_restraints.py:4303) D /trunk/python/user_defined_restraints.py Rename user_define(d)_restraints and distribute. ------------------------------------------------------------------------ r4303 | pemsley | 2012-07-27 15:01:22 +0100 (Fri, 27 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Correct position of user_defined_alerts_smarts_py declaration. ------------------------------------------------------------------------ r4302 | pemsley | 2012-07-27 13:39:52 +0100 (Fri, 27 Jul 2012) | 4 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot-utils.scm M /trunk/scheme/user-define-restraints.scm Add coot-replace string function and use it in constructing the file name for ProSMART output. Fix bad let form in transform-map-using-lsq-matrix. ------------------------------------------------------------------------ r4301 | pemsley | 2012-07-26 08:28:07 +0100 (Thu, 26 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/alerts.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/qed-interface.cc Rework user-defined alerts python interface. ------------------------------------------------------------------------ r4300 | pemsley | 2012-07-25 21:01:38 +0100 (Wed, 25 Jul 2012) | 6 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/alerts.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/flev.cc Add n_hydrogens() in the geometry dictionary. Add a function to check for hydrogens on the ligand and environment. Add extra items to lbg key. Add NULL protection for results of PyObject_GetAttrString() when looking for user-defined alert SMARTS. ------------------------------------------------------------------------ r4299 | pemsley | 2012-07-25 18:12:37 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/dnotes Notes on installing dependences for CentOS 6. ------------------------------------------------------------------------ r4298 | pemsley | 2012-07-25 18:00:19 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Partially implement the "show key" functionality. ------------------------------------------------------------------------ r4297 | pemsley | 2012-07-25 15:05:12 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/notes update notes. ------------------------------------------------------------------------ r4296 | pemsley | 2012-07-25 11:13:52 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/alerts.cc M /trunk/lbg/lbg.hh Add the ability to use user_defined alert SMARTS. ------------------------------------------------------------------------ r4295 | pemsley | 2012-07-25 10:21:55 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Add a save_molecule() to get_drug(). ------------------------------------------------------------------------ r4294 | pemsley | 2012-07-25 09:51:28 +0100 (Wed, 25 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Remove inappropriate function declaration. ------------------------------------------------------------------------ r4293 | pemsley | 2012-07-24 23:02:26 +0100 (Tue, 24 Jul 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add pubchem interface too (for chemical/drug lookups). ------------------------------------------------------------------------ r4292 | pemsley | 2012-07-24 23:01:30 +0100 (Tue, 24 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Add missing declaration. ------------------------------------------------------------------------ r4291 | pemsley | 2012-07-24 08:49:11 +0100 (Tue, 24 Jul 2012) | 5 lines Changed paths: M /trunk/ideal/simple-restraint.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/fitting.scm M /trunk/src/molecule-class-info-kk.cc Add start pos restraint only if it doesn't exist already for the atom. If it does, update it. Add a scripting layer wrapper to add starting position restraints for a given residue. ------------------------------------------------------------------------ r4290 | pemsley | 2012-07-24 08:43:02 +0100 (Tue, 24 Jul 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes Clear descriptor attributes on failure to kekulize. when generating SMILES string, don't strip hydrogens beforehand. ------------------------------------------------------------------------ r4289 | b.lohkamp | 2012-07-24 08:35:23 +0100 (Tue, 24 Jul 2012) | 1 line Changed paths: M /trunk/python/coot_toolbuttons.py Add a pre-defined cootilus button ------------------------------------------------------------------------ r4288 | b.lohkamp | 2012-07-24 08:34:54 +0100 (Tue, 24 Jul 2012) | 1 line Changed paths: M /trunk/src/c-interface.cc Fix typo: let molecule_name_stub_py be compiled with python ------------------------------------------------------------------------ r4287 | pemsley | 2012-07-23 17:03:26 +0100 (Mon, 23 Jul 2012) | 2 lines Changed paths: M /trunk/pixmaps/dna.svg tweak the dna icon. ------------------------------------------------------------------------ r4286 | pemsley | 2012-07-23 15:35:33 +0100 (Mon, 23 Jul 2012) | 2 lines Changed paths: M /trunk/src/c-interface-refine.cc M /trunk/src/molecule-class-info-refine.cc Fix up erase typo in extra bond restraint deletion. ------------------------------------------------------------------------ r4285 | pemsley | 2012-07-23 15:33:43 +0100 (Mon, 23 Jul 2012) | 3 lines Changed paths: M /trunk/src/molecule-class-info-build.cc Don't add hydrogen to residue if an atom of that name exists already (in that case, update the coords). ------------------------------------------------------------------------ r4284 | kevin.cowtan@gmail.com | 2012-07-23 15:17:44 +0100 (Mon, 23 Jul 2012) | 2 lines Changed paths: A /trunk/pixmaps/dna.svg svg DNA icon ------------------------------------------------------------------------ r4283 | pemsley | 2012-07-23 00:07:48 +0100 (Mon, 23 Jul 2012) | 2 lines Changed paths: M /trunk/python/prodrg_import.py M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.cc SBASE results overlay added. ------------------------------------------------------------------------ r4282 | pemsley | 2012-07-22 16:40:45 +0100 (Sun, 22 Jul 2012) | 4 lines Changed paths: M /trunk/dnotes M /trunk/python/redefine_functions.py M /trunk/rel-todo M /trunk/scheme/redefine-functions.scm M /trunk/scheme/user-define-restraints.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add molecule_name_stub function. Add simple ProSMART gui interface (user-defined-restraints). Use erase/remove_if to delete over-end-labels. ------------------------------------------------------------------------ r4281 | pemsley | 2012-07-21 11:10:55 +0100 (Sat, 21 Jul 2012) | 8 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ideal/extra-restraints.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/scheme/user-define-restraints.scm M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/utils/coot-utils.hh Additional handling of extra restraints. Use remove_if() to remove extra bond restraints that are too deviant. Add a refmac distance restraint reader (reading prosmart output). Delete extra distance restraints for a particular atom spec. Delete extra restraints for a particular residue. set_show_extra_restraints() for display toggling. NULL protection for operator<<() for CAtom * in mmdb.cc. ------------------------------------------------------------------------ r4280 | pemsley | 2012-07-19 16:56:46 +0100 (Thu, 19 Jul 2012) | 2 lines Changed paths: M /trunk/python/rcrane_loader.py Remove rcrane loading debugging. ------------------------------------------------------------------------ r4279 | pemsley | 2012-07-18 23:46:21 +0100 (Wed, 18 Jul 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use clipper_hack_version=2.1-110915-fixup-2 for updated clipper. ------------------------------------------------------------------------ r4278 | pemsley | 2012-07-18 23:44:46 +0100 (Wed, 18 Jul 2012) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.hh Energy lib get_torsion() now throws an exception on failing to find the torsion. ------------------------------------------------------------------------ r4277 | pemsley | 2012-07-17 14:27:38 +0100 (Tue, 17 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.hh M /trunk/lbg/notes sync notes. ------------------------------------------------------------------------ r4276 | pemsley | 2012-07-16 15:36:38 +0100 (Mon, 16 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/qed-interface.cc M /trunk/rel-todo Add a (by default, hidden) test-function button to lbg. ------------------------------------------------------------------------ r4275 | pemsley | 2012-07-16 15:32:15 +0100 (Mon, 16 Jul 2012) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Use clipper fixup-2, that contains fixes for reading mmcif files (initialization and r-free code corrected), ------------------------------------------------------------------------ r4274 | pemsley | 2012-07-14 17:36:31 +0100 (Sat, 14 Jul 2012) | 3 lines Changed paths: M /trunk/src/c-interface-network.cc Fix the problem of throwing an exception in get_drug_mdl_via_wikipedia_and_drugbank scripting functions. ------------------------------------------------------------------------ r4273 | pemsley | 2012-07-14 17:34:46 +0100 (Sat, 14 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Hide alerts gui elements without rdkit. ------------------------------------------------------------------------ r4272 | pemsley | 2012-07-13 22:25:37 +0100 (Fri, 13 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lig-build.hh Fix the problem of rotating dragged bond ignoring button-up. ------------------------------------------------------------------------ r4271 | pemsley | 2012-07-13 19:24:07 +0100 (Fri, 13 Jul 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debug $coot_dir_name link usage. ------------------------------------------------------------------------ r4270 | pemsley | 2012-07-13 14:09:53 +0100 (Fri, 13 Jul 2012) | 3 lines Changed paths: M /trunk/dnotes M /trunk/lbg/notes M /trunk/scheme/extensions.scm M /trunk/src/molecule-class-info-build.cc Trivial change: use coot-can-do-lidia? Clean up notes. ------------------------------------------------------------------------ r4269 | pemsley | 2012-07-13 00:05:16 +0100 (Fri, 13 Jul 2012) | 3 lines Changed paths: M /trunk/src/graphics-info-superpose.cc Fix up when writing out the alignment - by-passed crash ("strange" t_index values?) ------------------------------------------------------------------------ r4265 | pemsley | 2012-07-11 13:05:12 +0100 (Wed, 11 Jul 2012) | 2 lines Changed paths: M /trunk/python/rcrane_loader.py Remove debugging of rcrane loading. ------------------------------------------------------------------------ r4264 | pemsley | 2012-07-09 15:21:25 +0100 (Mon, 09 Jul 2012) | 4 lines Changed paths: M /trunk/build-it-gtk2-simple Update for systype, centos6 and debian. Add in hacks to get round york server failure. Use refmac dictionary from MRC. ------------------------------------------------------------------------ r4263 | b.lohkamp | 2012-07-09 09:19:59 +0100 (Mon, 09 Jul 2012) | 1 line Changed paths: M /trunk/lbg/alerts-list.cc M /trunk/lbg/alerts.cc M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-drag-and-drop.cc M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc Clean up python header include in lbg. ------------------------------------------------------------------------ r4261 | pemsley | 2012-07-05 22:41:02 +0100 (Thu, 05 Jul 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/notes Fill smiles strings for smiles lbg toolbar button. ------------------------------------------------------------------------ r4258 | b.lohkamp | 2012-07-02 12:33:34 +0100 (Mon, 02 Jul 2012) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/src/c-interface-network.cc Add pythonic version for get_drug_via_wikipedia_and_drugbank and get_drug_via_wikipedia_and_drugbank_py. ------------------------------------------------------------------------ r4257 | b.lohkamp | 2012-07-02 12:32:10 +0100 (Mon, 02 Jul 2012) | 1 line Changed paths: M /trunk/src/graphics-info.h Add .pha files to data file list. ------------------------------------------------------------------------ r4256 | b.lohkamp | 2012-07-02 12:31:19 +0100 (Mon, 02 Jul 2012) | 1 line Changed paths: M /trunk/src/c-interface-build.cc Protect get_monomer from empty strings. ------------------------------------------------------------------------ r4255 | b.lohkamp | 2012-07-02 12:30:05 +0100 (Mon, 02 Jul 2012) | 1 line Changed paths: M /trunk/src/c-interface-waters-gui.cc Save the correct min/max water-protein distances from the water search GUI. ------------------------------------------------------------------------ r4254 | pemsley | 2012-06-29 13:27:20 +0100 (Fri, 29 Jun 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes Show and hide manipulation for alerts. ------------------------------------------------------------------------ r4253 | pemsley | 2012-06-26 09:50:49 +0100 (Tue, 26 Jun 2012) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-network.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h When a molecule is closed, then the ligand thumbnail is no longer displayed. molecule_is_drawn_as_surface() predicate function added. Fix up hydrogen_grey_bond line-thinning logic. ------------------------------------------------------------------------ r4252 | pemsley | 2012-06-26 00:29:54 +0100 (Tue, 26 Jun 2012) | 3 lines Changed paths: M /trunk/src/molecule-class-info-build.cc Add protection for add_hydrogens_from_file, when the hydrogen file is not available. ------------------------------------------------------------------------ r4251 | pemsley | 2012-06-24 00:57:16 +0100 (Sun, 24 Jun 2012) | 2 lines Changed paths: A /trunk/src/cc-interface-network.hh Add missing network interface header. ------------------------------------------------------------------------ r4250 | pemsley | 2012-06-24 00:52:08 +0100 (Sun, 24 Jun 2012) | 7 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/wmolecule.cc M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-network.cc A /trunk/src/c-interface-network.hh M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Add another arg to the lbg() args, the function to get-drug given a drug name (gets the mdl mol file from drugbank via wikipedia). Scheme function get-drug-via-wikipedia added - python version needed. Add a user-agent header before curl_easy_perform(). Add a File -> Get Drug... menu item and hook it up to dialog and get-drug function. ------------------------------------------------------------------------ r4249 | b.lohkamp | 2012-06-23 17:18:41 +0100 (Sat, 23 Jun 2012) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/python/shelx.py Pythonic SHELX projects run on the 30/31st too. ------------------------------------------------------------------------ r4248 | pemsley | 2012-06-21 18:43:15 +0100 (Thu, 21 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade We want to see the alerts when we have rdkit and not python. ------------------------------------------------------------------------ r4247 | pemsley | 2012-06-19 14:20:53 +0100 (Tue, 19 Jun 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/lidia-core/rdkit-interface.cc M /trunk/scheme/extensions.scm Remove copying of files to biop in build-it. ------------------------------------------------------------------------ r4246 | pemsley | 2012-06-18 23:59:16 +0100 (Mon, 18 Jun 2012) | 2 lines Changed paths: M /trunk/scheme/generic-objects.scm For interactive-probe, use command-in-path-or-absolute? for *probe-command*. ------------------------------------------------------------------------ r4245 | pemsley | 2012-06-18 22:01:57 +0100 (Mon, 18 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Add protection for setting up silicos-it function. ------------------------------------------------------------------------ r4244 | pemsley | 2012-06-18 20:25:11 +0100 (Mon, 18 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/qed-interface.cc M /trunk/lbg/qed-interface.hh M /trunk/lbg/wmolecule.cc Add Python usage protection for qed functions. ------------------------------------------------------------------------ r4243 | pemsley | 2012-06-18 15:55:52 +0100 (Mon, 18 Jun 2012) | 2 lines Changed paths: M /trunk/scheme/shelx.scm For SHELX projects run on the 30/31st. Thanks Gabriele Balducci/ ------------------------------------------------------------------------ r4242 | pemsley | 2012-06-18 15:54:50 +0100 (Mon, 18 Jun 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Add a trap for invalid map when rigid body refining. Fixes Shawn W. bug I hope. ------------------------------------------------------------------------ r4241 | pemsley | 2012-06-16 13:09:25 +0100 (Sat, 16 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/qed-interface.cc M /trunk/lbg/qed-interface.hh Try to initialize qed on lbg start-up. ------------------------------------------------------------------------ r4240 | pemsley | 2012-06-15 11:59:11 +0100 (Fri, 15 Jun 2012) | 2 lines Changed paths: M /trunk/utils/coot-utils.cc Include unistd.h (for GCC 4.7?). ------------------------------------------------------------------------ r4239 | b.lohkamp | 2012-06-14 20:43:56 +0100 (Thu, 14 Jun 2012) | 1 line Changed paths: M /trunk/lbg/lbg.hh Initialise alert_group not only for ENTERPRISE_TOOLS ------------------------------------------------------------------------ r4238 | pemsley | 2012-06-14 13:45:47 +0100 (Thu, 14 Jun 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Assign hetatoms to all models (thanks Justin L.) ------------------------------------------------------------------------ r4237 | pemsley | 2012-06-14 13:44:28 +0100 (Thu, 14 Jun 2012) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc In create_mmdbmanager_from_mmdbmanager() transfer all models. (Thanks Justin L.) ------------------------------------------------------------------------ r4236 | pemsley | 2012-06-14 13:42:03 +0100 (Thu, 14 Jun 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc translate to origin for all models (thanks Justing L.). ------------------------------------------------------------------------ r4235 | pemsley | 2012-06-14 09:39:47 +0100 (Thu, 14 Jun 2012) | 6 lines Changed paths: M /trunk/lbg/alerts-list.cc M /trunk/lbg/alerts.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes Name alerts where I can, add a text label on the gui for the alert name. Show alerts. initialize draw_flev_annotations_flag. Improve memory management for query molecule. Add atom index properties to atoms (as strings). ------------------------------------------------------------------------ r4234 | pemsley | 2012-06-11 23:15:59 +0100 (Mon, 11 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/qed-interface.cc Check pFunc for null before calling PyCallable_Check(). ------------------------------------------------------------------------ r4233 | pemsley | 2012-06-11 12:30:14 +0100 (Mon, 11 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Clean up some lbg debugging. ------------------------------------------------------------------------ r4232 | pemsley | 2012-06-11 10:49:03 +0100 (Mon, 11 Jun 2012) | 2 lines Changed paths: A /trunk/lbg/alerts-list.cc Add alerts list. ------------------------------------------------------------------------ r4231 | pemsley | 2012-06-10 19:04:28 +0100 (Sun, 10 Jun 2012) | 6 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/dnotes M /trunk/lbg/Makefile.am M /trunk/lbg/alerts.cc M /trunk/lbg/alerts.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lidia-core/rdkit-interface.cc M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/flev.cc M /trunk/src/graphics-info.cc Add alerts notification. Rework qed notification. Add atom masses in rdkit_mol(widgeted_molecule_t). Add update_desciptor_attributes(). Remove some debuggings. ------------------------------------------------------------------------ r4230 | kevin.cowtan@gmail.com | 2012-06-08 16:59:29 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info.h Simplified updating of models using newly public update_model_after_additions ------------------------------------------------------------------------ r4229 | kevin.cowtan@gmail.com | 2012-06-08 15:23:37 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add new nucleotides to existing NuclAcid model if it exists. ------------------------------------------------------------------------ r4228 | pemsley | 2012-06-08 14:27:01 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/lbg/Makefile.am Add alerts.hh to the Makefile.am ------------------------------------------------------------------------ r4227 | pemsley | 2012-06-08 14:26:19 +0100 (Fri, 08 Jun 2012) | 4 lines Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/alerts.cc A /trunk/lbg/alerts.hh M /trunk/lbg/lbg.cc M /trunk/lbg/qed-interface.cc M /trunk/lbg/qed-interface.hh Improve the molecule manipulation and function look up so that calling qed's default() works. Add alerts, but not plugged in yet. ------------------------------------------------------------------------ r4226 | pemsley | 2012-06-08 14:17:50 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh Abstract rdkit_sanitize_mol() so that it works when called with a RWMol ref. ------------------------------------------------------------------------ r4225 | kevin.cowtan@gmail.com | 2012-06-08 13:37:14 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/cootilus/cootilus-build.cpp Shift built nucleic acids close to current view centre ------------------------------------------------------------------------ r4224 | kevin.cowtan@gmail.com | 2012-06-08 13:06:50 +0100 (Fri, 08 Jun 2012) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Nucleic acid autobuilding. (Preliminary) ------------------------------------------------------------------------ r4223 | b.lohkamp | 2012-06-07 22:24:30 +0100 (Thu, 07 Jun 2012) | 4 lines Changed paths: M /trunk/python/jligand.py M /trunk/scheme/jligand.scm Pythonic jligand, dont pass FILE for standard amino acids (maybe that was a previously problem for jligand on windows). Complete standard aa list in scheme. ------------------------------------------------------------------------ r4222 | kevin.cowtan@gmail.com | 2012-06-07 13:45:26 +0100 (Thu, 07 Jun 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am Add cootilus to include path ------------------------------------------------------------------------ r4221 | b.lohkamp | 2012-06-05 16:51:57 +0100 (Tue, 05 Jun 2012) | 1 line Changed paths: M /trunk/src/command-line.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh M /trunk/windows/WinCoot_install_masta.nsi Add mtz and script files to command-line. ------------------------------------------------------------------------ r4218 | pemsley | 2012-06-04 18:05:07 +0100 (Mon, 04 Jun 2012) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh Add simple_restraint (which refines given a dictionary_residue_restriants_t and a CResidue *. And update_coords() from an RDKit molecule from the coords in a CResidue *. ------------------------------------------------------------------------ r4217 | pemsley | 2012-06-04 18:02:45 +0100 (Mon, 04 Jun 2012) | 2 lines Changed paths: M /trunk/scheme/jligand.scm Don't pass FILE info for standard amino acids - JLigand doesn't like that. ------------------------------------------------------------------------ r4216 | b.lohkamp | 2012-06-03 19:05:38 +0100 (Sun, 03 Jun 2012) | 1 line Changed paths: M /trunk/coot-utils/elastic.cc Fix random for windows. ------------------------------------------------------------------------ r4213 | pemsley | 2012-06-03 13:42:44 +0100 (Sun, 03 Jun 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/lbg/Makefile.am M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh A /trunk/lbg/qed-interface.cc A /trunk/lbg/qed-interface.hh M /trunk/src/flev.cc Add qed interface functions - not working yet, not called. ------------------------------------------------------------------------ r4209 | pemsley | 2012-06-01 06:46:29 +0100 (Fri, 01 Jun 2012) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-mogul.cc M /trunk/src/graphics-info.cc Change colouring of solid tubes. Make arcs smoother. ------------------------------------------------------------------------ r4208 | pemsley | 2012-06-01 06:36:20 +0100 (Fri, 01 Jun 2012) | 2 lines Changed paths: M /trunk/python/redefine_functions.py Add redefine for get_residue_by_type. ------------------------------------------------------------------------ r4207 | pemsley | 2012-06-01 06:35:38 +0100 (Fri, 01 Jun 2012) | 2 lines Changed paths: M /trunk/coot-utils/test-elastic.cc Add maths testing function, not used. ------------------------------------------------------------------------ r4206 | kevin.cowtan@gmail.com | 2012-05-31 13:20:10 +0100 (Thu, 31 May 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am Add cootilus to dependencies. ------------------------------------------------------------------------ r4205 | pemsley | 2012-05-30 23:51:00 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/rel-todo M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/molecule-class-info-maps.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Add command-line pdbs. ------------------------------------------------------------------------ r4204 | pemsley | 2012-05-30 18:57:11 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Adjust drawing of solvent accessibility halos. ------------------------------------------------------------------------ r4203 | pemsley | 2012-05-30 18:55:52 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Extra docs for moving atoms. ------------------------------------------------------------------------ r4202 | pemsley | 2012-05-30 18:55:13 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Test altconfs for partially-split dictionary hetgroup. ------------------------------------------------------------------------ r4200 | pemsley | 2012-05-30 15:49:25 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add a function to remove redundant plane restraints. ------------------------------------------------------------------------ r4199 | pemsley | 2012-05-30 14:04:54 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.hh Don't allow bond order to change in get_bond(). ------------------------------------------------------------------------ r4198 | kevin.cowtan@gmail.com | 2012-05-30 09:29:00 +0100 (Wed, 30 May 2012) | 2 lines Changed paths: A /trunk/cootilus/nautilus_lib.pdb Add nautilus lib ------------------------------------------------------------------------ r4197 | kevin.cowtan@gmail.com | 2012-05-29 14:21:34 +0100 (Tue, 29 May 2012) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in Update build system to build cootilus.... .... if I'm very lucky ------------------------------------------------------------------------ r4196 | kevin.cowtan@gmail.com | 2012-05-29 14:16:35 +0100 (Tue, 29 May 2012) | 2 lines Changed paths: A /trunk/cootilus A /trunk/cootilus/Makefile.am A /trunk/cootilus/cootilus-build.cpp A /trunk/cootilus/cootilus-build.h A /trunk/cootilus/cootilus-demo.cpp A /trunk/cootilus/nautilus-join.cpp A /trunk/cootilus/nautilus-join.h A /trunk/cootilus/nautilus-ss-find.cpp A /trunk/cootilus/nautilus-ss-find.h A /trunk/cootilus/nautilus-target.cpp A /trunk/cootilus/nautilus-target.h A /trunk/cootilus/nautilus-tools.cpp A /trunk/cootilus/nautilus-tools.h A /trunk/cootilus/nucleicacid_db.cpp A /trunk/cootilus/nucleicacid_db.h Add cootilus files for fast Nucleic Acid building. ------------------------------------------------------------------------ r4195 | pemsley | 2012-05-28 13:48:09 +0100 (Mon, 28 May 2012) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh A /trunk/coot-utils/elastic.cc A /trunk/coot-utils/elastic.hh A /trunk/coot-utils/test-elastic.cc Add elastic: make atom-atom pairs given atom selection and distance criteria. ------------------------------------------------------------------------ r4194 | pemsley | 2012-05-27 18:39:17 +0100 (Sun, 27 May 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Map colouring changes for negative level too. ------------------------------------------------------------------------ r4193 | pemsley | 2012-05-27 18:31:54 +0100 (Sun, 27 May 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Tone down super-shiny solid-rendered maps. ------------------------------------------------------------------------ r4192 | b.lohkamp | 2012-05-27 16:48:42 +0100 (Sun, 27 May 2012) | 3 lines Changed paths: M /trunk/python/coot_utils.py Add truely pythonic versions of macros NoBackups, AutoAccept and UsingActiveAtom. To be used with 'with'. ------------------------------------------------------------------------ r4191 | pemsley | 2012-05-27 01:24:10 +0100 (Sun, 27 May 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Speed-up tweak to non-bonded and bond derivatives. ------------------------------------------------------------------------ r4190 | pemsley | 2012-05-24 10:30:33 +0100 (Thu, 24 May 2012) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Fix FAQ typo. ------------------------------------------------------------------------ r4189 | b.lohkamp | 2012-05-23 09:04:43 +0100 (Wed, 23 May 2012) | 1 line Changed paths: M /trunk/src/c-interface-ligands.cc Fix reference counting for get_residue_by_type_py. ------------------------------------------------------------------------ r4188 | pemsley | 2012-05-22 15:29:39 +0100 (Tue, 22 May 2012) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add a function to return a residue spec for a given residue type. ------------------------------------------------------------------------ r4187 | pemsley | 2012-05-22 11:25:00 +0100 (Tue, 22 May 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Remove pow() from torsion gradients. ------------------------------------------------------------------------ r4186 | b.lohkamp | 2012-05-20 18:05:37 +0100 (Sun, 20 May 2012) | 1 line Changed paths: M /trunk/python/coot_utils.py Rework pythonic using_active_atom to work with argument lists. ------------------------------------------------------------------------ r4185 | pemsley | 2012-05-19 08:45:24 +0100 (Sat, 19 May 2012) | 2 lines Changed paths: A /trunk/src/mmcif-sfs-to-mtz-main.cc Add mmcif-sfs-to-mtz-main.cc. ------------------------------------------------------------------------ r4184 | pemsley | 2012-05-19 01:26:44 +0100 (Sat, 19 May 2012) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Add molecule number protect in compate ligand atom types function. ------------------------------------------------------------------------ r4183 | b.lohkamp | 2012-05-17 21:14:28 +0100 (Thu, 17 May 2012) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/redefine_functions.py M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Add simple functio to display info_dialog and print text to console (usefull for warning and error messages). Used in make_backup. ------------------------------------------------------------------------ r4182 | b.lohkamp | 2012-05-17 21:10:27 +0100 (Thu, 17 May 2012) | 3 lines Changed paths: M /trunk/src/main.cc Disable new screen size determination for windows as gdk_property_get does not exist (yet). ------------------------------------------------------------------------ r4181 | b.lohkamp | 2012-05-17 21:07:54 +0100 (Thu, 17 May 2012) | 2 lines Changed paths: M /trunk/macros/with-python.m4 No extra_dl_lib for windows and cleanup gcc version testing. ------------------------------------------------------------------------ r4180 | pemsley | 2012-05-17 15:34:53 +0100 (Thu, 17 May 2012) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Use import_rcrane_wrapper() if possible. ------------------------------------------------------------------------ r4179 | pemsley | 2012-05-17 15:33:59 +0100 (Thu, 17 May 2012) | 2 lines Changed paths: M /trunk/python/rcrane_loader.py Rework pythonic rcrane loader. ------------------------------------------------------------------------ r4178 | pemsley | 2012-05-17 15:32:22 +0100 (Thu, 17 May 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/notes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r4177 | pemsley | 2012-05-17 15:28:53 +0100 (Thu, 17 May 2012) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Incorporate new ubuntu builds. ------------------------------------------------------------------------ r4176 | pemsley | 2012-05-16 15:42:13 +0100 (Wed, 16 May 2012) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Change test to use "test" not "]", "[" (which get substituted). ------------------------------------------------------------------------ r4175 | pemsley | 2012-05-16 13:03:59 +0100 (Wed, 16 May 2012) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Add hacky code to set extra_dl_lib (not sure when it is needed). First attempt. ------------------------------------------------------------------------ r4174 | pemsley | 2012-05-16 12:28:15 +0100 (Wed, 16 May 2012) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Add -Wno-unsed-but-set-variable for guile compilation. Update curl to 7.25.0. ------------------------------------------------------------------------ r4173 | pemsley | 2012-05-15 16:38:14 +0100 (Tue, 15 May 2012) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am protein-geometry, hence lidia-core depends on mini-mol includes (atom-quads.hh). ------------------------------------------------------------------------ r4171 | pemsley | 2012-05-14 15:56:39 +0100 (Mon, 14 May 2012) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/geometry-graphs.cc Improve energy lib bond lookup. Add coordinates from mol to dictionary and write them out. Don't manipulate ring torsions. ------------------------------------------------------------------------ r4170 | b.lohkamp | 2012-05-13 13:32:00 +0100 (Sun, 13 May 2012) | 1 line Changed paths: M /trunk/src/main.cc Better estimate of effective screen size for small screen testing. ------------------------------------------------------------------------ r4169 | b.lohkamp | 2012-05-13 13:31:25 +0100 (Sun, 13 May 2012) | 1 line Changed paths: M /trunk/geometry/energy-lib.cc Fix missing return in enery lib torsion. ------------------------------------------------------------------------ r4168 | b.lohkamp | 2012-05-13 13:11:01 +0100 (Sun, 13 May 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py Enable pythonic redefine_functions. ------------------------------------------------------------------------ r4167 | pemsley | 2012-05-12 17:18:52 +0100 (Sat, 12 May 2012) | 2 lines Changed paths: M /trunk/src/main.cc The setting of get_url_func_pointer is dependent on USE_LIBCURL. ------------------------------------------------------------------------ r4166 | b.lohkamp | 2012-05-12 14:01:35 +0100 (Sat, 12 May 2012) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py Add pythonic function set_alt_conf_occ to change occupancies of alt confs and add a slider gui for this Load all icons for toolbar manager at size 16x16 ------------------------------------------------------------------------ r4165 | pemsley | 2012-05-09 23:56:37 +0100 (Wed, 09 May 2012) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.hh Add bond types when looking up bonds. ------------------------------------------------------------------------ r4163 | pemsley | 2012-05-09 10:21:04 +0100 (Wed, 09 May 2012) | 2 lines Changed paths: M /trunk/coot-utils/read-sm-cif.cc Add an error message when failing to read small molecule cif. ------------------------------------------------------------------------ r4162 | b.lohkamp | 2012-05-09 09:33:50 +0100 (Wed, 09 May 2012) | 1 line Changed paths: M /trunk/python/user_defined_restraints.py M /trunk/scheme/user-define-restraints.scm fix refmac keyword for external restraints ------------------------------------------------------------------------ r4161 | pemsley | 2012-05-08 08:54:40 +0100 (Tue, 08 May 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Handle the addition of atoms at END card. ------------------------------------------------------------------------ r4160 | pemsley | 2012-05-07 15:07:49 +0100 (Mon, 07 May 2012) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc Angle lookup permissives should be 1 and 3. ------------------------------------------------------------------------ r4158 | pemsley | 2012-05-06 18:09:37 +0100 (Sun, 06 May 2012) | 11 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/dnotes M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add fall-back contacts-based apply_torsion() in torsion_match class. Add compare_ligand_atom_types_scm to compare residue atom types (based on a graph match). energy_lib cif functions into energy_lib_t class rather than protein_geometry. Fixups for energy lib parsers Fixups for monomer restraints write_cif(). look_ups for bonds, angles and torsion based on atom types. conservatively_replace_with_bonds() added, to replace restraints. is_ring_torsion() function added. torsion() function added to atom_name_quad class. ------------------------------------------------------------------------ r4157 | b.lohkamp | 2012-05-05 16:42:01 +0100 (Sat, 05 May 2012) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/src/c-interface-build.cc delete_atom deletes residue if there is only 1 atom left in residue. ------------------------------------------------------------------------ r4156 | KevKeating | 2012-05-04 19:49:22 +0100 (Fri, 04 May 2012) | 1 line Changed paths: M /trunk/rcrane/CHANGELOG.txt M /trunk/rcrane/README.txt M /trunk/rcrane/about.py M /trunk/rcrane/coot_gui_adapter.py M /trunk/rcrane/coot_utils_adapter.py M /trunk/rcrane/revisionNum.py update RCrane to work with the "outsourced" function redefinitions (r4146) ------------------------------------------------------------------------ r4155 | pemsley | 2012-05-03 13:28:49 +0100 (Thu, 03 May 2012) | 5 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/scheme/redefine-functions.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh Add pdbx descriptors to a dictionary residue restraint. Add auto_load_dictionary(comp_id) and reload_dictionary(comp_id). Add dictionary_entries() returning a string list of comp-ids. Add SMILES_for_comp_id() returning #f/False or a string. ------------------------------------------------------------------------ r4154 | b.lohkamp | 2012-05-02 16:21:49 +0100 (Wed, 02 May 2012) | 1 line Changed paths: M /trunk/python/mutate.py fix no of args in pythonic delete_sidechain_range ------------------------------------------------------------------------ r4153 | b.lohkamp | 2012-05-02 16:18:17 +0100 (Wed, 02 May 2012) | 1 line Changed paths: M /trunk/python/mutate.py fix typo in pythonic delete_sidechain_range ------------------------------------------------------------------------ r4151 | pemsley | 2012-05-02 12:52:59 +0100 (Wed, 02 May 2012) | 2 lines Changed paths: M /trunk/analysis/mogul.cc M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/src/flev.cc make_residue() now takes a residue name arg too. ------------------------------------------------------------------------ r4149 | b.lohkamp | 2012-05-01 17:40:00 +0100 (Tue, 01 May 2012) | 2 lines Changed paths: M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h Add full screen mode (using GTK) and python toolbuttons with it. ------------------------------------------------------------------------ r4148 | pemsley | 2012-05-01 13:35:13 +0100 (Tue, 01 May 2012) | 3 lines Changed paths: M /trunk/src/graphics-info-gui.cc Fixup for widget-attached chain-id handling on OXT addition. Fixes crash on mac? ------------------------------------------------------------------------ r4147 | b.lohkamp | 2012-05-01 12:08:56 +0100 (Tue, 01 May 2012) | 3 lines Changed paths: M /trunk/windows/WinCoot_install_masta.nsi A /trunk/windows/runwincoot.bat A /trunk/windows/runwincoot_ccp4.bat A /trunk/windows/runwincoot_ccp4_vista.bat Windows uses CLIBD_MON if available otherwise override with COOT_REFMAC_LIB_DIR using own dictionaries. ------------------------------------------------------------------------ r4146 | b.lohkamp | 2012-05-01 11:56:11 +0100 (Tue, 01 May 2012) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py A /trunk/python/redefine_functions.py M /trunk/src/c-interface.h Prepare to 'outsource' the redefining functions (but not done yet, breaks rcrane currently) ------------------------------------------------------------------------ r4143 | pemsley | 2012-04-30 14:24:25 +0100 (Mon, 30 Apr 2012) | 4 lines Changed paths: M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/geometry/protein-geometry.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/use-rdkit.hh Add "zero-number-of-restraints" protection when writing out mmCIF restraints (no empty loops). Extend mogul restraints interface. ------------------------------------------------------------------------ r4141 | pemsley | 2012-04-23 17:16:18 +0100 (Mon, 23 Apr 2012) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm A /trunk/scheme/redefine-functions.scm Move all the function redefinition (new names) to their own .scm file. ------------------------------------------------------------------------ r4140 | pemsley | 2012-04-23 11:00:52 +0100 (Mon, 23 Apr 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/notes Update notes. ------------------------------------------------------------------------ r4139 | pemsley | 2012-04-23 11:00:01 +0100 (Mon, 23 Apr 2012) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc Add a call to set_debug_wiggly_ligands() if ligand verbose reporting is on in exectute_ligand_search_internal(). ------------------------------------------------------------------------ r4138 | pemsley | 2012-04-23 10:43:26 +0100 (Mon, 23 Apr 2012) | 2 lines Changed paths: M /trunk/libgtkgraph/Makefile.am Add GLIB_CFLAGS to includes. ------------------------------------------------------------------------ r4137 | pemsley | 2012-04-23 10:42:52 +0100 (Mon, 23 Apr 2012) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh Make a write_file() function for a residue. ------------------------------------------------------------------------ r4136 | pemsley | 2012-04-23 10:08:00 +0100 (Mon, 23 Apr 2012) | 2 lines Changed paths: M /trunk/analysis/mogul-interface.hh Add a namespace to make_restraints() (for subsequent swig usage). ------------------------------------------------------------------------ r4135 | pemsley | 2012-04-21 15:55:57 +0100 (Sat, 21 Apr 2012) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh Move interface declarations to .hh, because the abstraction uses a std::vector. Python version enabled. ------------------------------------------------------------------------ r4134 | pemsley | 2012-04-20 13:32:20 +0100 (Fri, 20 Apr 2012) | 2 lines Changed paths: M /trunk/ligand/wligand.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h get_conformers() added to wligand.hh and made available to scripting. ------------------------------------------------------------------------ r4133 | pemsley | 2012-04-20 11:19:02 +0100 (Fri, 20 Apr 2012) | 2 lines Changed paths: M /trunk/ideal/torsion-bonds.cc Remove debugging output in torsion trial map fit. ------------------------------------------------------------------------ r4132 | KevKeating | 2012-04-17 15:36:02 +0100 (Tue, 17 Apr 2012) | 1 line Changed paths: M /trunk/python/rcrane_loader.py Simplify the warning message when an old version of RCrane is found ------------------------------------------------------------------------ r4131 | KevKeating | 2012-04-16 23:16:16 +0100 (Mon, 16 Apr 2012) | 1 line Changed paths: M /trunk/python/rcrane_loader.py Coot now checks for old versions of RCrane and prevents them from running (since they would conflict with the current version of RCrane) ------------------------------------------------------------------------ r4130 | pemsley | 2012-04-16 23:04:49 +0100 (Mon, 16 Apr 2012) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Remove some output about bad fits. ------------------------------------------------------------------------ r4129 | KevKeating | 2012-04-16 19:49:31 +0100 (Mon, 16 Apr 2012) | 1 line Changed paths: M /trunk/rcrane/CHANGELOG.txt M /trunk/rcrane/README.txt M /trunk/rcrane/about.py M /trunk/rcrane/revisionNum.py Updating RCrane to v1.0 (r439) ------------------------------------------------------------------------ r4128 | pemsley | 2012-04-16 18:24:57 +0100 (Mon, 16 Apr 2012) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Use hetify_residues_as_needed() on ligand fitting results. ------------------------------------------------------------------------ r4127 | pemsley | 2012-04-16 18:24:12 +0100 (Mon, 16 Apr 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add hetify_residues_as_needed (given a CMMDBManager). ------------------------------------------------------------------------ r4126 | pemsley | 2012-04-16 11:54:00 +0100 (Mon, 16 Apr 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix item_py typo in display_maps_py(). ------------------------------------------------------------------------ r4125 | b.lohkamp | 2012-04-15 14:03:31 +0100 (Sun, 15 Apr 2012) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python/clear_backup.py M /trunk/python/coot_utils.py M /trunk/python/jligand.py M /trunk/python/jligand_gui.py Enable use of FILE in pythonic jligand interface. ------------------------------------------------------------------------ r4124 | b.lohkamp | 2012-04-15 13:50:12 +0100 (Sun, 15 Apr 2012) | 1 line Changed paths: M /trunk/ccp4mg-utils/ppmutil.cc Fix ppmutil.cc for use with newer (1.4/5) libpng ------------------------------------------------------------------------ r4123 | pemsley | 2012-04-15 08:24:15 +0100 (Sun, 15 Apr 2012) | 2 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/src/c-interface.cc Fill display_maps_py(). ------------------------------------------------------------------------ r4122 | pemsley | 2012-04-13 19:49:55 +0100 (Fri, 13 Apr 2012) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add display-maps function (avoids the graphics_draw() when maps are undisplayed). ------------------------------------------------------------------------ r4121 | KevKeating | 2012-04-13 18:10:44 +0100 (Fri, 13 Apr 2012) | 2 lines Changed paths: M /trunk/rcrane/README.txt M /trunk/rcrane/menu.py M /trunk/rcrane/revisionNum.py M /trunk/windows/WinCoot_install_masta.nsi Update RCrane to r435 Add RCrane directories to WinCoot installer ------------------------------------------------------------------------ r4120 | KevKeating | 2012-04-12 21:52:46 +0100 (Thu, 12 Apr 2012) | 1 line Changed paths: M /trunk/python/rcrane_loader.py fix compatibility issue with the RCrane launch menu item ------------------------------------------------------------------------ r4119 | KevKeating | 2012-04-12 20:34:05 +0100 (Thu, 12 Apr 2012) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in A /trunk/python/rcrane_loader.py A /trunk/rcrane/Makefile.am M /trunk/rcrane/about.py M /trunk/rcrane/revisionNum.py Update RCrane to r433 RCrane is now properly installed with Coot ------------------------------------------------------------------------ r4118 | pemsley | 2012-04-12 16:36:43 +0100 (Thu, 12 Apr 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.hh Fix typo in endif documentation. ------------------------------------------------------------------------ r4117 | pemsley | 2012-04-12 16:10:12 +0100 (Thu, 12 Apr 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/notes Lighten and unref contour plots dashes. ------------------------------------------------------------------------ r4115 | KevKeating | 2012-04-12 15:58:43 +0100 (Thu, 12 Apr 2012) | 1 line Changed paths: M /trunk A /trunk/rcrane (from /branches/rcrane/rcrane:4114) Merge rcrane branch to trunk ------------------------------------------------------------------------ r4110 | pemsley | 2012-04-11 22:18:17 +0100 (Wed, 11 Apr 2012) | 2 lines Changed paths: M /trunk/src/Makefile.am Add dots-representation.hh to Makefile.am ------------------------------------------------------------------------ r4109 | KevKeating | 2012-04-11 19:25:38 +0100 (Wed, 11 Apr 2012) | 1 line Changed paths: M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface.h Add python_representation_kk() function that's faster than python_representation() ------------------------------------------------------------------------ r4108 | pemsley | 2012-04-11 14:43:35 +0100 (Wed, 11 Apr 2012) | 2 lines Changed paths: M /trunk/scheme/clear-backup.scm Don't print "There are xx old files (xxs bytes)" when cleaing backups. ------------------------------------------------------------------------ r4107 | pemsley | 2012-04-11 14:30:32 +0100 (Wed, 11 Apr 2012) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-colour.hh A /trunk/src/dots-representation.hh M /trunk/src/graphics-info.cc A /trunk/src/molecule-class-info-dots.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add (back) the ability to have atom selection dots be a single colour. unset_dots_colour() added (reverts to colour by atom-element). Rework dots_colour of molecule_class_info and split out dots-representation. ------------------------------------------------------------------------ r4106 | pemsley | 2012-04-11 14:21:48 +0100 (Wed, 11 Apr 2012) | 3 lines Changed paths: M /trunk/goograph/goograph.cc create a new goograph, no deletion (and subsequent crashing) when it goes out of scope. ------------------------------------------------------------------------ r4105 | pemsley | 2012-04-11 11:03:10 +0100 (Wed, 11 Apr 2012) | 2 lines Changed paths: M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4104 | pemsley | 2012-04-11 11:02:23 +0100 (Wed, 11 Apr 2012) | 2 lines Changed paths: M /trunk/pixmaps/glyco-structures.svg Shift the label a bit. ------------------------------------------------------------------------ r4103 | pemsley | 2012-04-09 22:10:38 +0100 (Mon, 09 Apr 2012) | 3 lines Changed paths: M /trunk/src/c-inner-main.c M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-test.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters-gui.cc M /trunk/src/c-interface.cc M /trunk/src/guile-fixups.h M /trunk/src/main.cc M /trunk/src/user-mods.hh Use libguile.h not guile/gh.h. Replace remaining gh functions. ------------------------------------------------------------------------ r4100 | pemsley | 2012-04-08 09:50:51 +0100 (Sun, 08 Apr 2012) | 3 lines Changed paths: M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Rework imol_molecule_map() so that, when unassigned, it checks (and assigns) if there is exactly one non-difference map. ------------------------------------------------------------------------ r4099 | b.lohkamp | 2012-04-07 13:57:53 +0100 (Sat, 07 Apr 2012) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/src/molecule-class-info-maps.cc M /trunk/src/read-phs.c Fix windows filenames in state phs files. Set phs cell chooser window transient for main window (still not fully focused though - seems tricky somehow). ------------------------------------------------------------------------ r4098 | pemsley | 2012-04-05 16:05:20 +0100 (Thu, 05 Apr 2012) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc deep_copy_this_residue() takes an extra arg, to optionally embed the residue in a chain. Add some notes on moving_atoms_asc memory leak. ------------------------------------------------------------------------ r4097 | pemsley | 2012-04-04 20:22:54 +0100 (Wed, 04 Apr 2012) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/dnotes M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/scheme/fitting.scm M /trunk/src/molecule-class-info-other.cc M /trunk/src/sdf-interface.cc Fix leak in GetResidue() i.e. deep_copy_residue() usage. Fix leak in write_atom_selection_file(). Turn off backup when doing rotamer part of fit-protein (also). ------------------------------------------------------------------------ r4096 | pemsley | 2012-04-04 13:53:51 +0100 (Wed, 04 Apr 2012) | 2 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h More is_hydrogen() abstraction. ------------------------------------------------------------------------ r4095 | pemsley | 2012-04-04 13:44:43 +0100 (Wed, 04 Apr 2012) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h is_hydrogen() abstraction for Bond_lines takes into account deuteriums. ------------------------------------------------------------------------ r4094 | pemsley | 2012-04-04 12:52:48 +0100 (Wed, 04 Apr 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4093 | pemsley | 2012-04-04 12:51:38 +0100 (Wed, 04 Apr 2012) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/lbg/lbg.cc Small fix - improve comments. ------------------------------------------------------------------------ r4092 | pemsley | 2012-04-03 18:03:51 +0100 (Tue, 03 Apr 2012) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Allow grokking of group type "P-peptide" in find_link_type(). ------------------------------------------------------------------------ r4091 | pemsley | 2012-04-03 17:36:33 +0100 (Tue, 03 Apr 2012) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc get_neighb_normal() now returns a synthetic value when not enough neighbours. Allow bond order representation of OXY. ------------------------------------------------------------------------ r4090 | pemsley | 2012-04-03 15:38:09 +0100 (Tue, 03 Apr 2012) | 2 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Filter out ring torsion variation in conformer generation. ------------------------------------------------------------------------ r4089 | b.lohkamp | 2012-04-02 09:02:55 +0100 (Mon, 02 Apr 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/jligand.py Only check for JLigand in CCP4_BIN if exists ------------------------------------------------------------------------ r4088 | b.lohkamp | 2012-04-01 17:43:26 +0100 (Sun, 01 Apr 2012) | 2 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/jligand.py A /trunk/python/jligand_gui.py Split out pythonic jligand_gui.py from jligand.py. ------------------------------------------------------------------------ r4087 | b.lohkamp | 2012-04-01 12:12:54 +0100 (Sun, 01 Apr 2012) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info-graphs.cc Block show_select_map_dialog for map selection in density fit graph. ------------------------------------------------------------------------ r4086 | b.lohkamp | 2012-03-31 16:44:54 +0100 (Sat, 31 Mar 2012) | 3 lines Changed paths: M /trunk/src/main.cc Make cootrc actually being executed (move before gtk_init), i.e. get back small icons. ------------------------------------------------------------------------ r4085 | pemsley | 2012-03-26 14:31:45 +0100 (Mon, 26 Mar 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in need_guile_unused_values_patch. ------------------------------------------------------------------------ r4084 | pemsley | 2012-03-26 14:31:04 +0100 (Mon, 26 Mar 2012) | 2 lines Changed paths: M /trunk/src/coot-nomenclature.cc Remove debugging. ------------------------------------------------------------------------ r4083 | b.lohkamp | 2012-03-23 16:48:16 +0000 (Fri, 23 Mar 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/Makefile.am M /trunk/python/prodrg_import.py Add a pythonic fle_view_to_png. ------------------------------------------------------------------------ r4082 | b.lohkamp | 2012-03-23 16:31:03 +0000 (Fri, 23 Mar 2012) | 1 line Changed paths: M /trunk/python/get_recent_pdbe.py Fix cancellation in pythonic get_recent_pdbe download ------------------------------------------------------------------------ r4081 | b.lohkamp | 2012-03-23 16:14:02 +0000 (Fri, 23 Mar 2012) | 1 line Changed paths: M /trunk/pixmaps/go-to-ligand.svg Fix font in go-to-ligand.svg for use in Windows ------------------------------------------------------------------------ r4080 | pemsley | 2012-03-23 13:02:17 +0000 (Fri, 23 Mar 2012) | 6 lines Changed paths: M /trunk/TODO M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py M /trunk/python/prodrg_import.py M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh Put Lidia in the extensions menu. bool coot_can_do_lidia_p() function aded (SWIG makes boolean types for the scripting interface. prodrg-import dropped from the Makefile.am and coot.scm and coot_load_modules.py.in. ------------------------------------------------------------------------ r4079 | pemsley | 2012-03-23 11:04:35 +0000 (Fri, 23 Mar 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Don't make a backup in list_nomenclature_errors(). ------------------------------------------------------------------------ r4078 | pemsley | 2012-03-23 10:53:55 +0000 (Fri, 23 Mar 2012) | 3 lines Changed paths: M /trunk/configure.in M /trunk/coot-surface/Makefile.am Tweak to the OpenGL configuration for coot-surface Makefile. We need this to resolve to blank in the case of Windows. ------------------------------------------------------------------------ r4077 | pemsley | 2012-03-23 10:46:47 +0000 (Fri, 23 Mar 2012) | 2 lines Changed paths: M /trunk/dnotes update ntoes. ------------------------------------------------------------------------ r4076 | pemsley | 2012-03-22 19:01:14 +0000 (Thu, 22 Mar 2012) | 3 lines Changed paths: M /trunk/pixmaps/anchor.svg M /trunk/pixmaps/go-to-atom.svg M /trunk/pixmaps/go-to-ligand.svg M /trunk/pixmaps/map.svg Sharpen the blury icons - by making document properties 48x48 pixels and scaling up. ------------------------------------------------------------------------ r4075 | pemsley | 2012-03-22 17:46:16 +0000 (Thu, 22 Mar 2012) | 5 lines Changed paths: M /trunk/configure.in M /trunk/coot-surface/Makefile.am We should provide the OpenGL library in the list of dependencies for libcoot-surface. So set this in configure.in. Usually it resolved to -lGL, but not on Windows - where it resolves to -lopengl32. ------------------------------------------------------------------------ r4074 | pemsley | 2012-03-22 12:08:22 +0000 (Thu, 22 Mar 2012) | 8 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/scheme/Makefile.am M /trunk/scheme/coot-utils.scm M /trunk/scheme/coot.scm A /trunk/scheme/jligand-gui.scm M /trunk/scheme/jligand.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh cif_for_comp_id() function added. So that we can know which cif file was responsible for a given comp-id. This is needed for JLigand to use the correct file when reading the restraints. cif_file_name field added to dictionary_residue_restraints_t(). jigand-gui.scm split out from jligand.scm and jligand.scm is no longer a gui-specific extension. ------------------------------------------------------------------------ r4073 | pemsley | 2012-03-22 10:10:12 +0000 (Thu, 22 Mar 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc Add some code to handle top-left recentering. Not complete and correct yet. ------------------------------------------------------------------------ r4072 | pemsley | 2012-03-21 09:48:05 +0000 (Wed, 21 Mar 2012) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/lbg/flev-annotations.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/residue-circles.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc M /trunk/src/main.cc Add determination of covalent bonds by examination of LINKs. Don't shorten covalent bonds. Use reposition_problematics_and_reoptimise() to annotate(). ------------------------------------------------------------------------ r4071 | pemsley | 2012-03-20 17:25:19 +0000 (Tue, 20 Mar 2012) | 3 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm A /trunk/scheme/prodrg-import-gui.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface.h M /trunk/src/flev.cc Batch mode fle-view using cprodrg: fle-view-to-png - no gui interface for this. ------------------------------------------------------------------------ r4070 | pemsley | 2012-03-19 10:43:56 +0000 (Mon, 19 Mar 2012) | 4 lines Changed paths: M /trunk/src/c-interface-build.cc Remove problematic debugging code. model_p need not be valid if no atoms selected. We shouldn't dereference it. ------------------------------------------------------------------------ r4069 | b.lohkamp | 2012-03-19 10:32:44 +0000 (Mon, 19 Mar 2012) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win Windows build use libccp4c-5.0.2-ysbl-3.tar.gz too ------------------------------------------------------------------------ r4068 | b.lohkamp | 2012-03-18 17:37:21 +0000 (Sun, 18 Mar 2012) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py M /trunk/python/get_recent_pdbe.py Get recent pdbs uses queues and sleeper functions now. No more gthreads. Re-activate get recent pdbs in extensions. ------------------------------------------------------------------------ r4067 | b.lohkamp | 2012-03-18 12:45:09 +0000 (Sun, 18 Mar 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc fix create_mmdbmanager_from_atom_selection to be able to use in ssm (thx Eugene) ------------------------------------------------------------------------ r4066 | pemsley | 2012-03-18 08:23:04 +0000 (Sun, 18 Mar 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Use g_type_init() so that goo_canvas_new() works without having called gtk_init(). ------------------------------------------------------------------------ r4065 | pemsley | 2012-03-18 08:14:19 +0000 (Sun, 18 Mar 2012) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix long-standing typo in using-active-atom. Test active-atom, not active-residue! ------------------------------------------------------------------------ r4064 | pemsley | 2012-03-18 07:50:49 +0000 (Sun, 18 Mar 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Remove PDBCleanup() usage debugging. ------------------------------------------------------------------------ r4063 | pemsley | 2012-03-17 15:13:55 +0000 (Sat, 17 Mar 2012) | 3 lines Changed paths: M /trunk/src/main.cc Only use gtk_init() if graphics are enabled - reverting previous change made for command-line fle-view. ------------------------------------------------------------------------ r4062 | pemsley | 2012-03-16 16:31:23 +0000 (Fri, 16 Mar 2012) | 6 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/main.cc command-line fle-view updates: in main.cc, initialize gtk even though we might be in no-graphics mode (we just won't gtk_widget_show(stuff)). lbg() ind lbg_info_t::init) reworked considering use_graphics_interface_flag. remove canvas add-image test cruft. ------------------------------------------------------------------------ r4061 | pemsley | 2012-03-16 13:35:49 +0000 (Fri, 16 Mar 2012) | 2 lines Changed paths: M /trunk/scheme/remote-control.scm Bug fixes for scheme-based remote control handling. ------------------------------------------------------------------------ r4060 | pemsley | 2012-03-16 13:35:13 +0000 (Fri, 16 Mar 2012) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r4059 | pemsley | 2012-03-15 16:50:21 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 M /trunk/rel-todo Remove out of data comment re: CISPEP code. ------------------------------------------------------------------------ r4058 | pemsley | 2012-03-15 16:49:40 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/src/testing.cc Fix up greg_test() for the case where COOT_TEST_DATA_DIR has been set. ------------------------------------------------------------------------ r4057 | pemsley | 2012-03-15 16:48:59 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/coot-surface/Makefile.am For cleanness, we need to add -lGL to _LIBADD. ------------------------------------------------------------------------ r4056 | pemsley | 2012-03-15 15:18:05 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.h Add scripting function set_go_to_atom_chain_residue_atom_name_full(). ------------------------------------------------------------------------ r4055 | pemsley | 2012-03-15 13:47:06 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r4054 | pemsley | 2012-03-15 13:46:48 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Null residue protection for intelligent_this_residue_atom(). ------------------------------------------------------------------------ r4053 | pemsley | 2012-03-15 13:45:30 +0000 (Thu, 15 Mar 2012) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Don't display (environment distance) text when the lights are on. ------------------------------------------------------------------------ r4052 | pemsley | 2012-03-15 12:56:16 +0000 (Thu, 15 Mar 2012) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/molecule-class-info-other.cc Ignore hydrogens when doing distance checks for waters. In the display manager, change the label on the delete buttons. ------------------------------------------------------------------------ r4051 | pemsley | 2012-03-13 16:33:32 +0000 (Tue, 13 Mar 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc More sigma -> rmsd changes (top right graphics window). ------------------------------------------------------------------------ r4050 | pemsley | 2012-03-13 16:25:12 +0000 (Tue, 13 Mar 2012) | 2 lines Changed paths: M /trunk/src/gtk-manual.cc remove debugging. ------------------------------------------------------------------------ r4049 | b.lohkamp | 2012-03-11 13:06:31 +0000 (Sun, 11 Mar 2012) | 1 line Changed paths: M /trunk/doc/tutorial.tex Tutorial uses toolbar rather than Model/Fit/Refine window. ------------------------------------------------------------------------ r4048 | pemsley | 2012-03-09 17:16:30 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/src/cc-interface.hh Add multi-residue torsions into a doxygen section. ------------------------------------------------------------------------ r4047 | pemsley | 2012-03-09 17:11:25 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/cc-interface.hh M /trunk/src/coot.in (Potential) fixes for automatic documentation generation for sectioning problems. ------------------------------------------------------------------------ r4046 | pemsley | 2012-03-09 16:42:27 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi Add name argument to dots command. ------------------------------------------------------------------------ r4045 | pemsley | 2012-03-09 12:38:47 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh Add get_minima_grid_points() function. ------------------------------------------------------------------------ r4044 | pemsley | 2012-03-09 01:03:26 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/molecule-class-info.cc Fix up intelligent_previous_atom() for the case of starting at the first residue. ------------------------------------------------------------------------ r4043 | pemsley | 2012-03-09 01:01:55 +0000 (Fri, 09 Mar 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Trivial fix, use bool for cleanliness. ------------------------------------------------------------------------ r4042 | pemsley | 2012-03-08 17:43:42 +0000 (Thu, 08 Mar 2012) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Handle NULL residue arg in constructor for residue_spec_t. ------------------------------------------------------------------------ r4041 | pemsley | 2012-03-08 17:42:33 +0000 (Thu, 08 Mar 2012) | 5 lines Changed paths: M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info.cc Fix go to next atom problems apparent after a residue deletion/addtion. (It seems that the residue indexing is broken (or changed in a way that I don't understand). So add a test for self-referencing via indexing, and if that fails use a fall-back based on residue number. ------------------------------------------------------------------------ r4040 | pemsley | 2012-02-29 11:45:46 +0000 (Wed, 29 Feb 2012) | 3 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Throw an exception if any non-H atom name is not found when constructing and rdkit_mol from a residue and restraints. ------------------------------------------------------------------------ r4039 | b.lohkamp | 2012-02-26 22:10:59 +0000 (Sun, 26 Feb 2012) | 2 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py A /trunk/python/jligand.py Add a pythonic version for JLigand interface. ------------------------------------------------------------------------ r4038 | pemsley | 2012-02-25 18:00:04 +0000 (Sat, 25 Feb 2012) | 3 lines Changed paths: M /trunk/src/graphics-info.cc Need to *disable* GL_COLOR_MATERIAL to have correct colours on solid generic objects (chemical features). ------------------------------------------------------------------------ r4037 | pemsley | 2012-02-25 16:00:46 +0000 (Sat, 25 Feb 2012) | 5 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/sdf-interface.cc Re-work the generic object tori. Add GL_NORMALIZE to improve "shading". Flatten delocalize tori. Adjust light positions. ------------------------------------------------------------------------ r4036 | pemsley | 2012-02-25 15:20:32 +0000 (Sat, 25 Feb 2012) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm M /trunk/scheme/jligand.scm Put JLigand into the Modelling menu (it creates a new menu/menu item when activated). ------------------------------------------------------------------------ r4035 | pemsley | 2012-02-25 12:36:01 +0000 (Sat, 25 Feb 2012) | 2 lines Changed paths: A /trunk/scheme/jligand.scm Add jligand.scm ------------------------------------------------------------------------ r4034 | pemsley | 2012-02-25 04:23:15 +0000 (Sat, 25 Feb 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/Makefile.am LDADDs that are files in this directory should not use $(top_builddir)/xx. ------------------------------------------------------------------------ r4033 | pemsley | 2012-02-24 16:34:21 +0000 (Fri, 24 Feb 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fixup libccp4c version patch. ------------------------------------------------------------------------ r4032 | pemsley | 2012-02-24 16:01:15 +0000 (Fri, 24 Feb 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use libccp4c-5.0.2-ysbl-3.tar.gz, that has libccp4c_la_LIBADD. ------------------------------------------------------------------------ r4031 | pemsley | 2012-02-24 12:23:28 +0000 (Fri, 24 Feb 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes Conditionally apply the guile usused values patch. ------------------------------------------------------------------------ r4030 | pemsley | 2012-02-24 12:22:41 +0000 (Fri, 24 Feb 2012) | 2 lines Changed paths: M /trunk/src/sdf-interface.cc Correct return value from show_feats(). Add some diagnostics for problems. ------------------------------------------------------------------------ r4029 | pemsley | 2012-02-24 12:20:47 +0000 (Fri, 24 Feb 2012) | 2 lines Changed paths: M /trunk/src/gl-matrix.cc Fix up indexing errors as per Ansgar Esztermann. ------------------------------------------------------------------------ r4028 | pemsley | 2012-02-23 16:20:53 +0000 (Thu, 23 Feb 2012) | 2 lines Changed paths: M /trunk/coot-surface/coot-surface.cc Fix up opacity for surface colour as per Ansgar Esztermann. ------------------------------------------------------------------------ r4027 | pemsley | 2012-02-22 09:19:55 +0000 (Wed, 22 Feb 2012) | 1 line Changed paths: M /trunk/coot-utils/Makefile.am Demote test-morph to a check program. ------------------------------------------------------------------------ r4026 | pemsley | 2012-02-22 07:38:51 +0000 (Wed, 22 Feb 2012) | 1 line Changed paths: M /trunk/src/Makefile.am Add mogul interface header to sources. ------------------------------------------------------------------------ r4025 | pemsley | 2012-02-21 08:47:21 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/c-interface-mogul.cc Remove reference to goograph for the moment. ------------------------------------------------------------------------ r4024 | pemsley | 2012-02-21 08:41:22 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/scheme/coot-utils.scm Update header (trivial). ------------------------------------------------------------------------ r4023 | pemsley | 2012-02-21 08:41:17 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/analysis/Makefile.am Add utils to INCLUDES for analysis. ------------------------------------------------------------------------ r4022 | pemsley | 2012-02-21 03:24:06 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface.h No public access to mogul functions yet. ------------------------------------------------------------------------ r4021 | pemsley | 2012-02-21 03:24:01 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/sdf-interface.cc Fix up merging duplications. ------------------------------------------------------------------------ r4020 | pemsley | 2012-02-21 03:23:56 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/c-interface-mogul.cc bonds treestore not filled yet. ------------------------------------------------------------------------ r4019 | pemsley | 2012-02-21 03:23:39 +0000 (Tue, 21 Feb 2012) | 5 lines Changed paths: M /trunk/README M /trunk/analysis/mogul-interface.hh M /trunk/analysis/mogul.cc M /trunk/coot-gtk2.glade M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-fffear.cc M /trunk/coot-utils/coot-map-heavy.hh A /trunk/coot-utils/test-morph.cc M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/ligand/Makefile.am M /trunk/ligand/test-fffear-in-coot.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mogul.cc A /trunk/src/cc-interface-mogul.hh M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Add some bug-fixing and testing to lbg canvas button presses (delete item). Add glade gui for mogul results. Update drawing of generic objects (arcs). Enable translate-only fffear search. Add test-tt-morph - just playing with some fffear searches. ------------------------------------------------------------------------ r4018 | pemsley | 2012-02-21 03:23:24 +0000 (Tue, 21 Feb 2012) | 3 lines Changed paths: M /trunk/analysis/Makefile.am A /trunk/analysis/mogul-interface.hh A /trunk/analysis/mogul.cc A /trunk/analysis/test-mogul.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc A /trunk/src/c-interface-mogul.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc Improve lighting on arcs (not ideal yet) - but at least now normals are unit vectors. Conservatively update restraints (using data from mogul). ------------------------------------------------------------------------ r4017 | pemsley | 2012-02-21 03:23:17 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/generic-objects.cc M /trunk/src/graphics-info.cc Colour passing for arcs improved. Normals still problematic. ------------------------------------------------------------------------ r4016 | pemsley | 2012-02-21 03:23:04 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/analysis/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/generic-display-object.hh A /trunk/src/generic-objects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/sdf-interface.cc internal_arcs positioned correctly now. Colouring and/or normals still wrong. ------------------------------------------------------------------------ r4015 | pemsley | 2012-02-21 03:22:57 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/Makefile.am Remove boost interface references. ------------------------------------------------------------------------ r4014 | pemsley | 2012-02-21 03:22:51 +0000 (Tue, 21 Feb 2012) | 6 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/src/coot-colour.hh M /trunk/src/graphics-info.cc M /trunk/src/sdf-interface.cc chemical_features now namespaced. Handle unit vector (currently called normal) for donor and acceptor features. LumpedHydrophobic spheres are smaller. Add GL_LIGHT2 for solid generic objects. Remove degugging. Remove GTK1 cruft. ------------------------------------------------------------------------ r4013 | pemsley | 2012-02-21 03:22:45 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/sdf-interface.cc aromatic rings work (but no colours there yet). ------------------------------------------------------------------------ r4012 | pemsley | 2012-02-21 03:22:40 +0000 (Tue, 21 Feb 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/src/coot-colour.hh Conflicts: lidia-core/rdkit-interface.cc ------------------------------------------------------------------------ r4011 | pemsley | 2012-02-21 03:22:34 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/lidia-core/rdkit-interface.cc M /trunk/src/Makefile.am some changes - confused. ------------------------------------------------------------------------ r4010 | pemsley | 2012-02-21 03:22:29 +0000 (Tue, 21 Feb 2012) | 1 line Changed paths: M /trunk/src/sdf-interface.cc Improvements to features - still problems with factory header. ------------------------------------------------------------------------ r4009 | pemsley | 2012-02-20 15:23:24 +0000 (Mon, 20 Feb 2012) | 2 lines Changed paths: M /trunk/src/sdf-interface.cc Initial Coord_orth return values - for compiler cleanness. ------------------------------------------------------------------------ r4008 | pemsley | 2012-02-20 11:19:06 +0000 (Mon, 20 Feb 2012) | 2 lines Changed paths: M /trunk/coords/mmdb.cc If mol2 format fails, try mdl molfile (bond orders ignored though). ------------------------------------------------------------------------ r4007 | pemsley | 2012-02-20 11:12:13 +0000 (Mon, 20 Feb 2012) | 2 lines Changed paths: M /trunk/coords/mmdb-extras.h Set default read_success values for atom-selection_container_t constructors. ------------------------------------------------------------------------ r4006 | b.lohkamp | 2012-02-19 19:19:23 +0000 (Sun, 19 Feb 2012) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/python/prodrg_import.py Create coot-ccp4 directory if it doesn't exist before running pythonic cprodrg. ------------------------------------------------------------------------ r4005 | b.lohkamp | 2012-02-19 17:37:43 +0000 (Sun, 19 Feb 2012) | 3 lines Changed paths: M /trunk/python/coot_utils.py A /trunk/python/with_jligand.py include actually centre residue when auto-weighting add draft for pythonic jligand interface ------------------------------------------------------------------------ r4004 | pemsley | 2012-02-16 02:44:35 +0000 (Thu, 16 Feb 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm residue-to-sdf-file is not available in standard build. ------------------------------------------------------------------------ r4003 | pemsley | 2012-02-14 22:49:14 +0000 (Tue, 14 Feb 2012) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Take into account pathological cases where auto-refine does not converge. Python version needs to be updated too, I think. ------------------------------------------------------------------------ r4002 | pemsley | 2012-02-11 03:37:07 +0000 (Sat, 11 Feb 2012) | 2 lines Changed paths: A /trunk/src/coot-colour.hh Add missing src/coot-colour.hh. ------------------------------------------------------------------------ r4001 | pemsley | 2012-02-11 03:36:22 +0000 (Sat, 11 Feb 2012) | 2 lines Changed paths: A /trunk/src/coot-colour.cc Add missing src/coot-colour.cc. ------------------------------------------------------------------------ r4000 | pemsley | 2012-02-11 03:28:39 +0000 (Sat, 11 Feb 2012) | 13 lines Changed paths: M /trunk/doc/coot-user-manual.texi M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/rel-todo M /trunk/scheme/get-recent-pdbe.scm M /trunk/src/Makefile.am M /trunk/src/coot-render.hh M /trunk/src/generic-display-object.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/sdf-interface.cc M /trunk/src/sdf-interface.hh A /trunk/src/sdf-internal.hh M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Show Chemical Features. Add show_feats() function. Add classes and functions to store and draw new generic objects, spheres, tori, arrows. rdkit_mol_sanitized() function added. chemical_features namespace added, which holds show() and normal/unit-vector calculators. coot.i now depends on sdf-interface.hh Remove some gtk1 cruft. Factor out undelocalization carboxylate inner test. coot-colour.hh split out and create new source file for the std::ostream writer. Document set-draw-axes. ------------------------------------------------------------------------ r3999 | b.lohkamp | 2012-02-06 10:42:36 +0000 (Mon, 06 Feb 2012) | 1 line Changed paths: M /trunk/src/testing.cc Make sure test_internal finds all the test data in greg-data dir ------------------------------------------------------------------------ r3998 | b.lohkamp | 2012-02-05 12:45:13 +0000 (Sun, 05 Feb 2012) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python-tests/03_ligand.py Fix pythonic shell_command_to_string for subprocess, and return False on fail. ------------------------------------------------------------------------ r3997 | b.lohkamp | 2012-02-04 18:09:33 +0000 (Sat, 04 Feb 2012) | 5 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python-tests/03_ligand.py Update pythonic auto-load restraints test - now accounting for CCP4 library version. Added python function shell_command_to_string. ------------------------------------------------------------------------ r3996 | pemsley | 2012-02-04 15:20:50 +0000 (Sat, 04 Feb 2012) | 1 line Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r3995 | pemsley | 2012-02-04 15:15:40 +0000 (Sat, 04 Feb 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Add mass to RDkit atoms. Some work on undelocalising oxygen-carbon bonds. ------------------------------------------------------------------------ r3994 | pemsley | 2012-02-04 08:48:30 +0000 (Sat, 04 Feb 2012) | 1 line Changed paths: M /trunk/src/sdf-interface.cc Add some molecule prep before moving on to writing the sdf file. ------------------------------------------------------------------------ r3993 | pemsley | 2012-02-04 08:48:24 +0000 (Sat, 04 Feb 2012) | 1 line Changed paths: M /trunk/src/lbg-interface.cc Catch null rdkit_mol on SmilesToMol() parse failure. ------------------------------------------------------------------------ r3992 | pemsley | 2012-02-04 08:48:15 +0000 (Sat, 04 Feb 2012) | 1 line Changed paths: M /trunk/lbg/lbg.cc Remove debugging. ------------------------------------------------------------------------ r3991 | pemsley | 2012-02-03 18:27:02 +0000 (Fri, 03 Feb 2012) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm Update auto-load restraints test - now accounting for CCP4 library version. ------------------------------------------------------------------------ r3990 | b.lohkamp | 2012-02-03 09:00:04 +0000 (Fri, 03 Feb 2012) | 3 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py Add pythonic test for peptide bond lengths in sphere refine test. Make the python test for auto-load residue name actually test. ------------------------------------------------------------------------ r3989 | pemsley | 2012-02-02 12:39:33 +0000 (Thu, 02 Feb 2012) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Add diacritical marks to "Angstrom" - remove plurals. ------------------------------------------------------------------------ r3988 | pemsley | 2012-01-31 13:48:59 +0000 (Tue, 31 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/read-sbase.cc Revert previous commit. ------------------------------------------------------------------------ r3987 | pemsley | 2012-01-31 13:44:45 +0000 (Tue, 31 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/read-sbase.cc Don't autoload SBase descriptions for non-autoload comp-ids. ------------------------------------------------------------------------ r3986 | pemsley | 2012-01-31 11:18:51 +0000 (Tue, 31 Jan 2012) | 2 lines Changed paths: A /trunk/src/sdf-interface.cc A /trunk/src/sdf-interface.hh Add missing files to repo. ------------------------------------------------------------------------ r3985 | pemsley | 2012-01-31 01:24:44 +0000 (Tue, 31 Jan 2012) | 6 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/read-sbase.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/ideal/simple-restraint.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.cc M /trunk/src/coot.i M /trunk/src/graphics-ligand-view.cc Fix M-peptide refinement links. Fix up non-auto-load test when SBASE is setup. Add test for peptide bond lengths in sphere refine test. Brighten blues in ligand view. Add residue->sdf interface. ------------------------------------------------------------------------ r3984 | pemsley | 2012-01-30 15:40:54 +0000 (Mon, 30 Jan 2012) | 1 line Changed paths: M /trunk/TODO M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3983 | pemsley | 2012-01-30 15:35:05 +0000 (Mon, 30 Jan 2012) | 6 lines Changed paths: M /trunk/coot-utils/bonded-pairs.cc M /trunk/coot-utils/bonded-pairs.hh M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Making a link now uses the dictionary for the link (if any) to apply link chem mods (currently only delete chem mods). To do this, restraints are generated between the linked residues. From there we get the bonded pair and it is in the bonded pairs that the chem mods are applied. ------------------------------------------------------------------------ r3982 | pemsley | 2012-01-30 15:30:04 +0000 (Mon, 30 Jan 2012) | 3 lines Changed paths: M /trunk/macros/goo-canvas.m4 Put goo-canvas.m4 back to how it was before 3947. Needs some more thought. ------------------------------------------------------------------------ r3981 | b.lohkamp | 2012-01-29 13:51:19 +0000 (Sun, 29 Jan 2012) | 4 lines Changed paths: M /trunk/python-tests/03_ligand.py M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Make functions remove-non-auto-load-residue-name and add-non-auto-load-residue-name available to python too. Add a pythonic test as well. ------------------------------------------------------------------------ r3980 | b.lohkamp | 2012-01-29 10:24:22 +0000 (Sun, 29 Jan 2012) | 1 line Changed paths: M /trunk/greg-tests/03-ligand.scm fix typo in non-auto-load greg test ------------------------------------------------------------------------ r3979 | pemsley | 2012-01-28 14:29:40 +0000 (Sat, 28 Jan 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add strip-leading-spaces to utils - used in parsing output of jligand. ------------------------------------------------------------------------ r3978 | pemsley | 2012-01-28 12:55:39 +0000 (Sat, 28 Jan 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Add some currently commented code to examine hetcompounds in no_dictionary_for_residue_types function. ------------------------------------------------------------------------ r3977 | pemsley | 2012-01-28 12:55:32 +0000 (Sat, 28 Jan 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh When bonding het groups check that the atoms match the dictionary, else fall back to basic bonding. ------------------------------------------------------------------------ r3976 | pemsley | 2012-01-28 05:54:34 +0000 (Sat, 28 Jan 2012) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/greg-tests/03-ligand.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Add functions remove-non-auto-load-residue-name and add-non-auto-load-residue-name. Add a test. ------------------------------------------------------------------------ r3975 | pemsley | 2012-01-28 05:54:27 +0000 (Sat, 28 Jan 2012) | 1 line Changed paths: M /trunk/TODO Update notes. ------------------------------------------------------------------------ r3974 | pemsley | 2012-01-27 13:58:07 +0000 (Fri, 27 Jan 2012) | 2 lines Changed paths: M /trunk/scheme/prodrg-import.scm Create coot-ccp4 directory if it doesn't exist before running cprodrg. ------------------------------------------------------------------------ r3973 | pemsley | 2012-01-27 11:12:37 +0000 (Fri, 27 Jan 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo Rework the code that decides how many processors to use, add low memory test. ------------------------------------------------------------------------ r3972 | pemsley | 2012-01-27 11:11:56 +0000 (Fri, 27 Jan 2012) | 2 lines Changed paths: A /trunk/scheme/with-jligand.scm Add jigand interface to repo. ------------------------------------------------------------------------ r3971 | b.lohkamp | 2012-01-26 13:37:31 +0000 (Thu, 26 Jan 2012) | 1 line Changed paths: M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py disable pythonic get_recent_pdbe until threads are fixed ------------------------------------------------------------------------ r3970 | pemsley | 2012-01-26 10:27:23 +0000 (Thu, 26 Jan 2012) | 1 line Changed paths: M /trunk/src/coot.in Absolutize COOT_PREFIX (needed for glade builder in lbg). ------------------------------------------------------------------------ r3969 | pemsley | 2012-01-26 01:26:02 +0000 (Thu, 26 Jan 2012) | 2 lines Changed paths: M /trunk/coords/Bond_lines.h Add constructor documentation. ------------------------------------------------------------------------ r3968 | b.lohkamp | 2012-01-25 22:50:02 +0000 (Wed, 25 Jan 2012) | 4 lines Changed paths: M /trunk/pixmaps/glyco-structures.svg M /trunk/windows/WinCoot_install_masta.nsi Windows fixes: add protein.db to installer fix fonts in glyco-structure.svg ------------------------------------------------------------------------ r3967 | b.lohkamp | 2012-01-25 22:48:43 +0000 (Wed, 25 Jan 2012) | 1 line Changed paths: M /trunk/lbg/lbg.glade fix default responses for filechoosers in lbg ------------------------------------------------------------------------ r3966 | b.lohkamp | 2012-01-25 17:16:57 +0000 (Wed, 25 Jan 2012) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c focus on OK in fix-nomenclature-errors-dialog ------------------------------------------------------------------------ r3965 | pemsley | 2012-01-24 20:59:13 +0000 (Tue, 24 Jan 2012) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc Update molecules with redraw if then contain residues with of specified type after an update of the restraints. ------------------------------------------------------------------------ r3964 | pemsley | 2012-01-24 20:56:52 +0000 (Tue, 24 Jan 2012) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Attempt to remove map_scroll_button_n warning messages by no looking up those widgets when attempting to get previous scroll radio button. ------------------------------------------------------------------------ r3963 | pemsley | 2012-01-24 17:03:28 +0000 (Tue, 24 Jan 2012) | 1 line Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Stop autoloading Refmac restraints for INH,DRG,LIG,XXX etc. ------------------------------------------------------------------------ r3962 | pemsley | 2012-01-24 01:15:33 +0000 (Tue, 24 Jan 2012) | 2 lines Changed paths: M /trunk/coot-utils/read-sm-cif.cc M /trunk/coot-utils/read-sm-cif.hh Fixes to element and oxidation state parsing in small-molecule CIF reading. ------------------------------------------------------------------------ r3961 | pemsley | 2012-01-24 01:14:27 +0000 (Tue, 24 Jan 2012) | 2 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Remove debugging. ------------------------------------------------------------------------ r3960 | pemsley | 2012-01-24 01:12:55 +0000 (Tue, 24 Jan 2012) | 2 lines Changed paths: M /trunk/src/c-interface-maps.cc M /trunk/src/cc-interface.hh Add ifdef oversights for scripting functions. ------------------------------------------------------------------------ r3959 | pemsley | 2012-01-23 13:10:59 +0000 (Mon, 23 Jan 2012) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc A /trunk/src/c-interface-maps.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh Add interface for variance_map, make_variance_map(). Add new source file c-interface-maps.cc, move map functions there. ------------------------------------------------------------------------ r3958 | pemsley | 2012-01-23 13:10:51 +0000 (Mon, 23 Jan 2012) | 1 line Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh Implement variance_map(). ------------------------------------------------------------------------ r3957 | pemsley | 2012-01-23 13:10:45 +0000 (Mon, 23 Jan 2012) | 1 line Changed paths: M /trunk/TODO M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3956 | pemsley | 2012-01-23 13:10:29 +0000 (Mon, 23 Jan 2012) | 2 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Add has_model() protection for no_dictionary_for_residue_type_as_yet(). Not sure that it does any good. ------------------------------------------------------------------------ r3955 | b.lohkamp | 2012-01-22 18:11:06 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/build-it-win update ccp4 for windows too (needed for clipper) ------------------------------------------------------------------------ r3954 | b.lohkamp | 2012-01-22 17:02:13 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/src/c-interface-refine.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc block refinement map selection dialog until selection is done ------------------------------------------------------------------------ r3953 | b.lohkamp | 2012-01-22 15:46:07 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/face-smile.svg M /trunk/lbg/lbg.glade distribute and use face-smile icon in lbg ------------------------------------------------------------------------ r3952 | b.lohkamp | 2012-01-22 13:37:04 +0000 (Sun, 22 Jan 2012) | 3 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py M /trunk/python/get_ebi.py M /trunk/python/get_recent_pdbe.py M /trunk/python/prodrg_import.py add pythonic get_recent_pdbe to Makefile, load the module and add to extensions ------------------------------------------------------------------------ r3951 | b.lohkamp | 2012-01-22 13:35:44 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/build-it-win update windows to mmdb 1.24 and clipper fixup ------------------------------------------------------------------------ r3950 | pemsley | 2012-01-22 02:24:54 +0000 (Sun, 22 Jan 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Remove save_molecule() call on clear_button_down_bond_addtion(). It was causing double saves and the need to do double deletes. ------------------------------------------------------------------------ r3949 | pemsley | 2012-01-22 02:24:48 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/src/c-interface-build.cc Remove hacky values for cif read_number when using try_dynamic_add(). ------------------------------------------------------------------------ r3948 | pemsley | 2012-01-22 01:59:34 +0000 (Sun, 22 Jan 2012) | 1 line Changed paths: M /trunk/geometry/protein-geometry.cc Remove debugging chem_comp reading. ------------------------------------------------------------------------ r3947 | pemsley | 2012-01-21 18:13:33 +0000 (Sat, 21 Jan 2012) | 2 lines Changed paths: M /trunk/autogen.sh M /trunk/configure.in M /trunk/macros/glut.m4 M /trunk/macros/goo-canvas.m4 D /trunk/macros/gtk.m4 M /trunk/macros/guile-gtk.m4 Configure and macr changes. Delete old GTK1 macro usage. ------------------------------------------------------------------------ r3946 | pemsley | 2012-01-21 18:13:28 +0000 (Sat, 21 Jan 2012) | 1 line Changed paths: M /trunk/rel-todo Add python configuration option. ------------------------------------------------------------------------ r3945 | pemsley | 2012-01-21 18:13:22 +0000 (Sat, 21 Jan 2012) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/src/c-interface.cc Better handle the cif file read_number. Now new files from add_cif_dictionary() have different read numbers, thus clearing the old restraints. ------------------------------------------------------------------------ r3944 | pemsley | 2012-01-21 18:13:16 +0000 (Sat, 21 Jan 2012) | 1 line Changed paths: M /trunk/src/lbg-interface.cc Simple reformat. ------------------------------------------------------------------------ r3943 | pemsley | 2012-01-21 18:13:10 +0000 (Sat, 21 Jan 2012) | 1 line Changed paths: M /trunk/src/c-interface-ligands.cc Remove comment cruft. ------------------------------------------------------------------------ r3942 | pemsley | 2012-01-21 18:13:03 +0000 (Sat, 21 Jan 2012) | 1 line Changed paths: M /trunk/src/c-interface-build.cc Add use_graphics_interface protection for handle_cif_dictionary(). ------------------------------------------------------------------------ r3941 | KevKeating | 2012-01-20 19:34:31 +0000 (Fri, 20 Jan 2012) | 1 line Changed paths: M /trunk/ideal/extra-restraints-kk.cc M /trunk/ideal/extra-restraints.cc remove debugging ------------------------------------------------------------------------ r3940 | pemsley | 2012-01-19 02:05:02 +0000 (Thu, 19 Jan 2012) | 1 line Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3938 | pemsley | 2012-01-17 18:29:45 +0000 (Tue, 17 Jan 2012) | 3 lines Changed paths: M /trunk/python/prodrg_import.py M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/lbg-interface.cc Make the "prodrg" import function (the function run when the lbg "Apply" button is clicked) more generic. ------------------------------------------------------------------------ r3937 | pemsley | 2012-01-17 11:34:09 +0000 (Tue, 17 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/chem_mods.cc In add_chem_mod_plane() allow an error on reading new_dist_esd if function is delete. ------------------------------------------------------------------------ r3936 | pemsley | 2012-01-16 16:28:02 +0000 (Mon, 16 Jan 2012) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/rel-todo Update notes. remove debugging. ------------------------------------------------------------------------ r3935 | pemsley | 2012-01-16 16:27:28 +0000 (Mon, 16 Jan 2012) | 2 lines Changed paths: M /trunk/scheme/get-ebi.scm Change the EDS unreliable map message a bit. ------------------------------------------------------------------------ r3934 | pemsley | 2012-01-16 16:26:57 +0000 (Mon, 16 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc Allow for M-peptide -> TRANS links. ------------------------------------------------------------------------ r3933 | pemsley | 2012-01-16 16:22:56 +0000 (Mon, 16 Jan 2012) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Remve flash bond debugging. ------------------------------------------------------------------------ r3932 | pemsley | 2012-01-16 13:46:22 +0000 (Mon, 16 Jan 2012) | 1 line Changed paths: A /trunk/doc/carbo.txt Add some sub notes on carbohydrate functions. ------------------------------------------------------------------------ r3931 | pemsley | 2012-01-16 13:45:29 +0000 (Mon, 16 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh When reading _chem_comp_atom coordinates, check that the atoms don't lie at the origin - and if they do, delete all the atom positions. ------------------------------------------------------------------------ r3930 | pemsley | 2012-01-14 14:16:31 +0000 (Sat, 14 Jan 2012) | 1 line Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r3929 | pemsley | 2012-01-14 08:56:07 +0000 (Sat, 14 Jan 2012) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h Chi angle editing, allow change of highlighting depending on the mouse motion deltas. ------------------------------------------------------------------------ r3928 | pemsley | 2012-01-13 21:42:11 +0000 (Fri, 13 Jan 2012) | 3 lines Changed paths: M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc Adjust formal charge on a atoms with energy type "P". Remove debugging. ------------------------------------------------------------------------ r3927 | pemsley | 2012-01-13 21:32:38 +0000 (Fri, 13 Jan 2012) | 1 line Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c M /trunk/src/callbacks.h Minor changes, remove some gtk1 code. ------------------------------------------------------------------------ r3926 | KevKeating | 2012-01-13 18:49:03 +0000 (Fri, 13 Jan 2012) | 1 line Changed paths: M /trunk/ideal/extra-restraints-kk.cc M /trunk/ideal/extra-restraints.cc M /trunk/src/graphics-info-modelling.cc non-bonded constraints no longer added between atoms with extra bond or angle restraints ------------------------------------------------------------------------ r3925 | pemsley | 2012-01-13 13:42:26 +0000 (Fri, 13 Jan 2012) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc Don't include OXT as a missing atom in a residue. ------------------------------------------------------------------------ r3924 | pemsley | 2012-01-12 17:03:08 +0000 (Thu, 12 Jan 2012) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a menu item for PDBe structure retrieval. ------------------------------------------------------------------------ r3923 | pemsley | 2012-01-12 17:02:06 +0000 (Thu, 12 Jan 2012) | 2 lines Changed paths: M /trunk/src/c-interface-superpose.cc Draw after lsq_improve(). ------------------------------------------------------------------------ r3922 | b.lohkamp | 2012-01-11 15:54:42 +0000 (Wed, 11 Jan 2012) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix python refinement test, allow more cycles to converge ------------------------------------------------------------------------ r3921 | pemsley | 2012-01-10 18:37:36 +0000 (Tue, 10 Jan 2012) | 2 lines Changed paths: M /trunk/src/coot.in Only run the crash catcher if coot was compile with guile. ------------------------------------------------------------------------ r3920 | b.lohkamp | 2012-01-10 12:18:43 +0000 (Tue, 10 Jan 2012) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/src/c-interface-wii.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h add wiiuse interface (simple bindings only so far). fixes/adds keypad_translate_xyz python scripting tet completion alphabetically sorted. ------------------------------------------------------------------------ r3919 | b.lohkamp | 2012-01-10 12:16:32 +0000 (Tue, 10 Jan 2012) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py New-style NBC, atoms move less in the pythonic test. ------------------------------------------------------------------------ r3918 | pemsley | 2012-01-10 11:10:52 +0000 (Tue, 10 Jan 2012) | 1 line Changed paths: M /trunk/TODO M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3917 | pemsley | 2012-01-10 07:07:29 +0000 (Tue, 10 Jan 2012) | 1 line Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm New-style NBC means that the atoms move less in this test. ------------------------------------------------------------------------ r3916 | pemsley | 2012-01-10 06:27:49 +0000 (Tue, 10 Jan 2012) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Connect (via a function pointer) a function to import an SBase residue given a comp_id from an lbg sbase search. ------------------------------------------------------------------------ r3915 | b.lohkamp | 2012-01-09 16:25:04 +0000 (Mon, 09 Jan 2012) | 1 line Changed paths: M /trunk/src/graphics-ligand-view.cc fix problem with variable name small on windows ------------------------------------------------------------------------ r3914 | pemsley | 2012-01-09 16:04:11 +0000 (Mon, 09 Jan 2012) | 4 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/wmolecule.cc M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Improve graphics ligand representation update after prodrg import. Fix typo to enable (loose) non-bonded contact distances that are dependent on type. Needs angle and torsion rejection to be better. ------------------------------------------------------------------------ r3913 | pemsley | 2012-01-09 16:00:21 +0000 (Mon, 09 Jan 2012) | 2 lines Changed paths: M /trunk/lidia-core/lig-build.hh Adjust NH tweaks. ------------------------------------------------------------------------ r3912 | pemsley | 2012-01-08 15:57:55 +0000 (Sun, 08 Jan 2012) | 2 lines Changed paths: M /trunk/dnotes update notes (gnome desktop icon labels). ------------------------------------------------------------------------ r3911 | pemsley | 2012-01-08 15:57:29 +0000 (Sun, 08 Jan 2012) | 2 lines Changed paths: M /trunk/lbg/lbg.cc gtk_drag_dest_add_uri_targets() for all platforms, not just windows. ------------------------------------------------------------------------ r3910 | pemsley | 2012-01-08 15:56:58 +0000 (Sun, 08 Jan 2012) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-network.cc M /trunk/src/graphics-ligand-view.hh M /trunk/src/molecule-class-info-other.cc graphics-ligand-view's display_list_tag is a GUint, so initial value should not be negative. ------------------------------------------------------------------------ r3909 | pemsley | 2012-01-08 11:42:06 +0000 (Sun, 08 Jan 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix script_version typo. ------------------------------------------------------------------------ r3908 | pemsley | 2012-01-08 11:41:35 +0000 (Sun, 08 Jan 2012) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use make not MAKE for guile-gtk. ------------------------------------------------------------------------ r3907 | pemsley | 2012-01-07 20:07:30 +0000 (Sat, 07 Jan 2012) | 2 lines Changed paths: A /trunk/build-it-gtk2-Darwin Add the ports-based Darwin build script. First bash. ------------------------------------------------------------------------ r3906 | pemsley | 2012-01-07 14:43:06 +0000 (Sat, 07 Jan 2012) | 2 lines Changed paths: M /trunk/src/c-interface-mmdb.cc Set initial values for aniso Bs from python expression. ------------------------------------------------------------------------ r3905 | pemsley | 2012-01-07 14:42:31 +0000 (Sat, 07 Jan 2012) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Use Delete(MMDBFCM_Coord) rather than DeleteAllModels() in replace_models(). Fixes crash. ------------------------------------------------------------------------ r3904 | pemsley | 2012-01-07 13:13:50 +0000 (Sat, 07 Jan 2012) | 2 lines Changed paths: M /trunk/goograph/Makefile.am Fix typo in SOURCES for goograph_la. ------------------------------------------------------------------------ r3903 | pemsley | 2012-01-07 13:05:02 +0000 (Sat, 07 Jan 2012) | 2 lines Changed paths: M /trunk/Makefile.am Remove template PDB fileanmes from top level Makefile.am EXTRA_DIST. ------------------------------------------------------------------------ r3902 | KevKeating | 2012-01-05 16:44:07 +0000 (Thu, 05 Jan 2012) | 1 line Changed paths: M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface.h add use_only_extra_torsion_restraints_for_torsions_state() function to Python and Scheme ------------------------------------------------------------------------ r3901 | KevKeating | 2012-01-04 18:55:47 +0000 (Wed, 04 Jan 2012) | 1 line Changed paths: M /trunk/ideal/extra-restraints-kk.cc M /trunk/ideal/extra-restraints.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-kk.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h add custom angle restraints (add_extra_angle_restraint() in Python and Scheme) ------------------------------------------------------------------------ r3900 | pemsley | 2012-01-04 17:05:03 +0000 (Wed, 04 Jan 2012) | 2 lines Changed paths: M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh Add angle_2() and angle_3() functions to quad. ------------------------------------------------------------------------ r3899 | pemsley | 2012-01-04 12:38:42 +0000 (Wed, 04 Jan 2012) | 3 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.hh A /trunk/coot-utils/helix-analysis.cc A /trunk/coot-utils/helix-analysis.hh M /trunk/coot-utils/test-utils.cc Add helix analysis. Currently fails to calculate zeta. ------------------------------------------------------------------------ r3898 | pemsley | 2012-01-04 09:39:28 +0000 (Wed, 04 Jan 2012) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix (valgrind) problem when dynamic adding residues with names short than 3 in length. ------------------------------------------------------------------------ r3897 | pemsley | 2012-01-02 16:48:51 +0000 (Mon, 02 Jan 2012) | 3 lines Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc M /trunk/src/globjects.cc Make goograph resizable, so interface changed slightly. ------------------------------------------------------------------------ r3896 | pemsley | 2012-01-01 18:11:36 +0000 (Sun, 01 Jan 2012) | 2 lines Changed paths: M /trunk/goograph/Makefile.am M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc Add copyright notices. ------------------------------------------------------------------------ r3895 | pemsley | 2012-01-01 17:15:51 +0000 (Sun, 01 Jan 2012) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc Make the graphics ligand view optional. ------------------------------------------------------------------------ r3894 | pemsley | 2012-01-01 16:42:14 +0000 (Sun, 01 Jan 2012) | 4 lines Changed paths: M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.h M /trunk/src/graphics-ligand-view.cc Change lidia text anchoring. Don't expand ligand view on graphics window resizing. make_canvas_text_item moved into wmolecule.cc. ------------------------------------------------------------------------ r3893 | pemsley | 2012-01-01 13:37:17 +0000 (Sun, 01 Jan 2012) | 3 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lig-build.hh M /trunk/src/graphics-ligand-view.cc M /trunk/src/graphics-ligand-view.hh Rework subscripted text, now make_atom_id_by_using_bonds is passed a renderer flag. ------------------------------------------------------------------------ r3892 | pemsley | 2012-01-01 09:46:20 +0000 (Sun, 01 Jan 2012) | 3 lines Changed paths: M /trunk/lidia-core/lig-build.cc M /trunk/lidia-core/lig-build.hh M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-ligand-view.cc M /trunk/src/graphics-ligand-view.hh Move some pos_t functions from lig-build.hh to lig-build.cc. Don't display old layout on hetgroups without restraints. Enable subscripted layout text. ------------------------------------------------------------------------ r3891 | pemsley | 2011-12-31 17:30:49 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lig-build.cc M /trunk/lidia-core/lig-build.hh M /trunk/lidia-core/rdkit-interface.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-test.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h A /trunk/src/graphics-ligand-view.cc A /trunk/src/graphics-ligand-view.hh Hetgroups are now displayed laid-out bottom left (if using rdkit). ------------------------------------------------------------------------ r3890 | pemsley | 2011-12-31 17:30:43 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/src/coot.in unsetenv PHTHONHOME and PYTHONPATH so that gdb (for crash catcher) will start. ------------------------------------------------------------------------ r3889 | pemsley | 2011-12-31 17:30:38 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh Extract the goo_canvas line, text, object creation function into wrap_goo. Next to see how to use GL instead/aswell... ------------------------------------------------------------------------ r3888 | pemsley | 2011-12-31 17:30:31 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/src/c-interface-analysis.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Put in place stub functions that setup and draw the ligand view. ------------------------------------------------------------------------ r3887 | pemsley | 2011-12-31 17:30:26 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/test-goograph.cc Trivial diffs - wrapping up goocanvas changes for now. ------------------------------------------------------------------------ r3886 | pemsley | 2011-12-31 17:30:21 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc Add coloured dashed lines. ------------------------------------------------------------------------ r3885 | pemsley | 2011-12-31 17:30:17 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh Add the title onto the canvas. ------------------------------------------------------------------------ r3884 | pemsley | 2011-12-31 17:30:12 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc Clean up debugging. ------------------------------------------------------------------------ r3883 | pemsley | 2011-12-31 17:30:08 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/rel-todo Comment not needed in notes. ------------------------------------------------------------------------ r3882 | pemsley | 2011-12-31 17:30:02 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc M /trunk/lbg/lbg.cc M /trunk/rel-todo More autotick improvements - now with good major tick labelling. Try and fail to use canvas scaling to get high-res png in lidia output. ------------------------------------------------------------------------ r3881 | pemsley | 2011-12-31 17:29:55 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc More impovements in auto-ticks. ------------------------------------------------------------------------ r3880 | pemsley | 2011-12-31 17:29:51 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh Minor diff: add commented out debugging of data ranges in set_data(). ------------------------------------------------------------------------ r3879 | pemsley | 2011-12-31 17:29:46 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc Extents correction in the light of multiple traces. Correction of position of Y axis label. ------------------------------------------------------------------------ r3878 | pemsley | 2011-12-31 17:29:40 +0000 (Sat, 31 Dec 2011) | 3 lines Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc More scaling and placement improvements. world_to_canvas() now takes account of extents_min_y. Auto-ticking. ------------------------------------------------------------------------ r3877 | pemsley | 2011-12-31 17:29:31 +0000 (Sat, 31 Dec 2011) | 3 lines Changed paths: M /trunk/goograph/Makefile.am M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-test.cc M /trunk/src/cc-interface.hh Remove the dialog destroy on out of goograph going out of scope. More adjustments to positions (non-zero data extents). Add goograph display option for hole probe radius. ------------------------------------------------------------------------ r3876 | pemsley | 2011-12-31 17:29:25 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/goograph/test-goograph.cc Minor changes to annotation when using unscaled test data. ------------------------------------------------------------------------ r3875 | pemsley | 2011-12-31 17:29:19 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc Add annotated line and text. Add smoothed line plot. ------------------------------------------------------------------------ r3874 | pemsley | 2011-12-31 17:29:11 +0000 (Sat, 31 Dec 2011) | 2 lines Changed paths: M /trunk/auxil/catcheck/catcheck.hh M /trunk/goograph/Makefile.am M /trunk/goograph/goograph.cc M /trunk/goograph/goograph.hh M /trunk/goograph/test-goograph.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Graph orientation sorted out, axes and ticks now work with various data. Line graphs added. ------------------------------------------------------------------------ r3873 | pemsley | 2011-12-31 17:29:00 +0000 (Sat, 31 Dec 2011) | 1 line Changed paths: M /trunk/Makefile.am M /trunk/configure.in A /trunk/goograph A /trunk/goograph/Makefile.am A /trunk/goograph/goograph.cc A /trunk/goograph/goograph.hh A /trunk/goograph/test-goograph.cc M /trunk/src/Makefile.am M /trunk/src/testing.cc M /trunk/utils/coot-utils.cc Initial add of goograph. Y scaling broken. ------------------------------------------------------------------------ r3872 | pemsley | 2011-12-20 23:53:43 +0000 (Tue, 20 Dec 2011) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/ideal/simple-restraint.hh M /trunk/ideal/torsion-bonds.cc M /trunk/mini-mol/atom-quads.hh convert from atom_quads to torsion_atom_quads for use in multi_residue_torsion_fit_map(). Add sp3 torsion-angle transition option to random angles. ------------------------------------------------------------------------ r3871 | pemsley | 2011-12-19 17:21:22 +0000 (Mon, 19 Dec 2011) | 2 lines Changed paths: M /trunk/pixmaps/glyco-structures.svg Fix up bonding errors. ------------------------------------------------------------------------ r3870 | b.lohkamp | 2011-12-18 22:10:16 +0000 (Sun, 18 Dec 2011) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h add sort_residue function (similar to sort_chain) fix phs map reading from state files for windows ------------------------------------------------------------------------ r3869 | pemsley | 2011-12-18 15:13:24 +0000 (Sun, 18 Dec 2011) | 2 lines Changed paths: M /trunk/coot-utils/bonded-pairs.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Add environmental atoms for NBCs of refining atoms. ------------------------------------------------------------------------ r3868 | pemsley | 2011-12-18 15:12:20 +0000 (Sun, 18 Dec 2011) | 2 lines Changed paths: M /trunk/pdb-templates/Makefile.am A /trunk/pdb-templates/pyranose-pyranose-via-ALPHA1-2.pdb Add alpha1-2 link template. ------------------------------------------------------------------------ r3867 | pemsley | 2011-12-18 15:10:35 +0000 (Sun, 18 Dec 2011) | 2 lines Changed paths: M /trunk/ccp4mg-utils/ppmutil.cc Close the ppm file when colourspace is not IMAGEINFO_RGB. ------------------------------------------------------------------------ r3866 | pemsley | 2011-12-18 10:49:59 +0000 (Sun, 18 Dec 2011) | 3 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Remove debugging. Remove GTK1 cruft. ------------------------------------------------------------------------ r3865 | b.lohkamp | 2011-12-16 17:16:58 +0000 (Fri, 16 Dec 2011) | 9 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-graphs.cc do not test reduce exit status and no more stdbonds in probe (python) add pythonic local map export fix pythonic add solvent gui add multi_residue_torsion_fit_py add test_function_py (un-tested strangely) fix rotamer graphs for non-standard-residue chains ------------------------------------------------------------------------ r3864 | pemsley | 2011-12-16 16:23:00 +0000 (Fri, 16 Dec 2011) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo Fix valgrind error in try_dynamic_add(). ------------------------------------------------------------------------ r3863 | pemsley | 2011-12-16 14:02:52 +0000 (Fri, 16 Dec 2011) | 2 lines Changed paths: D /trunk/libgtkgraph/Makefile.in D /trunk/libgtkgraph/TAGS D /trunk/libgtkgraph/docs Remove docs and TAGS from libgtkgraph ------------------------------------------------------------------------ r3862 | pemsley | 2011-12-16 14:01:21 +0000 (Fri, 16 Dec 2011) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in A /trunk/libgtkgraph A /trunk/libgtkgraph/Doxyfile A /trunk/libgtkgraph/Doxyfile.orig A /trunk/libgtkgraph/Makefile.am A /trunk/libgtkgraph/Makefile.in A /trunk/libgtkgraph/TAGS A /trunk/libgtkgraph/annotation.c A /trunk/libgtkgraph/axis.c A /trunk/libgtkgraph/docs A /trunk/libgtkgraph/docs/html A /trunk/libgtkgraph/docs/html/annotated.html A /trunk/libgtkgraph/docs/html/classes.html A /trunk/libgtkgraph/docs/html/doxygen.css A /trunk/libgtkgraph/docs/html/doxygen.png A /trunk/libgtkgraph/docs/html/files.html A /trunk/libgtkgraph/docs/html/globals.html A /trunk/libgtkgraph/docs/html/globals_defs.html A /trunk/libgtkgraph/docs/html/globals_enum.html A /trunk/libgtkgraph/docs/html/globals_eval.html A /trunk/libgtkgraph/docs/html/globals_func.html A /trunk/libgtkgraph/docs/html/gtkgraph_8h.html A /trunk/libgtkgraph/docs/html/index.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph_annotation.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph_axis.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph_polar_format.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph_trace.html A /trunk/libgtkgraph/docs/html/struct_gtk_graph_trace_format.html A /trunk/libgtkgraph/docs/html/tab_b.gif A /trunk/libgtkgraph/docs/html/tab_l.gif A /trunk/libgtkgraph/docs/html/tab_r.gif A /trunk/libgtkgraph/docs/html/tabs.css A /trunk/libgtkgraph/docs/latex A /trunk/libgtkgraph/docs/latex/Makefile A /trunk/libgtkgraph/docs/latex/annotated.tex A /trunk/libgtkgraph/docs/latex/doxygen.sty A /trunk/libgtkgraph/docs/latex/files.tex A /trunk/libgtkgraph/docs/latex/gtkgraph_8h.tex A /trunk/libgtkgraph/docs/latex/index.tex A /trunk/libgtkgraph/docs/latex/refman.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph_annotation.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph_axis.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph_polar_format.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph_trace.tex A /trunk/libgtkgraph/docs/latex/struct_gtk_graph_trace_format.tex A /trunk/libgtkgraph/gtkgraph.c A /trunk/libgtkgraph/gtkgraph.h A /trunk/libgtkgraph/gtkgraph_internal.h A /trunk/libgtkgraph/gtkgraph_original.h A /trunk/libgtkgraph/polar.c A /trunk/libgtkgraph/polar_util.c A /trunk/libgtkgraph/smith.c A /trunk/libgtkgraph/trace.c M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc M /trunk/src/cc-interface.hh Experimental: Add libgtkgraph and use it to draw the graph for the probe radius. ------------------------------------------------------------------------ r3861 | pemsley | 2011-12-16 13:29:55 +0000 (Fri, 16 Dec 2011) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/cc-interface.hh Add on_simple_text_dialog_close_button_pressed() so we can have a close button. (Some non-functional/commented references to gtkgraph). ------------------------------------------------------------------------ r3860 | pemsley | 2011-12-15 22:41:37 +0000 (Thu, 15 Dec 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/cc-interface.hh M /trunk/src/gtk2-interface.c Add a dialog for the text of the hole probe data points. ------------------------------------------------------------------------ r3859 | pemsley | 2011-12-15 17:55:49 +0000 (Thu, 15 Dec 2011) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-test.cc M /trunk/src/globjects.cc shift-control middle-mouse and control-shift middle mouse now behave the same way. ------------------------------------------------------------------------ r3858 | pemsley | 2011-12-15 15:30:40 +0000 (Thu, 15 Dec 2011) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Fix long-standing bug of link determination of consecutive residues but non-sequential residue numbering for non-peptide links. ------------------------------------------------------------------------ r3857 | pemsley | 2011-12-15 00:01:38 +0000 (Thu, 15 Dec 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a extensions menu item for map fragment export. ------------------------------------------------------------------------ r3856 | pemsley | 2011-12-14 23:55:15 +0000 (Wed, 14 Dec 2011) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-kdc.cc Call set_cell() when exporting an nxmap. ------------------------------------------------------------------------ r3855 | pemsley | 2011-12-14 23:42:29 +0000 (Wed, 14 Dec 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface.cc M /trunk/src/c-interface.h A /trunk/src/molecule-class-info-kdc.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add (non-working) map fragment export. Needs Kevin to look at it. ------------------------------------------------------------------------ r3854 | pemsley | 2011-12-14 21:03:00 +0000 (Wed, 14 Dec 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/utils/gdk-keysyms.cc Don't draw hetgroup bonds to hydrogens when hydrogens are switched off. Add "(" and ")" (back?) to key-bindings. ------------------------------------------------------------------------ r3853 | pemsley | 2011-12-14 19:03:03 +0000 (Wed, 14 Dec 2011) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Draw LINKRs (templated function). In autobuilder, use mmdb-1.24 which has working LINKRs. ------------------------------------------------------------------------ r3852 | pemsley | 2011-12-14 15:07:57 +0000 (Wed, 14 Dec 2011) | 4 lines Changed paths: M /trunk/dnotes M /trunk/ideal/torsion-bonds.cc M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc Add n_selected_atoms == 0 protection in multi_residue_torsion_fit_map(). Add make_backup() in add_residue(). Add SCM version of test_function. ------------------------------------------------------------------------ r3851 | pemsley | 2011-12-13 18:57:12 +0000 (Tue, 13 Dec 2011) | 2 lines Changed paths: M /trunk/src/graphics-info-render.cc Remove debugging. ------------------------------------------------------------------------ r3850 | pemsley | 2011-12-13 18:56:23 +0000 (Tue, 13 Dec 2011) | 2 lines Changed paths: M /trunk/src/graphics-info-render.cc Fix typo and increment frame counter. ------------------------------------------------------------------------ r3849 | pemsley | 2011-12-13 18:55:05 +0000 (Tue, 13 Dec 2011) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-ebi.scm Remove debugging when downloading files from EDS. string->list-of-strings now splits on tab too. ------------------------------------------------------------------------ r3848 | pemsley | 2011-12-13 12:05:26 +0000 (Tue, 13 Dec 2011) | 1 line Changed paths: M /trunk/lbg/wmolecule.cc Remove debugging. ------------------------------------------------------------------------ r3847 | pemsley | 2011-12-13 12:05:18 +0000 (Tue, 13 Dec 2011) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ideal/torsion-bonds.cc M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h SCM an Py interface for add_linked_residue. go_to_atom_from_res_spec SCM and Py interface. Add intelligent_this_residue_atom() taking a residue spec. Add a empty() function for an atom_spec_t. res-spec->chain-id, res-no ins-code extraction functions. tweak the multi-torsion-angle search algorithm. ------------------------------------------------------------------------ r3846 | pemsley | 2011-12-13 12:05:13 +0000 (Tue, 13 Dec 2011) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Add the distance check to smooth_scroll_maybe_sinusoidal_acceleration() so that NCS jumping works again. ------------------------------------------------------------------------ r3845 | pemsley | 2011-12-13 12:05:09 +0000 (Tue, 13 Dec 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Remove debugging. Add non-functional code trying to add an image to a canvas. ------------------------------------------------------------------------ r3844 | pemsley | 2011-12-11 23:04:07 +0000 (Sun, 11 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/ideal/torsion-bonds.cc M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh Add the quad name to an atom_quad (so that we can change the angle manipulation for a 1-6 link (if needed). ------------------------------------------------------------------------ r3843 | pemsley | 2011-12-11 18:58:18 +0000 (Sun, 11 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/src/molecule-class-info-residues.cc Rework the beam_in_residue constructor to work with comp_id-group pairs. This enables SIA-ALPHA2-3 link. ------------------------------------------------------------------------ r3842 | pemsley | 2011-12-11 15:49:49 +0000 (Sun, 11 Dec 2011) | 11 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/geometry/protein-geometry.cc M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-gui.cc M /trunk/src/molecule-class-info-residues.cc Rework atom_quad constructor (for link chiral) - now handled atom names for ALPHA2-3 links. Glycosidic link check for ALPHA2-3 now checks for SIA in residue_1. neighbouring residues at the start of glyco_tree_t constructor are now sorted (by residue spec). rooted tree construction can now add residues that need an order switch. tree comparison added. Fix oversight in solvent-ligands gui, we no longer try call get-monomer using the button-label, now the comp-id is used. Remove some GTK1 cruff from c-interface-gui.cc ------------------------------------------------------------------------ r3841 | pemsley | 2011-12-11 15:38:53 +0000 (Sun, 11 Dec 2011) | 2 lines Changed paths: M /trunk/pdb-templates/Makefile.am A /trunk/pdb-templates/SIA-pyranose-via-ALPHA2-3.pdb Add template for SIA-pyranose via ALPHA2-3. ------------------------------------------------------------------------ r3840 | pemsley | 2011-12-11 12:56:50 +0000 (Sun, 11 Dec 2011) | 2 lines Changed paths: M /trunk/Makefile.am Template pdb files have their own directory now - no need to refer to them in top Level Makefile. ------------------------------------------------------------------------ r3839 | pemsley | 2011-12-10 19:27:38 +0000 (Sat, 10 Dec 2011) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/macros/goo-canvas.m4 M /trunk/mini-mol/atom-quads.cc M /trunk/rel-todo Debugging added to finding glyco linkages. Fix ALPHA2-3 typo. atom-quads needs to be reworked with 2-linked residues in mind (new chiral centre is in Residue 1). ------------------------------------------------------------------------ r3838 | pemsley | 2011-12-09 16:44:30 +0000 (Fri, 09 Dec 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Fix typo in unsaved changes. ------------------------------------------------------------------------ r3837 | pemsley | 2011-12-09 16:43:40 +0000 (Fri, 09 Dec 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-glyco.cc Add in an initial value for current_torsion (obviates compiler warning). ------------------------------------------------------------------------ r3836 | pemsley | 2011-12-09 16:39:57 +0000 (Fri, 09 Dec 2011) | 3 lines Changed paths: D /trunk/ASN-NAG-via-NAG-ASN.pdb M /trunk/Makefile.am M /trunk/configure.in A /trunk/pdb-templates A /trunk/pdb-templates/ASN-NAG-via-NAG-ASN.pdb (from /trunk/ASN-NAG-via-NAG-ASN.pdb:3834) A /trunk/pdb-templates/Makefile.am A /trunk/pdb-templates/pyranose-pyranose-via-ALPHA1-3.pdb (from /trunk/pyranose-pyranose-via-ALPHA1-3.pdb:3834) A /trunk/pdb-templates/pyranose-pyranose-via-ALPHA1-6.pdb (from /trunk/pyranose-pyranose-via-ALPHA1-6.pdb:3834) A /trunk/pdb-templates/pyranose-pyranose-via-BETA1-4.pdb (from /trunk/pyranose-pyranose-via-BETA1-4.pdb:3834) A /trunk/pdb-templates/theor-helix-70.pdb (from /trunk/theor-helix-70.pdb:3834) D /trunk/pyranose-pyranose-via-ALPHA1-3.pdb D /trunk/pyranose-pyranose-via-ALPHA1-6.pdb D /trunk/pyranose-pyranose-via-BETA1-4.pdb M /trunk/rel-todo D /trunk/theor-helix-70.pdb Make a directory for template PDB files. Move pdb-files to template directory. ------------------------------------------------------------------------ r3835 | pemsley | 2011-12-09 16:18:01 +0000 (Fri, 09 Dec 2011) | 2 lines Changed paths: A /trunk/pixmaps/glyco-structures.svg Add glyco-structure svg. ------------------------------------------------------------------------ r3834 | pemsley | 2011-12-09 15:34:45 +0000 (Fri, 09 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/rel-todo M /trunk/src/molecule-class-info-residues.cc beam_in_residue() now works with 1-6 links (by rotation of new residue about reference residue's C5-C6 bond). add_residue() now sets have_unsaved_changes_flag. ------------------------------------------------------------------------ r3833 | pemsley | 2011-12-09 08:37:03 +0000 (Fri, 09 Dec 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/molecule-class-info.cc Fix additional_representation_by_attributes() when an altconf specified. mmdb_string() needed to write out the ins_code. ------------------------------------------------------------------------ r3832 | b.lohkamp | 2011-12-09 03:00:34 +0000 (Fri, 09 Dec 2011) | 1 line Changed paths: M /trunk/src/lbg-interface.cc fix python compilation for enterprise tools ------------------------------------------------------------------------ r3831 | pemsley | 2011-12-08 18:51:51 +0000 (Thu, 08 Dec 2011) | 2 lines Changed paths: M /trunk/compat/coot-getopt.h Hack out throw() in getopt declaration. Compiles fine on Fed15 it seems. ------------------------------------------------------------------------ r3830 | pemsley | 2011-12-08 18:40:16 +0000 (Thu, 08 Dec 2011) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am Add tree.hh to include_HEADERS. ------------------------------------------------------------------------ r3829 | pemsley | 2011-12-08 18:34:59 +0000 (Thu, 08 Dec 2011) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Alignment of widgets in Go To Atom. No longer able to tab to "Update from Current Position". ------------------------------------------------------------------------ r3828 | b.lohkamp | 2011-12-08 14:38:32 +0000 (Thu, 08 Dec 2011) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/c-inner-main.h M /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-python.hh M /trunk/src/c-interface-sfs.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-view.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/drag-and-drop.cc M /trunk/src/get-residue.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-network.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/graphics-info-scripting.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh reorder Python.h header to fix Mac compile issues (maybe) ------------------------------------------------------------------------ r3827 | pemsley | 2011-12-08 12:09:54 +0000 (Thu, 08 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc Add reference trees. Add a residue name to linked_residue_t, add == operator, change print() to print from right to left. ------------------------------------------------------------------------ r3826 | pemsley | 2011-12-08 12:09:50 +0000 (Thu, 08 Dec 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-utils-glyco.cc Trivial diff - shorten lines. ------------------------------------------------------------------------ r3825 | pemsley | 2011-12-08 06:18:09 +0000 (Thu, 08 Dec 2011) | 2 lines Changed paths: M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add glyco_test() to user-interface - currently prints the tree. ------------------------------------------------------------------------ r3824 | pemsley | 2011-12-08 06:16:23 +0000 (Thu, 08 Dec 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/test-utils.cc Add non-rooted trees. ------------------------------------------------------------------------ r3823 | pemsley | 2011-12-07 18:50:31 +0000 (Wed, 07 Dec 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Add #include (strncmp is used). ------------------------------------------------------------------------ r3822 | pemsley | 2011-12-07 18:46:28 +0000 (Wed, 07 Dec 2011) | 3 lines Changed paths: M /trunk/analysis/bfkurt.hh M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines_ext.cc M /trunk/coords/coot-close.hh M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/coot-utils/bonded-pairs.hh M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-h-bonds.hh M /trunk/coot-utils/coot-hole.hh M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-rama.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/coot-utils/peak-search.hh M /trunk/geometry/protein-geometry-mmdb.cc M /trunk/geometry/protein-geometry.hh M /trunk/high-res/sequence-assignment.hh M /trunk/ideal/molmantest.cc M /trunk/ideal/pepflip.hh M /trunk/ideal/simple-restraint.hh M /trunk/ideal/test-indexing.cc M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/lbg/flev-annotations.cc M /trunk/lbg/lbg.hh M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/rdkit-interface.hh M /trunk/ligand/base-pairing.hh M /trunk/ligand/dipole.hh M /trunk/ligand/ideal-rna.hh M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/monomer-utils.hh M /trunk/ligand/primitive-chi-angles.hh M /trunk/macros/mmdb.m4 M /trunk/mini-mol/atom-quads.hh M /trunk/mini-mol/mini-mol.hh M /trunk/skeleton/BuildCas.h M /trunk/skeleton/graphical_skel.cc M /trunk/src/align.cc M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-test.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters-gui.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/coot-align.cc M /trunk/src/coot-hydrogens.cc M /trunk/src/coot-nomenclature.hh M /trunk/src/density-score-by-residue-src.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-ribbons.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/molecule-class-info.cc M /trunk/src/nsv.hh M /trunk/src/pick.cc M /trunk/src/pick.h M /trunk/src/rama_plot.hh M /trunk/src/sequence-view.cc M /trunk/src/sequence-view.hh M /trunk/surface/CXXBall.h M /trunk/surface/CXXCircle.cpp M /trunk/surface/CXXCircle.h M /trunk/surface/CXXCircleNode.h M /trunk/surface/CXXCreator.h M /trunk/surface/CXXNewHood.cpp M /trunk/surface/CXXNewHood.h M /trunk/surface/CXXQADSurface.h M /trunk/surface/CXXSpace.h M /trunk/surface/CXXSphereElement.cpp M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXUtils.h M /trunk/surface/ElectroSurface.cpp M /trunk/surface/surface.h Convert to #include (etc) usage. Ajust configure test for same. ------------------------------------------------------------------------ r3821 | pemsley | 2011-12-07 18:00:25 +0000 (Wed, 07 Dec 2011) | 3 lines Changed paths: M /trunk/scheme/generic-objects.scm No longer use --std-bonds argument to probe. This fixes carbohydrate linkage clashes. Not sure what it will break... ------------------------------------------------------------------------ r3820 | pemsley | 2011-12-07 17:58:48 +0000 (Wed, 07 Dec 2011) | 3 lines Changed paths: M /trunk/analysis/Makefile.am M /trunk/lbg/Makefile.am Makefile.am changes to account for protein-geometry dependency on mini-mol on Ubuntu 10.04. ------------------------------------------------------------------------ r3819 | pemsley | 2011-12-07 17:13:40 +0000 (Wed, 07 Dec 2011) | 5 lines Changed paths: M /trunk/Makefile.am M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc A /trunk/coot-utils/tree.hh M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh M /trunk/mini-mol/mini-mol.cc M /trunk/rel-todo Add glyco_tree analysis - first bash. Add chiral test for glycosidic link determination. protein-geometry now depends on mini-mol via atom-quads. So Makefile.am LIBADDs and build order changed to reflect that. Test it in testcootutils. ------------------------------------------------------------------------ r3818 | pemsley | 2011-12-06 23:45:29 +0000 (Tue, 06 Dec 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Add some protection for null model in get_residue(). ------------------------------------------------------------------------ r3817 | pemsley | 2011-12-06 23:45:25 +0000 (Tue, 06 Dec 2011) | 1 line Changed paths: M /trunk/ideal/torsion-bonds.cc No differences - AFAICS. ------------------------------------------------------------------------ r3816 | pemsley | 2011-12-06 23:45:20 +0000 (Tue, 06 Dec 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-tree-extras.cc remove debugging. ------------------------------------------------------------------------ r3815 | pemsley | 2011-12-06 22:10:38 +0000 (Tue, 06 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/test-utils.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo Inital glyco_tree analysis. Testing added to testcootutils. Begin to construct an ASN-rooted tree. ------------------------------------------------------------------------ r3814 | pemsley | 2011-12-06 15:56:04 +0000 (Tue, 06 Dec 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-residues.cc Remove debugging. ------------------------------------------------------------------------ r3813 | pemsley | 2011-12-05 23:24:24 +0000 (Mon, 05 Dec 2011) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/pyranose-pyranose-via-ALPHA1-3.pdb M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add multi_residue_torsion_fit() c++ function. add_linked_residue returns a residue spec for new residue. ------------------------------------------------------------------------ r3812 | pemsley | 2011-12-05 22:47:31 +0000 (Mon, 05 Dec 2011) | 2 lines Changed paths: A /trunk/pyranose-pyranose-via-ALPHA1-6.pdb Add pyranose-pyranose-via-ALPHA1-6.pdb. ------------------------------------------------------------------------ r3811 | pemsley | 2011-12-05 13:15:06 +0000 (Mon, 05 Dec 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-utils-glyco.cc Add a warning message for the case of link template file not existing. ------------------------------------------------------------------------ r3810 | pemsley | 2011-12-05 13:15:02 +0000 (Mon, 05 Dec 2011) | 1 line Changed paths: M /trunk/Makefile.am Fix typo for alpha1-3 template file. ------------------------------------------------------------------------ r3809 | pemsley | 2011-12-05 12:47:46 +0000 (Mon, 05 Dec 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-extras.cc static cast the NULL initial value of a vector of CAtom *s. ------------------------------------------------------------------------ r3808 | pemsley | 2011-12-05 12:25:17 +0000 (Mon, 05 Dec 2011) | 5 lines Changed paths: M /trunk/Makefile.am M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/torsion-bonds.cc M /trunk/ligand/Makefile.am M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh A /trunk/pyranose-pyranose-via-ALPHA1-3.pdb M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/skeleton/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add a c-interface.h function for torsion fitting. Remove pyranose ring link torsions from the manipulatable set. 200 trials currently. Add a template for an alpha-1-3 link. Torsion manipulation seems to work crudely. ------------------------------------------------------------------------ r3807 | b.lohkamp | 2011-12-04 15:08:52 +0000 (Sun, 04 Dec 2011) | 1 line Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c resize phs_cell_dialog ------------------------------------------------------------------------ r3806 | pemsley | 2011-12-04 14:30:14 +0000 (Sun, 04 Dec 2011) | 1 line Changed paths: M /trunk/generate-svn-revision-cc.sh Update generate-svn-revision-cc.sh to handle non-svn repo. ------------------------------------------------------------------------ r3805 | pemsley | 2011-12-04 14:30:10 +0000 (Sun, 04 Dec 2011) | 1 line Changed paths: M /trunk/autogen.sh Tidy up autogen.sh a bit. ------------------------------------------------------------------------ r3804 | pemsley | 2011-12-04 14:30:06 +0000 (Sun, 04 Dec 2011) | 1 line Changed paths: M /trunk/dnotes Clean up dnotes. ------------------------------------------------------------------------ r3803 | pemsley | 2011-12-04 12:41:56 +0000 (Sun, 04 Dec 2011) | 1 line Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3802 | pemsley | 2011-12-03 19:27:10 +0000 (Sat, 03 Dec 2011) | 2 lines Changed paths: M /trunk/Makefile.am Put back linked pdb files into EXTRA_DIST. ------------------------------------------------------------------------ r3801 | pemsley | 2011-12-03 16:59:15 +0000 (Sat, 03 Dec 2011) | 3 lines Changed paths: M /trunk/lidia-core/Makefile.am lidia-core depends on geometry and utils. Add them to the libcoot_lidia_core_la_LIBADD line. ------------------------------------------------------------------------ r3800 | b.lohkamp | 2011-12-03 16:21:49 +0000 (Sat, 03 Dec 2011) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py python test update for new ccp4 ------------------------------------------------------------------------ r3799 | pemsley | 2011-12-03 13:36:18 +0000 (Sat, 03 Dec 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh A /trunk/ideal/torsion-bonds.cc M /trunk/src/c-interface-test.cc Move multi_residue_torsion_fit_map to ideal (it uses restraints). Break out torsion functions to new source file. ------------------------------------------------------------------------ r3798 | pemsley | 2011-12-03 12:12:51 +0000 (Sat, 03 Dec 2011) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-residues.cc M /trunk/src/molecule-class-info.cc Fix up reverse-fragment mode of multi-residue torsion (gui). ------------------------------------------------------------------------ r3797 | pemsley | 2011-12-02 13:00:03 +0000 (Fri, 02 Dec 2011) | 2 lines Changed paths: A /trunk/pyranose-pyranose-via-BETA1-4.pdb Add missing file. ------------------------------------------------------------------------ r3796 | pemsley | 2011-12-02 12:02:57 +0000 (Fri, 02 Dec 2011) | 14 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/geometry/chem_mods.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc Updates to beam_in_linked_residue class. Now take a pointer to a protein_geometry. matching_chem_link() returns all links. find_glycosidic_linkage_type moved to protein_geometry class. atom_id_expand() function added (used in chem mods when we don't know the group until we get a residue). Apply the link's mods after adding a new monomer. delete_atom() created to deal with mod atom deletes. lsq_fit() function factored out, matrix is determined from one pair of residues and applied to a third. deep_copy_residue() tests for null atoms. tests updated for new ccp4 (libcheck torsion restraints) and allow for different default sampling rates in difference map test. ------------------------------------------------------------------------ r3795 | pemsley | 2011-12-01 08:15:50 +0000 (Thu, 01 Dec 2011) | 4 lines Changed paths: M /trunk/Makefile.am M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/lsq-improve.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/molecule-class-info-residues.cc M /trunk/src/testing.cc Rework beam_in_linked_residue. The constructor now takes a protein_geometry (and so the class has moved to coot-coord-extras.hh). setup_be_group() filled. ------------------------------------------------------------------------ r3794 | pemsley | 2011-11-30 20:11:28 +0000 (Wed, 30 Nov 2011) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi Add documentation for refine-residues. ------------------------------------------------------------------------ r3793 | pemsley | 2011-11-30 17:46:05 +0000 (Wed, 30 Nov 2011) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add the parsing of torsion and chiral info from structures (in addition to loops) in mmCIF files. ------------------------------------------------------------------------ r3792 | pemsley | 2011-11-29 16:09:12 +0000 (Tue, 29 Nov 2011) | 2 lines Changed paths: M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3791 | pemsley | 2011-11-29 16:07:42 +0000 (Tue, 29 Nov 2011) | 3 lines Changed paths: M /trunk/src/globjects.cc Don't scale the orientation axes as the screen is widened (the placement is a bit non-optimal, but all together things are better). ------------------------------------------------------------------------ r3790 | pemsley | 2011-11-29 14:16:46 +0000 (Tue, 29 Nov 2011) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3789 | pemsley | 2011-11-29 14:16:11 +0000 (Tue, 29 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm M /trunk/scheme/refmac.scm More cleanups when running refmac for recent PDBe entries. ------------------------------------------------------------------------ r3788 | pemsley | 2011-11-29 12:36:05 +0000 (Tue, 29 Nov 2011) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Fix problem of translation when using solid generic objects (stray GL_LINES). ------------------------------------------------------------------------ r3787 | pemsley | 2011-11-28 21:37:48 +0000 (Mon, 28 Nov 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Upcase the user-defined Atom at pointer. ------------------------------------------------------------------------ r3786 | pemsley | 2011-11-28 21:36:22 +0000 (Mon, 28 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm Move make-and-draw-map-local to where it's needed. ------------------------------------------------------------------------ r3785 | pemsley | 2011-11-28 20:51:38 +0000 (Mon, 28 Nov 2011) | 6 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm M /trunk/scheme/prodrg-import.scm Promote pdbe-get-pdb-and-sfs-cif promoted to top level. Remove debugging. Limit concurrent curl requests to 20 (otherwise connections dropped). Add new curl objects to the back of the queue (popping from the front, as before). ------------------------------------------------------------------------ r3784 | b.lohkamp | 2011-11-28 06:48:32 +0000 (Mon, 28 Nov 2011) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/lbg/lbg.cc M /trunk/python/extensions.py M /trunk/python/prodrg_import.py M /trunk/python/refmac.py fix dnd for lbg in windows pythonic prodrg_import has errors log now, activated hydrogenation and de- activated non-working and non-public functions add a pythonic extension of compid to resname pythonic rotamer search submenu selectable (finally) ------------------------------------------------------------------------ r3783 | pemsley | 2011-11-25 14:25:37 +0000 (Fri, 25 Nov 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Improve function name documentation. ------------------------------------------------------------------------ r3782 | pemsley | 2011-11-25 11:02:09 +0000 (Fri, 25 Nov 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info.cc Fix up material colour for solid generic objects and environment distances. ------------------------------------------------------------------------ r3781 | pemsley | 2011-11-25 00:03:43 +0000 (Fri, 25 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-recent-pdbe.scm M /trunk/scheme/refmac.scm Enable quiet mode for refmac usage. ------------------------------------------------------------------------ r3780 | pemsley | 2011-11-24 15:54:43 +0000 (Thu, 24 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a "What's this?" to modelling menu (uses comp-id->name). ------------------------------------------------------------------------ r3779 | pemsley | 2011-11-24 13:57:52 +0000 (Thu, 24 Nov 2011) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/lbg/lbg.cc M /trunk/python/extensions.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/generic-objects.scm M /trunk/scheme/get-recent-pdbe.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h dots() now takes a name argument. clear_dots_by_name() function added. dots are coloured by atom element. dots are generated using (simple) atom element-based radii. Remove some lbg debugging. ------------------------------------------------------------------------ r3778 | pemsley | 2011-11-24 11:34:41 +0000 (Thu, 24 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/refmac.scm Turn off screen output of refmac when make-molecules-flag is 0. ------------------------------------------------------------------------ r3777 | pemsley | 2011-11-22 23:44:13 +0000 (Tue, 22 Nov 2011) | 2 lines Changed paths: M /trunk/lidia-core/lbg-shared.cc M /trunk/lidia-core/lbg-shared.hh Add copyright notices. ------------------------------------------------------------------------ r3776 | pemsley | 2011-11-22 23:43:54 +0000 (Tue, 22 Nov 2011) | 2 lines Changed paths: M /trunk/lbg/lbg-drag-and-drop.cc Remove debugging. ------------------------------------------------------------------------ r3775 | pemsley | 2011-11-22 23:11:29 +0000 (Tue, 22 Nov 2011) | 2 lines Changed paths: M /trunk/lidia-core/lbg-shared.cc Fix up quotation of include file ------------------------------------------------------------------------ r3774 | pemsley | 2011-11-22 19:11:46 +0000 (Tue, 22 Nov 2011) | 4 lines Changed paths: M /trunk/coot-utils/coot-h-bonds.cc M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.cc M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/lbg-molfile.cc A /trunk/lidia-core/lbg-shared.cc M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/flev.cc Enable CCP4 (Prodrg+refmac) path for ligand layout (flev). remove debugging. Clear up Lidia menu. ------------------------------------------------------------------------ r3773 | pemsley | 2011-11-21 12:27:49 +0000 (Mon, 21 Nov 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh Fix up map transformations so that grid points close to the middle of the target position are set last - fixes symmetry overwritting (in tests so far). ------------------------------------------------------------------------ r3772 | pemsley | 2011-11-18 12:04:31 +0000 (Fri, 18 Nov 2011) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-gui.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Some changes with Accept/Reject dialog position. I give up - I don't know why it sometimes is misplaced. is_standard_amino_acid_name() introduced (for rotamer analysis filter). ------------------------------------------------------------------------ r3771 | pemsley | 2011-11-17 16:37:07 +0000 (Thu, 17 Nov 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove debugging. ------------------------------------------------------------------------ r3770 | pemsley | 2011-11-17 15:34:09 +0000 (Thu, 17 Nov 2011) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/mmdb-crystal.cc M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-defines.cc Clean up symm_trans_t::str(). Use 1-index not zero index for outputing symm op numbers. Pymol-esque (AFAICT) symmetry filenames. ------------------------------------------------------------------------ r3769 | pemsley | 2011-11-17 13:43:14 +0000 (Thu, 17 Nov 2011) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/coords/Bond_lines.cc M /trunk/python/coot_load_modules.py.in M /trunk/python/prodrg_import.py M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Use (use_gui_qm == 2) test for pythonic LIDIA additions. Remove testing functions from LIDIA menu. python_prefered() made available at the scripting layer. Notes updated. ------------------------------------------------------------------------ r3768 | pemsley | 2011-11-15 14:20:21 +0000 (Tue, 15 Nov 2011) | 6 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lidia-core/rdkit-interface.cc M /trunk/lidia-core/rdkit-interface.hh M /trunk/python/prodrg_import.py M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-scripting.cc M /trunk/src/graphics-info.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Rework the usage of prodrg on pressing "Accept" in the Ligand Builder. No more timeout functions waiting for new prodrg-in.mdl. Instead pass a function pointer to lbg that is called when "Accept" is clicked (prodrg_import_function). prefer_python correctly set when not compiled with guile. ------------------------------------------------------------------------ r3767 | pemsley | 2011-11-14 16:46:17 +0000 (Mon, 14 Nov 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/src/molecule-class-info.cc Don't add_bonds_het_residues() if are_different_atom_selections (X-H bonding), (we only need it once). ------------------------------------------------------------------------ r3766 | pemsley | 2011-11-14 15:13:49 +0000 (Mon, 14 Nov 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-navigation.cc Fix updating of Go To Atom window after change_chain_id()/merge water chains. ------------------------------------------------------------------------ r3765 | pemsley | 2011-11-14 15:12:07 +0000 (Mon, 14 Nov 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi update dependency text. ------------------------------------------------------------------------ r3764 | pemsley | 2011-11-13 23:26:35 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/ideal/Makefile.am M /trunk/ligand/Makefile.am More Makefile.am updates. ------------------------------------------------------------------------ r3763 | b.lohkamp | 2011-11-13 17:22:01 +0000 (Sun, 13 Nov 2011) | 3 lines Changed paths: M /trunk/lbg/lbg-drag-and-drop.cc M /trunk/python/libcheck.py M /trunk/src/drag-and-drop.cc fix (some) drag and drop for windows ------------------------------------------------------------------------ r3762 | pemsley | 2011-11-13 15:28:22 +0000 (Sun, 13 Nov 2011) | 3 lines Changed paths: M /trunk/src/Makefile.am Update Makefile.ams to add RDKIT_LIBS to executable LDADDs. Not sure why this is needed (Ubuntu 10.04). ------------------------------------------------------------------------ r3761 | pemsley | 2011-11-13 15:26:13 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/src/command-arg.hh M /trunk/src/graphics-info-scripting.cc Better output as string when command_arg_t is a bool. ------------------------------------------------------------------------ r3760 | pemsley | 2011-11-13 15:24:14 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Use new-style scripting_function() for get_coords_for_accession_code(). ------------------------------------------------------------------------ r3759 | pemsley | 2011-11-13 15:22:38 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/lbg/lbg-drag-and-drop.cc Add a return value for on_lbg_drag_drop(). ------------------------------------------------------------------------ r3758 | pemsley | 2011-11-13 14:46:35 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh Fix typo in simplex function setup function name. ------------------------------------------------------------------------ r3757 | pemsley | 2011-11-13 14:45:21 +0000 (Sun, 13 Nov 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc Add a return value for rotate_about() with int args. ------------------------------------------------------------------------ r3756 | pemsley | 2011-11-12 22:57:59 +0000 (Sat, 12 Nov 2011) | 2 lines Changed paths: M /trunk/src/Makefile.am Put command-arg.hh into Makefile.am ------------------------------------------------------------------------ r3755 | pemsley | 2011-11-12 15:57:50 +0000 (Sat, 12 Nov 2011) | 2 lines Changed paths: A /trunk/src/graphics-info-scripting.cc Add missing file. ------------------------------------------------------------------------ r3754 | pemsley | 2011-11-12 15:44:01 +0000 (Sat, 12 Nov 2011) | 7 lines Changed paths: M /trunk/lbg/lbg-drag-and-drop.cc M /trunk/lbg/lbg-drag-and-drop.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Send a function pointer to lbg so that it can get urls (coot_get_url and its handlers are at the top (src) level). Allow the dropping of mol/sdf/mol2 files URLs onto the lbg canvas. Also allow dropping of drugbank images (parsed to construct the URL for the mol file). Conditionally compile on HAVE_GOOCANAS. ------------------------------------------------------------------------ r3753 | pemsley | 2011-11-12 07:20:50 +0000 (Sat, 12 Nov 2011) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Remove some debugging from get_monomer(). ------------------------------------------------------------------------ r3752 | pemsley | 2011-11-12 00:43:57 +0000 (Sat, 12 Nov 2011) | 2 lines Changed paths: A /trunk/src/command-arg.hh Add command-arg.hh to repo. ------------------------------------------------------------------------ r3751 | pemsley | 2011-11-12 00:42:57 +0000 (Sat, 12 Nov 2011) | 9 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/scheme/libcheck.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/drag-and-drop.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Change get_monomer() to use the new scripting_function() system. add_cif_dictionary() and handle_cif_dictionary() return a value now, which we can use to see if the cif file was a restraints dictionary (it had bond restraints). And that is used for dragging and droping. command_arg_t abstracted to its own source file. Fix long-standing typo in simple_cif_reader, so that it now correctly sets the three letter code from _chem_comp loop. ------------------------------------------------------------------------ r3750 | pemsley | 2011-11-11 22:00:33 +0000 (Fri, 11 Nov 2011) | 2 lines Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/lbg-drag-and-drop.cc A /trunk/lbg/lbg-drag-and-drop.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Add drag and drop for the lbg canvas (mol and mol2 files). ------------------------------------------------------------------------ r3749 | b.lohkamp | 2011-11-09 15:34:05 +0000 (Wed, 09 Nov 2011) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/windows/WinCoot_install_masta.nsi Fix Windows installer to make correct runwincoot.bat update python refmac to display molecules after making phases and prodrg-ify add_ligand_delete_residue_copy_molecule (just make it and undisplay it) ------------------------------------------------------------------------ r3748 | pemsley | 2011-11-09 02:19:39 +0000 (Wed, 09 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc Fix up scheme code for running refmac normal/gui mode (incorrect arg order). ------------------------------------------------------------------------ r3747 | pemsley | 2011-11-08 16:41:59 +0000 (Tue, 08 Nov 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc rotate_about() with int args can be called from the residue path, so take acount of that. ------------------------------------------------------------------------ r3746 | pemsley | 2011-11-08 15:45:54 +0000 (Tue, 08 Nov 2011) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm On prodrg-ify, don't swap to the result of add-ligand-delete-residue-copy-molecule (just make it and undisplay it). ------------------------------------------------------------------------ r3745 | pemsley | 2011-11-08 15:31:33 +0000 (Tue, 08 Nov 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh M /trunk/rel-todo Factor out atom_tree_t's set_dihedral() given a set of map_index_ts. ------------------------------------------------------------------------ r3744 | b.lohkamp | 2011-11-08 14:41:14 +0000 (Tue, 08 Nov 2011) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/get_recent_pdbe.py M /trunk/python/refmac.py fix stdin parsing for python popen command clean up and fix (some) threading for get_recent_pdbe ------------------------------------------------------------------------ r3743 | pemsley | 2011-11-07 15:07:03 +0000 (Mon, 07 Nov 2011) | 2 lines Changed paths: M /trunk/TODO M /trunk/geometry/read-sbase.cc M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-residues.cc Tidy up the types-with-no-dictionary (sbase-usage) code. ------------------------------------------------------------------------ r3742 | pemsley | 2011-11-05 18:03:11 +0000 (Sat, 05 Nov 2011) | 2 lines Changed paths: M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Sinusoidal acceleration-based motion on smooth screen recentering. ------------------------------------------------------------------------ r3741 | pemsley | 2011-11-05 14:25:35 +0000 (Sat, 05 Nov 2011) | 3 lines Changed paths: M /trunk/lidia-core/rdkit-interface.cc Rework the extraction of bonds in rdkit_mol() so that it works when given a residue that has alt confs. ------------------------------------------------------------------------ r3740 | pemsley | 2011-11-05 01:29:03 +0000 (Sat, 05 Nov 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/coot-coord-utils.hh Refactor beam_in_linked_residue() constructor. ------------------------------------------------------------------------ r3739 | pemsley | 2011-11-04 15:31:09 +0000 (Fri, 04 Nov 2011) | 2 lines Changed paths: M /trunk/src/c-interface-build-gui.cc Improve the wording of the nomenclature errors dialog. ------------------------------------------------------------------------ r3738 | pemsley | 2011-11-04 12:55:35 +0000 (Fri, 04 Nov 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h move_hetgroups_to_around_protein() function implemented - like the water-only version, but moving HETATM residues (based on residue centre). ------------------------------------------------------------------------ r3737 | pemsley | 2011-11-04 01:42:54 +0000 (Fri, 04 Nov 2011) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am Rework the libs again (back on Fed 15). ------------------------------------------------------------------------ r3736 | pemsley | 2011-11-04 00:06:01 +0000 (Fri, 04 Nov 2011) | 3 lines Changed paths: M /trunk/coords/Makefile.am M /trunk/ideal/Makefile.am M /trunk/ligand/Makefile.am M /trunk/src/Makefile.am Additions to Makefiles to resolve make_residue() usage. I don't understand why these are needed (on Ubuntu 10.04 - but not Fed 15). ------------------------------------------------------------------------ r3735 | pemsley | 2011-11-03 18:28:22 +0000 (Thu, 03 Nov 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/pick.cc Remove debugging. Update notes. ------------------------------------------------------------------------ r3734 | pemsley | 2011-11-03 15:18:22 +0000 (Thu, 03 Nov 2011) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Rework the keyboarding go to residue code. Strip out constructing text from button press and release callbacks in the graphics window and use a (currently) modal undecorated entry widget. ------------------------------------------------------------------------ r3733 | pemsley | 2011-11-03 08:03:04 +0000 (Thu, 03 Nov 2011) | 2 lines Changed paths: M /trunk/src/globjects.cc ifdef the GTK version for gtk_drag_dest_add_uri_targets() usage. ------------------------------------------------------------------------ r3732 | pemsley | 2011-11-02 19:43:54 +0000 (Wed, 02 Nov 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc remove debugging. ------------------------------------------------------------------------ r3731 | pemsley | 2011-11-02 19:42:02 +0000 (Wed, 02 Nov 2011) | 2 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm clean up JSON parser, check for presence of gui. ------------------------------------------------------------------------ r3730 | pemsley | 2011-11-02 19:22:26 +0000 (Wed, 02 Nov 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Fix std::cout typo (how did it compile before!?). ------------------------------------------------------------------------ r3729 | pemsley | 2011-11-01 20:57:57 +0000 (Tue, 01 Nov 2011) | 10 lines Changed paths: M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh A /trunk/src/drag-and-drop.cc A /trunk/src/drag-and-drop.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc Update utils simplex function names to give space for more simplex functions later. Add drag and drop support, URL and URI and multiple strings (presume separated by \n). factor out get_coords_for_accession_code() function. file_type_coords() function added. Remove GTK1 code from globjects.cc set_bond_colour() makes darker bonds if the background is white - needs more work - nothing appears to happen on changing background colour. ------------------------------------------------------------------------ r3728 | KevKeating | 2011-10-31 20:40:53 +0000 (Mon, 31 Oct 2011) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface.h added regularize_zone_with_score() scripting function (Python and Scheme) ------------------------------------------------------------------------ r3727 | b.lohkamp | 2011-10-30 18:08:38 +0000 (Sun, 30 Oct 2011) | 4 lines Changed paths: M /trunk/ideal/with-map.cc M /trunk/python/coot_utils.py A /trunk/python/get_recent_pdbe.py M /trunk/python/refmac.py M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h add first draft for get_recent_pdbe (some more threading cleverness in progress) fix MINGW getopt in with-map add pythonic multi_residue_torsion_py ------------------------------------------------------------------------ r3726 | pemsley | 2011-10-30 09:09:09 +0000 (Sun, 30 Oct 2011) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Add gui for multi-residue torsion (on Other Modelling Tools). Add function rotate_multi_residue_torsion() to handle mouse motion. ------------------------------------------------------------------------ r3725 | pemsley | 2011-10-30 01:26:36 +0000 (Sun, 30 Oct 2011) | 2 lines Changed paths: A /trunk/src/graphics-info-residues.cc Add missing graphics-info-residues.cc ------------------------------------------------------------------------ r3724 | pemsley | 2011-10-30 01:25:40 +0000 (Sun, 30 Oct 2011) | 7 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/testing.cc Updates for multi-residue torsions. add a constructor that takes pairs of CAtoms for link bonds. contact_info constructor common code factored out. Add a dialog for multi-residue torsion bonds chooser. pyranose ring torsion test corrected. torsionable_bonds_monomer_internal() no longer returns const torsions. ------------------------------------------------------------------------ r3723 | pemsley | 2011-10-28 00:48:55 +0100 (Fri, 28 Oct 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Revome unneeded casting. ------------------------------------------------------------------------ r3722 | pemsley | 2011-10-27 20:43:09 +0100 (Thu, 27 Oct 2011) | 3 lines Changed paths: M /trunk/coot-gtk2.glade Remove sigmas from interface. XML file only - this needs a build (source) later. ------------------------------------------------------------------------ r3721 | pemsley | 2011-10-27 20:39:27 +0100 (Thu, 27 Oct 2011) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/bonded-pairs.hh M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/testing.cc M /trunk/src/testing.hh More update to torsions and link torsions. order_switch code changed on find_link_type_rigourous(). torsionable_bonds() added to simple-restraints.hh ------------------------------------------------------------------------ r3720 | pemsley | 2011-10-27 20:36:28 +0100 (Thu, 27 Oct 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple fix up strange syntax on handling error from guile compile. ------------------------------------------------------------------------ r3719 | pemsley | 2011-10-27 20:35:04 +0100 (Thu, 27 Oct 2011) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/notes update notes. ------------------------------------------------------------------------ r3718 | pemsley | 2011-10-27 20:34:31 +0100 (Thu, 27 Oct 2011) | 2 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm Back to PDB files for PDBe downloads. ------------------------------------------------------------------------ r3717 | pemsley | 2011-10-27 20:33:56 +0100 (Thu, 27 Oct 2011) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 Test that mmdb has LINKR interface. ------------------------------------------------------------------------ r3716 | pemsley | 2011-10-27 20:33:17 +0100 (Thu, 27 Oct 2011) | 3 lines Changed paths: M /trunk/compat/coot-getopt.h Add a throw() to getop() prototype. Needed for gcc 4.6.1 Fed 15. Will this pass in other compilers? ------------------------------------------------------------------------ r3715 | pemsley | 2011-10-27 03:03:08 +0100 (Thu, 27 Oct 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Add a FAQ for the menu font size on Mac. ------------------------------------------------------------------------ r3714 | KevKeating | 2011-10-25 16:36:18 +0100 (Tue, 25 Oct 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix bug where adding a 3' terminal residue was failing for nucleic acids when the 3' residue was a C (fix courtesy of Huw Jenkins) ------------------------------------------------------------------------ r3713 | pemsley | 2011-10-24 17:09:08 +0100 (Mon, 24 Oct 2011) | 10 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/bonded-pairs.cc A /trunk/coot-utils/bonded-pairs.hh M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/skeleton/Makefile.am M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Bonded pairs moved to their own file. Add a new constructor for contact_info taking an atom_selection and a bonded pairs container (to describe the link). Add a select_atoms() method for a residue_spec_t. Change the interface of atom_tree_t::rotate_about() to be degrees. New rotate_about() for atom_tree_t taking atom indices. A new constructor for atom_tree_t taking a (potentially multi-residue) set of contacts. Add multi-residue torsion test. ------------------------------------------------------------------------ r3712 | pemsley | 2011-10-24 15:51:51 +0100 (Mon, 24 Oct 2011) | 2 lines Changed paths: M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/rdkit-interface.cc Fix up rdkit-interface includes. ------------------------------------------------------------------------ r3711 | b.lohkamp | 2011-10-23 16:24:07 +0100 (Sun, 23 Oct 2011) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/compat/coot-sysdep.h M /trunk/lidia-core/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh M /trunk/windows/WinCoot_install_masta.nsi disable dialogs for windows uninstaller render main toolbar icons fix label radiobutton for environment distances fixups for move of lbg/rdk files windows fixup for nomenclature_error_handle_type enum ------------------------------------------------------------------------ r3710 | pemsley | 2011-10-23 04:41:07 +0100 (Sun, 23 Oct 2011) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/lbg/notes Update notes. ------------------------------------------------------------------------ r3709 | pemsley | 2011-10-23 03:58:27 +0100 (Sun, 23 Oct 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-view.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add single-model-view (for NMR models in particular), including (wrapping) next and previous models. ------------------------------------------------------------------------ r3708 | pemsley | 2011-10-22 20:27:26 +0100 (Sat, 22 Oct 2011) | 5 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Add ability to set mode for nomenclature errors on reading coordinates: ignore, auto-correct, and prompt (default is prompt). delete_restraints() function added. Added a hack for conditionally compiling bitmapcharacters (printString). ------------------------------------------------------------------------ r3707 | pemsley | 2011-10-21 20:39:34 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh mdl mol/mol2 extension check function renamed for clarity. ------------------------------------------------------------------------ r3706 | pemsley | 2011-10-21 19:34:29 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: D /trunk/lbg/use-rdkit.hh A /trunk/lidia-core/use-rdkit.hh (from /trunk/lbg/use-rdkit.hh:3703) Move use-rdkit.hh to match rdkit-interface. ------------------------------------------------------------------------ r3705 | pemsley | 2011-10-21 19:16:23 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3704 | pemsley | 2011-10-21 19:14:51 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Add rotamer dialog position setting to state file. ------------------------------------------------------------------------ r3703 | pemsley | 2011-10-21 19:12:05 +0100 (Fri, 21 Oct 2011) | 7 lines Changed paths: M /trunk/coords/Makefile.am M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh D /trunk/lbg/rdkit-interface.cc D /trunk/lbg/rdkit-interface.hh M /trunk/lidia-core/Makefile.am A /trunk/lidia-core/rdkit-interface.cc (from /trunk/lbg/rdkit-interface.cc:3697) A /trunk/lidia-core/rdkit-interface.hh (from /trunk/lbg/rdkit-interface.hh:3697) M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc Add mol_to_asc_rdkit() for reading of mol2 files as 3d molecules, import_mol_file() and import_mol_from_file(). rdkit-interface.cc/hh moved down to lower level (and directory changed). Add rotamer dialog position setting to state file. Label atom on user-defined pick. Some debugging in window position of accept/reject dialog (needs more work). ------------------------------------------------------------------------ r3702 | pemsley | 2011-10-21 18:58:58 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/coot-utils/read-sm-cif.cc Add an mmdb-version dependent hack for string list casting. ------------------------------------------------------------------------ r3701 | pemsley | 2011-10-21 18:53:50 +0100 (Fri, 21 Oct 2011) | 7 lines Changed paths: M /trunk/build-it-gtk2-simple update python version to 2.7. Update guile version to 1.8.8 Add guile patch. Add n-processors (max 4). Note that ncurses needs to be installed for guile-readline config test to work and be linked. ------------------------------------------------------------------------ r3700 | pemsley | 2011-10-21 18:42:29 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/pixmaps/go-to-ligand.svg Thicken up the go-to-ligand icon bonds. ------------------------------------------------------------------------ r3699 | pemsley | 2011-10-21 18:41:57 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/autogen.sh libtoolize with --copy argument. ------------------------------------------------------------------------ r3698 | pemsley | 2011-10-21 18:40:51 +0100 (Fri, 21 Oct 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add an extra note in the save dialog positions dialog for chi angles. ------------------------------------------------------------------------ r3697 | pemsley | 2011-10-18 11:49:51 +0100 (Tue, 18 Oct 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info-build.cc on making a LINK, treat it as a model modification - so that it can be undone. ------------------------------------------------------------------------ r3696 | pemsley | 2011-10-18 11:48:04 +0100 (Tue, 18 Oct 2011) | 3 lines Changed paths: M /trunk/src/cc-interface.hh atom_name_info_text_for_statusbar should not be an unsectioned function (nothing should be). ------------------------------------------------------------------------ r3695 | pemsley | 2011-10-18 11:46:55 +0100 (Tue, 18 Oct 2011) | 3 lines Changed paths: M /trunk/scheme/extensions.scm Now that CCP4 PISA is updated, we can bring back the interface into the gui (scheme version). ------------------------------------------------------------------------ r3694 | pemsley | 2011-10-18 11:45:49 +0100 (Tue, 18 Oct 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Add overlap info to Coot FAQ. ------------------------------------------------------------------------ r3693 | pemsley | 2011-10-12 12:22:10 +0100 (Wed, 12 Oct 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Try to add /usr/X11R6/bin to path on RH4 (for freeglut configure). ------------------------------------------------------------------------ r3692 | pemsley | 2011-10-06 17:40:01 +0100 (Thu, 06 Oct 2011) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Don't try to make restraints if no atoms selected (protects against array usage by inappropriate atom indices). ------------------------------------------------------------------------ r3691 | pemsley | 2011-10-05 18:42:02 +0100 (Wed, 05 Oct 2011) | 2 lines Changed paths: M /trunk/rel-todo Update todo items. ------------------------------------------------------------------------ r3690 | pemsley | 2011-10-05 18:39:13 +0100 (Wed, 05 Oct 2011) | 3 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h Quick hack to fix up element names from mmdb mmCIF reading (this is more properly done with an fix to mmdb). ------------------------------------------------------------------------ r3689 | b.lohkamp | 2011-10-03 09:58:27 +0100 (Mon, 03 Oct 2011) | 4 lines Changed paths: M /trunk/analysis/Makefile.am M /trunk/bldnotes M /trunk/coot-surface/Makefile.am M /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/lbg/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-info.cc update and fix pythonic tests (goto atom ins code) include mini-mol for atom-quads.h (analysis, lbg, coot-surface) fix windows AddAtom stuff in coot-coord-utils-glyco.cc ------------------------------------------------------------------------ r3688 | pemsley | 2011-10-02 01:07:58 +0100 (Sun, 02 Oct 2011) | 2 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm Download coordinate mmCIF files, not pdbs. ------------------------------------------------------------------------ r3687 | pemsley | 2011-10-02 00:20:22 +0100 (Sun, 02 Oct 2011) | 6 lines Changed paths: A /trunk/ASN-NAG-via-NAG-ASN.pdb (from /trunk/N-linked-NAG-ref.pdb:3683) M /trunk/Makefile.am D /trunk/N-linked-NAG-ref.pdb M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/coot-coord-utils-glyco.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/scheme/get-recent-pdbe.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh More progress on the simple-minded NAG addition: add-linked-residue. The position of the carbohydrate residue is based on template and LSQing. Currently only template for ASN+NAG. The type is looked up in the residue for a LINK record addition. copy_and_add_residue_to_chain() now returns the new residue. ------------------------------------------------------------------------ r3686 | pemsley | 2011-10-01 11:24:24 +0100 (Sat, 01 Oct 2011) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Make the test for dictionary residue names less specific (less dependent on CCP4 version). ------------------------------------------------------------------------ r3685 | pemsley | 2011-10-01 10:06:36 +0100 (Sat, 01 Oct 2011) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add some diagnostic output for dictionary names test. ------------------------------------------------------------------------ r3684 | pemsley | 2011-09-30 23:40:29 +0100 (Fri, 30 Sep 2011) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Catch the clipper runtime exception of import_hkl_info() on reading a reflection cif file with no cell. ------------------------------------------------------------------------ r3683 | pemsley | 2011-09-30 18:52:07 +0100 (Fri, 30 Sep 2011) | 2 lines Changed paths: M /trunk/Makefile.am A /trunk/N-linked-NAG-ref.pdb M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add N-linked-NAG-ref.pdb and a few notes on how to use it for adding NAGs. ------------------------------------------------------------------------ r3682 | pemsley | 2011-09-30 17:26:25 +0100 (Fri, 30 Sep 2011) | 4 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/chi-angles.cc M /trunk/ligand/monomer-utils.cc M /trunk/ligand/primitive-chi-angles.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh M /trunk/mini-mol/mini-mol.cc M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Fix up ins-code change and GoTo atom test for new atom navigation code (r3673). Atom name quads are now an array of strings and no longer publically accessible. Partial (failing) test for rotation of residue by internal coords added. ------------------------------------------------------------------------ r3681 | pemsley | 2011-09-30 02:04:22 +0100 (Fri, 30 Sep 2011) | 2 lines Changed paths: M /trunk/rel-todo update todo. ------------------------------------------------------------------------ r3680 | pemsley | 2011-09-29 23:11:16 +0100 (Thu, 29 Sep 2011) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/rel-todo M /trunk/src/graphics-info-pick.cc Don't allow picking of symmetry atoms for distance pick when symmetry is not displayed. Don't make long bonds in CA or P backbone mode. ------------------------------------------------------------------------ r3679 | pemsley | 2011-09-29 18:22:59 +0100 (Thu, 29 Sep 2011) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/restraints-editor.cc Read in bond orders from Chemical Component Dictionary (or such-like). Need to handle cases were attempts are made to use the distance/eds information but it is not available. ------------------------------------------------------------------------ r3678 | pemsley | 2011-09-29 18:21:49 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/src/post-process-coot-wrap-python.sh Revert r3670 for the moment. ------------------------------------------------------------------------ r3677 | pemsley | 2011-09-29 14:44:39 +0100 (Thu, 29 Sep 2011) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh comp-id -> comp-id (molecule/chemical) name function added and used in solvent-ligands-gui. remove_trailing_whitespace() function added and test. ------------------------------------------------------------------------ r3676 | pemsley | 2011-09-29 12:58:33 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/pick.cc No picking on non-CA or ligand in Rainbow mode. ------------------------------------------------------------------------ r3675 | pemsley | 2011-09-29 12:25:07 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/coot-nomenclature.cc M /trunk/src/graphics-info-state.cc Add geometry distances to state script. ------------------------------------------------------------------------ r3674 | pemsley | 2011-09-29 11:23:30 +0100 (Thu, 29 Sep 2011) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/restraints-editor.cc Matching names from the dictionary, scripting interface and test. comp_id removed from dictionary_residue_restraints_t. Now the comp_id is in the residue_info. simple_monomer_descriptions changed from a vector to a map (with key comp_id). Startup-time improved. ------------------------------------------------------------------------ r3673 | pemsley | 2011-09-29 11:14:04 +0100 (Thu, 29 Sep 2011) | 3 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc Intelligent next atom now takes account of where we are. Allow the setting of the default representation type. ------------------------------------------------------------------------ r3672 | pemsley | 2011-09-29 11:13:25 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/autogen.sh Add extra dir for aclocal search. ------------------------------------------------------------------------ r3671 | pemsley | 2011-09-29 11:12:10 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r3670 | pemsley | 2011-09-29 11:10:59 +0100 (Thu, 29 Sep 2011) | 2 lines Changed paths: M /trunk/src/post-process-coot-wrap-python.sh Fix up for post-processing swig on new machine. ------------------------------------------------------------------------ r3669 | b.lohkamp | 2011-09-28 08:29:04 +0100 (Wed, 28 Sep 2011) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/python-tests/01_pdb_mtz.py add pythonic test for renumber residues move stdlib include to avoid getopt conflicts in windows (find-waters.cc) ------------------------------------------------------------------------ r3668 | pemsley | 2011-09-26 15:25:40 +0100 (Mon, 26 Sep 2011) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3667 | pemsley | 2011-09-26 15:24:09 +0100 (Mon, 26 Sep 2011) | 2 lines Changed paths: M /trunk/geometry/read-sbase.cc Residues from SBASe have hetatms. ------------------------------------------------------------------------ r3666 | pemsley | 2011-09-26 00:32:44 +0100 (Mon, 26 Sep 2011) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test-case for renumber residues. ------------------------------------------------------------------------ r3665 | pemsley | 2011-09-26 00:32:22 +0100 (Mon, 26 Sep 2011) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Fix up renumber_residues so that the affected residues are now correctly positioned in the chain - slightly awkward mmdb manipulations. ------------------------------------------------------------------------ r3664 | pemsley | 2011-09-26 00:30:07 +0100 (Mon, 26 Sep 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Improve documentation for deep_copy_residue(). ------------------------------------------------------------------------ r3663 | pemsley | 2011-09-25 21:44:37 +0100 (Sun, 25 Sep 2011) | 2 lines Changed paths: M /trunk/rel-todo Update rel-todo. ------------------------------------------------------------------------ r3662 | pemsley | 2011-09-23 17:46:36 +0100 (Fri, 23 Sep 2011) | 3 lines Changed paths: M /trunk/scheme/get-recent-pdbe.scm Remove refmac progress bar debugging. Add ligand codes to button labels. ------------------------------------------------------------------------ r3661 | pemsley | 2011-09-23 16:14:52 +0100 (Fri, 23 Sep 2011) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Fix typo in (new) test for terminal residue by phi_psi. ------------------------------------------------------------------------ r3660 | pemsley | 2011-09-23 15:55:26 +0100 (Fri, 23 Sep 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/scheme/get-recent-pdbe.scm Use a thread dispatcher to throttle the spawning of (too) many threads. ------------------------------------------------------------------------ r3659 | pemsley | 2011-09-21 20:40:00 +0100 (Wed, 21 Sep 2011) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Hack in a temporary solution for the new clipper libs (new clipper with cif tools needs new libtools/configure and new ccp4 libs (underlay-2). ------------------------------------------------------------------------ r3658 | pemsley | 2011-09-21 20:38:14 +0100 (Wed, 21 Sep 2011) | 2 lines Changed paths: M /trunk/cootaneer/cootaneer-demo.cpp Needs stdlib.h for exit() - (new clipper libs, presumably). ------------------------------------------------------------------------ r3657 | pemsley | 2011-09-21 20:34:26 +0100 (Wed, 21 Sep 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Take out the PDBe recent structures browswer - too crashy. ------------------------------------------------------------------------ r3656 | pemsley | 2011-09-21 18:01:18 +0100 (Wed, 21 Sep 2011) | 2 lines Changed paths: M /trunk/autogen.sh Clean up autogen.sh. Don't use old macros. ------------------------------------------------------------------------ r3655 | pemsley | 2011-09-21 15:45:57 +0100 (Wed, 21 Sep 2011) | 3 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/cootaneer/buccaneer-prot.cpp M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/ligand.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-ncs.cc Include algorithm explicitly (mostly for std::sort()) - it is no longer implicitly provided by (new) clippper code includes. ------------------------------------------------------------------------ r3654 | pemsley | 2011-09-20 18:30:44 +0100 (Tue, 20 Sep 2011) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/get-recent-pdbe.scm Tidy up, don't double-load the json-reader, remove debugging output. ------------------------------------------------------------------------ r3653 | pemsley | 2011-09-20 16:41:42 +0100 (Tue, 20 Sep 2011) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/Makefile.am M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm A /trunk/scheme/get-recent-pdbe.scm A /trunk/scheme/json-reader.scm Add PDBe recent structure browswer. Needs json parser. Added. Add menu item in Extensions menu. ------------------------------------------------------------------------ r3652 | b.lohkamp | 2011-09-20 13:43:51 +0100 (Tue, 20 Sep 2011) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/refmac.py fix python refmac for phases incl make_molecules_flag ------------------------------------------------------------------------ r3651 | b.lohkamp | 2011-09-19 16:23:03 +0100 (Mon, 19 Sep 2011) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/graphics-info-network.cc fix pygtk tooltip(s) typo add pythonic test to add residue by phi psi fix sleep issue in curl functions for windows ------------------------------------------------------------------------ r3650 | pemsley | 2011-09-19 13:10:34 +0100 (Mon, 19 Sep 2011) | 12 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/read-sm-cif.cc M /trunk/coot-utils/read-sm-cif.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python/refmac.py M /trunk/rel-todo M /trunk/scheme/check-for-updates.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/refmac.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc A /trunk/src/c-interface-sfs.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-network.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add make_molecules_flag arg to run_refmac_by_filename() so that we can run this function in a thread. Running assoc on a curl-info returns a pair, not a list. Fix up problem of adding a residue by phi phi - (udd atom indices needed updating). Add a test. Add mmcif_sfs_to_mtz() function to interface (new c-interface-sfs.cc). lock curl handlers - for multi-threaded usage (we still need to cache (and check cache so that the ligand files are not downloaded multiple times simultaneously). coot::smcif::get_space_group() now returns a pair (with status), rather than throwing an exception. ------------------------------------------------------------------------ r3649 | pemsley | 2011-09-16 17:23:10 +0100 (Fri, 16 Sep 2011) | 5 lines Changed paths: M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.cc M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc execute_simple_nucleotide_addition() has protection for correct terminal type before addition. Rename statusbar_text function to be more consistent with the c-interface function. ------------------------------------------------------------------------ r3648 | pemsley | 2011-09-13 16:58:21 +0100 (Tue, 13 Sep 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Additions to three_letter_to_one_letter() to handle v3 DNA names. ------------------------------------------------------------------------ r3647 | b.lohkamp | 2011-09-13 08:33:29 +0100 (Tue, 13 Sep 2011) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix typos in pythonic test for TER placement after nucleotide mutation ------------------------------------------------------------------------ r3646 | b.lohkamp | 2011-09-12 15:52:20 +0100 (Mon, 12 Sep 2011) | 1 line Changed paths: M /trunk/scheme/coot-utils.scm fix scheme command-in-path-or-absolute ------------------------------------------------------------------------ r3645 | b.lohkamp | 2011-09-12 10:41:28 +0100 (Mon, 12 Sep 2011) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/read-sm-cif.cc M /trunk/python/refmac.py M /trunk/python-tests/01_pdb_mtz.py fix refmac log reader for newer refmac versions add pythonic test for TER placement after nucleotide mutation fix windows AddAtom issue for read-sm-cif ------------------------------------------------------------------------ r3644 | pemsley | 2011-09-12 02:29:36 +0100 (Mon, 12 Sep 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove udd handle debugging. ------------------------------------------------------------------------ r3643 | b.lohkamp | 2011-09-11 16:09:54 +0100 (Sun, 11 Sep 2011) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/read-sm-cif.cc M /trunk/python/prodrg_import.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-view.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c preferences options for the main toolbar (similar to refinement toolbar) re-ordering of preferences notebook pages fix return value for smcif::get_cell (hack) ------------------------------------------------------------------------ r3642 | pemsley | 2011-09-09 14:16:17 +0100 (Fri, 09 Sep 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Improve bonding (particularly to waters from small molecule cifs (they are not marked with residue name HOH)). ------------------------------------------------------------------------ r3641 | pemsley | 2011-09-08 22:55:05 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/read-sm-cif.cc A /trunk/coot-utils/read-sm-cif.hh M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Add small molecule cif reader - needs testing. ------------------------------------------------------------------------ r3640 | pemsley | 2011-09-08 18:44:36 +0100 (Thu, 08 Sep 2011) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm Fix TER placement on mutation of a nucleotide with a TER. Add a test. ------------------------------------------------------------------------ r3639 | pemsley | 2011-09-08 18:44:00 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3638 | pemsley | 2011-09-08 18:38:29 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple A bit more debugging on the freeglut configure patch. ------------------------------------------------------------------------ r3637 | pemsley | 2011-09-08 18:37:17 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc no need to cast the category names any longer. ------------------------------------------------------------------------ r3636 | pemsley | 2011-09-08 18:35:33 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add another build host. ------------------------------------------------------------------------ r3635 | pemsley | 2011-09-08 18:34:48 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: D /trunk/burn-up/new-graph.py Remove graph script, it only makes sense on the server machine. Reduce noise. ------------------------------------------------------------------------ r3634 | pemsley | 2011-09-08 18:34:06 +0100 (Thu, 08 Sep 2011) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New graph script. ------------------------------------------------------------------------ r3633 | KevKeating@gmail.com | 2011-09-02 22:02:10 +0100 (Fri, 02 Sep 2011) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h residue_info() no longer includes erroneous "blank" atoms in place of TER records (both Python and Scheme) clear_and_update_molecule() no longer removes header information from a model (Python only) ------------------------------------------------------------------------ r3632 | b.lohkamp | 2011-08-28 14:09:38 +0100 (Sun, 28 Aug 2011) | 9 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/macros/coot-windows.m4 M /trunk/macros/goo-canvas.m4 M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/ncs.py M /trunk/python-tests/03_ligand.py M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/main.cc M /trunk/src/pick.cc add consolidated loop molecule for python db_loops fix error python ncs skipping with some non-ncs chains fail python ligand test if we cannot get 3GP monomer clean up and fix windows goocanvas configure ignore python swig for list_nomenclature_errors since it conflicts atom info in status bar has own function, so space bar updates atom info (maybe not in an ideal place though) ------------------------------------------------------------------------ r3631 | KevKeating | 2011-08-25 22:23:54 +0100 (Thu, 25 Aug 2011) | 1 line Changed paths: M /trunk/src/c-interface-mmdb.cc clear_and_update_molecule() now works with anisotropic temperature records (Python only) ------------------------------------------------------------------------ r3630 | pemsley | 2011-08-23 15:46:09 +0100 (Tue, 23 Aug 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Add bug report info to the FAQ. ------------------------------------------------------------------------ r3629 | pemsley | 2011-08-18 17:17:30 +0100 (Thu, 18 Aug 2011) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/ligand/ideal-rna.cc M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Fixup for missing C7 in mutating to a DT - correct the atom name at atom addition time, not at atom name addition time. Add name_sans_extension() function to utils. ------------------------------------------------------------------------ r3628 | KevKeating | 2011-08-16 20:57:38 +0100 (Tue, 16 Aug 2011) | 1 line Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix bug where do-add-terminal-residue was failing for RNA ------------------------------------------------------------------------ r3627 | pemsley | 2011-08-14 09:53:32 +0100 (Sun, 14 Aug 2011) | 2 lines Changed paths: M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r3626 | b.lohkamp | 2011-08-13 17:19:13 +0100 (Sat, 13 Aug 2011) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/WinCoot_install_masta.nsi M /trunk/windows/wincoot-autobuild-all update windows build system for 0.7-pre ------------------------------------------------------------------------ r3625 | pemsley | 2011-08-12 14:47:05 +0100 (Fri, 12 Aug 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc Add some protection for failure to init widgets from lbg glade file. ------------------------------------------------------------------------ r3624 | pemsley | 2011-08-12 14:45:52 +0100 (Fri, 12 Aug 2011) | 2 lines Changed paths: M /trunk/rel-todo Add some todo items. ------------------------------------------------------------------------ r3623 | pemsley | 2011-08-12 14:37:05 +0100 (Fri, 12 Aug 2011) | 2 lines Changed paths: D /trunk/burn-up/burn-up.tab Delete burn-up.tab (generated file for server). ------------------------------------------------------------------------ r3622 | pemsley | 2011-08-12 14:36:24 +0100 (Fri, 12 Aug 2011) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab last burn up update - delete. ------------------------------------------------------------------------ r3621 | pemsley | 2011-08-11 10:53:04 +0100 (Thu, 11 Aug 2011) | 3 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Add the fuctions set_display_generic_objects_as_solid() and set_show_environment_distances_as_solid(). ------------------------------------------------------------------------ r3620 | pemsley | 2011-08-10 22:19:54 +0100 (Wed, 10 Aug 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc Generic display items ass solid objects. Off by default. ------------------------------------------------------------------------ r3619 | pemsley | 2011-08-10 17:35:01 +0100 (Wed, 10 Aug 2011) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/burn-up/process-rel-todo.awk M /trunk/rel-todo Burn-up reset for 0.7. ------------------------------------------------------------------------ r3618 | pemsley | 2011-08-10 14:09:52 +0100 (Wed, 10 Aug 2011) | 4 lines Changed paths: M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/lbg/notes M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc Part-way through adding solid model (gluCylinders and gluDisks) for environment distances. Currently failure with colours and text in lighting mode. Disabled currently. ------------------------------------------------------------------------ r3617 | pemsley | 2011-08-09 20:43:12 +0100 (Tue, 09 Aug 2011) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/src/molecule-class-info-other.cc In make_environment_bonds_box(), use the atom index to get the residue, don't do a residue selection (ignoring the insertion code). Adjust the environment distance shortening for hydrogens. ------------------------------------------------------------------------ r3616 | pemsley | 2011-08-09 20:10:09 +0100 (Tue, 09 Aug 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in sed line for freeglut's configure. ------------------------------------------------------------------------ r3615 | pemsley | 2011-08-09 17:16:20 +0100 (Tue, 09 Aug 2011) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple On 64 bit redhat 4, building freeglut, we need to use /usr/X11R6/lib64, not /usr/X11R6/lib, edit configure. ------------------------------------------------------------------------ r3614 | pemsley | 2011-08-05 14:06:34 +0100 (Fri, 05 Aug 2011) | 2 lines Changed paths: M /trunk/src/gtk-manual.cc Tidy up get_radio_button_in_scroll_group() somewhat (now that it works). ------------------------------------------------------------------------ r3613 | pemsley | 2011-08-04 17:04:58 +0100 (Thu, 04 Aug 2011) | 4 lines Changed paths: M /trunk/src/graphics-info-gui.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-maps.cc Better handling of the scroll wheel map radio button. No longer do we check that the map is displayed before chekcking for the existance of the scroll button for that map. ------------------------------------------------------------------------ r3612 | pemsley | 2011-08-04 14:53:47 +0100 (Thu, 04 Aug 2011) | 4 lines Changed paths: M /trunk/dnotes M /trunk/python/coot_gui.py M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh Add the molecule for the consolidated loops in the return value of protein_db_loops(). Use it to add a button (in the scheme version) to toggle the display of this molecule. ------------------------------------------------------------------------ r3611 | pemsley | 2011-08-04 14:51:48 +0100 (Thu, 04 Aug 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Trivial debugging of goocanvas dependencies. ------------------------------------------------------------------------ r3610 | pemsley | 2011-08-04 14:50:33 +0100 (Thu, 04 Aug 2011) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc Add diagnosis for failure to read chem link. Clean up debugging of links when making restraints. ------------------------------------------------------------------------ r3609 | pemsley | 2011-08-04 14:12:59 +0100 (Thu, 04 Aug 2011) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Update to reflect currently building targets. ------------------------------------------------------------------------ r3608 | pemsley | 2011-08-02 12:23:07 +0100 (Tue, 02 Aug 2011) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Use the more generic package_data_dir() to get the directory in which the lbg.glade file is to be found. ------------------------------------------------------------------------ r3607 | b.lohkamp | 2011-07-31 14:39:48 +0100 (Sun, 31 Jul 2011) | 5 lines Changed paths: M /trunk/lbg/wmolecule.cc M /trunk/python/coot_utils.py M /trunk/python/get_ebi.py M /trunk/python-tests/01_pdb_mtz.py make sure the reverse_iterators in wmolecule are const update python test formatting pythonic EDS download check for reliable map too ------------------------------------------------------------------------ r3606 | b.lohkamp | 2011-07-28 14:44:15 +0100 (Thu, 28 Jul 2011) | 5 lines Changed paths: M /trunk/build-it-win M /trunk/macros/goo-canvas.m4 use CXX rather than libtool for windows goocanvas configure (goo-canvas.m4 needs cleanup though) fix typos in windows build script ------------------------------------------------------------------------ r3605 | pemsley | 2011-07-27 16:34:59 +0100 (Wed, 27 Jul 2011) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc Add Ligand Builder menu item to the interface and desensitise when we don't have goocanvas. ------------------------------------------------------------------------ r3604 | pemsley | 2011-07-27 16:09:54 +0100 (Wed, 27 Jul 2011) | 8 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.hh M /trunk/cycle-page-builder.scm M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-ebi.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/coot-nomenclature.cc M /trunk/src/coot-nomenclature.hh M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc M /trunk/src/restraints-editor.cc Introduce the nomenclature error tester on reading coordinate files. Display a dialog of violations if not clean. On reading a structure from the EDS, check the web page to see if it was a reliable map (or not - and if not, give a warning dialog). Clean up tests output a bit. Allow for compilation without guile or python (need string.hs). Only display pointer distances to molecules that are active/pickable. ------------------------------------------------------------------------ r3603 | pemsley | 2011-07-26 23:22:05 +0100 (Tue, 26 Jul 2011) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc find_link_type() now returns "TRANS" for a peptide link involving an MSE with the new dictionary (MSE group is "peptide). ------------------------------------------------------------------------ r3602 | pemsley | 2011-07-26 08:58:35 +0100 (Tue, 26 Jul 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo of goocanvas arg to coot's configure. ------------------------------------------------------------------------ r3601 | pemsley | 2011-07-25 17:54:10 +0100 (Mon, 25 Jul 2011) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Add test for gtk and cairo before going ahead with compiling and using goocanvas. ------------------------------------------------------------------------ r3600 | pemsley | 2011-07-25 15:50:56 +0100 (Mon, 25 Jul 2011) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Remove non-gtk2 builds. ------------------------------------------------------------------------ r3599 | pemsley | 2011-07-25 15:22:36 +0100 (Mon, 25 Jul 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add goocanvas, simple-mindedly currently. ------------------------------------------------------------------------ r3598 | pemsley | 2011-07-25 09:44:26 +0100 (Mon, 25 Jul 2011) | 2 lines Changed paths: M /trunk/lbg/rdkit-interface.cc Trivial debugging change. ------------------------------------------------------------------------ r3597 | pemsley | 2011-07-25 09:14:37 +0100 (Mon, 25 Jul 2011) | 3 lines Changed paths: M /trunk/src/c-interface-info.cc Fix 'integer constant too large for long type' when setting initial best_dist for text_index_near_position(), GCC 4.1.2. ------------------------------------------------------------------------ r3596 | pemsley | 2011-07-24 23:08:46 +0100 (Sun, 24 Jul 2011) | 2 lines Changed paths: M /trunk/coot-utils/test-hole.cc Add include of string.h, needed for GCC 4.1.2, it seems. ------------------------------------------------------------------------ r3595 | b.lohkamp | 2011-07-21 10:07:44 +0100 (Thu, 21 Jul 2011) | 4 lines Changed paths: M /trunk/build-it-win M /trunk/doc/crib-sheet.tex patch mmdb so that windows doesnt write double EOLs add Redo shortcut to crib sheet ------------------------------------------------------------------------ r3594 | b.lohkamp | 2011-07-20 15:10:40 +0100 (Wed, 20 Jul 2011) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/macros/goo-canvas.m4 M /trunk/macros/libpng.m4 M /trunk/python/clear_backup.py M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/unittest_extensions.py M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-network.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h update pygtk use of tooltip(s) coot python module only loaded and checked once (have_coot_python) fix typo in pythonic (stable) update enable windows libpng14 use pkg-config for goocanvas on windows (simple implementation) add short cut for redo (Crtl-y) ------------------------------------------------------------------------ r3593 | pemsley | 2011-07-19 14:28:48 +0100 (Tue, 19 Jul 2011) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi Add a function index. ------------------------------------------------------------------------ r3592 | pemsley | 2011-07-18 13:55:08 +0100 (Mon, 18 Jul 2011) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi Clear up node and section issues for texi2html. ------------------------------------------------------------------------ r3591 | pemsley | 2011-07-18 13:54:03 +0100 (Mon, 18 Jul 2011) | 3 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Change order or scheme texi files in coot-scheme-functions.texi for better texi2html. ------------------------------------------------------------------------ r3590 | pemsley | 2011-07-18 12:53:27 +0100 (Mon, 18 Jul 2011) | 2 lines Changed paths: M /trunk/src/c-interface.h Adjust comments for better doxygenation. ------------------------------------------------------------------------ r3589 | pemsley | 2011-07-15 14:34:34 +0100 (Fri, 15 Jul 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi M /trunk/doc/coot-user-manual.texi Documentaion fixups so that makeinfo works. ------------------------------------------------------------------------ r3588 | pemsley | 2011-07-15 14:23:36 +0100 (Fri, 15 Jul 2011) | 2 lines Changed paths: M /trunk/scheme/user-define-restraints.scm Move RNA base names to PDB v3 format. ------------------------------------------------------------------------ r3587 | pemsley | 2011-07-15 14:22:50 +0100 (Fri, 15 Jul 2011) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add extra debugging (when snarfing fails). ------------------------------------------------------------------------ r3586 | pemsley | 2011-07-15 14:21:17 +0100 (Fri, 15 Jul 2011) | 2 lines Changed paths: M /trunk/scheme/fitting.scm Fix up for doc snarfing. ------------------------------------------------------------------------ r3585 | pemsley | 2011-07-15 12:54:50 +0100 (Fri, 15 Jul 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.hh M /trunk/src/c-interface-test.cc fixups (add #ifdefs) to compile without GOOCANVAS. ------------------------------------------------------------------------ r3584 | pemsley | 2011-07-12 13:39:58 +0100 (Tue, 12 Jul 2011) | 3 lines Changed paths: M /trunk/cycle-page-builder.scm In source-code-url-info, return the correct number of values when latest-file is #f. ------------------------------------------------------------------------ r3583 | pemsley | 2011-07-12 13:38:22 +0100 (Tue, 12 Jul 2011) | 2 lines Changed paths: M /trunk/doc/crib-sheet.tex Update quick save documentation. ------------------------------------------------------------------------ r3582 | pemsley | 2011-07-07 16:27:02 +0100 (Thu, 07 Jul 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Also make holding directory for stable builds. ------------------------------------------------------------------------ r3581 | pemsley | 2011-07-06 10:28:17 +0100 (Wed, 06 Jul 2011) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Return state for undo and redo functions. ------------------------------------------------------------------------ r3580 | pemsley | 2011-07-02 07:19:28 +0100 (Sat, 02 Jul 2011) | 15 lines Changed paths: M /trunk/TODO M /trunk/doc/coot-faq.texi M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/python/coot_gui.py M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot-nomenclature.cc M /trunk/src/coot-nomenclature.hh M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Hamburg mishmash. list_nomenclature_errors() called on reading a pdb file - needes testing. fix_nomenclature_errors_gui() needs filling - to use a new window created using glade-2. optimize_rotamer_by_atom_names() takes an arg to flag whether to actually apply the atom swap. edit_text() and text_index_near_position() added for manipulation of 3d text. If NCS master is not found when applying residue range edit, then write an error message to the console. apply_undo() and apply_redo now return ints (i.e. return 1 if the undo was applied). add_terminal_residue_using_phi_psi() function added. Needs testing. On adding molecules after ligand fitting, use assign_hetatoms(). Added TRS to solvent molecule list. ------------------------------------------------------------------------ r3579 | pemsley | 2011-06-29 19:45:43 +0100 (Wed, 29 Jun 2011) | 2 lines Changed paths: M /trunk/src/main.cc ligand_builder_gui depends on goocanvas, not enterprise. ------------------------------------------------------------------------ r3578 | pemsley | 2011-06-28 16:26:30 +0100 (Tue, 28 Jun 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/coot-0.7-pre-1.png M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c New splashscreen for 0.7-pre. ------------------------------------------------------------------------ r3577 | b.lohkamp | 2011-06-26 18:20:17 +0100 (Sun, 26 Jun 2011) | 12 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/lbg/use-rdkit.hh M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/prodrg_import.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc new pythonic release time get_first_master_chain function for python created and used in NCS copy residue range get_lsq_matrix() pythonic function created update python overlap ligand in prodrg import add python function (extension) to make link update python tests (add delete all-molecule hydrogens and chirals test) add comment on molecule and map for raster3d files optional render water as spheres in raster3d (only for normal bonds so far - maybe requires different bonds_box for bonded and non-bonded atom bonds) ------------------------------------------------------------------------ r3576 | pemsley | 2011-06-26 00:56:31 +0100 (Sun, 26 Jun 2011) | 11 lines Changed paths: M /trunk/TODO M /trunk/coords/mmdb.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/ligand/base-pairing.cc M /trunk/ligand/ideal-rna.cc M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Fix up base pairing for modern dictionary. Add function watson_crick_pair_for_residue_range which creates a new chain and adds it to the passed/reference molecule. ncs_master_chains function created. get-first-master-chain function created and used in NCS copy residue range (it gets the master chain id of the first molecule with ncs chains), used as a default for user. get-lsq_matrix() function created - same as apply_lsq, but the matrix is only generated, not applied - to be used in local NCS transformations. Update notes. ------------------------------------------------------------------------ r3575 | pemsley | 2011-06-22 18:38:02 +0100 (Wed, 22 Jun 2011) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info.h Add a LINK record to molecule. Currently the function takes name and length arg, but these are ignored. ------------------------------------------------------------------------ r3574 | pemsley | 2011-06-22 18:33:04 +0100 (Wed, 22 Jun 2011) | 3 lines Changed paths: M /trunk/scheme/prodrg-import.scm Updates to importing from prodrg. Tidy ups and a bit of debugging. ------------------------------------------------------------------------ r3573 | pemsley | 2011-06-22 18:29:07 +0100 (Wed, 22 Jun 2011) | 5 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc reposition the molecule on the canvas on import. Function needs extra arg for flagging that this is laid out in FLEV? Set the default file name when using "save as..." status bar is updated with SMILES string on reading a mdl file. ------------------------------------------------------------------------ r3572 | pemsley | 2011-06-20 14:13:31 +0100 (Mon, 20 Jun 2011) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add all-molecule hydrogen deletion function, delete_hydrogens(). ------------------------------------------------------------------------ r3571 | pemsley | 2011-06-20 12:14:26 +0100 (Mon, 20 Jun 2011) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/use-rdkit.hh Use Lipinski descriptors to get number of rotatable bonds for depiction. Update notes. ------------------------------------------------------------------------ r3570 | pemsley | 2011-06-20 12:12:23 +0100 (Mon, 20 Jun 2011) | 3 lines Changed paths: M /trunk/src/c-interface-superpose.cc M /trunk/src/graphics-info-preferences.cc apply_lsq no longer needs cell and symmetry - python interface. Remove some GTK1 checking. ------------------------------------------------------------------------ r3569 | pemsley | 2011-06-20 12:10:42 +0100 (Mon, 20 Jun 2011) | 2 lines Changed paths: M /trunk/src/coot-hydrogens.cc Return correct value type when calling add_hydrogens_with_ccp4_tools(). ------------------------------------------------------------------------ r3568 | pemsley | 2011-06-20 12:09:37 +0100 (Mon, 20 Jun 2011) | 2 lines Changed paths: M /trunk/doc/crib-sheet.tex Update crib sheet. ------------------------------------------------------------------------ r3567 | pemsley | 2011-06-20 12:09:11 +0100 (Mon, 20 Jun 2011) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Merge 3566 to trunk. ------------------------------------------------------------------------ r3565 | pemsley | 2011-06-15 18:02:15 +0100 (Wed, 15 Jun 2011) | 2 lines Changed paths: M /trunk M /trunk/geometry/protein-geometry.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-state.cc Merge r3561-3562 to trunk. ------------------------------------------------------------------------ r3564 | pemsley | 2011-06-15 17:49:16 +0100 (Wed, 15 Jun 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple biop -> lmb.bioch ------------------------------------------------------------------------ r3563 | b.lohkamp | 2011-06-14 22:56:02 +0100 (Tue, 14 Jun 2011) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/python/coot_utils.py M /trunk/python/prodrg_import.py M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h update prodrg_import for python make writing CONECT records optional (default no CONECT records!) ------------------------------------------------------------------------ r3556 | pemsley | 2011-06-09 14:21:49 +0100 (Thu, 09 Jun 2011) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-h-bonds.cc M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Go to ligands must have at least 6 atoms - add set_go_to_ligand_n_atoms_limit() function to allow users to change this. After applying torsions, check them (helps diagnose ring torsion problems). Remove some debugging. ------------------------------------------------------------------------ r3555 | pemsley | 2011-06-09 01:23:53 +0100 (Thu, 09 Jun 2011) | 5 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/lbg/rdkit-interface.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/flev.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h check_waters_baddies() added for scripting. Remove the cell and symmetry args from apply_lsq(). match_ligand_torsions() no longer runs prodrg. Remove debugging in rdkit interface. ------------------------------------------------------------------------ r3554 | pemsley | 2011-06-09 01:20:22 +0100 (Thu, 09 Jun 2011) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.hh Add energy_lib_bonds parsing. ------------------------------------------------------------------------ r3553 | pemsley | 2011-06-09 01:19:39 +0100 (Thu, 09 Jun 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info-residues.cc Fix typo in indexing atoms in get_vector() (between residues). ------------------------------------------------------------------------ r3552 | pemsley | 2011-06-09 01:17:59 +0100 (Thu, 09 Jun 2011) | 3 lines Changed paths: M /trunk/scheme/prodrg-import.scm Improve the handling the prodrg results - accept regularizement before setting the torsions. ------------------------------------------------------------------------ r3551 | pemsley | 2011-06-07 21:40:13 +0100 (Tue, 07 Jun 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Correctly bond het residues with alt-confs. ------------------------------------------------------------------------ r3550 | pemsley | 2011-06-07 21:39:32 +0100 (Tue, 07 Jun 2011) | 2 lines Changed paths: M /trunk/src/lbg-interface.cc M /trunk/src/lbg-interface.hh Add weight_for_3d_distances to interface for residue->2d-layout. ------------------------------------------------------------------------ r3549 | pemsley | 2011-06-07 21:38:34 +0100 (Tue, 07 Jun 2011) | 2 lines Changed paths: M /trunk/src/coot.i Add std::pair for swigging. Needs more, I think. ------------------------------------------------------------------------ r3548 | b.lohkamp | 2011-06-07 12:49:19 +0100 (Tue, 07 Jun 2011) | 1 line Changed paths: M /trunk/pixmaps/go-to-ligand.svg fix windows font in go-to-ligand icon ------------------------------------------------------------------------ r3547 | pemsley | 2011-06-07 00:13:00 +0100 (Tue, 07 Jun 2011) | 2 lines Changed paths: A /trunk/pixmaps/go-to-ligand.svg Add the go-to-ligand icon. ------------------------------------------------------------------------ r3546 | b.lohkamp | 2011-06-06 20:44:49 +0100 (Mon, 06 Jun 2011) | 1 line Changed paths: M /trunk/python/generic_objects.py M /trunk/python/prodrg_import.py fix some python scripting typos ------------------------------------------------------------------------ r3545 | b.lohkamp | 2011-06-06 20:37:32 +0100 (Mon, 06 Jun 2011) | 10 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/prodrg_import.py A /trunk/python/test_hole.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/cc-interface.hh add a few coot_util python functions (file2string, load_default_sequence, residue_is_close_to_screen_centre_qm) rework reduce het dictionary usage (use build in db file otherwise use a connect file) use old_pdb_style to use (or not) -olpdb in reduce fix pythonic ligand overlap in prodrg import add and make python (test) hole gui enable hydrogenate_region for python ------------------------------------------------------------------------ r3544 | pemsley | 2011-06-06 17:56:08 +0100 (Mon, 06 Jun 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add a button to go to the (next) ligand of the "active" molecule. ------------------------------------------------------------------------ r3543 | pemsley | 2011-06-06 14:42:25 +0100 (Mon, 06 Jun 2011) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Remove chiral filtering debugging. ------------------------------------------------------------------------ r3542 | pemsley | 2011-06-06 13:45:39 +0100 (Mon, 06 Jun 2011) | 4 lines Changed paths: M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/lbg/use-rdkit.hh Add interface to chiral info and wedge bonds on rdkit-based layout. Add call to WedgeMolBonds() so that rdkit uses chiral info to return wedged bonds. ------------------------------------------------------------------------ r3541 | pemsley | 2011-06-06 13:40:45 +0100 (Mon, 06 Jun 2011) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh Trivial tidy of topological_equivalence_chiral_centres(). Add some documentation for add_terminal_residue(). ------------------------------------------------------------------------ r3540 | pemsley | 2011-06-06 13:37:25 +0100 (Mon, 06 Jun 2011) | 2 lines Changed paths: M /trunk/lidia-core/lbg-molfile.cc Remove debugging. ------------------------------------------------------------------------ r3539 | pemsley | 2011-06-06 13:37:09 +0100 (Mon, 06 Jun 2011) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Remove chiral centres that are bonded to more than one hydrogen at restraints-reading time. Thus comp_chiral() returns a list of comp_ids. ------------------------------------------------------------------------ r3538 | pemsley | 2011-06-06 13:34:36 +0100 (Mon, 06 Jun 2011) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc Remove debugging for probe dots parsing. ------------------------------------------------------------------------ r3537 | pemsley | 2011-06-06 13:33:44 +0100 (Mon, 06 Jun 2011) | 3 lines Changed paths: M /trunk/src/coot.i Allow scripting interface for std::string and std::vector return values. ------------------------------------------------------------------------ r3536 | pemsley | 2011-06-06 13:32:47 +0100 (Mon, 06 Jun 2011) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add test for 0.7 for hydrogen-based chiral filtering (currently commented). ------------------------------------------------------------------------ r3535 | pemsley | 2011-06-06 13:32:01 +0100 (Mon, 06 Jun 2011) | 3 lines Changed paths: M /trunk/scheme/generic-objects.scm Use *old-pdb-style* to determine if -oldpdb is passed to reduce (default now is #f -> not). ------------------------------------------------------------------------ r3534 | pemsley | 2011-06-02 18:20:17 +0100 (Thu, 02 Jun 2011) | 3 lines Changed paths: M /trunk/lbg/rdkit-interface.cc Call calcExplicitValence() with strict=false - helps with formal charge vs. valence dilemma (in tests so far). ------------------------------------------------------------------------ r3533 | pemsley | 2011-06-02 18:18:43 +0100 (Thu, 02 Jun 2011) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Redraw graphics after torsion match. ------------------------------------------------------------------------ r3532 | pemsley | 2011-06-02 18:18:09 +0100 (Thu, 02 Jun 2011) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add Fed 14 build target. ------------------------------------------------------------------------ r3531 | pemsley | 2011-06-02 18:15:36 +0100 (Thu, 02 Jun 2011) | 2 lines Changed paths: M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-validate.cc Fix up forgotten mutation and alignment python-interfaced functions. ------------------------------------------------------------------------ r3530 | pemsley | 2011-06-02 15:47:11 +0100 (Thu, 02 Jun 2011) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Add rama triples to to make_link_restraints_from_res_vec(). ------------------------------------------------------------------------ r3528 | pemsley | 2011-06-01 23:38:00 +0100 (Wed, 01 Jun 2011) | 4 lines Changed paths: M /trunk/dnotes M /trunk/geometry/chem_mods.cc M /trunk/src/align.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh align_to_closest_chain() function added. Add test for COO modification. Adjust environment bond distance colours for non-black background. ------------------------------------------------------------------------ r3527 | pemsley | 2011-06-01 23:35:05 +0100 (Wed, 01 Jun 2011) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Apply chem mods to the restraints (bonds, angles, planes). ------------------------------------------------------------------------ r3526 | pemsley | 2011-06-01 23:33:19 +0100 (Wed, 01 Jun 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix base name bug (nucleotide_to_nucleotide). ------------------------------------------------------------------------ r3525 | pemsley | 2011-06-01 23:31:31 +0100 (Wed, 01 Jun 2011) | 2 lines Changed paths: M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Add remove_whitespace() function. ------------------------------------------------------------------------ r3524 | pemsley | 2011-06-01 06:07:37 +0100 (Wed, 01 Jun 2011) | 4 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/prodrg-import.scm Fix typo in ligand overlap when importing prodrg result. add load-default-sequence function, which is a wrapper for align-to-closest-chain. ------------------------------------------------------------------------ r3523 | b.lohkamp | 2011-05-30 16:50:03 +0100 (Mon, 30 May 2011) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/callbacks.c fix typo in fast secondary structure find ------------------------------------------------------------------------ r3521 | b.lohkamp | 2011-05-29 17:34:35 +0100 (Sun, 29 May 2011) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-state.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh fix python pir string association (EOL issue) add pythonic reduce_on_pdb_file (needs testing) fix pythonic hydrogenation (and typo) ------------------------------------------------------------------------ r3517 | pemsley | 2011-05-25 21:31:45 +0100 (Wed, 25 May 2011) | 7 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-hole.hh M /trunk/coot-utils/hole.cc M /trunk/coot-utils/test-hole.cc M /trunk/doc/coot-user-manual.texi M /trunk/geometry/chem_mods.cc M /trunk/geometry/protein-geometry.cc A /trunk/scheme/test-hole.scm M /trunk/src/Makefile.am A /trunk/src/c-interface-analysis.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/utils/Makefile.am M /trunk/utils/coot-utils.hh A /trunk/utils/hsv-rgb.cc Update to hole representation. Now built into main executable, split writing surface and generation of surface points. Hex strings for colours - and conversion using string streams. convert_hsv_to_rgb() moved to utils from src. Fix up partial charge reading from old dictionary. ------------------------------------------------------------------------ r3516 | pemsley | 2011-05-25 12:33:24 +0100 (Wed, 25 May 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-hole.hh M /trunk/coot-utils/hole.cc M /trunk/coot-utils/test-hole.cc Updates to hole, use spheres for the probe path. ------------------------------------------------------------------------ r3515 | pemsley | 2011-05-25 12:32:25 +0100 (Wed, 25 May 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix typo in setting python list variables. ------------------------------------------------------------------------ r3514 | pemsley | 2011-05-24 09:57:24 +0100 (Tue, 24 May 2011) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/coot-hole.hh A /trunk/coot-utils/hole.cc A /trunk/coot-utils/test-hole.cc Add hole/channel finding class - preliminary version. ------------------------------------------------------------------------ r3513 | pemsley | 2011-05-24 09:55:38 +0100 (Tue, 24 May 2011) | 3 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Fix typo when setting vdwH_radius. Add get_vdw_radius() function. ------------------------------------------------------------------------ r3512 | pemsley | 2011-05-20 17:50:02 +0100 (Fri, 20 May 2011) | 3 lines Changed paths: M /trunk/lbg/notes M /trunk/scheme/coot-utils.scm M /trunk/scheme/prodrg-import.scm Add a function residue-is-close-to-screen-centre? and use it in prodrg importing. ------------------------------------------------------------------------ r3511 | pemsley | 2011-05-20 17:48:28 +0100 (Fri, 20 May 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add a funtion to return the residue centre.( ------------------------------------------------------------------------ r3510 | pemsley | 2011-05-19 14:32:52 +0100 (Thu, 19 May 2011) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3509 | pemsley | 2011-05-19 14:31:25 +0100 (Thu, 19 May 2011) | 5 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/Makefile.am A /trunk/ideal/chirals.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/src/coot-hydrogens.cc M /trunk/src/coot-hydrogens.hh M /trunk/src/flev.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Sprout hydrogens returns a pair, including a error message string. add_hydrogens_with_rdkit() checks for hydrogen presence first. Chiral functions moved to their own file in ideal directory. chiral_hydrogen_needs_pushing now only checks bad angles involving the hydrogen. ------------------------------------------------------------------------ r3508 | pemsley | 2011-05-19 06:22:22 +0100 (Thu, 19 May 2011) | 5 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/rdkit-interface.cc M /trunk/lidia-core/lig-build.hh M /trunk/src/c-interface.cc On reading PDB coordinates, only check for the dictionary if the read of the file was successful. Turn off/on all flev annotions with the "+" button on the LBG gui. Introduce clear_and_redraw() for lidia. ------------------------------------------------------------------------ r3506 | pemsley | 2011-05-18 00:34:31 +0100 (Wed, 18 May 2011) | 2 lines Changed paths: M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Add energy lib atom type non-bonded contact distances. ------------------------------------------------------------------------ r3505 | pemsley | 2011-05-17 09:50:23 +0100 (Tue, 17 May 2011) | 3 lines Changed paths: M /trunk/lbg/graphics-c-interface-functions-blanks.cc M /trunk/lbg/notes M /trunk/lbg/test_lbg_functions.cc M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/src/molecule-class-info-residues.cc Add formal charges holder to lbg_molfile_molecule atoms. Spell equivalence correctly. ------------------------------------------------------------------------ r3504 | pemsley | 2011-05-17 09:46:28 +0100 (Tue, 17 May 2011) | 2 lines Changed paths: M /trunk/scheme/prodrg-import.scm Trivial change to molecule handing on prodruging residue. ------------------------------------------------------------------------ r3503 | pemsley | 2011-05-17 09:45:35 +0100 (Tue, 17 May 2011) | 3 lines Changed paths: M /trunk/doc/coot-faq.texi M /trunk/doc/coot-user-manual.texi M /trunk/doc/validation-tutorial.tex Add documentation for Patterson and sphere refinement doc adjustment. Also how to use Coot on mac without mouse. ------------------------------------------------------------------------ r3502 | pemsley | 2011-05-13 16:57:38 +0100 (Fri, 13 May 2011) | 12 lines Changed paths: M /trunk/coot-utils/coot-h-bonds.cc M /trunk/lbg/flev-annotations.hh M /trunk/lbg/graphics-c-interface-functions.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lidia-main.cc M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Sometimes reduce works but has status 1, so fix up return value from reduce-on-pdb-file. Rocking uses a timeout now. Much nicer - now we can refine when rocking. all_additional_representations_off_except() now takes an extra arg to not turn off ball-and-stick representations (e.g. the ligand). pi stacking type is now enumerated (was an int). pi stacking significance test split depending on pi-pi or pi-cation. ligand interactions don't use LIGHT2 (commented out). H-bond analysis: Acceptor on ligand, hydrogen on environment has a special case for water (no H). Fix typo in an angle calculation with H on ligand. ------------------------------------------------------------------------ r3501 | pemsley | 2011-05-12 13:22:39 +0100 (Thu, 12 May 2011) | 8 lines Changed paths: M /trunk/coot-utils/coot-h-bonds.cc M /trunk/coot-utils/coot-h-bonds.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/notes M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/utils/coot-utils.cc Add hydrogenate_region() function - which calls reduce on a part of the struture and then reads in and adds the hydrogens from reduce output. Needs python version. flev analysis switched to use McDonald & Thornton hydrogen bonds. solvent exposure difference calculation atom selection excludes hydrogens. animated_ligand_interaction_t now inherits from fle_ligand_bond_t. Sidechain interactions are now green (dotted tubes). ------------------------------------------------------------------------ r3500 | pemsley | 2011-05-10 17:06:00 +0100 (Tue, 10 May 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Try to get rid of include/python-2.6 error message. ------------------------------------------------------------------------ r3499 | pemsley | 2011-05-10 17:04:45 +0100 (Tue, 10 May 2011) | 4 lines Changed paths: M /trunk/lbg/flev-annotations.cc M /trunk/lbg/flev-annotations.hh M /trunk/lbg/graphics-c-interface-functions.hh M /trunk/lbg/lbg.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface-test.cc M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/flev.hh M /trunk/src/junk.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h fle_ligand_bond_t objects now contain atom information. animated ligand interactions now work with fle_ligand_bond_t objects - not simple specs. ------------------------------------------------------------------------ r3498 | pemsley | 2011-05-10 09:50:32 +0100 (Tue, 10 May 2011) | 4 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-test.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a ligand interaction timeout function for animated bonds (pulsing tranparent cylinders currently). In build script, comment out the libtool updating of coot build. ------------------------------------------------------------------------ r3497 | b.lohkamp | 2011-05-08 14:30:45 +0100 (Sun, 08 May 2011) | 3 lines Changed paths: M /trunk/build-it-win M /trunk/python-tests/01_pdb_mtz.py update build script to new refmac dictionary v5.29 new RNA tests for python ------------------------------------------------------------------------ r3494 | pemsley | 2011-05-07 11:03:57 +0100 (Sat, 07 May 2011) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple update build script for refmac dictionary 5.29 ------------------------------------------------------------------------ r3493 | pemsley | 2011-05-06 15:25:43 +0100 (Fri, 06 May 2011) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ligand/ideal-rna.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Merge 3489 to trunk. ------------------------------------------------------------------------ r3492 | pemsley | 2011-05-06 11:22:40 +0100 (Fri, 06 May 2011) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3491 | pemsley | 2011-05-06 11:20:20 +0100 (Fri, 06 May 2011) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm update RNA/DNA tests in the light of new base names. ------------------------------------------------------------------------ r3490 | pemsley | 2011-05-06 11:19:31 +0100 (Fri, 06 May 2011) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple New build scripts (using new Refmac dictionary). ------------------------------------------------------------------------ r3488 | pemsley | 2011-05-04 16:14:25 +0100 (Wed, 04 May 2011) | 2 lines Changed paths: M /trunk M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh Merge 3487 to trunk. ------------------------------------------------------------------------ r3486 | pemsley | 2011-05-04 13:25:33 +0100 (Wed, 04 May 2011) | 2 lines Changed paths: M /trunk M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ideal-rna.hh M /trunk/python/prodrg_import.py M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/lbg-interface.cc Merge 3482-3484 to trunk. ------------------------------------------------------------------------ r3485 | pemsley | 2011-05-04 12:34:34 +0100 (Wed, 04 May 2011) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/lbg/notes clean up debugging, add a note. ------------------------------------------------------------------------ r3481 | pemsley | 2011-04-30 10:34:19 +0100 (Sat, 30 Apr 2011) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Clean up the patterson function a bit - remove the weights from the parameters, remove debugging, improve the map name. ------------------------------------------------------------------------ r3480 | pemsley | 2011-04-29 16:22:44 +0100 (Fri, 29 Apr 2011) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h make_and_draw_patterson() with tweak to contour change code. n_residues() function added. ------------------------------------------------------------------------ r3479 | pemsley | 2011-04-29 15:56:36 +0100 (Fri, 29 Apr 2011) | 2 lines Changed paths: M /trunk/geometry/Makefile.am A /trunk/geometry/chem_mods.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add chem mods holders to geometry (chem_mod_atom, chem_mod_bond etc.). ------------------------------------------------------------------------ r3478 | b.lohkamp | 2011-04-25 18:21:47 +0100 (Mon, 25 Apr 2011) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/fitting.py M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc sphere regularization for python (incl toolbuttons) docked accept/reject dialog desensitised upon Esc ------------------------------------------------------------------------ r3477 | b.lohkamp | 2011-04-24 13:36:47 +0100 (Sun, 24 Apr 2011) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/cootrc.template M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh fix icon sizes for toolbar preferences and other modelling toolbar (this is configurable via cootrc now too) fix windows usleep in rocking ------------------------------------------------------------------------ r3476 | pemsley | 2011-04-14 11:48:01 +0100 (Thu, 14 Apr 2011) | 2 lines Changed paths: M /trunk/doc/coot-user-manual.texi fix typo in mutate documentation. ------------------------------------------------------------------------ r3475 | pemsley | 2011-04-14 11:42:02 +0100 (Thu, 14 Apr 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c Add rock function to GUI (under spin). ------------------------------------------------------------------------ r3474 | pemsley | 2011-04-13 13:18:37 +0100 (Wed, 13 Apr 2011) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc Remove initial angle jump on rocking. ------------------------------------------------------------------------ r3473 | pemsley | 2011-04-13 12:15:30 +0100 (Wed, 13 Apr 2011) | 3 lines Changed paths: M /trunk/src/c-interface-view.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info.h Add rocking function toggle_idle_rock_function() with scale factors. Not in the GUI yet. ------------------------------------------------------------------------ r3472 | pemsley | 2011-04-12 22:17:31 +0100 (Tue, 12 Apr 2011) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lidia-core/lig-build.hh Add a fix-up for rotating wedge bonds with 2 and 3 bond to sharp-end wedge bond atom. ------------------------------------------------------------------------ r3471 | b.lohkamp | 2011-04-12 16:50:11 +0100 (Tue, 12 Apr 2011) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/protein_db/protein_db.cpp M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/gap.py M /trunk/python/prodrg_import.py M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc click_protein_db_loop_gui for python (uses dialog of buttons and not radio buttons currently) update python prodrg_import to actually function properly Fix sequence error in old python loop fitting make protein_db_loops_py return the loop imols fix reading protein.db file ------------------------------------------------------------------------ r3470 | pemsley | 2011-04-11 07:31:38 +0100 (Mon, 11 Apr 2011) | 2 lines Changed paths: M /trunk/lidia-core/lig-build.hh Tweak the HN, NH, OH layout a tiny bit. ------------------------------------------------------------------------ r3469 | pemsley | 2011-04-10 21:20:13 +0100 (Sun, 10 Apr 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lig-build.cc M /trunk/lidia-core/lig-build.hh Implicit (non-polar) hydrogen canvas positioning improved. ------------------------------------------------------------------------ r3468 | pemsley | 2011-04-09 15:15:06 +0100 (Sat, 09 Apr 2011) | 4 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lidia-core/lbg-molfile.cc fix up the stereo bond direction on reading. Add cheesy dialog to set the atom "X" (using lbg.glade), on_lbg_atom_x_entry_changed handles the dynamic text change. ------------------------------------------------------------------------ r3467 | pemsley | 2011-04-09 10:45:10 +0100 (Sat, 09 Apr 2011) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-test.cc M /trunk/src/cc-interface.hh Add a constructor of a molfile_molecule_t using only restraints. Remove atoms and bonds from function params of topological equivalence class. Swap highlighted bond info indices when wedge bond direction changes. ------------------------------------------------------------------------ r3466 | pemsley | 2011-04-09 09:59:19 +0100 (Sat, 09 Apr 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm fix typo in the menu for hetify-residue function. ------------------------------------------------------------------------ r3465 | pemsley | 2011-04-08 20:25:34 +0100 (Fri, 08 Apr 2011) | 3 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh Tweak the wedge representation - now a quad. Add ability to convert a single bond to a wedge. ------------------------------------------------------------------------ r3464 | pemsley | 2011-04-08 12:12:12 +0100 (Fri, 08 Apr 2011) | 2 lines Changed paths: A /trunk/lbg/Trash-hydrogens-Andy_Trash_Can.svg Add a hydrogen trash can icon. ------------------------------------------------------------------------ r3463 | pemsley | 2011-04-08 12:11:44 +0100 (Fri, 08 Apr 2011) | 8 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/Makefile.am M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lig-build.hh M /trunk/src/Makefile.am A /trunk/src/c-interface-test.cc M /trunk/src/c-interface.cc Add molfile_molecule_t constructor from a residue and resetraints. Add Molfile bond type supports into lidia-core bond types, read and write them. However, display of such things as "double or single" is a hack (displayed as single). Delete hydrogen function added to lidia interface, functioned added to widgeted_molecule_t to do the deletion. Move out test_function to its own file. ------------------------------------------------------------------------ r3462 | pemsley | 2011-04-07 14:35:20 +0100 (Thu, 07 Apr 2011) | 2 lines Changed paths: M /trunk M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Merge 3461 to trunk. ------------------------------------------------------------------------ r3460 | pemsley | 2011-04-07 09:17:33 +0100 (Thu, 07 Apr 2011) | 2 lines Changed paths: M /trunk M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc Merge 3441 to trunk. ------------------------------------------------------------------------ r3459 | pemsley | 2011-04-07 09:10:22 +0100 (Thu, 07 Apr 2011) | 2 lines Changed paths: M /trunk M /trunk/protein_db/Makefile.am A /trunk/protein_db/rna_db.cpp A /trunk/protein_db/rna_db.h Stub for RNA version of Protein DB. ------------------------------------------------------------------------ r3458 | pemsley | 2011-04-07 09:07:21 +0100 (Thu, 07 Apr 2011) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3457 | pemsley | 2011-04-07 08:51:19 +0100 (Thu, 07 Apr 2011) | 2 lines Changed paths: M /trunk/src/c-interface.h Fix typo in set-convert-to-v2-atom-names documentation string. ------------------------------------------------------------------------ r3456 | pemsley | 2011-04-07 08:33:52 +0100 (Thu, 07 Apr 2011) | 4 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/lbg/test_lbg_functions.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.cc Fix up the stereo bond issues on reading and writing mol2 files. Add addition of assignment of invariant sequence number for widgeted molecules. Includes debugging that should be cleaned up. Needs tests. ------------------------------------------------------------------------ r3455 | pemsley | 2011-04-05 12:21:57 +0100 (Tue, 05 Apr 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm fix-up hetify residue menu item. ------------------------------------------------------------------------ r3454 | pemsley | 2011-04-05 11:35:29 +0100 (Tue, 05 Apr 2011) | 3 lines Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/graphics-c-interface-functions-blanks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/notes A /trunk/lbg/test_lbg_functions.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh First bash at equivalent class analysis for topological equivalence (currently gets the same answer as Gasteiger&Engel Phe test - but with one more round). ------------------------------------------------------------------------ r3453 | pemsley | 2011-04-05 09:37:39 +0100 (Tue, 05 Apr 2011) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Tidy up stabilisation in angle restraints. ------------------------------------------------------------------------ r3452 | pemsley | 2011-04-05 09:36:45 +0100 (Tue, 05 Apr 2011) | 2 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/lbg-interface.cc catch ... exception in SMILES generation. ------------------------------------------------------------------------ r3451 | pemsley | 2011-04-05 09:35:51 +0100 (Tue, 05 Apr 2011) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a menu item for hetify-residue. ------------------------------------------------------------------------ r3450 | pemsley | 2011-03-29 12:13:30 +0100 (Tue, 29 Mar 2011) | 6 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h M /trunk/src/protein_db-interface.cc M /trunk/src/protein_db-interface.hh protein_db_loops_scm returns a SCM values (the molecule for a copy of the original loop and the list of loop molecules). New function get_chain() added to molecule class. New function copy_residue_range() created. click-protein-db-gui updated to use copy-residue-range. ------------------------------------------------------------------------ r3448 | pemsley | 2011-03-28 12:08:35 +0100 (Mon, 28 Mar 2011) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add triple bond representation, add_neighb_normal() optionally includes second order atoms. ------------------------------------------------------------------------ r3447 | pemsley | 2011-03-28 07:38:04 +0100 (Mon, 28 Mar 2011) | 2 lines Changed paths: M /trunk/dnotes M /trunk/lbg/notes Update notes. ------------------------------------------------------------------------ r3446 | pemsley | 2011-03-28 07:37:14 +0100 (Mon, 28 Mar 2011) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Tidy up in add_ligand_delete_residue_copy_molecule(). ------------------------------------------------------------------------ r3445 | pemsley | 2011-03-28 07:34:47 +0100 (Mon, 28 Mar 2011) | 2 lines Changed paths: M /trunk/doc/validation-tutorial.tex Add a note about 3f1l. ------------------------------------------------------------------------ r3444 | pemsley | 2011-03-28 07:33:40 +0100 (Mon, 28 Mar 2011) | 3 lines Changed paths: M /trunk/scheme/prodrg-import.scm Better handle the case where, on importing a prodrg ligand, there is no ligand to overlap (or it does not have restraints). ------------------------------------------------------------------------ r3443 | pemsley | 2011-03-28 07:32:30 +0100 (Mon, 28 Mar 2011) | 2 lines Changed paths: M /trunk/coords/mmdb.cc In mdl_mol_to_asc(), don't set the ResID with an non-blank ins-code. ------------------------------------------------------------------------ r3439 | KevKeating | 2011-03-16 15:37:11 +0000 (Wed, 16 Mar 2011) | 6 lines Changed paths: M /trunk/ideal/Makefile.am A /trunk/ideal/extra-restraints-kk.cc M /trunk/ideal/extra-restraints.cc A /trunk/ideal/simple-restraint-kk.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/python/coot_utils.py M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h A /trunk/src/molecule-class-info-kk.cc M /trunk/src/molecule-class-info.h added start position/harmonic restraints (add_extra_start_pos_restraint() Python and Scheme function) added refine_zone_with_score() Python and Scheme function added mark_multiple_atoms_as_fixed() Python function delete_extra_restraint() can now delete torsion and start position restraints minimizations now return scores even when gsl_multimin_fdfminimizer_iterate() returns a GSL_ENOPROG signal added additional kk source code files ------------------------------------------------------------------------ r3438 | pemsley | 2011-03-16 14:56:23 +0000 (Wed, 16 Mar 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Merge 3437 to trunk. ------------------------------------------------------------------------ r3436 | pemsley | 2011-03-15 21:07:08 +0000 (Tue, 15 Mar 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc set_monomer_restraints_py(), bond restraint length should be 5 now [KK]. ------------------------------------------------------------------------ r3434 | pemsley | 2011-03-14 12:53:44 +0000 (Mon, 14 Mar 2011) | 2 lines Changed paths: M /trunk M /trunk/rel-todo M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-refine.cc Merge 3432-3433 to trunk. ------------------------------------------------------------------------ r3431 | pemsley | 2011-03-14 11:21:21 +0000 (Mon, 14 Mar 2011) | 2 lines Changed paths: M /trunk M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c Merge 3430 to trunk. ------------------------------------------------------------------------ r3429 | pemsley | 2011-03-13 23:27:29 +0000 (Sun, 13 Mar 2011) | 2 lines Changed paths: M /trunk M /trunk/geometry/protein-geometry.cc M /trunk/src/c-interface.h Merge rev 3428 to trunk. ------------------------------------------------------------------------ r3427 | pemsley | 2011-03-10 11:37:55 +0000 (Thu, 10 Mar 2011) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.hh M /trunk/scheme/extensions.scm Make the new chiral centre functions private. Put the inverter menu item into the correct menu. ------------------------------------------------------------------------ r3426 | pemsley | 2011-03-10 11:24:35 +0000 (Thu, 10 Mar 2011) | 11 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc Chiral centre inverter. Restraints are converted to scm expression, manipulated, and added back (currently in scheme, should be c++). Add Chiral hydrogen pusher (pushes an incorrectly positioned single hydrogen attached to a chiral centre through to the other side of the chiral centre) added to the minimizer. get_chiral_hydrogen_index() used to set the index on that atom (if it exists) when restraints are generated. check_pushable_chiral_hydrogens() and push_chiral_hydrogen() do the deed. Less updates for graphics when in regularization mode (steps per frame). Python and scheme expressions for bond restraints now contain bond type info. replace_monomer_restraints() now calls assign_chiral_volume_targets(). ------------------------------------------------------------------------ r3425 | pemsley | 2011-03-09 11:34:51 +0000 (Wed, 09 Mar 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-widgets.cc M /trunk/src/gtk2-interface.c Clean-up on the Remarks browswer - move it to About menu. ------------------------------------------------------------------------ r3424 | pemsley | 2011-03-09 06:43:31 +0000 (Wed, 09 Mar 2011) | 2 lines Changed paths: M /trunk/scheme/coot.scm prodrg-import.scm needs the graphics. ------------------------------------------------------------------------ r3423 | pemsley | 2011-03-08 23:20:05 +0000 (Tue, 08 Mar 2011) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/callbacks.c connect up the remarks dialog to the remarks molecule chooser. ------------------------------------------------------------------------ r3422 | pemsley | 2011-03-08 21:51:02 +0000 (Tue, 08 Mar 2011) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h remarks browser molecule chooser. ------------------------------------------------------------------------ r3421 | pemsley | 2011-03-08 14:56:52 +0000 (Tue, 08 Mar 2011) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/coot-nomenclature.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc Bad chiral centres should really be called "inverted". ------------------------------------------------------------------------ r3420 | b.lohkamp | 2011-03-06 15:59:14 +0000 (Sun, 06 Mar 2011) | 1 line Changed paths: M /trunk/src/graphics-info-render.cc fix povray view matrix (zoom still problematic though) ------------------------------------------------------------------------ r3419 | pemsley | 2011-03-05 16:35:05 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r3418 | pemsley | 2011-03-05 16:16:52 +0000 (Sat, 05 Mar 2011) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/rel-todo M /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.h Remarks dialog. Fixup button-up status to stop rotating bond after button-up. ------------------------------------------------------------------------ r3417 | pemsley | 2011-03-05 16:14:38 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update for OpenSuse 11.3 build. ------------------------------------------------------------------------ r3416 | pemsley | 2011-03-05 16:13:28 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi RHEL 6 note added to FAQ. ------------------------------------------------------------------------ r3415 | pemsley | 2011-03-05 15:16:44 +0000 (Sat, 05 Mar 2011) | 3 lines Changed paths: M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Enable the search similarity from the search combo box. In a few tests that I have done, exact matches match nothing - Hmm... ------------------------------------------------------------------------ r3414 | pemsley | 2011-03-05 14:15:58 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/scheme/prodrg-import.scm mdl-latest-time is not necessarily a number. Test for a number before using. ------------------------------------------------------------------------ r3413 | pemsley | 2011-03-05 14:00:16 +0000 (Sat, 05 Mar 2011) | 3 lines Changed paths: M /trunk/scheme/prodrg-import.scm sbase-transfer-latest-time is not always a number. Test for a number before using the > operator. ------------------------------------------------------------------------ r3412 | pemsley | 2011-03-05 11:58:44 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.h Merge rev 3409 to trunk. ------------------------------------------------------------------------ r3411 | pemsley | 2011-03-05 11:57:54 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc Merge rev 3407 to trunk. ------------------------------------------------------------------------ r3410 | pemsley | 2011-03-05 11:44:50 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/lbg/notes M /trunk/ltmain.sh-unneeded M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3408 | pemsley | 2011-03-05 11:41:22 +0000 (Sat, 05 Mar 2011) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points ------------------------------------------------------------------------ r3406 | pemsley | 2011-02-27 15:10:31 +0000 (Sun, 27 Feb 2011) | 2 lines Changed paths: M /trunk M /trunk/RELEASE-NOTES M /trunk/src/c-interface.h M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc Merge rev 3405 to trunk. ------------------------------------------------------------------------ r3404 | b.lohkamp | 2011-02-26 16:53:34 +0000 (Sat, 26 Feb 2011) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/lbg/lbg.glade M /trunk/lbg/rdkit-interface.cc M /trunk/pixmaps/side-chain-180.svg M /trunk/pixmaps/torsion-general.svg M /trunk/python/coot_gui.py M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh M /trunk/src/lbg-interface.cc fix font in some icons for windows protein_db_loops for python remove protection around rdkit assignRadicals for windows better icon for lbg (?) ------------------------------------------------------------------------ r3403 | pemsley | 2011-02-24 17:56:22 +0000 (Thu, 24 Feb 2011) | 2 lines Changed paths: M /trunk M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.h M /trunk/src/restraints-editor.cc Merge 3399 to trunk. ------------------------------------------------------------------------ r3402 | pemsley | 2011-02-24 17:38:02 +0000 (Thu, 24 Feb 2011) | 2 lines Changed paths: M /trunk/lbg/notes Another lbg problem (maybe prodrg). ------------------------------------------------------------------------ r3401 | pemsley | 2011-02-24 17:19:02 +0000 (Thu, 24 Feb 2011) | 2 lines Changed paths: M /trunk/doc/validation-tutorial.tex M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc Hetify residue atoms (if non-standard residue type). ------------------------------------------------------------------------ r3400 | pemsley | 2011-02-24 17:17:46 +0000 (Thu, 24 Feb 2011) | 7 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc Pi-cation additions. Debugging. Formal charge for atom type NT. Testing undelocalise() in add_hydrogens_with_rdkit(). unresolved. ------------------------------------------------------------------------ r3398 | pemsley | 2011-02-21 15:02:12 +0000 (Mon, 21 Feb 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix up so that ccp4mg runs given the picture description. ------------------------------------------------------------------------ r3397 | pemsley | 2011-02-21 15:01:05 +0000 (Mon, 21 Feb 2011) | 2 lines Changed paths: M /trunk/doc/validation-tutorial.tex Add 2XDE to tutorial. ------------------------------------------------------------------------ r3396 | b.lohkamp | 2011-02-20 16:47:26 +0000 (Sun, 20 Feb 2011) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-test-cc.cc M /trunk/lbg/lbg.hh M /trunk/lbg/rdkit-interface.cc M /trunk/python/prodrg_import.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/coot-hydrogens.cc M /trunk/src/lbg-interface.cc update python prodrg_import some windowsy fixes for lbg add pythonic all_molecule_ramachandran_score and all_molecule_rotamer_score ------------------------------------------------------------------------ r3395 | b.lohkamp | 2011-02-20 12:34:25 +0000 (Sun, 20 Feb 2011) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc merge 3380 and 3387 into trunk ------------------------------------------------------------------------ r3393 | pemsley | 2011-02-19 14:06:58 +0000 (Sat, 19 Feb 2011) | 2 lines Changed paths: M /trunk/coot-surface/Makefile.am Add coot-utils to INCUDES, now that we use CXX_UNSET_CHARGE. ------------------------------------------------------------------------ r3392 | pemsley | 2011-02-18 15:09:44 +0000 (Fri, 18 Feb 2011) | 2 lines Changed paths: M /trunk/doc/Makefile.am M /trunk/doc/coot-user-manual.texi Tidy up double target for coot-user-manual.ps ------------------------------------------------------------------------ r3391 | pemsley | 2011-02-18 12:33:28 +0000 (Fri, 18 Feb 2011) | 2 lines Changed paths: A /trunk/doc/coot-user-manual.texi (from /trunk/doc/user-manual.texi:3379) D /trunk/doc/user-manual.texi Rename coot-user-manual. ------------------------------------------------------------------------ r3390 | pemsley | 2011-02-17 16:30:02 +0000 (Thu, 17 Feb 2011) | 2 lines Changed paths: M /trunk M /trunk/coot-gtk2.glade M /trunk/coot-surface/coot-surface.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h Merge 3388 to trunk. ------------------------------------------------------------------------ r3389 | pemsley | 2011-02-17 16:04:09 +0000 (Thu, 17 Feb 2011) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-surface/coot-surface.cc M /trunk/doc/user-manual.texi M /trunk/lbg/notes M /trunk/rel-todo M /trunk/src/c-interface.h M /trunk/surface/CXXBall.h NEED_OPENMP_PRAGMA_HACK enabled for (__GNUC_MINOR__ == 3) (Ubuntu 9.04). pkg-config gtk+-2.0 test to 2.16 for gtkglext (Ubuntu 9.04). Add small bit of documentation for surfaces. Update notes. ------------------------------------------------------------------------ r3386 | pemsley | 2011-02-16 12:45:41 +0000 (Wed, 16 Feb 2011) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3385 | pemsley | 2011-02-16 12:45:16 +0000 (Wed, 16 Feb 2011) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/flev.cc Tweak debugging. ------------------------------------------------------------------------ r3384 | pemsley | 2011-02-16 12:44:04 +0000 (Wed, 16 Feb 2011) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm M /trunk/scheme/generic-objects.scm Add prodrg-import. ------------------------------------------------------------------------ r3383 | pemsley | 2011-02-16 12:43:41 +0000 (Wed, 16 Feb 2011) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add krosp to the builds. ------------------------------------------------------------------------ r3382 | pemsley | 2011-02-16 12:42:44 +0000 (Wed, 16 Feb 2011) | 2 lines Changed paths: M /trunk/doc/Makefile.am rename user-manual coot-user-manual. ------------------------------------------------------------------------ r3379 | pemsley | 2011-02-14 17:35:20 +0000 (Mon, 14 Feb 2011) | 2 lines Changed paths: D /trunk/protein_db/Makefile.in Delete the Makefile.in from protein_db. ------------------------------------------------------------------------ r3378 | pemsley | 2011-02-14 17:33:40 +0000 (Mon, 14 Feb 2011) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/mini-mol/mini-mol-utils.cc M /trunk/mini-mol/mini-mol-utils.hh M /trunk/mini-mol/mini-mol.hh A /trunk/protein_db A /trunk/protein_db/Makefile.am A /trunk/protein_db/Makefile.in A /trunk/protein_db/protein.db A /trunk/protein_db/protein_db.cpp A /trunk/protein_db/protein_db.h A /trunk/protein_db/protein_db_utils.cpp A /trunk/protein_db/protein_db_utils.h M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/user-define-restraints.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh A /trunk/src/molecule-class-info-build.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h A /trunk/src/protein_db-interface.cc A /trunk/src/protein_db-interface.hh Add an interface to protein_db. Cheap as chips. Simple residue numbers, no merging/replacement tools. ------------------------------------------------------------------------ r3377 | pemsley | 2011-02-14 11:09:21 +0000 (Mon, 14 Feb 2011) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/lsq-improve.cc M /trunk/coot-utils/lsq-improve.hh M /trunk/coot-utils/test-utils.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Create user interface to lsq_improve. Add atom selections to lsq_improve(). Make a stub for protein_db_loops(). ------------------------------------------------------------------------ r3376 | pemsley | 2011-02-14 02:00:50 +0000 (Mon, 14 Feb 2011) | 2 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/notes M /trunk/lbg/some-coot-utils.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add lsq-improve to the interface. Needs an atom selection too. ------------------------------------------------------------------------ r3375 | pemsley | 2011-02-11 12:35:24 +0000 (Fri, 11 Feb 2011) | 5 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/lsq-improve.cc M /trunk/coot-utils/lsq-improve.hh M /trunk/coot-utils/test-utils.cc get_lsq_matrix() now has an optional arg, saying if the summary should be written to the screen. General clean-up of lsq-improve, make the max number of rounds be a class variable. ------------------------------------------------------------------------ r3374 | pemsley | 2011-02-10 07:41:42 +0000 (Thu, 10 Feb 2011) | 2 lines Changed paths: M /trunk/coot-utils/lsq-improve.cc Comment typo so that things compile. ------------------------------------------------------------------------ r3373 | pemsley | 2011-02-10 07:40:22 +0000 (Thu, 10 Feb 2011) | 2 lines Changed paths: M /trunk/coot-utils/lsq-improve.cc M /trunk/coot-utils/lsq-improve.hh const the arg to get_new_matches(). ------------------------------------------------------------------------ r3372 | pemsley | 2011-02-10 03:31:08 +0000 (Thu, 10 Feb 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/lsq-improve.cc Core function of lsq-improve filled: get_new_matches(contact_residues). ------------------------------------------------------------------------ r3371 | pemsley | 2011-02-08 09:36:35 +0000 (Tue, 08 Feb 2011) | 2 lines Changed paths: M /trunk/coot-utils/lsq-improve.cc M /trunk/coot-utils/lsq-improve.hh M /trunk/src/mol-hierachy.cc Factor out a get_new_matches() that takes a vector of residue contacts. ------------------------------------------------------------------------ r3370 | pemsley | 2011-02-08 00:34:37 +0000 (Tue, 08 Feb 2011) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/lsq-improve.cc A /trunk/coot-utils/lsq-improve.hh M /trunk/coot-utils/test-utils.cc LSQ-Improve initial check-in, many stub functions, nothing clever yet. ------------------------------------------------------------------------ r3369 | pemsley | 2011-02-07 13:02:22 +0000 (Mon, 07 Feb 2011) | 2 lines Changed paths: M /trunk M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/high-res/sequence-assignment.cc M /trunk/python/get_ebi.py M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.h A /trunk/src/gtk-widget-conversion-utils.cc (from /branches/release-0.6.2/src/gtk-widget-conversion-utils.cc:3365) A /trunk/src/gtk-widget-conversion-utils.h (from /branches/release-0.6.2/src/gtk-widget-conversion-utils.h:3365) M /trunk/src/gtk2-interface.c M /trunk/src/junk.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/read-phs.c M /trunk/src/testing.cc M /trunk/utils/gdk-keysyms.cc Merge 3347:3351 and 3355:3365 to trunk. ------------------------------------------------------------------------ r3368 | pemsley | 2011-02-07 12:30:17 +0000 (Mon, 07 Feb 2011) | 2 lines Changed paths: M /trunk M /trunk/TODO M /trunk/rel-todo M /trunk/src/c-interface.h update notes ------------------------------------------------------------------------ r3367 | pemsley | 2011-02-07 12:25:48 +0000 (Mon, 07 Feb 2011) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple SWIG 1.3.29 doesn't work for 32 bits either. ------------------------------------------------------------------------ r3366 | pemsley | 2011-02-07 12:24:52 +0000 (Mon, 07 Feb 2011) | 2 lines Changed paths: M /trunk/doc/Makefile.am Add ligand-fitting figures to Makefile.am ------------------------------------------------------------------------ r3355 | pemsley | 2011-01-28 15:27:23 +0000 (Fri, 28 Jan 2011) | 2 lines Changed paths: M /trunk/TODO M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/dnotes M /trunk/lbg/notes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3354 | pemsley | 2011-01-28 15:26:17 +0000 (Fri, 28 Jan 2011) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc change max_dist for conventional distance-based bonding from 1.64 to 1.71 ------------------------------------------------------------------------ r3353 | pemsley | 2011-01-28 13:42:26 +0000 (Fri, 28 Jan 2011) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Merge 3352 to trunk. ------------------------------------------------------------------------ r3347 | pemsley | 2011-01-25 11:21:36 +0000 (Tue, 25 Jan 2011) | 2 lines Changed paths: M /trunk/pixmaps/add-alt-conf.svg M /trunk/pixmaps/add-peptide-1.svg M /trunk/pixmaps/add-water.svg M /trunk/pixmaps/atom-at-pointer.svg M /trunk/pixmaps/auto-fit-rotamer.svg M /trunk/pixmaps/azerbaijan.svg M /trunk/pixmaps/edit-backbone.svg M /trunk/pixmaps/edit-chi.svg M /trunk/pixmaps/flip-peptide.svg M /trunk/pixmaps/mutate-auto-fit.svg M /trunk/pixmaps/mutate.svg M /trunk/pixmaps/refine-1.svg M /trunk/pixmaps/regularize-1.svg M /trunk/pixmaps/rigid-body.svg M /trunk/pixmaps/rotamers.svg M /trunk/pixmaps/rtz.svg M /trunk/pixmaps/side-chain-180.svg M /trunk/pixmaps/torsion-general.svg Change to 48x48 svgs. ------------------------------------------------------------------------ r3346 | pemsley | 2011-01-23 12:53:56 +0000 (Sun, 23 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Remove operator<< for coot::bash_distance_t now that we have integrated the build into the main line. ------------------------------------------------------------------------ r3345 | pemsley | 2011-01-22 17:47:06 +0000 (Sat, 22 Jan 2011) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Include normal coot-utils.hh not some-coot-utils.hh for lbg. ------------------------------------------------------------------------ r3344 | pemsley | 2011-01-21 11:25:03 +0000 (Fri, 21 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/Makefile.am No need for some-coot-utils now that we link with conventional util libs for lidia. ------------------------------------------------------------------------ r3343 | pemsley | 2011-01-20 14:21:02 +0000 (Thu, 20 Jan 2011) | 4 lines Changed paths: M /trunk M /trunk/coords/Bond_lines.cc M /trunk/doc/user-manual.texi M /trunk/lbg/Makefile.am M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h Merge 3342 to trunk. Cut down hydrogen bumps by restricting dist_max for hydrogens. Add dot_size_scale_factor for molprobity dots. Should be user parameter? ------------------------------------------------------------------------ r3341 | b.lohkamp | 2011-01-20 10:44:48 +0000 (Thu, 20 Jan 2011) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/WinCoot_install_masta.nsi update windows installer, grant execute access and add windows feelin. ------------------------------------------------------------------------ r3340 | pemsley | 2011-01-19 14:54:36 +0000 (Wed, 19 Jan 2011) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Fix typo in delete_residue() model test. ------------------------------------------------------------------------ r3337 | pemsley | 2011-01-12 14:24:48 +0000 (Wed, 12 Jan 2011) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-defines.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc M /trunk/src/pick.h Merge 3332 into trunk. ------------------------------------------------------------------------ r3336 | pemsley | 2011-01-12 14:18:20 +0000 (Wed, 12 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/src/main.cc Bernie fixes up file chooser dialogs, adds default file names. Modal file choosers. ------------------------------------------------------------------------ r3334 | pemsley | 2011-01-11 18:23:21 +0000 (Tue, 11 Jan 2011) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Remove deleted alt-confed residue test until delete-residue-with-full-spec makes it to trunk. ------------------------------------------------------------------------ r3331 | pemsley | 2011-01-10 15:31:57 +0000 (Mon, 10 Jan 2011) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-validate.cc For greying out the probe validation menu, check that the file exists in addition to testing that the command exists in path. ------------------------------------------------------------------------ r3330 | pemsley | 2011-01-10 15:30:40 +0000 (Mon, 10 Jan 2011) | 2 lines Changed paths: M /trunk/scheme/generic-objects.scm write-file-for-molprobity no longer provided. ------------------------------------------------------------------------ r3329 | pemsley | 2011-01-10 15:27:36 +0000 (Mon, 10 Jan 2011) | 2 lines Changed paths: M /trunk/lbg/use-rdkit.hh Not using NLS seems to help get past gettext issues with boost/rdkit on Windows. ------------------------------------------------------------------------ r3328 | pemsley | 2011-01-09 23:49:12 +0000 (Sun, 09 Jan 2011) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Explicitly give the vertext type for MatchGraph(). ------------------------------------------------------------------------ r3327 | pemsley | 2011-01-09 16:37:50 +0000 (Sun, 09 Jan 2011) | 6 lines Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/lbg-callbacks-outer.cc M /trunk/src/Makefile.am A /trunk/src/lbg-callbacks-outer.cc OK, this is a bit of a hack. We have not yet managed to get the Windows build to use the reentrant callbacks of lbg when they are defined in a library. So, let's put them in the executable, by using a wrapper that includes lbg-callbacks.cc. That way both executables can get the functions directly (not in a library). ------------------------------------------------------------------------ r3326 | pemsley | 2011-01-09 16:24:43 +0000 (Sun, 09 Jan 2011) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fill the Python remarks function. ------------------------------------------------------------------------ r3325 | pemsley | 2011-01-09 16:14:45 +0000 (Sun, 09 Jan 2011) | 7 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add a function for all-molecule-rotamer-score. Add a function for all-molecule-ramachandran-score. Add a function to return remarks to the scripting level. Python version needs to be filled. Add a few new files to the Makefile.am so that they are added to the file on make dist. ------------------------------------------------------------------------ r3324 | pemsley | 2011-01-09 16:09:44 +0000 (Sun, 09 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/some-coot-utils.hh Trivial formatting changes. Add some notes. ------------------------------------------------------------------------ r3323 | pemsley | 2011-01-09 16:08:08 +0000 (Sun, 09 Jan 2011) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/user-define-restraints.scm Change default weight for simple user-define bond restraint to 0.05 ------------------------------------------------------------------------ r3322 | pemsley | 2011-01-09 16:07:07 +0000 (Sun, 09 Jan 2011) | 2 lines Changed paths: M /trunk/ligand/rotamer.hh trivial formatting changes. ------------------------------------------------------------------------ r3321 | pemsley | 2011-01-09 11:09:26 +0000 (Sun, 09 Jan 2011) | 3 lines Changed paths: D /trunk/ltmain.sh A /trunk/ltmain.sh-unneeded (from /trunk/ltmain.sh:3319) Do the ltmain.sh deed! Bernie thinks that ltmain.sh should not be in the repo. PE now agrees with him. ------------------------------------------------------------------------ r3320 | pemsley | 2011-01-08 22:03:05 +0000 (Sat, 08 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc Close the stream of the write_mdl_molfile() function before returning. Fixed crash on stream deconstruction? ------------------------------------------------------------------------ r3319 | pemsley | 2011-01-08 18:17:59 +0000 (Sat, 08 Jan 2011) | 2 lines Changed paths: M /trunk/ltmain.sh Try a new ltmain.sh ------------------------------------------------------------------------ r3318 | pemsley | 2011-01-08 18:15:46 +0000 (Sat, 08 Jan 2011) | 2 lines Changed paths: M /trunk/configure.in Check for a specific version of glib, fails less. ------------------------------------------------------------------------ r3317 | pemsley | 2011-01-08 17:59:38 +0000 (Sat, 08 Jan 2011) | 4 lines Changed paths: M /trunk/scheme/prodrg-import.scm Update prodrg result importing. Speed up refinement, Tweak/improve the timeout new file function handler. ------------------------------------------------------------------------ r3316 | pemsley | 2011-01-08 17:53:22 +0000 (Sat, 08 Jan 2011) | 3 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes Put the enumeration of UNASSIGNED_INDEX in the lbg class. Use it to test penultimate_atom_index in rotate_latest_bond(). ------------------------------------------------------------------------ r3314 | pemsley | 2010-12-30 17:18:43 +0000 (Thu, 30 Dec 2010) | 3 lines Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.hh Add all-molecule ramachandran score (SCM interface only currently). Add a stub for related rotamer score. ------------------------------------------------------------------------ r3313 | pemsley | 2010-12-29 15:36:53 +0000 (Wed, 29 Dec 2010) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc Add a water max distance to flev. Use the max water distance cutoff in coot-utils filter_residues_by_solvent_contact(). In the lbg gui, make the residue addition a check button and set a state for displaying residues. ------------------------------------------------------------------------ r3312 | pemsley | 2010-12-29 15:32:18 +0000 (Wed, 29 Dec 2010) | 2 lines Changed paths: M /trunk/configure.in Enable PKG_CHECK_MODULES for GPP4. Rearrange package checking, add some notes. ------------------------------------------------------------------------ r3311 | pemsley | 2010-12-26 15:32:26 +0000 (Sun, 26 Dec 2010) | 3 lines Changed paths: M /trunk/configure.in M /trunk/macros/clipper.m4 gpp4 updates for configure. Clean up prefix use logic in clipper.m4. ------------------------------------------------------------------------ r3310 | pemsley | 2010-12-23 18:24:21 +0000 (Thu, 23 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/scheme/fitting.scm M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc Merge 3308, 3309 into trunk. ------------------------------------------------------------------------ r3307 | b.lohkamp | 2010-12-21 16:42:13 +0000 (Tue, 21 Dec 2010) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/libcheck.py M /trunk/python/ncs.py M /trunk/python/user_defined_restraints.py M /trunk/scheme/coot-utils.scm merge python r3300 and r3306 into trunk ------------------------------------------------------------------------ r3305 | pemsley | 2010-12-20 12:44:44 +0000 (Mon, 20 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface.h Merge 3304 into trunk. ------------------------------------------------------------------------ r3303 | pemsley | 2010-12-20 12:30:06 +0000 (Mon, 20 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/coot-rama.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/surface/Makefile.am Merge 3301, 3302 into trunk. ------------------------------------------------------------------------ r3299 | pemsley | 2010-12-15 18:21:00 +0000 (Wed, 15 Dec 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Merge 3288 to trunk. ------------------------------------------------------------------------ r3297 | b.lohkamp | 2010-12-14 16:53:08 +0000 (Tue, 14 Dec 2010) | 1 line Changed paths: M /trunk/src/main.cc fix typo from merge ------------------------------------------------------------------------ r3296 | b.lohkamp | 2010-12-14 16:28:05 +0000 (Tue, 14 Dec 2010) | 1 line Changed paths: M /trunk/src/main.cc merge 3295 (main.cc only) into trunk ------------------------------------------------------------------------ r3294 | pemsley | 2010-12-14 10:53:14 +0000 (Tue, 14 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface-preferences.cc Merge 3293 into trunk. ------------------------------------------------------------------------ r3292 | b.lohkamp | 2010-12-13 22:13:37 +0000 (Mon, 13 Dec 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/src/callbacks.c M /trunk/src/coot-hydrogens.cc M /trunk/src/main.cc M /trunk/surface/CXXBall.cpp M /trunk/surface/CXXCircleNode.cpp add some gtk2 protections (for older versions) fix some casting and compiler errors ------------------------------------------------------------------------ r3291 | pemsley | 2010-12-12 17:20:17 +0000 (Sun, 12 Dec 2010) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Rework CA or P bonds internal function. Rework the setting of the rainbow colours - now taking into account waters and based on the sequence number (not the residue number). ------------------------------------------------------------------------ r3290 | pemsley | 2010-12-11 13:51:07 +0000 (Sat, 11 Dec 2010) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r3289 | pemsley | 2010-12-11 12:49:35 +0000 (Sat, 11 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/src/pick.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Merge to trunk: CA+ligands pick patch. ------------------------------------------------------------------------ r3287 | b.lohkamp | 2010-12-10 15:57:50 +0000 (Fri, 10 Dec 2010) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/src/main.cc merge 3286 to trunk ------------------------------------------------------------------------ r3285 | pemsley | 2010-12-09 14:23:34 +0000 (Thu, 09 Dec 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm merge the ball and stick atom selection patch to trunk. ------------------------------------------------------------------------ r3283 | pemsley | 2010-12-08 15:16:59 +0000 (Wed, 08 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-preferences.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/mol-hierachy.cc Merge to trunk the fixes for ins code in Rot/Trans. ------------------------------------------------------------------------ r3281 | pemsley | 2010-12-06 16:19:00 +0000 (Mon, 06 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/testing.cc Merge 3280 into trunk - optional hydrogens in graph matching. ------------------------------------------------------------------------ r3279 | pemsley | 2010-12-06 15:23:24 +0000 (Mon, 06 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Commit 3278 (atom name mapping) to trunk. ------------------------------------------------------------------------ r3277 | b.lohkamp | 2010-12-05 23:03:02 +0000 (Sun, 05 Dec 2010) | 1 line Changed paths: M /trunk/build-it-win M /trunk/coords/Bond_lines.cc M /trunk/coot-gtk2.glade M /trunk/coot-surface/coot-surface.cc M /trunk/doc/scripting_tutorial.tex M /trunk/geometry/protein-geometry.cc M /trunk/ideal/logparse.awk M /trunk/ltmain.sh M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/generic_objects.py M /trunk/python/povray.py M /trunk/python/prodrg_import.py M /trunk/python/raster3d.py M /trunk/python/refmac.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-inner-main.c M /trunk/src/c-inner-main.h M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/read-phs.c M /trunk/src/testing.cc merge all of 0.6.2 (as of rev 3274) to trunk ------------------------------------------------------------------------ r3276 | b.lohkamp | 2010-12-05 12:28:13 +0000 (Sun, 05 Dec 2010) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/macros/goo-canvas.m4 M /trunk/src/globjects.cc (quick) fix for windows goo-canvas configure make filechooser default ------------------------------------------------------------------------ r3275 | pemsley | 2010-12-01 11:36:20 +0000 (Wed, 01 Dec 2010) | 2 lines Changed paths: M /trunk M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/python/coot_utils.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc Apply 3274 to trunk. ------------------------------------------------------------------------ r3273 | pemsley | 2010-11-30 14:15:36 +0000 (Tue, 30 Nov 2010) | 2 lines Changed paths: M /trunk M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ideal/extra-restraints.cc M /trunk/lbg/notes M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/callbacks.c M /trunk/src/read-phs.c M /trunk/src/restraints-editor.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Merge 3271 and 3272 into trunk. ------------------------------------------------------------------------ r3269 | pemsley | 2010-11-29 16:03:45 +0000 (Mon, 29 Nov 2010) | 3 lines Changed paths: M /trunk M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-preferences.cc M /trunk/src/graphics-info-modelling.cc Merge 3268 into trunk. Fix compilation warning issues on strings. ------------------------------------------------------------------------ r3264 | pemsley | 2010-11-27 12:23:16 +0000 (Sat, 27 Nov 2010) | 3 lines Changed paths: M /trunk M /trunk/RELEASE-NOTES M /trunk/coords/mmdb-crystal.cc M /trunk/db-main/db-main.cc M /trunk/db-main/train-pepflip.cc M /trunk/high-res/high-res.cc M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc Merge in releaese-0.6.2 branch, minimol residue unset runtime error usage, rev 3261. ------------------------------------------------------------------------ r3263 | pemsley | 2010-11-27 12:18:01 +0000 (Sat, 27 Nov 2010) | 3 lines Changed paths: M /trunk M /trunk/dnotes M /trunk/rel-todo update notes. property change on . ------------------------------------------------------------------------ r3262 | pemsley | 2010-11-27 11:00:56 +0000 (Sat, 27 Nov 2010) | 2 lines Changed paths: M /trunk/rel-todo update todo notes, now with estimates. ------------------------------------------------------------------------ r3259 | pemsley | 2010-11-26 12:06:21 +0000 (Fri, 26 Nov 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-preferences.cc Merge in no-coot-tips commit 3258. ------------------------------------------------------------------------ r3257 | pemsley | 2010-11-24 11:24:33 +0000 (Wed, 24 Nov 2010) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Merge commit 3256: torsion angle refinement. ------------------------------------------------------------------------ r3255 | pemsley | 2010-11-22 15:53:00 +0000 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/ncs.scm Add snarfable documentation for ncs-ligand. ------------------------------------------------------------------------ r3254 | pemsley | 2010-11-22 15:51:56 +0000 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /trunk/src/c-interface.h Fix a quotation in documentation (for snarfing). ------------------------------------------------------------------------ r3253 | pemsley | 2010-11-22 15:42:34 +0000 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /trunk/configure.in M /trunk/lbg/Makefile.am M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc Include a preprocessor option so that we can compile in lbg without a canvas. ------------------------------------------------------------------------ r3252 | pemsley | 2010-11-22 15:41:04 +0000 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Use os process from the library, not goosh. ------------------------------------------------------------------------ r3251 | pemsley | 2010-11-22 15:40:11 +0000 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add link representation in colour_by_chain. ------------------------------------------------------------------------ r3250 | pemsley | 2010-11-21 14:31:32 +0000 (Sun, 21 Nov 2010) | 6 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/use-rdkit.hh M /trunk/rel-todo M /trunk/src/flev.cc M /trunk/src/molecule-class-info-residues.cc Use get_monomer_restraints_at_least_minimal() instead of get_monomer_restraints() in flev functions. Layout works now without full restraints. Fix typo in lbg in creating a rectangle. Add some notes. ------------------------------------------------------------------------ r3249 | pemsley | 2010-11-17 15:58:57 +0000 (Wed, 17 Nov 2010) | 2 lines Changed paths: A /trunk/force-field A /trunk/force-field/Makefile.simple A /trunk/force-field/ff-bits.cc A /trunk/force-field/make-3d-from-smiles.cc Add some force-field testing/play code. ------------------------------------------------------------------------ r3245 | pemsley | 2010-11-16 13:14:53 +0000 (Tue, 16 Nov 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Fix up drawing of missing atoms in colour by chain mode (PRE bug). ------------------------------------------------------------------------ r3244 | pemsley | 2010-11-15 13:56:29 +0000 (Mon, 15 Nov 2010) | 12 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/rdkit-interface.cc M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Add initialiser for the default constructor of grid_index_t. Add an operator== for this class too. find_nearest_zero() function added, returning (in part) a grid_index_t. We don't want to find layout solutions for residues where other residues are, so find the nearest point that has a grid value sufficiently small (close to zero). In annotate(), reorder the render_from_molecule() and refine_residue_circle_positions() so that the grid is in position when refining (for debugging grid). Add an extra arg to lbg() so that (in future) we can use it without showing the window. ------------------------------------------------------------------------ r3243 | pemsley | 2010-11-14 20:43:13 +0000 (Sun, 14 Nov 2010) | 4 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes position_non_primaries() function added in an attempt to untrap residues. adjust debugging of grid - problems showing ligand rejections? Add some more notes. ------------------------------------------------------------------------ r3242 | pemsley | 2010-11-14 20:14:54 +0000 (Sun, 14 Nov 2010) | 5 lines Changed paths: M /trunk/geometry/read-sbase.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/rdkit-interface.cc M /trunk/src/molecule-class-info-residues.cc Improve stabilisation of angles terms in idealisation. Use RDKit::MolOps::sanitizeMol(m) in rdkit construction from residue. Add ForceField minimizer for rdkit molecule after adding hydrogens. Remove NBCs from first round of idealization after adding hydrogens. ------------------------------------------------------------------------ r3241 | pemsley | 2010-11-14 11:59:23 +0000 (Sun, 14 Nov 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/rdkit-interface.cc More flip trials for 3d mimic layout. solvent accessability of atoms depends on the LIGAND_TO_CANVAS_SCALE_FACTOR. ------------------------------------------------------------------------ r3240 | pemsley | 2010-11-13 19:12:49 +0000 (Sat, 13 Nov 2010) | 2 lines Changed paths: M /trunk/lbg/Makefile.am M /trunk/lbg/flev-annotations.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/wmolecule.cc M /trunk/scheme/prodrg-import.scm Rework compilation params, so that lidia is built if goo canvas prefix is given. ------------------------------------------------------------------------ r3239 | pemsley | 2010-11-13 15:29:45 +0000 (Sat, 13 Nov 2010) | 2 lines Changed paths: A /trunk/src/c-interface-view.cc Add forgotten interface file (for orienting the view). ------------------------------------------------------------------------ r3237 | pemsley | 2010-11-11 12:03:51 +0000 (Thu, 11 Nov 2010) | 3 lines Changed paths: M /trunk/lbg/graphics-c-interface-functions.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lidia-main.cc M /trunk/lbg/notes M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a function all_additional_representations_off_except(). Rework get_vector() so that it returns the vector of the midpoints. ------------------------------------------------------------------------ r3236 | pemsley | 2010-11-07 18:26:09 +0000 (Sun, 07 Nov 2010) | 8 lines Changed paths: A /trunk/lbg/graphics-c-interface-functions.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/src/Makefile.am M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/flev.hh M /trunk/src/lbg-interface.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Tidy up the callbacks a bit - add infrastructure for a function that orients the view give a residue pair (e.g. (and typically) from lbg residue circle). Pre-calculate add-reps before calling lbg and pass the vector of handles to lbg. Pass the view name to lbg (not displayed yet). Add lbg/graphics-c-interface-functions.hh for functions whereby lbg manipulates the graphics window. Show the add-reps on mousing over residue circles. ------------------------------------------------------------------------ r3235 | pemsley | 2010-11-06 20:08:16 +0000 (Sat, 06 Nov 2010) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/lbg/Makefile.am M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/c-interface-build.cc M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc M /trunk/src/main.cc Add the molecule number to the lbg_info_type constructor. Add a user data int placeholder in residue_spec. Rework the canvas button presses to use the 4 arg callback using G_CALLBACK. Add new callbacks for mouse motion and button click. ------------------------------------------------------------------------ r3233 | pemsley | 2010-11-02 20:52:33 +0000 (Tue, 02 Nov 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Correct directory for previoius patch. ------------------------------------------------------------------------ r3232 | pemsley | 2010-11-02 20:39:09 +0000 (Tue, 02 Nov 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Dependency check for gtkglext patch (compatibility with gtk+ version). ------------------------------------------------------------------------ r3231 | pemsley | 2010-11-02 10:07:51 +0000 (Tue, 02 Nov 2010) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/gtk2-interface.c Rename the PDB (and MTZ) getting functions (Now Fetch...). Added a residue spec to the residue circle class - to be used in a callback. Try to add a callback for the residue circle - currently fails. ------------------------------------------------------------------------ r3230 | pemsley | 2010-11-01 16:12:37 +0000 (Mon, 01 Nov 2010) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/lbg.cc M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/src/flev.cc M /trunk/src/lbg-interface.cc Add special rule for aromatic nitrogen attached to a (missing) hydrogen (in that case, add a hydrogen to the created rdkit molecule) so that kekulization works. ------------------------------------------------------------------------ r3229 | pemsley | 2010-10-31 05:22:23 +0000 (Sun, 31 Oct 2010) | 5 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/src/flev.cc weight for 3d distance matching of 2d layout back to 0.4 show_contour() now takes ring_atom_list because ring atom markers are now separate, not embedded in atoms (and contour cutting is different for ring and non-ring atoms). ------------------------------------------------------------------------ r3228 | pemsley | 2010-10-30 16:25:14 +0100 (Sat, 30 Oct 2010) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Minor updates for ring centre additions to the substition grid. ------------------------------------------------------------------------ r3227 | pemsley | 2010-10-29 17:39:17 +0100 (Fri, 29 Oct 2010) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/src/flev.cc M /trunk/src/graphics-info-modelling.cc Add restraints to lbg's annotate() function (to be use for ring centre avoidance in the layout). ------------------------------------------------------------------------ r3226 | pemsley | 2010-10-29 08:16:12 +0100 (Fri, 29 Oct 2010) | 5 lines Changed paths: M /trunk/lbg/flev-annotations.hh M /trunk/lbg/lbg.cc M /trunk/lbg/wmolecule.hh M /trunk/src/flev.cc flev_attached_hydrogens_t class updated to be used with rdkit-based hydrogens (rather than maping hydrogen positions from a reference ligand in a different orientation (cprodrg)). Layout has debugging for unlimited atoms and ring centres. ------------------------------------------------------------------------ r3225 | pemsley | 2010-10-27 21:33:30 +0100 (Wed, 27 Oct 2010) | 2 lines Changed paths: A /trunk/src/coot-hydrogens.cc A /trunk/src/coot-hydrogens.hh Add missing files. ------------------------------------------------------------------------ r3224 | pemsley | 2010-10-27 09:12:17 +0100 (Wed, 27 Oct 2010) | 2 lines Changed paths: M /trunk M /trunk/coords/Bond_lines.cc M /trunk/ideal/simple-restraint.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc M /trunk/src/pick.h Apply 3223 (hydrogen bond zero occ spots and picking) to trunk. ------------------------------------------------------------------------ r3221 | pemsley | 2010-10-26 18:09:31 +0100 (Tue, 26 Oct 2010) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/molecule-class-info-residues.cc Fix up for NBC fixed atoms. ------------------------------------------------------------------------ r3220 | pemsley | 2010-10-26 16:06:26 +0100 (Tue, 26 Oct 2010) | 10 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/doc/validation-tutorial.tex M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/lbg/Makefile.am M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/flev.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/lbg-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h D /trunk/src/rdkit-interface.hh Add in SBase support to the dictionary. We can store the bond orders so that hetatoms (that are in SBase) get rendered with double bonds etc without needing to read a dictionary. Switch to get_monomer_restraints_at_least_minimal() usage when needed. get_monomer_restraints() now checks for not sbase/minimal. sprout_hydrogens() function added. Currently only the rdkit-using path is filled (non-stub). Layout (vs 3d geometry) weight exposed in add_2d_conformer(). Add graphical debugging for substitution contour. ------------------------------------------------------------------------ r3217 | pemsley | 2010-10-19 01:56:11 +0100 (Tue, 19 Oct 2010) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/cycle-page-builder.scm M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc Add a function to return the model resolution, if it was in the input (pdb) file. ------------------------------------------------------------------------ r3216 | pemsley | 2010-10-19 01:52:08 +0100 (Tue, 19 Oct 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-h-bonds.cc M /trunk/coot-utils/coot-h-bonds.hh M /trunk/dnotes M /trunk/geometry/energy-lib.cc A /trunk/geometry/lbg-graph.cc-m (from /trunk/src/lbg-graph.cc:3144) A /trunk/geometry/lbg-graph.hh-m (from /trunk/src/lbg-graph.hh:3144) A /trunk/lbg/Makefile-dummy (from /trunk/lbg/Makefile:3145) M /trunk/lbg/Makefile.am A /trunk/lbg/flev-annotations.cc A /trunk/lbg/flev-annotations.hh M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc A /trunk/src/flev.hh M /trunk/src/lbg-interface.cc M /trunk/src/main.cc M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info-other.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Updates to lidia, largly interfacing RDKit between flev and lidia. ------------------------------------------------------------------------ r3215 | pemsley | 2010-10-19 01:15:35 +0100 (Tue, 19 Oct 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Update manual, adding a brief note for non-standard nucleic acids. ------------------------------------------------------------------------ r3209 | pemsley | 2010-10-08 12:58:26 +0100 (Fri, 08 Oct 2010) | 4 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/lbg/rdkit-interface.cc M /trunk/lbg/rdkit-interface.hh M /trunk/lbg/use-rdkit.hh M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/lidia-core/lbg-shared.hh M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/junk.cc Add fle_view_using_rdkit() - use RDKit for 2D depiction of ligand (given restraints). Add a function to remove polar hydrogens. Transfer atom name using a "name" property of an rdkit Atom. ------------------------------------------------------------------------ r3208 | pemsley | 2010-10-08 12:51:10 +0100 (Fri, 08 Oct 2010) | 2 lines Changed paths: M /trunk/src/lbg-interface.cc More tinkering to get include files in order. ------------------------------------------------------------------------ r3207 | pemsley | 2010-10-08 12:49:16 +0100 (Fri, 08 Oct 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove debugging output. ------------------------------------------------------------------------ r3205 | pemsley | 2010-10-06 13:19:23 +0100 (Wed, 06 Oct 2010) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3204 | pemsley | 2010-10-06 13:19:00 +0100 (Wed, 06 Oct 2010) | 3 lines Changed paths: M /trunk/src/lbg-interface.cc A tweak to get round compilation problems of RDKit (libitl dcgettext() problems). ------------------------------------------------------------------------ r3203 | pemsley | 2010-10-06 13:17:20 +0100 (Wed, 06 Oct 2010) | 3 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/scheme/libcheck.scm Add a menu item to turn on backrub rotamers. Simple reformated in libcheck interface. ------------------------------------------------------------------------ r3202 | pemsley | 2010-10-06 13:15:08 +0100 (Wed, 06 Oct 2010) | 2 lines Changed paths: M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/rdkit-interface.cc Improve the residue->RDKit mol converter. ------------------------------------------------------------------------ r3201 | pemsley | 2010-10-06 13:13:16 +0100 (Wed, 06 Oct 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Clearer documentation for backrub rotamers. ------------------------------------------------------------------------ r3197 | pemsley | 2010-09-30 13:12:49 +0100 (Thu, 30 Sep 2010) | 2 lines Changed paths: M /trunk/lbg/rdkit-interface.cc Use renamed include file: rdkit-interface.hh ------------------------------------------------------------------------ r3196 | pemsley | 2010-09-30 12:14:16 +0100 (Thu, 30 Sep 2010) | 2 lines Changed paths: M /trunk/dnotes Add some valgrind output to think about. ------------------------------------------------------------------------ r3195 | pemsley | 2010-09-30 12:13:31 +0100 (Thu, 30 Sep 2010) | 2 lines Changed paths: M /trunk/lbg/Makefile.am Add in needed include dirs. ------------------------------------------------------------------------ r3194 | pemsley | 2010-09-30 12:13:07 +0100 (Thu, 30 Sep 2010) | 2 lines Changed paths: M /trunk/geometry/protein-geometry-mmdb.cc Apply CC fix-up (from release branch). ------------------------------------------------------------------------ r3191 | pemsley | 2010-09-23 23:39:58 +0100 (Thu, 23 Sep 2010) | 13 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lidia-main.cc M /trunk/macros/goo-canvas.m4 M /trunk/python/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface.h M /trunk/src/graphics-info.h M /trunk/src/restraints-editor.cc Remove coot-python-functions.texi from the Makefile - I don't see how they are generated. use libtool in macros/goo-canvas.m4 to test linking - this may need to be revisited. Better document refine_residues_scm(). Add "mrc" as a valid map format. Fix up cif reading of _chem_comp info with no loop. Fix autobuild script to test for patch of gtkglext being applied properly. Return refinement results even on a GSL_ENOPROG. Pass stand_alone flag to lbg() so that the close button can act differently vs built-in. Add openmp flag to link line for coot-real. ------------------------------------------------------------------------ r3189 | pemsley | 2010-09-22 11:20:23 +0100 (Wed, 22 Sep 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Update to use lmb.bioch instead of www.biop. ------------------------------------------------------------------------ r3188 | pemsley | 2010-09-21 17:51:34 +0100 (Tue, 21 Sep 2010) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Add match-ligand-torsions (and an extra refinement) to mutate-by-overlap. (Fixed as in release-0.6.2). ------------------------------------------------------------------------ r3185 | pemsley | 2010-09-21 12:58:57 +0100 (Tue, 21 Sep 2010) | 5 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/user-define-restraints.scm Remove match ligand torsion from the processing of the output of prodrg (there is a problem with chirality or some such). Add refmac style output of user-defined restraints. Show default file-name text in generic-chooser-and-file-selector. ------------------------------------------------------------------------ r3182 | pemsley | 2010-09-18 16:52:52 +0100 (Sat, 18 Sep 2010) | 5 lines Changed paths: M /trunk M /trunk/build-it-gtk2-simple M /trunk/python/coot_utils.py M /trunk/python/what_check.py M /trunk/src/c-interface-gui.cc M /trunk/windows/wincoot-autobuild-all Merge in changes from release-0.6.2 branch: mmdb version update. Windows-build fixups. vu-file reading in Python. ------------------------------------------------------------------------ r3181 | pemsley | 2010-09-18 16:49:01 +0100 (Sat, 18 Sep 2010) | 2 lines Changed paths: M /trunk D /trunk/lbg/Makefile A /trunk/lbg/Makefile.simple (from /trunk/lbg/Makefile:3180) Trivial changes, book-keeping. ------------------------------------------------------------------------ r3180 | pemsley | 2010-09-18 16:07:58 +0100 (Sat, 18 Sep 2010) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/lbg/lbg.cc M /trunk/src/lbg-interface.cc M /trunk/src/lbg-interface.hh Improve bond representation for deloc bonds (for an atom that has 2 deloc bonds). Addd smiles_to_ligand_builder(). ------------------------------------------------------------------------ r3179 | pemsley | 2010-09-17 14:58:59 +0100 (Fri, 17 Sep 2010) | 2 lines Changed paths: M /trunk/src/main.cc Fixup dependency include. ------------------------------------------------------------------------ r3178 | pemsley | 2010-09-17 14:16:25 +0100 (Fri, 17 Sep 2010) | 6 lines Changed paths: M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/mmdb.h M /trunk/lbg/Makefile.am D /trunk/lbg/enterprise.cc D /trunk/lbg/enterprise.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh A /trunk/lbg/rdkit-interface.cc (from /trunk/lbg/enterprise.cc:3176) A /trunk/lbg/rdkit-interface.hh (from /trunk/lbg/enterprise.hh:3176) A /trunk/lbg/use-rdkit.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/lidia-core/lbg-molfile.cc M /trunk/lidia-core/lbg-molfile.hh M /trunk/macros/goo-canvas.m4 M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/coot.i A /trunk/src/lbg-interface.cc A /trunk/src/lbg-interface.hh A /trunk/src/rdkit-interface.hh Improve bonding of het residues (rules for SE, S and P fixed up). Show delocalised bonds. SWIG flags take enterprise args now. Add conversion between residue ligand and rdkit molecule. Add residue_to_ligand_builder() function. ------------------------------------------------------------------------ r3174 | pemsley | 2010-09-12 21:40:08 +0100 (Sun, 12 Sep 2010) | 2 lines Changed paths: A /trunk/lbg/enterprise.cc Add forgotten file for mol and SMILES manipulation. ------------------------------------------------------------------------ r3173 | pemsley | 2010-09-12 21:28:40 +0100 (Sun, 12 Sep 2010) | 2 lines Changed paths: M /trunk/lbg/Makefile.am A /trunk/lbg/enterprise.hh M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/src/Makefile.am M /trunk/src/main.cc Add statusbar text that is the current SMILES string. ------------------------------------------------------------------------ r3172 | pemsley | 2010-09-12 21:26:57 +0100 (Sun, 12 Sep 2010) | 2 lines Changed paths: M /trunk/configure.in Add AC_SUBST for flags for RDKit. ------------------------------------------------------------------------ r3171 | pemsley | 2010-09-12 21:26:23 +0100 (Sun, 12 Sep 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Remove debugging. ------------------------------------------------------------------------ r3170 | pemsley | 2010-09-12 21:25:44 +0100 (Sun, 12 Sep 2010) | 2 lines Changed paths: M /trunk/macros/goo-canvas.m4 M /trunk/macros/libglade.m4 Fix up typos for saving and restoring CXXFLAGS and CFLAGS. ------------------------------------------------------------------------ r3169 | pemsley | 2010-09-11 21:00:17 +0100 (Sat, 11 Sep 2010) | 2 lines Changed paths: A /trunk/macros/goo-canvas.m4 Add goo-canvas macros. ------------------------------------------------------------------------ r3168 | pemsley | 2010-09-11 12:05:21 +0100 (Sat, 11 Sep 2010) | 2 lines Changed paths: A /trunk/lbg/Makefile.am A /trunk/lbg/lidia-main.cc Add extra files for lidia merge. ------------------------------------------------------------------------ r3167 | pemsley | 2010-09-11 12:04:11 +0100 (Sat, 11 Sep 2010) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/scheme/coot-gui.scm M /trunk/src/Makefile.am M /trunk/src/c-interface.h M /trunk/src/junk.cc M /trunk/src/main.cc Add lidia to the main executable. ------------------------------------------------------------------------ r3165 | pemsley | 2010-09-08 17:03:14 +0100 (Wed, 08 Sep 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust mmdb and guile-gui patches. ------------------------------------------------------------------------ r3164 | pemsley | 2010-09-08 12:52:29 +0100 (Wed, 08 Sep 2010) | 2 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-refine.cc Apply 3162:3163, fixing add_extra_bond_restraint() bug. ------------------------------------------------------------------------ r3161 | pemsley | 2010-09-08 06:46:31 +0100 (Wed, 08 Sep 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Update docs strings for snarfing. ------------------------------------------------------------------------ r3160 | pemsley | 2010-09-07 13:32:47 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple swig version 1.3.29 seems broken too - exit if found. ------------------------------------------------------------------------ r3159 | pemsley | 2010-09-07 11:35:10 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk M /trunk/build-it-gtk2-simple M /trunk/coords/Bond_lines.cc M /trunk/src/c-interface-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Apply release-0.6.2 merge 3147:3152. ------------------------------------------------------------------------ r3158 | pemsley | 2010-09-07 11:21:48 +0100 (Tue, 07 Sep 2010) | 5 lines Changed paths: M /trunk M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gl-matrix.cc M /trunk/src/gl-matrix.h M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc Add a constructor for a GL_matrix given a normal. Updates for state script writing (python too). After a dictionary library is read, rebond molecules. In build script, override STD_PKGCONFIG_DIR to lib64 dir if we are in 64 bit. ------------------------------------------------------------------------ r3157 | pemsley | 2010-09-07 11:14:54 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp Rework for debugging (not really needed, bad centre passed). ------------------------------------------------------------------------ r3156 | pemsley | 2010-09-07 11:14:02 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Clear up debugging in bonding. ------------------------------------------------------------------------ r3155 | pemsley | 2010-09-07 11:13:26 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: A /trunk/doc/validation-tutorial.tex Add validation tutorial. ------------------------------------------------------------------------ r3154 | pemsley | 2010-09-07 11:13:00 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex Update tutorial docs (for summer school). ------------------------------------------------------------------------ r3153 | pemsley | 2010-09-07 11:07:51 +0100 (Tue, 07 Sep 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc TREF is a shelx keyword. ------------------------------------------------------------------------ r3145 | pemsley | 2010-08-31 23:41:04 +0100 (Tue, 31 Aug 2010) | 8 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/Cartesian.h M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/geometry/Makefile.am A /trunk/geometry/lbg-graph.cc (from /trunk/src/lbg-graph.cc:3143) A /trunk/geometry/lbg-graph.hh (from /trunk/src/lbg-graph.hh:3143) M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/scheme/extensions.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/flev.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/junk.cc D /trunk/src/lbg-graph.cc D /trunk/src/lbg-graph.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Improvements to dictionary bonding and solid modelling for dictionary bonding. add_double_bond(), get_neighb_normal(), add_bonds_het_residues(), het_residue_aromatic_rings(), add_aromatic_ring_bond_lines(). functions added. protein_geometry pointer passed down in molecule_class_info additional-representatation functions. map segmentation reworked to add a different segmentation algorithm. ------------------------------------------------------------------------ r3144 | pemsley | 2010-08-28 08:34:00 +0100 (Sat, 28 Aug 2010) | 2 lines Changed paths: M /trunk M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-burn-point.sh M /trunk/burn-up/process-rel-todo.awk M /trunk/dnotes-2008 M /trunk/macros/guile-lib-guile-gui.m4 M /trunk/mini-mol/atom-quads.hh M /trunk/rel-todo-0.6 M /trunk/src/seq-view-interface.c M /trunk/src/seq-view-interface.h M /trunk/src/sequence-view.cc M /trunk/src/sequence-view.hh M /trunk/utils/atomic-numbers.cc M /trunk/utils/coot-fasta.cc M /trunk/utils/coot-fasta.hh M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh M /trunk/utils/gdk-keysym.awk M /trunk/utils/gdk-keysyms.cc Apply property changes to trunk. ------------------------------------------------------------------------ r3141 | pemsley | 2010-08-28 08:10:09 +0100 (Sat, 28 Aug 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Make save_state() save a python script too. ------------------------------------------------------------------------ r3139 | pemsley | 2010-08-26 13:31:05 +0100 (Thu, 26 Aug 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple swig 1.3.29 may be broken, make a note. Needs updating ------------------------------------------------------------------------ r3138 | pemsley | 2010-08-26 13:29:03 +0100 (Thu, 26 Aug 2010) | 2 lines Changed paths: M /trunk/TODO update notes. ------------------------------------------------------------------------ r3137 | pemsley | 2010-08-26 13:26:57 +0100 (Thu, 26 Aug 2010) | 2 lines Changed paths: M /trunk/lbg/lbg.cc Don't draw the substitution contour when there are no bash distances. ------------------------------------------------------------------------ r3136 | b.lohkamp | 2010-08-25 16:22:49 +0100 (Wed, 25 Aug 2010) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc check for underscore in python main menubar names exit() in gtk2 and gtk_exit() in gtk1 disable threading in Windows clipper (for now) ------------------------------------------------------------------------ r3135 | pemsley | 2010-08-24 14:47:15 +0100 (Tue, 24 Aug 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/ideal/simple-restraint.cc M /trunk/lbg/Makefile M /trunk/rel-todo M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-surface.cc Pass a flag to the surface creation routine for the assigning of charges. Change to RMS Z values for the stats - update the traffic light color maping. ------------------------------------------------------------------------ r3134 | pemsley | 2010-08-20 09:55:26 +0100 (Fri, 20 Aug 2010) | 2 lines Changed paths: M /trunk/TODO Add extra item to consider for sequence view problems. ------------------------------------------------------------------------ r3133 | pemsley | 2010-08-19 17:27:33 +0100 (Thu, 19 Aug 2010) | 3 lines Changed paths: M /trunk/surface/CXXBall.cpp M /trunk/surface/CXXBall.h Try again with the OpenMP pragma work-around. Hopefully fixes up the "no contactmap" intersecting balls problem. ------------------------------------------------------------------------ r3132 | pemsley | 2010-08-18 15:06:55 +0100 (Wed, 18 Aug 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/burn-up/burn-up.tab M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/graphics-info.cc User-defined torsion restraints moderate the flags for minimize(). Remove (char *) casting in simple-restraint.cc. ------------------------------------------------------------------------ r3131 | pemsley | 2010-08-18 15:04:27 +0100 (Wed, 18 Aug 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Rework debugging code for sharpening. ------------------------------------------------------------------------ r3130 | pemsley | 2010-08-18 15:03:20 +0100 (Wed, 18 Aug 2010) | 2 lines Changed paths: M /trunk/autogen.sh Bernie want's libtoolize - OK! ------------------------------------------------------------------------ r3129 | pemsley | 2010-08-18 12:20:40 +0100 (Wed, 18 Aug 2010) | 2 lines Changed paths: M /trunk/configure.in test for libtool ------------------------------------------------------------------------ r3128 | pemsley | 2010-08-18 12:19:59 +0100 (Wed, 18 Aug 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm More conversions from old-style getting to new-style getting of web pages. ------------------------------------------------------------------------ r3127 | pemsley | 2010-08-18 12:18:30 +0100 (Wed, 18 Aug 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Fix (i.e. don't draw) the LINK between symmetry-related molcules. ------------------------------------------------------------------------ r3126 | pemsley | 2010-08-17 20:57:54 +0100 (Tue, 17 Aug 2010) | 2 lines Changed paths: M /trunk/surface/CXXBall.h Add GCC 4.2 to OpenMP pragma reference work-around. ------------------------------------------------------------------------ r3125 | pemsley | 2010-08-17 16:27:45 +0100 (Tue, 17 Aug 2010) | 3 lines Changed paths: M /trunk/surface/CXXBall.cpp M /trunk/surface/CXXBall.h Fixup defines for OpenMP pragma issue on some compilers (currently only GCC 4.1). ------------------------------------------------------------------------ r3124 | pemsley | 2010-08-17 12:08:55 +0100 (Tue, 17 Aug 2010) | 6 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-defines.cc M /trunk/src/testing.cc Add multiscale (scale-space filtering) reworking of the map. Interesting, not happy with it yet. After ligand fitting, if no ligands added, then don't display the post-ligand-fitting-gui. ener_lib.cif now gets read when ccp4 is setup. ------------------------------------------------------------------------ r3123 | pemsley | 2010-08-16 18:37:53 +0100 (Mon, 16 Aug 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up node problem in documentation. ------------------------------------------------------------------------ r3122 | b.lohkamp | 2010-08-15 14:11:02 +0100 (Sun, 15 Aug 2010) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/extensions.py M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/command-line.cc no waters for pythonic clipped surface quick fix for python-getopt conflict in windows fix typo in list_extra_restraints_scm() export screen_vectors_py protect gtk_adjustment_get_value in GTK1 ------------------------------------------------------------------------ r3121 | pemsley | 2010-08-13 17:08:57 +0100 (Fri, 13 Aug 2010) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/globjects.cc Set the line thickness of screen axes in draw_axes(). Now using generic objects does not affect the line thickness of the axes. ------------------------------------------------------------------------ r3120 | pemsley | 2010-08-13 15:15:23 +0100 (Fri, 13 Aug 2010) | 6 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/doc/user-manual.texi M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Export the max_closeness for difference map peaks to the user level. difference_map_peaks() interface changed to accommodate this parameter. Hopefully that won't bite. set_use_only_extra_torsion_restraints_for_torsions() function and static var added. Not activated in the refinement yet. ------------------------------------------------------------------------ r3119 | pemsley | 2010-08-13 10:26:18 +0100 (Fri, 13 Aug 2010) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-h-bonds.cc M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-network.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters-gui.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.cc M /trunk/src/cmtz-interface.cc M /trunk/src/command-line.cc M /trunk/src/coot_pythonmodule.cc M /trunk/src/flev.cc M /trunk/src/geometry-graphs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.cc M /trunk/src/nsv.cc M /trunk/src/pick.cc M /trunk/src/post-process-coot-wrap-guile.sh M /trunk/src/rama_mousey.cc M /trunk/src/rama_plot.cc M /trunk/src/restraints-editor.cc M /trunk/src/sequence-view.cc M /trunk/src/testing.hh M /trunk/src/user-mods.cc Tedious fixups for python includes. Fixups Makefile.am libs definitions of some test programs to resolve get_h_bond_type(). ------------------------------------------------------------------------ r3118 | pemsley | 2010-08-13 09:46:35 +0100 (Fri, 13 Aug 2010) | 3 lines Changed paths: M /trunk/src/c-interface-refine.cc Fix up typo in python code. The first of the header changes to fixup "_POSIX_C_SOURCE" redefined problems. ------------------------------------------------------------------------ r3117 | pemsley | 2010-08-13 03:00:45 +0100 (Fri, 13 Aug 2010) | 2 lines Changed paths: M /trunk/src/c-interface-refine.cc More typos in python list_extra_restraints_py(). ------------------------------------------------------------------------ r3116 | pemsley | 2010-08-13 01:59:29 +0100 (Fri, 13 Aug 2010) | 2 lines Changed paths: M /trunk/src/c-interface-refine.cc Fixup bond/torsion typo in python list for extra restraints. ------------------------------------------------------------------------ r3115 | pemsley | 2010-08-12 16:33:14 +0100 (Thu, 12 Aug 2010) | 3 lines Changed paths: M /trunk/coot-surface/coot-surface.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ideal/simple-restraint.hh M /trunk/python/coot_utils.py M /trunk/rel-todo M /trunk/src/c-interface-kk.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h M /trunk/surface/surface.cpp Add new code for torsion restraints. We can now list torsion restraints. clear_extra_restraints() function added. ------------------------------------------------------------------------ r3114 | pemsley | 2010-08-12 12:47:46 +0100 (Thu, 12 Aug 2010) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/peak-search.cc M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/c-interface.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Remove waters from clipped surface calculation. Add in XMap reading code, but not activated yet (lots of xmap dependencies elsewhere). is_em_map() function added to test the CCP4MAPfile. ------------------------------------------------------------------------ r3113 | pemsley | 2010-08-12 12:39:22 +0100 (Thu, 12 Aug 2010) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix crash when "Use weights" button was clicked but mtz had no weights. ------------------------------------------------------------------------ r3112 | b.lohkamp | 2010-08-12 09:40:22 +0100 (Thu, 12 Aug 2010) | 1 line Changed paths: M /trunk/src/globjects.cc exclude wglext.h for MINGW (doesnt seem to work with older msys) ------------------------------------------------------------------------ r3111 | pemsley | 2010-08-11 19:07:56 +0100 (Wed, 11 Aug 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi M /trunk/doc/user-manual.texi Update FAQ for geometry graph bars. ------------------------------------------------------------------------ r3110 | pemsley | 2010-08-11 14:22:44 +0100 (Wed, 11 Aug 2010) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fixup in cif atom reading - the setting of the index and the setting of the 'found' flag were inconsistent. ------------------------------------------------------------------------ r3109 | b.lohkamp | 2010-08-11 14:13:32 +0100 (Wed, 11 Aug 2010) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/src/c-interface.h update python scripts (Prodrg-ify creates new mol now...) ------------------------------------------------------------------------ r3108 | pemsley | 2010-08-11 13:20:14 +0100 (Wed, 11 Aug 2010) | 2 lines Changed paths: M /trunk/surface/CXXSphereFlatTriangle.h Add a newline. ------------------------------------------------------------------------ r3107 | pemsley | 2010-08-11 11:18:30 +0100 (Wed, 11 Aug 2010) | 6 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/high-res/Makefile.am M /trunk/ideal/extra-restraints.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/Makefile.am M /trunk/ligand/find-ligand.cc M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc Remove 'make check' programs from the Makefile.ams. Fix up find-ligand to use an absolute level for the map density cut-off. Add a flag for user_defined_restraints into basic restraint. Not really used (except add_user_defined_torsion_restraint() which sets the flag). Some debugging (switched off) in geometry cif reading. ------------------------------------------------------------------------ r3106 | pemsley | 2010-08-11 10:40:21 +0100 (Wed, 11 Aug 2010) | 4 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/generic-objects.scm Prodrg-ify now creates a new molecule, using the prodrg coordinates file, rather than replacing the residue in the current one (so that hydrogens can be "transfered"). ------------------------------------------------------------------------ r3105 | pemsley | 2010-08-10 11:20:10 +0100 (Tue, 10 Aug 2010) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/user-mods.cc HOH is no longer a non-standard residue (at the interface level). Rework the probe function so that the ligand/het-group connectivity is written to a file that is read with with the -DB argument to reduce. ------------------------------------------------------------------------ r3104 | b.lohkamp | 2010-08-10 08:55:19 +0100 (Tue, 10 Aug 2010) | 1 line Changed paths: M /trunk/surface/Makefile.am include missing CXXAlloc.h ------------------------------------------------------------------------ r3103 | pemsley | 2010-08-09 15:53:41 +0100 (Mon, 09 Aug 2010) | 10 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ideal/extra-restraints.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-superpose.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h Fill out the code for the addition of user-defined torsion restraints. Needs testing. Implememt transparent_draw() of coot surface. It uses screendoor stippling to represent the transparency. It is very slow though. Added set_transparent_electrostatic_surface() to allow user access to transparent molecular/electrostatic surfaces. change_model_representation_mode() added - bound to scroll wheel when Ctrl and Shift are used. "Copy of " replaced by "Copy_of_". ------------------------------------------------------------------------ r3102 | b.lohkamp | 2010-08-08 17:56:12 +0100 (Sun, 08 Aug 2010) | 1 line Changed paths: M /trunk/src/coot.in fix MINGW recognition in coot script ------------------------------------------------------------------------ r3101 | b.lohkamp | 2010-08-08 17:16:16 +0100 (Sun, 08 Aug 2010) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/compat/coot-sysdep.h M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/prodrg_import.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.in M /trunk/src/globjects.cc enable simple Control bound user defined python keys (use "Control_X") rework pythonic prodrg_import to not use using_active_atom update python surface extensions (and put surface in scheme representation menu) clipped surface for python fix some newer openGL functions for windows some windows fixes (enable all MINGW shells in coot script, undef far and near) ------------------------------------------------------------------------ r3100 | pemsley | 2010-08-07 13:49:45 +0100 (Sat, 07 Aug 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Adjust doc strings so that they get snarfed. ------------------------------------------------------------------------ r3099 | pemsley | 2010-08-07 13:34:50 +0100 (Sat, 07 Aug 2010) | 3 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Enough of dummy values for new function in doc snarfing. Copy necessary functions into snarf-coot-docs.scm directly. ------------------------------------------------------------------------ r3098 | pemsley | 2010-08-07 13:29:19 +0100 (Sat, 07 Aug 2010) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add snarf workaround. ------------------------------------------------------------------------ r3097 | pemsley | 2010-08-07 13:28:37 +0100 (Sat, 07 Aug 2010) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix typo in snarf workaround. ------------------------------------------------------------------------ r3096 | pemsley | 2010-08-07 13:27:42 +0100 (Sat, 07 Aug 2010) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix typo in snarf workaround. ------------------------------------------------------------------------ r3095 | pemsley | 2010-08-07 12:19:41 +0100 (Sat, 07 Aug 2010) | 2 lines Changed paths: M /trunk/Makefile.am Reorder the directories (lidia-core before coords). ------------------------------------------------------------------------ r3094 | pemsley | 2010-08-07 12:13:38 +0100 (Sat, 07 Aug 2010) | 4 lines Changed paths: M /trunk/coords/Makefile.am M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/high-res/Makefile.am M /trunk/ideal/Makefile.am M /trunk/lbg/Makefile D /trunk/lbg/lbg-molfile.cc D /trunk/lbg/lbg-molfile.hh D /trunk/lbg/lig-build.cc D /trunk/lbg/lig-build.hh M /trunk/lidia-core/Makefile.am A /trunk/lidia-core/lbg-molfile.cc (from /trunk/lbg/lbg-molfile.cc:3093) A /trunk/lidia-core/lbg-molfile.hh (from /trunk/lbg/lbg-molfile.hh:3093) A /trunk/lidia-core/lig-build.cc (from /trunk/lbg/lig-build.cc:3093) A /trunk/lidia-core/lig-build.hh (from /trunk/lbg/lig-build.hh:3093) M /trunk/ligand/Makefile.am M /trunk/src/Makefile.am M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Rework so that lig-build and lbg-molfile are part of lidia core. get_atom_selection() now tests extension for an MDL mol file and uses reader in lidia-core if so. ------------------------------------------------------------------------ r3093 | pemsley | 2010-08-06 14:53:59 +0100 (Fri, 06 Aug 2010) | 8 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h Fix up for Rotate/Translate a ligand in CA+Ligand mode. Fix unset active item for molecule in move molecule here dialog when using big molecules. Set atom charges for electrostatic surface using CXXUtils::assignCharge(). Add New extension representations for full and clipped surface around active residue. Add dummy function for transparent draw of surface. ------------------------------------------------------------------------ r3092 | pemsley | 2010-08-06 10:58:43 +0100 (Fri, 06 Aug 2010) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix misordered orth to frac conversion in new_molecule_by_symop(). ------------------------------------------------------------------------ r3091 | pemsley | 2010-08-06 00:59:25 +0100 (Fri, 06 Aug 2010) | 7 lines Changed paths: M /trunk/coot-surface/coot-surface.cc M /trunk/density-contour/CIsoSurface.cpp M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXUtils.cpp M /trunk/surface/ElectroSurface.cpp M /trunk/surface/Makefile.am Push the colour scale to the user level (set with set_electrostatic_surface_charge_range()). surface::fill_from() calls assignCharge() now. CXXUtils.cpp and CXXUtils.h properly addded to the Makefile.am Fixup normals for the negative contour level (there are (of course) artifacts in drawing 2 transparent surfaces because they are sorted independently). ------------------------------------------------------------------------ r3090 | pemsley | 2010-08-05 20:57:41 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: M /trunk/auxil/strand-analysis/strand-analysis.cc M /trunk/high-res/globularize.cc M /trunk/high-res/testseqassignment.cc M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-ligand.cc M /trunk/src/molecule-class-info-maps.cc Make make check pass. ------------------------------------------------------------------------ r3089 | pemsley | 2010-08-05 20:57:20 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXSpace.cpp Fixes for picky compiler. User logical operators not bit operators. ------------------------------------------------------------------------ r3088 | pemsley | 2010-08-05 20:09:15 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: A /trunk/surface/CXXAlloc.h A /trunk/surface/CXXBall.cpp A /trunk/surface/CXXBall.h A /trunk/surface/DummyMginterrupt.cpp A /trunk/surface/mginterrupt.h Add missing surface files. ------------------------------------------------------------------------ r3087 | pemsley | 2010-08-05 19:58:12 +0100 (Thu, 05 Aug 2010) | 10 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/configure.in M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h M /trunk/surface/CXXChargeTable.cpp M /trunk/surface/CXXChargeTable.h M /trunk/surface/CXXCircle.cpp M /trunk/surface/CXXCircle.h M /trunk/surface/CXXCircleNode.cpp M /trunk/surface/CXXCircleNode.h M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCoord.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/CXXException.cpp M /trunk/surface/CXXException.h M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXFFTSolventMap.h M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h M /trunk/surface/CXXMatrix4x4.h M /trunk/surface/CXXNewHood.cpp M /trunk/surface/CXXNewHood.h M /trunk/surface/CXXPointyBit.h M /trunk/surface/CXXQADSurface.cpp M /trunk/surface/CXXQADSurface.h M /trunk/surface/CXXQADSurfaceStaticData.cpp M /trunk/surface/CXXSpace.cpp M /trunk/surface/CXXSpace.h M /trunk/surface/CXXSphereElement.cpp M /trunk/surface/CXXSphereElement.h M /trunk/surface/CXXSphereFlatTriangle.h M /trunk/surface/CXXSphereNode.cpp M /trunk/surface/CXXSphereNode.h M /trunk/surface/CXXSphereTriangle.cpp M /trunk/surface/CXXSphereTriangle.h M /trunk/surface/CXXSphereTriangleEdge.cpp M /trunk/surface/CXXSphereTriangleEdge.h M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXSurfaceVertex.cpp M /trunk/surface/CXXSurfaceVertex.h M /trunk/surface/CXXTorusElement.cpp M /trunk/surface/CXXTorusElement.h M /trunk/surface/CXXTorusNode.cpp M /trunk/surface/CXXTorusNode.h M /trunk/surface/CXXTriangle.cpp M /trunk/surface/CXXTriangle.h M /trunk/surface/CXXUtils.cpp M /trunk/surface/CXXUtils.h M /trunk/surface/ElectroSurface.cpp M /trunk/surface/Makefile.am M /trunk/surface/TokenIterator.h M /trunk/surface/surface.cpp Update to Martin's new surface code. This uses 2 atom selections, one for the atoms for the electrostatics and the other for the surface fragment to display - this is not implemented fully yet. Introduce col_scale argument, so that the colour gradient on the electrostatic surface can be set by the user (partially implemented). Configure check or openmp. Partially implement surfaces for difference map (currently the triangles are not sorted). New burn up graph (after 2 months delay). ------------------------------------------------------------------------ r3086 | pemsley | 2010-08-05 12:13:41 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3085 | pemsley | 2010-08-05 12:13:07 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: M /trunk/ligand/find-ligand.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh Add absolute level for findligand. Need testing. ------------------------------------------------------------------------ r3084 | pemsley | 2010-08-05 12:10:53 +0100 (Thu, 05 Aug 2010) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info.cc Respect thin lines flag when displaying bonds, now that we use GL_QUADs. 50 segments at maximum in map segmentation. ------------------------------------------------------------------------ r3083 | pemsley | 2010-08-05 12:08:36 +0100 (Thu, 05 Aug 2010) | 3 lines Changed paths: M /trunk/src/globjects.cc On ctrl-right-mouse, do *either* z-trans or clipping, not both. Widen the clipping width max to 15 (from 10). ------------------------------------------------------------------------ r3082 | pemsley | 2010-08-05 12:01:53 +0100 (Thu, 05 Aug 2010) | 2 lines Changed paths: M /trunk/coords/mmdb-extras.cc Correctly resize the atom_radii vector. ------------------------------------------------------------------------ r3081 | pemsley | 2010-08-04 15:24:34 +0100 (Wed, 04 Aug 2010) | 15 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/lbg/Makefile M /trunk/lbg/lbg.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Add add_ligand_delete_residue_copy_molecule() function. Add segment_map function - simple version - no iterative map smoothing and segment merging. On reading an EM map, try to fill an nxmap version of it - needs more work. Add test_map_segmentation() test function. Tweek the parameters for material in setup_density_surface_material(). Move molecule_class_info::quick_save() to its proper place. Add some test code for trying out various parameters for fogging when not using (the standard) esoteric depth cueing. Add get_contour_level() function to molecule class. Reverse the order of cut-glass and transparent in the map properties dialog. Improve the look of the check/delete waters gui by reboxing the difference map option menu. Comment out use of coot-sysdep.h in lbg.hh - don't see (yet) why it is needed. ------------------------------------------------------------------------ r3080 | pemsley | 2010-08-04 15:11:57 +0100 (Wed, 04 Aug 2010) | 2 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/CIsoSurface.h A bit of code to implement contouring of NXmaps. Not useful yet. ------------------------------------------------------------------------ r3079 | pemsley | 2010-08-04 15:11:08 +0100 (Wed, 04 Aug 2010) | 2 lines Changed paths: M /trunk/ligand/find-ligand.cc findligand now takes a position argument (needs testing). ------------------------------------------------------------------------ r3078 | pemsley | 2010-08-04 15:10:15 +0100 (Wed, 04 Aug 2010) | 3 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/scheme/prodrg-import.scm Add an auto-save timeout. prodrg-import now uses add-ligand-delete-residue-copy-molecule. ------------------------------------------------------------------------ r3077 | pemsley | 2010-08-04 15:07:27 +0100 (Wed, 04 Aug 2010) | 3 lines Changed paths: M /trunk/Makefile.am A /trunk/fix-cif-loops.awk Add an awk script to fix up broken cif files (empty loops) (written by other programs). ------------------------------------------------------------------------ r3076 | pemsley | 2010-08-03 10:57:54 +0100 (Tue, 03 Aug 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh A start at map segmentation. Not called yet. ------------------------------------------------------------------------ r3075 | pemsley | 2010-08-03 01:12:22 +0100 (Tue, 03 Aug 2010) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Use the correct path to get to ener_lib.cif in the monomers directory. ------------------------------------------------------------------------ r3074 | pemsley | 2010-08-02 17:07:50 +0100 (Mon, 02 Aug 2010) | 3 lines Changed paths: M /trunk/src/c-interface-validate.cc Gtk1 version does not have check_waters_by_difference_map_active_checkbutton - so don't try to use it the lookup returns null. ------------------------------------------------------------------------ r3073 | pemsley | 2010-08-02 15:09:49 +0100 (Mon, 02 Aug 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Don't draw environment distances to atoms with non-blank different alt-locs. ------------------------------------------------------------------------ r3072 | pemsley | 2010-07-31 18:28:48 +0100 (Sat, 31 Jul 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-tree-extras.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r3071 | pemsley | 2010-07-31 18:27:57 +0100 (Sat, 31 Jul 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Make the build page builder work with guile-www. ------------------------------------------------------------------------ r3070 | pemsley | 2010-07-30 15:22:53 +0100 (Fri, 30 Jul 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/lbg/notes M /trunk/rel-todo Update notes - from ACA Chicago. ------------------------------------------------------------------------ r3069 | pemsley | 2010-07-30 14:21:46 +0100 (Fri, 30 Jul 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fixup map draw flags so that it works (by default) like it used to. ------------------------------------------------------------------------ r3068 | pemsley | 2010-07-29 23:19:39 +0100 (Thu, 29 Jul 2010) | 3 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c fill_single_map_properties_dialog() now sets radio buttons for slider and display style correctly. ------------------------------------------------------------------------ r3067 | b.lohkamp | 2010-07-29 22:04:02 +0100 (Thu, 29 Jul 2010) | 1 line Changed paths: M /trunk/build-it-win build alias for windows autobuild ------------------------------------------------------------------------ r3066 | pemsley | 2010-07-29 16:24:53 +0100 (Thu, 29 Jul 2010) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a gui (a frame in single_map_properties dialog) for transparent, cut-glass and standard lines. Activate representation on these button presses. Add a transparency slider too. The frame needs to be filled on show (in the fill_single_map_properties_dialog function). ------------------------------------------------------------------------ r3065 | pemsley | 2010-07-28 20:38:56 +0100 (Wed, 28 Jul 2010) | 2 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/src/molecule-class-info-maps.cc Fix up a couple of warnings - more picky compiler options. ------------------------------------------------------------------------ r3064 | pemsley | 2010-07-27 15:40:18 +0100 (Tue, 27 Jul 2010) | 4 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h setup_density_surface_material now takes the opacity as an argument, colour materials are enabled using the opacity. Reorder drawing of objects, transparent objects drawn later. ------------------------------------------------------------------------ r3063 | pemsley | 2010-07-26 16:13:44 +0100 (Mon, 26 Jul 2010) | 2 lines Changed paths: A /trunk/ideal/extra-restraints.cc Add missing extra-restraints.cc ------------------------------------------------------------------------ r3062 | pemsley | 2010-07-26 15:38:18 +0100 (Mon, 26 Jul 2010) | 15 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-extras.cc M /trunk/dnotes M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/rel-todo M /trunk/scheme/fitting.scm M /trunk/scheme/prodrg-import.scm M /trunk/scheme/user-define-restraints.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h A /trunk/src/density-score-by-residue-src.cc (from /trunk/src/density-score-by-residue.cc:3060) D /trunk/src/density-score-by-residue.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.h Changes from GRC Lewiston and ACA Chicago. Add paladium, lead and silver to atoms with long bonds - that whole bonding section needs rethinking. density-score-by-residue.cc renamed to density-score-by-residue-src.cc to get past build strangeness on make density-score-by-residue maps lighting works with LIGHT2 now - better, but still not completely dark in ambiently lit regions. wrapping for add_extra_torsion_restraint() added, but the actuall addition in simple-restraint.cc still needs work. Fix up safe_python_command() usage in the prodrugification of a monomer. Don't draw the substitution contour if there are no atoms. Additions to the subsitution contour work. add-extra-restraints-to-other-molecule template added, not working yet (needs extra restraint type: distance to point. ------------------------------------------------------------------------ r3061 | pemsley | 2010-07-26 15:17:15 +0100 (Mon, 26 Jul 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Make the use of the first keyword in SHELX input case insensitive. ------------------------------------------------------------------------ r3060 | b.lohkamp | 2010-07-25 16:58:40 +0100 (Sun, 25 Jul 2010) | 1 line Changed paths: A /trunk/python/prodrg_import.py add pythonic prodrg_import (still work to do) ------------------------------------------------------------------------ r3059 | b.lohkamp | 2010-07-25 16:57:53 +0100 (Sun, 25 Jul 2010) | 5 lines Changed paths: M /trunk/compat/coot-sysdep.h M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc fix 'small' variable issue for windows in lbg enable match_ligand_torsions for python set prefer_python for windows ------------------------------------------------------------------------ r3058 | pemsley | 2010-07-21 02:21:19 +0100 (Wed, 21 Jul 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Add immediate backup clearup hint. ------------------------------------------------------------------------ r3057 | pemsley | 2010-07-21 02:05:07 +0100 (Wed, 21 Jul 2010) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Try to write gdb strings to the screen in --no-graphics mode. ------------------------------------------------------------------------ r3056 | pemsley | 2010-07-21 01:52:06 +0100 (Wed, 21 Jul 2010) | 3 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm M /trunk/src/coot.in coot-crash-catcher knows about --no-graphics, and if so, doesn't run the gui. ------------------------------------------------------------------------ r3055 | pemsley | 2010-07-20 13:02:02 +0100 (Tue, 20 Jul 2010) | 7 lines Changed paths: M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand.cc M /trunk/src/align.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/density-score-by-residue.cc M /trunk/src/fix-nomenclature.cc M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc get_atom_selection() and handle_read_draw_molecule() now take an extra argument, a flag for resetting the residue and atom names of nucleotides to match the (current) dictionary. Add a scripting function to set this flag. Add a scripting function to set flat (vs smooth) shading for the solid density surface. ------------------------------------------------------------------------ r3054 | pemsley | 2010-07-19 13:51:06 +0100 (Mon, 19 Jul 2010) | 4 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/Makefile.am A /trunk/density-contour/density-contour-triangles.cc M /trunk/density-contour/density-contour-triangles.hh M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc Reorganise density contour triangle code. Add a container for the vertex normals. Use calculate_normals() to fill them (Gouraund shading). ------------------------------------------------------------------------ r3053 | pemsley | 2010-07-18 22:15:26 +0100 (Sun, 18 Jul 2010) | 3 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/density-contour-triangles.hh M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Enable flat shading for transparent density. Still a bug with interaction with ball&stick objects. ------------------------------------------------------------------------ r3052 | b.lohkamp | 2010-07-18 18:59:11 +0100 (Sun, 18 Jul 2010) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/fitting.py A /trunk/python/user_defined_restraints.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/07_ncs.py M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h don't do backups in stepped/rama/rotamer python fitting functions add pythonic user_defined_restraints add python tests for strange HAT file fix NCS map names in python tests add pythonic versions of list_extra_restraints and delete_extra_restraint ------------------------------------------------------------------------ r3051 | b.lohkamp | 2010-07-18 18:32:11 +0100 (Sun, 18 Jul 2010) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/graphics-info-navigation.cc fix gtk1 tree navigation fix add_extra_restraints to work(?) without residues_vec ------------------------------------------------------------------------ r3050 | pemsley | 2010-07-18 09:58:42 +0100 (Sun, 18 Jul 2010) | 4 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/density-contour-triangles.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h If solid density is transparent, then depth sort the triangles before drawing them. Add functions to turn on/off drawing of solid surface and set its opacity. ------------------------------------------------------------------------ r3049 | pemsley | 2010-07-16 23:56:11 +0100 (Fri, 16 Jul 2010) | 2 lines Changed paths: A /trunk/density-contour/density-contour-triangles.hh Add forgotten header. ------------------------------------------------------------------------ r3048 | pemsley | 2010-07-16 23:36:13 +0100 (Fri, 16 Jul 2010) | 4 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/CIsoSurface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Get map triangles and use them to display transparent triangles for the density. Triangles will need to be depth sorted for sensible rendering - later. ------------------------------------------------------------------------ r3047 | pemsley | 2010-07-16 19:42:21 +0100 (Fri, 16 Jul 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Oops fill_fobs_sigfobs() should fill original_fobs_sigfobs - crash fixed. ------------------------------------------------------------------------ r3046 | pemsley | 2010-07-16 19:26:41 +0100 (Fri, 16 Jul 2010) | 3 lines Changed paths: M /trunk/src/graphics-info-gui.cc M /trunk/src/molecule-class-info-maps.cc Some addition to sharpening scaling. Now use get_data() given an HKL on the original F and sigFs, but it crashes - not sure why. ------------------------------------------------------------------------ r3045 | pemsley | 2010-07-15 17:28:21 +0100 (Thu, 15 Jul 2010) | 3 lines Changed paths: M /trunk/scheme/user-define-restraints.scm For user-defined bonds, allow the user to specify the bond length (use generic-single-entry). ------------------------------------------------------------------------ r3044 | pemsley | 2010-07-15 15:19:12 +0100 (Thu, 15 Jul 2010) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Adjust sharpening interface to allow for a gompertz function depending on F/sigF - needs further work. ------------------------------------------------------------------------ r3043 | pemsley | 2010-07-15 12:12:14 +0100 (Thu, 15 Jul 2010) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm A /trunk/scheme/user-define-restraints.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc A /trunk/src/molecule-class-info-refine.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add the ability to add, delete, list and display extra bond restraints (remarkably little code needed to do this). ------------------------------------------------------------------------ r3042 | pemsley | 2010-07-13 18:55:04 +0100 (Tue, 13 Jul 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Add a bit of smoothing for small bash distances. substitution_value() needs more work. ------------------------------------------------------------------------ r3041 | pemsley | 2010-07-13 15:57:27 +0100 (Tue, 13 Jul 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/greg-tests/02-shelx.scm M /trunk/rel-todo Add a test case for crashing on reading strange HAT file. Fix crash. ------------------------------------------------------------------------ r3040 | pemsley | 2010-07-13 14:30:25 +0100 (Tue, 13 Jul 2010) | 2 lines Changed paths: M /trunk/scheme/fitting.scm Don't do backups in stepped/rama/rotamer fitting functions. ------------------------------------------------------------------------ r3039 | pemsley | 2010-07-13 14:11:29 +0100 (Tue, 13 Jul 2010) | 3 lines Changed paths: M /trunk/greg-tests/07-ncs.scm M /trunk/rel-todo M /trunk/src/c-interface-ncs.cc M /trunk/src/graphics-info.cc Fix issue of non-matching NCS map names now that they are tagged with the map number. ------------------------------------------------------------------------ r3038 | pemsley | 2010-07-13 14:10:44 +0100 (Tue, 13 Jul 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Comment out some debugging. Tweak residue solvent exposure difference radius scaling. ------------------------------------------------------------------------ r3037 | pemsley | 2010-07-13 09:29:45 +0100 (Tue, 13 Jul 2010) | 3 lines Changed paths: M /trunk/src/flev.cc Add some bash-related debugging to distances_to_protein(). They change on rerunning FLEV - Hmm.. ------------------------------------------------------------------------ r3036 | pemsley | 2010-07-13 09:27:58 +0100 (Tue, 13 Jul 2010) | 2 lines Changed paths: M /trunk/src/rama_plot.cc Fix problem of finding the next residue for PRE_PRO test in map_mouse_pos(). ------------------------------------------------------------------------ r3035 | pemsley | 2010-07-12 15:42:44 +0100 (Mon, 12 Jul 2010) | 2 lines Changed paths: A /trunk/lidia-core/Makefile.am Add Makefile.am ------------------------------------------------------------------------ r3034 | pemsley | 2010-07-12 13:27:25 +0100 (Mon, 12 Jul 2010) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/lbg/Makefile D /trunk/lbg/lbg-shared.hh A /trunk/lidia-core A /trunk/lidia-core/lbg-shared.hh (from /trunk/lbg/lbg-shared.hh:3033) M /trunk/src/Makefile.am Fix-ups for proper compilation with lbg-shared.hh - now in dependency directory. ------------------------------------------------------------------------ r3033 | pemsley | 2010-07-12 00:42:16 +0100 (Mon, 12 Jul 2010) | 3 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh show_contour() takes a vector of atoms with ring centres. Use ring centre to test for non-plotting of substitution contour. ------------------------------------------------------------------------ r3032 | pemsley | 2010-07-12 00:38:31 +0100 (Mon, 12 Jul 2010) | 3 lines Changed paths: M /trunk/src/flev.cc Restore the sensible cut-off for pi interaction cut-off. Add sampling for rotatable hydrogens for subsitution contour analysis. ------------------------------------------------------------------------ r3031 | b.lohkamp | 2010-07-08 13:31:17 +0100 (Thu, 08 Jul 2010) | 4 lines Changed paths: A /trunk/doc/scripting_tutorial.tex A /trunk/lbg/lbg-shared.hh M /trunk/src/globjects.cc add lbg-shared.hh (as instucted by Paul) add first draft of scripting manual/tutorial change default sigma in water search to 1.8 (as in tooltip) ------------------------------------------------------------------------ r3030 | pemsley | 2010-07-08 07:58:44 +0100 (Thu, 08 Jul 2010) | 2 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh More additions to contour plotting. ------------------------------------------------------------------------ r3029 | pemsley | 2010-07-08 07:57:46 +0100 (Thu, 08 Jul 2010) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.hh Header definitions for flev functions - got lost? ------------------------------------------------------------------------ r3028 | pemsley | 2010-07-07 16:42:15 +0100 (Wed, 07 Jul 2010) | 6 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/junk.cc Add "bash distances" to the solvent ligand accessibilities tmp file. The operator<<() function for bash_distances is copied from here into lbg.cc, it should be removed at some stage. find_bash_distance() and close_atoms() added to flev_attached_hydrogens_t class. ------------------------------------------------------------------------ r3027 | pemsley | 2010-07-07 16:27:56 +0100 (Wed, 07 Jul 2010) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh Update for handingly "bash" distances - distances from ligand atom to the surrounding protein distances - represent distances on the grid and contour - partial implementation. ------------------------------------------------------------------------ r3026 | pemsley | 2010-07-07 16:20:27 +0100 (Wed, 07 Jul 2010) | 2 lines Changed paths: M /trunk/ltmain.sh new ltmain.sh ------------------------------------------------------------------------ r3025 | b.lohkamp | 2010-07-06 11:46:00 +0100 (Tue, 06 Jul 2010) | 1 line Changed paths: M /trunk/src/gtk-manual.cc map name update in display manager ------------------------------------------------------------------------ r3024 | b.lohkamp | 2010-07-05 16:50:36 +0100 (Mon, 05 Jul 2010) | 2 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/src/c-interface-ncs.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h include map number for ncs maps names (we may want to revisit the format) ------------------------------------------------------------------------ r3023 | pemsley | 2010-07-02 11:57:44 +0100 (Fri, 02 Jul 2010) | 5 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h create get_contact_indices_with_reverse_contacts() for use with atom tree when the tree is not present in the cif file. residue_type_next_residue_by_alignment() now additionally takes the gap and space penalty. ------------------------------------------------------------------------ r3022 | pemsley | 2010-06-29 18:40:34 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add brief documentation for geometry graphs. ------------------------------------------------------------------------ r3021 | pemsley | 2010-06-29 18:39:57 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3020 | pemsley | 2010-06-29 18:39:43 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc Fix up crash on 2vtu - only do a geometry analysis on the first model. ------------------------------------------------------------------------ r3019 | pemsley | 2010-06-29 18:38:50 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/src/nsv.cc Change fixed font to Sans 9. ------------------------------------------------------------------------ r3018 | pemsley | 2010-06-29 15:13:29 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Document change chain ids. ------------------------------------------------------------------------ r3017 | pemsley | 2010-06-29 13:41:01 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/graphics-info-gui.cc Fix up renumber residue coordinates option menu. ------------------------------------------------------------------------ r3016 | pemsley | 2010-06-29 13:20:39 +0100 (Tue, 29 Jun 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/src/nsv.cc M /trunk/src/sequence-view.cc Centre the layout of the residue letters in nsv. Use three_letter_to_one_letter_with_specials() for residue letters in nsv. ------------------------------------------------------------------------ r3015 | pemsley | 2010-06-29 13:18:09 +0100 (Tue, 29 Jun 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Update Add Terminal Residue documentation. ------------------------------------------------------------------------ r3014 | pemsley | 2010-06-28 18:29:01 +0100 (Mon, 28 Jun 2010) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r3013 | pemsley | 2010-06-28 13:23:54 +0100 (Mon, 28 Jun 2010) | 10 lines Changed paths: M /trunk/TODO M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.hh M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/utils/coot-utils.cc Introduce the running of 3d prodrg into fle_view, so that the hydrogens can be analysed. Prodrg ligand hydrogen analysis added, torsion specified by named atoms and distance, angle and torsion angle. These will be mapped onto real ligand. Marching squares fragment contouring. Rework the handling of the atom list in the go to atom window (now you can no longer cause coot to crash by clicking on an atom label of an atom in a deleted residue). Fix up problem of unassigned chiral volume restraints being used in refinement. ------------------------------------------------------------------------ r3012 | b.lohkamp | 2010-06-23 16:22:14 +0100 (Wed, 23 Jun 2010) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/python/python_coot_docs.py fix typos in lbg.hh comment out is_hint in lbg.cc (not needed for goocanvas?) more cleanup of python docs ------------------------------------------------------------------------ r3011 | b.lohkamp | 2010-06-21 17:09:44 +0100 (Mon, 21 Jun 2010) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/doc/user-manual.texi M /trunk/python/coot_gui.py M /trunk/python/python_coot_docs.py M /trunk/src/callbacks.c M /trunk/utils/coot-utils.cc update documentation for command line options: small-screen and zalman-stereo change url for online docs sanitise python function documentation absolutise_file_name does not depend on MAXs any more (so for everyone now) ------------------------------------------------------------------------ r3010 | pemsley | 2010-06-18 11:04:41 +0100 (Fri, 18 Jun 2010) | 2 lines Changed paths: M /trunk/utils/coot-utils.cc _fullpath() is a windows thing. ------------------------------------------------------------------------ r3009 | b.lohkamp | 2010-06-18 10:35:24 +0100 (Fri, 18 Jun 2010) | 1 line Changed paths: M /trunk/src/c-interface-build.cc fix typos in fffear_search ------------------------------------------------------------------------ r3008 | pemsley | 2010-06-17 13:27:03 +0100 (Thu, 17 Jun 2010) | 4 lines Changed paths: M /trunk/TODO M /trunk/doc/user-manual.texi M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm Update notes. Document (in main text) user_defined_clicks. Initial work on marching squares. ------------------------------------------------------------------------ r3007 | pemsley | 2010-06-17 13:23:49 +0100 (Thu, 17 Jun 2010) | 8 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/coot-dox.cfg M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.cc Clean up unsectioned functions documentation in c-interface.h Add a stub function exchange_ligands(). Add documentation for user_defined_click(), but it fails on doxygenation. Switch back to gl_lines=1 for now (my desktop machine fails to draw anything with gl_lines=0). Change the default alignment wgap penalty. Better warning feedback from fffear_search(). ------------------------------------------------------------------------ r3006 | b.lohkamp | 2010-06-16 22:47:20 +0100 (Wed, 16 Jun 2010) | 12 lines Changed paths: M /trunk/bldnotes M /trunk/lbg/lig-build.hh M /trunk/lbg/wmolecule.cc M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py A /trunk/python/with_pisa_gui.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh add with_gui_gui module for python rework python using_active_atom to take all sorts of args add python test for 'empty NCS from mmCIF file' add background colours for povray and ccp4mg files/scripts write full path for files in ccp4mg definition file make pythonic get_map_colour_py write atom info in statusbar when label with 'l' add function to absolutify file names change 'small' to 'small_t' in lbg files since they conflict with windows system ------------------------------------------------------------------------ r3005 | b.lohkamp | 2010-06-16 16:02:13 +0100 (Wed, 16 Jun 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc actually show the GL quads ------------------------------------------------------------------------ r3004 | pemsley | 2010-06-16 14:34:30 +0100 (Wed, 16 Jun 2010) | 2 lines Changed paths: A /trunk/doc/texinfo.tex Add texinfo.tex, it's needed to run texi2dvi. ------------------------------------------------------------------------ r3003 | pemsley | 2010-06-16 14:32:19 +0100 (Wed, 16 Jun 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Fix menu problem for function key binding FAQ. ------------------------------------------------------------------------ r3002 | pemsley | 2010-06-15 09:45:01 +0100 (Tue, 15 Jun 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/flev.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add code to use GL quads, not GL lines for bond representation. ------------------------------------------------------------------------ r3001 | pemsley | 2010-06-14 17:08:30 +0100 (Mon, 14 Jun 2010) | 5 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add a function that checks for blueness of the map before making a simple screenshot - I've seen too many coot screenshots in which the map was too dark - the one that broke the camel's back was in today's presentation by Barry Trotter. ------------------------------------------------------------------------ r3000 | pemsley | 2010-06-14 17:04:42 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am Fix up the building of testcootutils ------------------------------------------------------------------------ r2999 | pemsley | 2010-06-14 17:02:40 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/src/pick.cc Quote the atom and element names in pick output. ------------------------------------------------------------------------ r2998 | pemsley | 2010-06-14 17:01:30 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2997 | pemsley | 2010-06-14 17:00:40 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/ltmain.sh update to a more modern ltmain.sh ------------------------------------------------------------------------ r2996 | pemsley | 2010-06-14 16:07:27 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/lbg/notes Add an sbase problem to notes. ------------------------------------------------------------------------ r2995 | pemsley | 2010-06-14 13:52:35 +0100 (Mon, 14 Jun 2010) | 2 lines Changed paths: M /trunk/TODO Add item about mutation. ------------------------------------------------------------------------ r2994 | pemsley | 2010-06-11 13:06:15 +0100 (Fri, 11 Jun 2010) | 26 lines Changed paths: M /trunk/dnotes M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc Turn off add reps objects in the state file if they were not being displayed. Default views play speed set to 10 (was 1). Change to ostream operator for views, rather than ofstream. Does this fix the crash on the Mac when writing views? Create an ostream operator for pi_stacking_instance_t. Add a placeholder for the 3D coordinates from prodrg in fle_view_internal(). Clean up sloppy thinking re: ring systems and pi overlapping (now cations have overlaps). get_ligand_cations() introduced (may need some reworking for other charged atoms). write_fle_centres() now writes out the different types of stacking. Cation stacking represented in lbg (using a "+"). Add a routine to read prodrg hybridisations from the log file - not sure that this is needed. Placeholder for canonball vectors. Some test code in lbg for trying to handle bond rotation and snapping on mouse down and drag. Needs to be reworked to be good. New lbg.glade - with orientations removed and adding a callback on_lbg_smiles_dialog_ok_button_clicked(). orthogonalise_2_bonds() bug fixed. Use graph_2->Build(False) rather than graph_2->Build(True) addressing bond-order related problem, perhaps. In prodrg-import.scm, adjust the order of the chi angle matching and overlaying. Add prodrg-plain, which creates tmp files (using getpid) and runs prodrg in 3D mode (for the generation of hydrogens). Add essay on the substitution contour. ------------------------------------------------------------------------ r2993 | pemsley | 2010-06-11 12:47:15 +0100 (Fri, 11 Jun 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-h-bonds.cc Turn on some debugging, other debugging off. ------------------------------------------------------------------------ r2992 | pemsley | 2010-06-11 12:46:02 +0100 (Fri, 11 Jun 2010) | 3 lines Changed paths: M /trunk/src/rama_plot.cc Add in fix to set residue type - hence (re-)enable dynarama. Add in support for pre-PRO distribution, which will be in clipper one day. ------------------------------------------------------------------------ r2991 | pemsley | 2010-06-11 12:43:53 +0100 (Fri, 11 Jun 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Tidy up comments. ------------------------------------------------------------------------ r2990 | pemsley | 2010-06-11 12:43:21 +0100 (Fri, 11 Jun 2010) | 2 lines Changed paths: M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Add split_string_no_blanks(). ------------------------------------------------------------------------ r2989 | pemsley | 2010-06-11 12:42:45 +0100 (Fri, 11 Jun 2010) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc clean up debugging. ------------------------------------------------------------------------ r2988 | pemsley | 2010-06-09 21:16:32 +0100 (Wed, 09 Jun 2010) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Add documentation for map-molecule-chooser-gui. ------------------------------------------------------------------------ r2987 | pemsley | 2010-06-08 08:23:18 +0100 (Tue, 08 Jun 2010) | 2 lines Changed paths: A /trunk/scheme/with-pisa-gui.scm Add a trivial temporary wrapper for PISA functions. ------------------------------------------------------------------------ r2986 | b.lohkamp | 2010-06-06 19:34:17 +0100 (Sun, 06 Jun 2010) | 2 lines Changed paths: M /trunk/build-it-win M /trunk/python/coot_utils.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h set_torsion for python ------------------------------------------------------------------------ r2985 | pemsley | 2010-06-06 11:53:42 +0100 (Sun, 06 Jun 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for mutate-nucleotide-range. ------------------------------------------------------------------------ r2984 | pemsley | 2010-06-04 09:38:42 +0100 (Fri, 04 Jun 2010) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-tree-extras.cc M /trunk/lbg/Makefile M /trunk/lbg/notes M /trunk/scheme/coot-utils.scm M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Fix set_dihedral() for the case of a reversed index set. Add a function (at scripting level) set_torsion(). Remove some debugging. ------------------------------------------------------------------------ r2983 | pemsley | 2010-06-03 21:20:06 +0100 (Thu, 03 Jun 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc Static cast the null pointer for the vector initialisation. ------------------------------------------------------------------------ r2982 | pemsley | 2010-06-02 18:44:23 +0100 (Wed, 02 Jun 2010) | 10 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.hh M /trunk/lbg/Makefile M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.hh M /trunk/lbg/notes M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/ligand/rotamer.cc M /trunk/mini-mol/atom-quads.hh M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add match_ligand_torsions() function, which does a graph match of the 2 residues and finds the torsions of the reference ligand and maps them onto the moving residue - currently there is a problem of seting the correct dihedral angle on the moving residue. lbg additions mainly to handle snap (bond extensions to atoms) and mouse-based bond-rotation. Still has a problem of when adding an atom to a CH4, the CH4 label remains. Changes to lbg-search, correcting the argument order of generation of the CVertex list. graph->Build() now called with arg False. ------------------------------------------------------------------------ r2981 | pemsley | 2010-06-01 16:35:51 +0100 (Tue, 01 Jun 2010) | 2 lines Changed paths: M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r2980 | pemsley | 2010-06-01 16:35:02 +0100 (Tue, 01 Jun 2010) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test case for reading a PDB mmCIF (should not fail on NCS). ------------------------------------------------------------------------ r2979 | pemsley | 2010-06-01 16:32:07 +0100 (Tue, 01 Jun 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New burn-up points and annotations. ------------------------------------------------------------------------ r2978 | pemsley | 2010-06-01 16:22:18 +0100 (Tue, 01 Jun 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Add entry for NCS chain problem for mmCIFs from PDB. ------------------------------------------------------------------------ r2977 | pemsley | 2010-06-01 16:19:32 +0100 (Tue, 01 Jun 2010) | 3 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc Fix problem of crashing on NCS detection of mmCIF files from the PDB (bogus (empty, which was the lower-level problem) chains, it seems to me). ------------------------------------------------------------------------ r2976 | pemsley | 2010-05-31 17:48:11 +0100 (Mon, 31 May 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES update release notes. ------------------------------------------------------------------------ r2975 | pemsley | 2010-05-31 17:47:47 +0100 (Mon, 31 May 2010) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Move to mmdb version 1.23 ------------------------------------------------------------------------ r2974 | pemsley | 2010-05-31 17:46:43 +0100 (Mon, 31 May 2010) | 2 lines Changed paths: M /trunk/src/c-interface-superpose.cc Fix the default active molecules in the SSM superpose dialog. ------------------------------------------------------------------------ r2973 | pemsley | 2010-05-29 12:37:23 +0100 (Sat, 29 May 2010) | 7 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/src/align.cc M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc M /trunk/src/junk.cc If we send a conventional residue to flev, we don't want to read in the resulting dictionary, because that will be a non-polymer (as opposed to L-peptide) and that would mess up future refinement. Some placeholders for pi-cation analysis. Refactor pi overlap code for use with pi-cation overlaps. DNA and RNA added to environment residues with ring systems. ------------------------------------------------------------------------ r2972 | pemsley | 2010-05-25 11:36:22 +0100 (Tue, 25 May 2010) | 7 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc Add RU as an atom that can have long bonds. Add qualifying distance to protein of waters in residue infos (flev.cc) Add metal bonds to get_fle_ligand_bonds(). Add not-yet-working covalent bonds to get_fle_ligand_bonds(). Allow public access to restraints find_link_type_rigourous() (used in above). In lbg.cc, filter residue circles based on water cut-off distance. ------------------------------------------------------------------------ r2971 | pemsley | 2010-05-24 14:33:48 +0100 (Mon, 24 May 2010) | 12 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-h-bonds.cc M /trunk/coot-utils/coot-h-bonds.hh M /trunk/coot-utils/test-h-bonds.cc M /trunk/dnotes M /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/lbg/lbg.cc M /trunk/lbg/notes M /trunk/lbg/residue-circles.cc M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc HOH added to standard residues. get_h_bond_type() introduced into protein_geometry. Based on energy dictionary lookup. New style (energy dictionary-based) get_fle_ligand_bonds() for H-bonds. make_neighbour_map(): find the neigbhours of the H-bonding atoms and sort the atoms contacts (by residue then distance). After importing a ligand from lbg->prodrg, ligand-overlay it to the active resdue. Fix up canvas sizes for PNG and pdf (a bit of a hack, but works OK). Problematically placed residues can be trapped in a big ring of 5 (or more) less close ligand atoms (cut-offs here may need tweaking). ------------------------------------------------------------------------ r2970 | pemsley | 2010-05-24 14:19:21 +0100 (Mon, 24 May 2010) | 2 lines Changed paths: A /trunk/lbg/Anonymous_Architetto_--_Chiave.svg Add the "key" icon. ------------------------------------------------------------------------ r2969 | pemsley | 2010-05-21 13:34:09 +0100 (Fri, 21 May 2010) | 2 lines Changed paths: A /trunk/coot-utils/test-h-bonds.cc Add dummy test-h-bonds.cc for now. ------------------------------------------------------------------------ r2968 | pemsley | 2010-05-21 12:00:07 +0100 (Fri, 21 May 2010) | 2 lines Changed paths: A /trunk/coot-utils/coot-h-bonds.cc A /trunk/coot-utils/coot-h-bonds.hh Add missing coot-h-bonds files. ------------------------------------------------------------------------ r2967 | pemsley | 2010-05-21 11:07:46 +0100 (Fri, 21 May 2010) | 11 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/coot-gtk2.glade M /trunk/coot-utils/Makefile.am M /trunk/db-main/Makefile.am M /trunk/geometry/Makefile.am A /trunk/geometry/energy-lib.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a filter for removing hydrogens and another for removing ANISO records from the saved PDB file - add the filter functions in mmdb.cc - which is the file that (also) contains write_atom_selection_file(). write_atom_selection_file() now takes optional args for the filtering of hydrogens and ANISO records. Add checkbuttons in the classic and modern file chooser/selectors. Add a reader for refmac energy lib cif into protein-geometry (currently only reader for atoms, but classes added for bond, angles and torsions). Add a lookup function get_h_bond_type() given an atom name and a residue type. This has caused the need for tweaking of libs in the Makefile - not sure why. ------------------------------------------------------------------------ r2966 | b.lohkamp | 2010-05-20 15:56:53 +0100 (Thu, 20 May 2010) | 4 lines Changed paths: M /trunk/bldnotes A /trunk/doc/3-amino-benzamide-2.png M /trunk/doc/crib-sheet.tex M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex M /trunk/python/coot_gui.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/nsv.cc update tutorials and fix some typos add pythonic auto-read mtz test fix sequence view (nsv) font for windows ------------------------------------------------------------------------ r2965 | pemsley | 2010-05-19 13:24:21 +0100 (Wed, 19 May 2010) | 5 lines Changed paths: M /trunk/coot-utils/coot-rama.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/lbg.cc M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/flev.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Add extra greg tests - internal tests that use data from greg data dir. Add test_phi_psi_values() test. Fix for the generation of phi_psi_t when the bonding residues are too far apart. Traffic lights are now called "Estimated RMS Z score". ------------------------------------------------------------------------ r2964 | pemsley | 2010-05-18 21:01:07 +0100 (Tue, 18 May 2010) | 3 lines Changed paths: M /trunk/greg-tests/Makefile.am Put internal test scm file into the Makefile, so that it becomes part of the tarball and internal tests are run for binary builds. ------------------------------------------------------------------------ r2963 | pemsley | 2010-05-18 13:44:25 +0100 (Tue, 18 May 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2962 | pemsley | 2010-05-18 13:38:21 +0100 (Tue, 18 May 2010) | 6 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc Fix problem of trying to edit chi angles when there is a dictionary, but no tree in the dictionary. Use atom name and dictionary, new getcontacts() function added, falling back to the old distance-based search. atom_tree_index_t renamed map_index_t and made more accessible (used in above getcontacts() function). ------------------------------------------------------------------------ r2961 | pemsley | 2010-05-17 16:49:46 +0100 (Mon, 17 May 2010) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc Fix up incorrect toggling of env distances when molecules display toggled off. Symmetry update on SSM superposition. lbg: grease colour adjustment. ------------------------------------------------------------------------ r2960 | pemsley | 2010-05-17 16:18:09 +0100 (Mon, 17 May 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Improve FAQ documentation of Rotate/Translate menu tool button. ------------------------------------------------------------------------ r2959 | pemsley | 2010-05-17 14:33:48 +0100 (Mon, 17 May 2010) | 5 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/nsv.cc M /trunk/src/nsv.hh do_sequence_view() should be used for big shelx molecules so that the X axis of the sequence view (nsv) doesn't go beyond 32700 (or so). Improve the position of the canvas items in nsv by using x_offset (reduces wasted space on the left of the sequences). ------------------------------------------------------------------------ r2958 | pemsley | 2010-05-17 14:31:39 +0100 (Mon, 17 May 2010) | 2 lines Changed paths: M /trunk/coords/mmdb.cc remove anachronistic char * casting. ------------------------------------------------------------------------ r2957 | pemsley | 2010-05-17 14:30:56 +0100 (Mon, 17 May 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc Tweak the "bond" length of pi-pi stacking interaction. Tweak the text position in residue circles. ------------------------------------------------------------------------ r2956 | pemsley | 2010-05-17 09:09:46 +0100 (Mon, 17 May 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/rel-todo Add in patch for gtkglext for specific versions of GTK+. ------------------------------------------------------------------------ r2955 | pemsley | 2010-05-14 18:51:53 +0100 (Fri, 14 May 2010) | 3 lines Changed paths: M /trunk/coords/mmdb.cc Rename DT, DG, DA, DC to old (Refmac) names. This is a hack. The correct solution is to fix the dictionary on the fly. ------------------------------------------------------------------------ r2954 | pemsley | 2010-05-14 17:47:48 +0100 (Fri, 14 May 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add update to Map Sharpening. ------------------------------------------------------------------------ r2953 | pemsley | 2010-05-14 14:59:47 +0100 (Fri, 14 May 2010) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/c-interface-ligands.hh M /trunk/src/flev.cc M /trunk/src/gtk2-interface.c Remove superfluous button in Bond Parameters dialog. Add metal contact bond type in ligand interaction analysis. Update todo list. Fix typo in prodrg-import. ------------------------------------------------------------------------ r2952 | pemsley | 2010-05-14 14:55:44 +0100 (Fri, 14 May 2010) | 2 lines Changed paths: M /trunk/lbg/lbg.hh Make the residue circles a touch bigger. ------------------------------------------------------------------------ r2951 | pemsley | 2010-05-14 13:58:31 +0100 (Fri, 14 May 2010) | 4 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh Add metal contact bond type (and rendereing colour). reposition_problematics_and_reoptimise() factored out and reworked. In ligand_grid::fill, exp_scale changed to 0.0011 - experimental. ------------------------------------------------------------------------ r2950 | pemsley | 2010-05-14 11:52:18 +0100 (Fri, 14 May 2010) | 6 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/residue-circles.cc Pass the primary residue indices to the optimise_residue_circles constructor because primary indices are used to optimise the bonds between the residues and ligand atoms. Add a toggle button for the key/legend - callback function not yet filled. Derivatives for score_vs_ligand_atom_bond_length added. ------------------------------------------------------------------------ r2949 | kevin.cowtan | 2010-05-14 10:58:19 +0100 (Fri, 14 May 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix for CNS read to check for a valid extended CNS file. ------------------------------------------------------------------------ r2948 | pemsley | 2010-05-13 19:33:08 +0100 (Thu, 13 May 2010) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix typo in greg test. ------------------------------------------------------------------------ r2947 | pemsley | 2010-05-13 18:04:29 +0100 (Thu, 13 May 2010) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test for auto-reading of MTZ data. ------------------------------------------------------------------------ r2946 | pemsley | 2010-05-13 18:03:29 +0100 (Thu, 13 May 2010) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/align.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Fix ups for auto-reading an MTZ file and going down auto-read CNS path. Use const char * to stored return value of GetChainID(). ------------------------------------------------------------------------ r2945 | pemsley | 2010-05-13 18:01:19 +0100 (Thu, 13 May 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Unmodelled blobs FAQ documentation ------------------------------------------------------------------------ r2944 | pemsley | 2010-05-13 18:00:22 +0100 (Thu, 13 May 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2943 | pemsley | 2010-05-10 15:11:06 +0100 (Mon, 10 May 2010) | 13 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.hh M /trunk/lbg/notes M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc get_attachment_points() now returns a vector of pairs of positions and bond lengths (so that we can add a term in the minimiser which tries to idealise the length of the ligand interaction bonds). Add terms for idealisation of angle (residue-ligand_atom-residue) terms (not yet turned on). Add a test for problematic residue (typically trapped in open ring systems). If so, move the residue (like a primary) and reminimise. initial_primary_residue_cirles_layout() factored out - so that it can be used for problematic residues. SMILES toolbutton added (requires babel). I mean dot product, not cross in pos_t function. Add residue colours for some metals. ------------------------------------------------------------------------ r2942 | pemsley | 2010-05-04 14:50:31 +0100 (Tue, 04 May 2010) | 2 lines Changed paths: M /trunk/Makefile.am Not ready to introduce lbg into main line yet - revert this for now. ------------------------------------------------------------------------ r2941 | pemsley | 2010-05-03 17:52:49 +0100 (Mon, 03 May 2010) | 20 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/dnotes M /trunk/lbg/Makefile M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.hh M /trunk/lbg/notes M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh M /trunk/rel-todo M /trunk/scheme/prodrg-import.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface.h M /trunk/src/flev.cc M /trunk/src/globjects.cc M /trunk/src/lbg-graph.cc M /trunk/src/lbg-graph.hh M /trunk/src/test-lbg-graph.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Pass the prodrg output cif to fle-view-internal. flev.cc now includes lbg-graph.hh functions. Add pi-pi stacking analysis and drawing functions. Place-holders for Pi-cation, but not searched for yet. ring_atom_names() give a residue type working for PHE, TYR, PTY and TRP - needs extension for DNA/RNA bases. Add internal test: test_flev_aromatics(). widgeted_molecule_t has new function get_ring_centre() give atom names and get_ring_centres() which caches the return value. ligand_grid class added to help with the initial placement of residues that bond to the ligand. Also added: fill() add_quadratic() and find_minimum_position() and canvas coordinates conversion functions. Also show_grid() and show_mol_ring_centres() for visual debugging. minimisation using ligand ring centres is done from a list of ring centres, no longer with the ring centres of each bond. residue->residue minimisation penalty function is now a Gaussian, not a reciprocal. handle_read_draw_coords_mol_and_solv_acc() function added so that I can run from the command line, rather than touching a "ready" file from coot. ------------------------------------------------------------------------ r2940 | b.lohkamp | 2010-04-27 16:23:36 +0100 (Tue, 27 Apr 2010) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/refmac.py fix pythonic auto_weight refinement (factor should be 1 otherwise no convergence - at least here) fix python refmac, ncs properly used only for more than 1 chains ------------------------------------------------------------------------ r2939 | pemsley | 2010-04-26 23:34:40 +0100 (Mon, 26 Apr 2010) | 3 lines Changed paths: M /trunk/TODO M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h superpose_with_atom_selection() now returns a model number. Adjustments to the chi_squareds output. ------------------------------------------------------------------------ r2938 | pemsley | 2010-04-25 19:29:06 +0100 (Sun, 25 Apr 2010) | 3 lines Changed paths: A /trunk/src/lbg-graph.cc A /trunk/src/lbg-graph.hh A /trunk/src/test-lbg-graph.cc Add the code for a class that detects aromatic ring systems. Not fully working yet, aromatic_graph_t. ------------------------------------------------------------------------ r2937 | pemsley | 2010-04-24 15:10:50 +0100 (Sat, 24 Apr 2010) | 4 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h Fixups for alt confs in geometry graph problem, and leading to restraints fixups for residues with alt confs in chiral restraints, link bond restraints, link angle restraints and link plane restraints. ------------------------------------------------------------------------ r2936 | pemsley | 2010-04-23 19:56:32 +0100 (Fri, 23 Apr 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update notes ------------------------------------------------------------------------ r2935 | pemsley | 2010-04-23 19:56:17 +0100 (Fri, 23 Apr 2010) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Pass a pointer to the atom_colour_map as an additional argument to atom_colour() and the functions that call it. Fixes the colour index problems of colour by chain c-only mode. ------------------------------------------------------------------------ r2934 | pemsley | 2010-04-23 19:52:40 +0100 (Fri, 23 Apr 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New burn up points and graph annotation. ------------------------------------------------------------------------ r2933 | pemsley | 2010-04-22 16:43:43 +0100 (Thu, 22 Apr 2010) | 10 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/check-for-updates.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-network.cc M /trunk/src/graphics-info-network.cc Address Bernie-race-condition-on-downloading-binary problem. I think. On cancel button press, set pending-install-in-place before stoping the curl download. pending-install-in-place is reset to #f on re-running download-binary-dialog. Only go on to check md5 sums and install if the result of coot-get-url-and-activate-curl-hook was a success. Accept Bernie suggestion of opening binary tar FILE as "wb". In curl_handler_stop_it_flag_set() only check the stop status of the given CURL pointer (not any of them). ------------------------------------------------------------------------ r2932 | pemsley | 2010-04-22 09:29:39 +0100 (Thu, 22 Apr 2010) | 3 lines Changed paths: M /trunk/TODO M /trunk/lbg/notes M /trunk/rel-todo M /trunk/src/c-interface.h M /trunk/src/rama_plot.cc Fix problem of misindenification of molecule number in callback of ramachandran residue click. ------------------------------------------------------------------------ r2931 | pemsley | 2010-04-21 14:36:59 +0100 (Wed, 21 Apr 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build.cc On merge molecules, make the merged molecule inactive (as well as undisplayed). ------------------------------------------------------------------------ r2930 | pemsley | 2010-04-21 14:00:06 +0100 (Wed, 21 Apr 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/lbg/notes M /trunk/rel-todo Make phosphodiester linkages correctly for RNA and DNA in sphere refinement. ------------------------------------------------------------------------ r2929 | pemsley | 2010-04-19 16:27:34 +0100 (Mon, 19 Apr 2010) | 2 lines Changed paths: A /trunk/scheme/prodrg-import.scm Add trivial prodrg communication script. Not added to main-line yet. ------------------------------------------------------------------------ r2928 | pemsley | 2010-04-19 16:24:19 +0100 (Mon, 19 Apr 2010) | 8 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.cc M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc A /trunk/src/c-interface-ligands.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/coot-nomenclature.cc A /trunk/src/flev.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Rework the output of optimize_rotamer_by_atom_names(). Still need some improvement. In the ligand fitting dialog, put the chooser for the ligand molecule first. Add functions for Flatland Ligand Environment View, handling the results of PRODRG/REFMAC and calculating solvent exposure differences (for environment residues) and solvent accessibility for ligand atoms. Also bonds from residues to the ligand atoms are calculated (and written). ------------------------------------------------------------------------ r2927 | pemsley | 2010-04-19 13:17:59 +0100 (Mon, 19 Apr 2010) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add filter_residues_by_solvent_contact() and get_residue_centre() functions. create_mmdbmanager_from_residue_vector() now sets the chain_id to match those of the added residues. ------------------------------------------------------------------------ r2926 | pemsley | 2010-04-19 13:13:38 +0100 (Mon, 19 Apr 2010) | 5 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc M /trunk/lbg/wmolecule.hh Add the reading of solvent exposures and put then on the canvas. ligand_centre() function added so the direction of the solvent ring offset can be determined. Tweak the layout scale factors. ------------------------------------------------------------------------ r2925 | pemsley | 2010-04-18 01:36:14 +0100 (Sun, 18 Apr 2010) | 3 lines Changed paths: M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh HIS is basic. sort out H-bond donor and acceptor logic. ------------------------------------------------------------------------ r2924 | pemsley | 2010-04-17 22:14:13 +0100 (Sat, 17 Apr 2010) | 7 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-junk.cc M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.hh M /trunk/lbg/residue-circles.cc M /trunk/lbg/wmolecule.cc A /trunk/lbg/wmolecule.hh Change what was "atom_name" to "atom_id" (i.e. the text on the canvas) in preparation for atom names (from the PDB file). So add a PDB reader. Rearrange the setting of the solvent accessibility attributes. Now do it by atom name, rather than by atom position. Add environment bonds. ------------------------------------------------------------------------ r2923 | pemsley | 2010-04-17 13:01:52 +0100 (Sat, 17 Apr 2010) | 2 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh A /trunk/lbg/wmolecule.cc move widgeted molecule bond and atom stuff from lbg.cc to wmolecule.cc ------------------------------------------------------------------------ r2922 | pemsley | 2010-04-16 15:12:40 +0100 (Fri, 16 Apr 2010) | 8 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.glade M /trunk/lbg/lbg.hh M /trunk/lbg/residue-circles.cc optimise_residue_circle_positions() takes an extra argument, the current positions (as opposed to the starting positions (which are the constants restrained against). Use gaussian rejection function for ring centres and ligand atoms. Add a diagnositic numerical_gradients() function. Residue centres are added with a "Residues" button, not Info dialog. TYRs are not grease. Waters need white fill. ------------------------------------------------------------------------ r2921 | pemsley | 2010-04-15 18:30:27 +0100 (Thu, 15 Apr 2010) | 2 lines Changed paths: M /trunk/src/c-interface.h Add/rework documentation for the setting of the scroll whell map. ------------------------------------------------------------------------ r2920 | pemsley | 2010-04-15 18:29:35 +0100 (Thu, 15 Apr 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Extend map masking docs. ------------------------------------------------------------------------ r2919 | pemsley | 2010-04-15 13:30:07 +0100 (Thu, 15 Apr 2010) | 4 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg-junk.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh A /trunk/lbg/residue-circles.cc Add in a minimiser to optimise the placement of the residues around the flat ligand. This minimises in several rounds, so that the "trajectory" of the residue circles is displayed (for the moment). ------------------------------------------------------------------------ r2918 | pemsley | 2010-04-15 12:23:43 +0100 (Thu, 15 Apr 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Improve CIS peptide documentation. ------------------------------------------------------------------------ r2917 | pemsley | 2010-04-15 12:21:54 +0100 (Thu, 15 Apr 2010) | 4 lines Changed paths: M /trunk/ideal/simple-restraint.cc In find_link_type_rigourous(), force all peptide links to be TRANS - we don't yet do a geometry analysis to distinguish CIS and TRANS (and TRANS has the peptide plane restraints). ------------------------------------------------------------------------ r2916 | pemsley | 2010-04-14 14:30:01 +0100 (Wed, 14 Apr 2010) | 5 lines Changed paths: M /trunk/lbg/lbg-junk.cc M /trunk/lbg/lbg-molfile.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/some-coot-utils.cc M /trunk/lbg/some-coot-utils.hh Add an ugly mechanism for transfering solvent accessibilities from a file. There is currently a synchronisation/timing issue re the generation of the files from coot and prodrg. Add split_string_no_blanks() function to some-coot-utils. ------------------------------------------------------------------------ r2915 | pemsley | 2010-04-13 20:59:57 +0100 (Tue, 13 Apr 2010) | 7 lines Changed paths: M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-molfile.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes M /trunk/lbg/some-coot-utils.cc M /trunk/lbg/some-coot-utils.hh Copy the scale and offset parameters when constructing and drawing from a widgeted_molecule. Add code to read and draw residue cirles to surround the ligand. Reading of file is attached for the moment to the info button. Add split_string() and downcase() to some-coot-utils. Make the wedge without using GooCanvasPoints. ------------------------------------------------------------------------ r2914 | pemsley | 2010-04-13 17:13:22 +0100 (Tue, 13 Apr 2010) | 6 lines Changed paths: M /trunk/lbg/Makefile M /trunk/lbg/lbg-molfile.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/notes Factor out the scaling and offsets for input coords to canvas coordinates conversion. Read the first arg on the command line as a mol file. Fix atom name problem on undo. Invert and re-invert coordinates on save as molfile, so that the orientation on the canvas is the same way up as a molecule drawn in JME. ------------------------------------------------------------------------ r2913 | b.lohkamp | 2010-04-13 10:16:45 +0100 (Tue, 13 Apr 2010) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/create_input_server.py M /trunk/python/remote_control.py M /trunk/src/graphics-info.cc remove obsolete guile packages from windows build system fix user defined python clicks (takes a model number properly too now) adjust pythonic annotation at click accordingly fix some python typos in cis_peptides_gui and user_mods_gui properly describe toolbutton for swap stereo sides use host_address rather than host_name in remote_control ------------------------------------------------------------------------ r2912 | pemsley | 2010-04-12 11:40:02 +0100 (Mon, 12 Apr 2010) | 2 lines Changed paths: D /trunk/lbg/a.cc D /trunk/lbg/b.cc M /trunk/lbg/lbg-callbacks.cc M /trunk/lbg/lbg-molfile.cc M /trunk/lbg/lbg-molfile.hh M /trunk/lbg/lbg-search.cc M /trunk/lbg/lbg-test-cc.cc M /trunk/lbg/lbg.cc M /trunk/lbg/lbg.hh M /trunk/lbg/lig-build.cc M /trunk/lbg/lig-build.hh M /trunk/lbg/some-coot-utils.cc M /trunk/lbg/some-coot-utils.hh D /trunk/lbg/test-inh.cc M /trunk/lbg/test-lbg.cc M /trunk/lbg/test-lig-build.cc M /trunk/lbg/test-read-molfile.cc D /trunk/lbg/test.cc Tidy up import - add license notices. ------------------------------------------------------------------------ r2911 | pemsley | 2010-04-12 11:25:31 +0100 (Mon, 12 Apr 2010) | 2 lines Changed paths: A /trunk/lbg A /trunk/lbg/3-c-new.svg A /trunk/lbg/3-c-other.svg A /trunk/lbg/3-c.svg A /trunk/lbg/4-c.svg A /trunk/lbg/5-c.svg A /trunk/lbg/6-c-arom.svg A /trunk/lbg/6-c-exp-2.svg A /trunk/lbg/6-c-shadow-experiment.svg A /trunk/lbg/6-c.svg A /trunk/lbg/7-c.svg A /trunk/lbg/8-c.svg A /trunk/lbg/Makefile A /trunk/lbg/TheStructorr_magnifying_glass-32.svg A /trunk/lbg/TheStructorr_magnifying_glass.svg A /trunk/lbg/a.cc A /trunk/lbg/b.cc A /trunk/lbg/charge.svg A /trunk/lbg/coot-favicon.png A /trunk/lbg/coot-icon.png A /trunk/lbg/double.svg A /trunk/lbg/lbg-callbacks.cc A /trunk/lbg/lbg-junk.cc A /trunk/lbg/lbg-molfile.cc A /trunk/lbg/lbg-molfile.hh A /trunk/lbg/lbg-search.cc A /trunk/lbg/lbg-test-cc.cc A /trunk/lbg/lbg.cc A /trunk/lbg/lbg.glade A /trunk/lbg/lbg.hh A /trunk/lbg/lig-build.cc A /trunk/lbg/lig-build.hh A /trunk/lbg/notes A /trunk/lbg/single.svg A /trunk/lbg/some-coot-utils.cc A /trunk/lbg/some-coot-utils.hh A /trunk/lbg/sp3.svg A /trunk/lbg/stereo-out.svg A /trunk/lbg/test-inh.cc A /trunk/lbg/test-lbg.cc A /trunk/lbg/test-lig-build.cc A /trunk/lbg/test-read-molfile.cc A /trunk/lbg/test.cc A /trunk/lbg/triple.svg Add the lbg project. ------------------------------------------------------------------------ r2910 | pemsley | 2010-04-10 10:03:36 +0100 (Sat, 10 Apr 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo Update todo notes. ------------------------------------------------------------------------ r2909 | pemsley | 2010-04-09 01:37:34 +0100 (Fri, 09 Apr 2010) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Remove glClearColor() call in make_ball_and_stick() - fixes reversion to black background (from white) after ball and stick model(s) added. ------------------------------------------------------------------------ r2908 | pemsley | 2010-04-07 07:08:42 +0100 (Wed, 07 Apr 2010) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Fix typo in general_link_find_close_link_inner(), use the correct atom name from residue r2. ------------------------------------------------------------------------ r2907 | b.lohkamp | 2010-04-06 09:13:05 +0100 (Tue, 06 Apr 2010) | 4 lines Changed paths: M /trunk/bldnotes A /trunk/bldnotes-2009 M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/python/check_for_updates.py M /trunk/src/c-interface.cc cleanup bldnotes scheme scripting window only for GTK2 png fixes for libpng 1.4 ------------------------------------------------------------------------ r2906 | b.lohkamp | 2010-04-05 14:10:53 +0100 (Mon, 05 Apr 2010) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h simple gtk2 window for scheme scripting when we dont have guile-gtk/gui ------------------------------------------------------------------------ r2905 | pemsley | 2010-04-04 00:25:25 +0100 (Sun, 04 Apr 2010) | 3 lines Changed paths: M /trunk/cycle-page-builder.scm Fix-ups for when the most recent file is not the bottom of the list when matching file names. ------------------------------------------------------------------------ r2904 | b.lohkamp | 2010-04-02 21:09:27 +0100 (Fri, 02 Apr 2010) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/parse_pisa_xml.py in pythonic mutate_by_overlap, use dictionary and model of item if it already exists. add pythonic prodrg_ify ------------------------------------------------------------------------ r2903 | pemsley | 2010-04-02 20:35:18 +0100 (Fri, 02 Apr 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Added documentation for the Rotate/Translate menu button. ------------------------------------------------------------------------ r2902 | pemsley | 2010-04-02 09:50:16 +0100 (Fri, 02 Apr 2010) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Fix up clipper::Message_base catch again for other compilers. ------------------------------------------------------------------------ r2901 | pemsley | 2010-04-02 09:25:38 +0100 (Fri, 02 Apr 2010) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/callbacks.c M /trunk/src/pisa-interface.hh M /trunk/utils/coot-utils.cc Clean-up pisa gui interface, removing unneeded argument. Minor typesetting issues elsewhere. ------------------------------------------------------------------------ r2900 | pemsley | 2010-04-02 09:21:38 +0100 (Fri, 02 Apr 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Update docs for the Coot reference. ------------------------------------------------------------------------ r2899 | pemsley | 2010-04-02 09:21:03 +0100 (Fri, 02 Apr 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add HG as a long-bonded atom. ------------------------------------------------------------------------ r2898 | pemsley | 2010-04-02 09:18:05 +0100 (Fri, 02 Apr 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-map.cc M /trunk/rel-todo Fix up "tangled disulfides in sphere refinement" problem. Fix up catch in with-map on bad read of MTZ. ------------------------------------------------------------------------ r2897 | pemsley | 2010-04-02 09:15:50 +0100 (Fri, 02 Apr 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2896 | pemsley | 2010-03-30 17:40:45 +0100 (Tue, 30 Mar 2010) | 3 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm In replace residue, use dictionary and model of item if it already exists. Load tutorial data uses COOT_PREFIX to find its data, not a built-in value. ------------------------------------------------------------------------ r2895 | pemsley | 2010-03-30 17:36:21 +0100 (Tue, 30 Mar 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2894 | b.lohkamp | 2010-03-29 13:16:22 +0100 (Mon, 29 Mar 2010) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/libcheck.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-waters.cc pythonic prodrg_ify (needs testing) pythonic water_coordination_gui (and friends, i.e. highly_coordinated_waters_py) sort python extensions alphabetically too python test for writing mmCIF restraints properly update citation in References dialog fix some python reference counting (hopefully !?) ------------------------------------------------------------------------ r2893 | b.lohkamp | 2010-03-28 16:12:27 +0100 (Sun, 28 Mar 2010) | 2 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/parse_pisa_xml.py M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh pythonic parsing of PISA interfaces ------------------------------------------------------------------------ r2892 | pemsley | 2010-03-26 02:00:37 +0000 (Fri, 26 Mar 2010) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Update Coot FAQ with new paper details. ------------------------------------------------------------------------ r2891 | pemsley | 2010-03-25 12:40:07 +0000 (Thu, 25 Mar 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/burn-up/burn-up.tab New burn points. Fix typo in release notes. ------------------------------------------------------------------------ r2890 | pemsley | 2010-03-25 02:24:23 +0000 (Thu, 25 Mar 2010) | 3 lines Changed paths: M /trunk/coot-utils/water-coordination.cc M /trunk/rel-todo Hydrogens are now filtered from neighbour contacts in highly coordinated waters search. ------------------------------------------------------------------------ r2889 | pemsley | 2010-03-25 01:58:57 +0000 (Thu, 25 Mar 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update release-notes for latest revision. ------------------------------------------------------------------------ r2888 | pemsley | 2010-03-25 01:55:34 +0000 (Thu, 25 Mar 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-rama.cc M /trunk/coot-utils/coot-rama.hh M /trunk/rel-todo M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/graphics-info.cc M /trunk/src/mol-hierachy.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh The long-needed rama-plot rewrite. Now the internals work by model and a residue_spec_t map to hold the phi_psi values. So now ramachandran plots work with chains with breaks in them all the way to the end. ------------------------------------------------------------------------ r2887 | pemsley | 2010-03-25 00:57:16 +0000 (Thu, 25 Mar 2010) | 3 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/pisa-interface.hh PISA interface fixups. Fix the number of bonds in the treeview dialog. Update notes. ------------------------------------------------------------------------ r2886 | pemsley | 2010-03-25 00:56:12 +0000 (Thu, 25 Mar 2010) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Catch the clipper exception on not making a map (bad mtz or so). ------------------------------------------------------------------------ r2885 | pemsley | 2010-03-24 19:36:01 +0000 (Wed, 24 Mar 2010) | 3 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Fix typo in pisa-make-atom-selection-string, use the correct string for the chain id to make the atom selection. ------------------------------------------------------------------------ r2884 | pemsley | 2010-03-24 18:03:40 +0000 (Wed, 24 Mar 2010) | 2 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Tiny fixups for handling pisa assemblies. ------------------------------------------------------------------------ r2883 | pemsley | 2010-03-21 21:30:35 +0000 (Sun, 21 Mar 2010) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc Thin down the ball/sphere/atom size for hydrogens (too) in ball-and-stick representation. ------------------------------------------------------------------------ r2882 | pemsley | 2010-03-21 20:20:50 +0000 (Sun, 21 Mar 2010) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-validate.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/rama_mousey.cc M /trunk/src/rama_plot.cc Use static_casts instead of c-style casting for rama plot usage. Thin down ball-and-stick bond lines to hydrogens. ------------------------------------------------------------------------ r2881 | pemsley | 2010-03-21 20:18:56 +0000 (Sun, 21 Mar 2010) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Set include_map_terms_flag = 0 in the constructor used by idle function minimisation. ------------------------------------------------------------------------ r2880 | pemsley | 2010-03-21 20:17:30 +0000 (Sun, 21 Mar 2010) | 2 lines Changed paths: M /trunk/doc/ligand-fitting-tutorial.tex Fix a typo. ------------------------------------------------------------------------ r2879 | pemsley | 2010-03-18 16:49:21 +0000 (Thu, 18 Mar 2010) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Don't test TER atoms when checking atom names against the dictionary. ------------------------------------------------------------------------ r2878 | pemsley | 2010-03-17 17:11:09 +0000 (Wed, 17 Mar 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add PT to long_bonded_atoms. ------------------------------------------------------------------------ r2877 | b.lohkamp | 2010-03-14 17:41:58 +0000 (Sun, 14 Mar 2010) | 11 lines Changed paths: M /trunk/bldnotes M /trunk/python/americanisms.py M /trunk/python/check_for_updates.py M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-network.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/main.cc modify and update pythonic update system: add update_self and possibility to use curl for update move some functions to coot_utils add pythonic new_molecule_by_smiles_string add possibility to run python threads without graohics (gtk.idle_add) update highly_coordinated_waters_py add pythonic curl_progress_info add matching_compound_names_from_sbase_py add and update pythonic regularize_residues, refine_residues_with_alt_conf, regularize_residues_with_alt_conf, and py_to_residue_specs ------------------------------------------------------------------------ r2876 | pemsley | 2010-03-12 15:51:40 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Alphabetise the extension modelling menu. ------------------------------------------------------------------------ r2875 | pemsley | 2010-03-12 15:26:38 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Remove const CMMDBManager * usage. ------------------------------------------------------------------------ r2874 | pemsley | 2010-03-12 15:26:05 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo Re-estimate to-do items. ------------------------------------------------------------------------ r2873 | pemsley | 2010-03-12 13:18:39 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/src/command-line.cc Fix up the formatting of the help text. ------------------------------------------------------------------------ r2872 | pemsley | 2010-03-12 12:49:05 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/libcheck.scm clean libcheck debugging. ------------------------------------------------------------------------ r2871 | pemsley | 2010-03-12 12:43:16 +0000 (Fri, 12 Mar 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h Add a interface to nearest_residue_by_sequence(). use it in the validate by sequence gui, to go to the nearest residue on needing an insertion. ------------------------------------------------------------------------ r2870 | pemsley | 2010-03-12 01:08:09 +0000 (Fri, 12 Mar 2010) | 3 lines Changed paths: M /trunk/macros/clipper.m4 Factor out mac changes, make editing easier. This is a temporary fix until clipper-config does the right thing. ------------------------------------------------------------------------ r2869 | pemsley | 2010-03-12 01:07:16 +0000 (Fri, 12 Mar 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2868 | pemsley | 2010-03-12 00:58:50 +0000 (Fri, 12 Mar 2010) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Add try/catch protection for writing formatted shelx output. Seems to be needed on the Mac - problem reported by Derek Logan. Now the backup .res file does not cause a crash, but the .res file is empty (in my tests). ------------------------------------------------------------------------ r2867 | pemsley | 2010-03-12 00:54:20 +0000 (Fri, 12 Mar 2010) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc Fix problem of recursive addition of looping forward atoms. Now forward atoms indices are checked against the base atom index. ------------------------------------------------------------------------ r2866 | pemsley | 2010-03-10 10:18:07 +0000 (Wed, 10 Mar 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add util function nearest_residue_by_sequence(). ------------------------------------------------------------------------ r2865 | pemsley | 2010-03-09 16:08:15 +0000 (Tue, 09 Mar 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Sanitise zoom scale before writing it to the state file. ------------------------------------------------------------------------ r2864 | pemsley | 2010-03-04 19:06:50 +0000 (Thu, 04 Mar 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/cycle-page-builder.scm M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/molecule-class-info-maps.cc Fix log files for f12 build. Anomalous maps are properly recorded in state file. Prodrg-ify has a menu item. ------------------------------------------------------------------------ r2863 | pemsley | 2010-03-04 19:05:11 +0000 (Thu, 04 Mar 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New burn points, graph annotation. ------------------------------------------------------------------------ r2862 | pemsley | 2010-03-04 18:24:14 +0000 (Thu, 04 Mar 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Trivial comment fix. ------------------------------------------------------------------------ r2861 | pemsley | 2010-03-04 18:23:18 +0000 (Thu, 04 Mar 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix $install_top_dir typos. ------------------------------------------------------------------------ r2860 | pemsley | 2010-03-04 15:47:39 +0000 (Thu, 04 Mar 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2859 | pemsley | 2010-03-04 15:39:44 +0000 (Thu, 04 Mar 2010) | 4 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/geometry/read-sbase.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.hh M /trunk/rel-todo M /trunk/src/globjects.cc Water fitting default distances less generous - more reasonable. Water fitting distance check to protein and other water sites improved. Atoms from SBase now are sanity checked for x,y,z postions (database corruption). ------------------------------------------------------------------------ r2858 | pemsley | 2010-03-04 11:32:59 +0000 (Thu, 04 Mar 2010) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/graphics-info-gui.cc M /trunk/src/gtk2-interface.c M /trunk/src/mol-hierachy.cc Update GUI text for SSM. Remove debugging on coordinates option menu generation. ------------------------------------------------------------------------ r2857 | pemsley | 2010-03-04 11:30:16 +0000 (Thu, 04 Mar 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Prodrgify should run regularize-residue, not refinement, I think. ------------------------------------------------------------------------ r2856 | pemsley | 2010-03-04 11:28:49 +0000 (Thu, 04 Mar 2010) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/with-map.cc Remove verbose info/debugging on generating links. Use residue vector interface to restraints generation in with-map. ------------------------------------------------------------------------ r2855 | pemsley | 2010-03-03 21:06:48 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/doc/ligand-fitting-tutorial.tex M /trunk/rel-todo update notes. Tiny edit to tutorial. ------------------------------------------------------------------------ r2854 | pemsley | 2010-03-03 20:22:49 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add prodrg-ify ligand (i.e. make restraints for) function. ------------------------------------------------------------------------ r2853 | pemsley | 2010-03-03 20:21:38 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Improve 4char atom name generation for SBAse atom names - now using element. ------------------------------------------------------------------------ r2852 | pemsley | 2010-03-03 17:47:02 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/doc/ligand-fitting-tutorial.tex Update SMILES text in ligand tutorial. ------------------------------------------------------------------------ r2851 | pemsley | 2010-03-03 16:21:54 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/parse-pisa-xml.scm Test pisa version before running it - pisa-new-enough? function added. ------------------------------------------------------------------------ r2850 | pemsley | 2010-03-03 15:23:41 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/dnotes M /trunk/rel-todo M /trunk/src/molecule-class-info.cc Fix thin-lines mode in colour-by-chain for many molecules. ------------------------------------------------------------------------ r2849 | pemsley | 2010-03-03 13:04:41 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Remove waters from NCS differences graph. ------------------------------------------------------------------------ r2848 | pemsley | 2010-03-03 13:03:29 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: A /trunk/doc/3-amino-benzamide-2.eps A /trunk/doc/ligand-fitting-tutorial.tex Add ligand-fitting tutorial. ------------------------------------------------------------------------ r2847 | pemsley | 2010-03-03 13:02:48 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/scheme/ncs.scm remove NCS skipping debugging. ------------------------------------------------------------------------ r2846 | b.lohkamp | 2010-03-03 07:52:33 +0000 (Wed, 03 Mar 2010) | 1 line Changed paths: M /trunk/src/c-interface.cc fix reference counting for space_group_py ------------------------------------------------------------------------ r2845 | pemsley | 2010-03-03 00:36:52 +0000 (Wed, 03 Mar 2010) | 2 lines Changed paths: M /trunk/src/c-interface.h Add forgotten interface declaration space_group_py(). ------------------------------------------------------------------------ r2844 | pemsley | 2010-03-02 15:19:29 +0000 (Tue, 02 Mar 2010) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h Fix up move molecule here set and unset "move big molecules" check button problem. Fixed up and changed active item setting in graphics_info_t::fill_option_menu_with_coordinates_options_internal_3(). ------------------------------------------------------------------------ r2843 | pemsley | 2010-03-02 14:39:11 +0000 (Tue, 02 Mar 2010) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h show_spacegroup() deprecated, now we have space_group_scm and space_group_py() with redefines. ------------------------------------------------------------------------ r2842 | pemsley | 2010-03-02 14:21:30 +0000 (Tue, 02 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.cc Move NCS functions from c-interface.cc into c-interface-ncs.cc ------------------------------------------------------------------------ r2841 | pemsley | 2010-03-02 14:20:50 +0000 (Tue, 02 Mar 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New burn points - extend the graph. ------------------------------------------------------------------------ r2840 | pemsley | 2010-03-02 09:21:21 +0000 (Tue, 02 Mar 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo Rearrange todo list - punt some items. ------------------------------------------------------------------------ r2839 | pemsley | 2010-03-01 17:31:40 +0000 (Mon, 01 Mar 2010) | 2 lines Changed paths: M /trunk/Makefile.am Restore the build order of mini-mol and coot-utils - recently changed. ------------------------------------------------------------------------ r2838 | pemsley | 2010-03-01 16:15:32 +0000 (Mon, 01 Mar 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-waters.cc Use guile-fixups.h in c-interface-waters.cc ------------------------------------------------------------------------ r2837 | pemsley | 2010-03-01 15:54:47 +0000 (Mon, 01 Mar 2010) | 13 lines Changed paths: M /trunk/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/water-coordination.cc M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/testing.cc M /trunk/src/testing.hh PISA interface - looks like it works now. untangle_mmdb_chain_id_string() function added. bonds dashed line drawing fixed. Coordinated waters GUI improved to account for extra metal sites which are passed. Brown&Wu (1976) and Nayal & Di Cera (1996) logic added for metals (particularly Na+). Coordinated waters test for symmetry. Add coordinated waters GUI to the Validate menu. copy_molecule() taking a CMMDBManager util function added. In coot-utils member? change test to (deeper) equal? from eqv? Add test test_translate_close_to_origin(). ------------------------------------------------------------------------ r2836 | pemsley | 2010-02-27 10:31:55 +0000 (Sat, 27 Feb 2010) | 4 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/ligand/rotamer.cc M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/coot-nomenclature.cc Add water coordination to coot-gui, but don't add it to the GUI yet. Clean up fix nomenclature errors screen output. Add a line in the documentation about the GUI for superposing ligands. ------------------------------------------------------------------------ r2835 | pemsley | 2010-02-26 15:31:24 +0000 (Fri, 26 Feb 2010) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Add target-auto-weighting-value as a user-definable variable, target 0.25 after Ian Tickle's suggestion. ------------------------------------------------------------------------ r2834 | pemsley | 2010-02-26 15:30:13 +0000 (Fri, 26 Feb 2010) | 2 lines Changed paths: M /trunk/src/c-interface.h Fix documentation for reverse_fragment(). ------------------------------------------------------------------------ r2833 | pemsley | 2010-02-26 15:29:47 +0000 (Fri, 26 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo Add puntable item. ------------------------------------------------------------------------ r2832 | pemsley | 2010-02-26 13:47:47 +0000 (Fri, 26 Feb 2010) | 6 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/cc-interface.hh M /trunk/src/pisa-interface.hh New util function: centre_of_molecule(). Extend pisa interfaces to 12 columns, including the pvalue. make_complementary_dotted_surfaces() now returns the centre of the interface. pisa_interfaces_display_only() function introduced, turn off all molecules except the 2 in this interface. ------------------------------------------------------------------------ r2831 | pemsley | 2010-02-25 07:20:20 +0000 (Thu, 25 Feb 2010) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo Update notes. ------------------------------------------------------------------------ r2830 | pemsley | 2010-02-25 07:17:39 +0000 (Thu, 25 Feb 2010) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in comment - minor. ------------------------------------------------------------------------ r2829 | pemsley | 2010-02-25 07:16:51 +0000 (Thu, 25 Feb 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add SBASE environment variable description. ------------------------------------------------------------------------ r2828 | pemsley | 2010-02-25 07:15:34 +0000 (Thu, 25 Feb 2010) | 2 lines Changed paths: M /trunk/python/check_for_updates.py Minor formatting cleanup. ------------------------------------------------------------------------ r2827 | b.lohkamp | 2010-02-24 08:49:46 +0000 (Wed, 24 Feb 2010) | 2 lines Changed paths: M /trunk/src/Makefile.am add pisa-interface.hh to Makefile.am ------------------------------------------------------------------------ r2826 | pemsley | 2010-02-23 14:18:43 +0000 (Tue, 23 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/rel-todo M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/pisa-interface.hh Add a selection changed callback for pisa interfaces. Doesn't do much. ------------------------------------------------------------------------ r2825 | pemsley | 2010-02-23 12:16:09 +0000 (Tue, 23 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc Add includes to compile on FC4. ------------------------------------------------------------------------ r2824 | pemsley | 2010-02-23 12:13:26 +0000 (Tue, 23 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New day range, points range. ------------------------------------------------------------------------ r2823 | pemsley | 2010-02-23 02:47:18 +0000 (Tue, 23 Feb 2010) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/pisa-interface.hh More parsing and processing of pisa interface statistics. Molecule records seem to be reversed currently (h-bonds etc mis-indexed). ------------------------------------------------------------------------ r2822 | pemsley | 2010-02-23 01:10:25 +0000 (Tue, 23 Feb 2010) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh A /trunk/src/c-interface-pisa-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h A /trunk/src/pisa-interface.hh M /trunk/src/support.h Add a treeview GUI for presentation of PISA interfaces - basic at the moment with some dummy values. Pass back extra interface info (area solv-en pvalue stab-en) from the interface description. Add a test for cif writing. ------------------------------------------------------------------------ r2821 | pemsley | 2010-02-23 00:58:03 +0000 (Tue, 23 Feb 2010) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix up mmCIF writing as per Eugene's advice. ------------------------------------------------------------------------ r2820 | b.lohkamp | 2010-02-22 16:35:47 +0000 (Mon, 22 Feb 2010) | 2 lines Changed paths: M /trunk/src/c-interface-pisa.cc M /trunk/src/graphics-info.cc typo fixes ------------------------------------------------------------------------ r2819 | pemsley | 2010-02-22 13:46:51 +0000 (Mon, 22 Feb 2010) | 3 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-pisa.cc Remove some debugging. Reorganise (clean-up) the molecule-record usage. ------------------------------------------------------------------------ r2818 | pemsley | 2010-02-22 13:37:01 +0000 (Mon, 22 Feb 2010) | 2 lines Changed paths: M /trunk/scheme/americanisms.scm M /trunk/scheme/parse-pisa-xml.scm Fix typo in set-dots-color definition. ------------------------------------------------------------------------ r2817 | pemsley | 2010-02-22 13:16:03 +0000 (Mon, 22 Feb 2010) | 20 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/americanisms.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Changes for PISA interfaces handling. handle_pisa_interfaces_scm() function added. handling of XML molecule entity is common to assemblies and interfaces, so promote it to top-level and modify to return molecule info in the case of interfaces. Add pisa-molecule-record and pisa-residue-record. Handle the reading of bonds from the interface description. Add set_dots_colour() function. make_complementary_dotted_surfaces() function added. residue_records_list_scm_to_residue_specs() and add_pisa_interface_bond_scm() pisa_molecule_record_residues() pisa_molecule_record_chain_id() functions introduced. (Corresponding Python functions not done yet and non-trivial to implement.) dots_representation_info_t class extended to make its own dots. Utility function added get_residue() given a residue spec. coot::util::create_mmdbmanager_from_points() added. Not used yet. The model number is now added to atom spec attributes. The model number is now added to the atom_specs that are passed to the user-defined clicks function (now the list contains 6 items, not 5). ------------------------------------------------------------------------ r2816 | b.lohkamp | 2010-02-17 23:24:42 +0000 (Wed, 17 Feb 2010) | 1 line Changed paths: M /trunk/src/c-interface-pisa.cc protect pisa_interface_scm ------------------------------------------------------------------------ r2815 | pemsley | 2010-02-16 22:14:51 +0000 (Tue, 16 Feb 2010) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/water-coordination.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface.h Rework the pisa interface scheme code - still in progress, but should be compatible with assemblies use. Now with molecule records and residue records. Add a pisa_interface_scm() scripting function. Currently a stub. ------------------------------------------------------------------------ r2814 | pemsley | 2010-02-16 21:46:41 +0000 (Tue, 16 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2813 | pemsley | 2010-02-14 18:56:13 +0000 (Sun, 14 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo update todo list. ------------------------------------------------------------------------ r2812 | pemsley | 2010-02-14 01:58:18 +0000 (Sun, 14 Feb 2010) | 2 lines Changed paths: M /trunk/scheme/ncs.scm Comment out debugging of NCS skipping operations. ------------------------------------------------------------------------ r2811 | pemsley | 2010-02-14 01:57:00 +0000 (Sun, 14 Feb 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/doc/tutorial-2.tex M /trunk/geometry/protein-geometry.cc M /trunk/python/ncs.py M /trunk/rel-todo M /trunk/scheme/ncs.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h NCS skipping backward enabled (in scheme). dictionary_residue_restraints_t::write_cif() is still broken. (changed slightly here). ------------------------------------------------------------------------ r2810 | pemsley | 2010-02-12 16:57:19 +0000 (Fri, 12 Feb 2010) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Make new interface using new protection from post-gtk2.sh ------------------------------------------------------------------------ r2809 | pemsley | 2010-02-12 16:44:31 +0000 (Fri, 12 Feb 2010) | 3 lines Changed paths: M /trunk/src/post-gtk2-glade.sh We also need to #ifdef protect gtk_tool_item_set_tooltip() for the rotate/translate gtk_menu_tool_button_new(). ------------------------------------------------------------------------ r2808 | pemsley | 2010-02-12 15:38:51 +0000 (Fri, 12 Feb 2010) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/cycle-page-builder.scm A /trunk/find-in-code.sh M /trunk/python/parse_pisa_xml.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/testing.cc PISTORE_DIR for pisa config file. Add fedora 12 binaries to the summary page. Add highly-coordinated-waters interface (scheme only). ------------------------------------------------------------------------ r2807 | pemsley | 2010-02-12 15:35:35 +0000 (Fri, 12 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Tweak prediction algorithm, new burn points. ------------------------------------------------------------------------ r2806 | pemsley | 2010-02-12 15:33:32 +0000 (Fri, 12 Feb 2010) | 5 lines Changed paths: M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc Fix NCS differences graph problem where a chain break (of a different length) causes the differences graph to terminate early. Now we GetResidue() based on the master residue SeqNum() and InsCode() rather than by index of the peer chain. ------------------------------------------------------------------------ r2805 | pemsley | 2010-02-12 00:26:02 +0000 (Fri, 12 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build.cc Undisplay the merged molecules. ------------------------------------------------------------------------ r2804 | pemsley | 2010-02-11 23:24:23 +0000 (Thu, 11 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-waters.cc M /trunk/src/graphics-info.cc Update pointer distances on go-to-blob. ------------------------------------------------------------------------ r2803 | pemsley | 2010-02-11 22:59:01 +0000 (Thu, 11 Feb 2010) | 14 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Accepting sphere-refined atoms with the geometry graph up caused a crash. This fixes that. Now there is need for linear residue selection in render_geometry_distortion_blocks_internal(). Now we use map iterators. Old version is now called ..._linear(). make_distortion_string() factored out to make function shorter. New plot_blocks() function added. The residues for the restraints in graphics-info-graphs.cc's geometric_distortions_from_mol() now use the constructor that uses a vector of residues. geometry_distortion_info_t and geometry_distortion_info_container_t have << stream operators. Added a test. ------------------------------------------------------------------------ r2802 | pemsley | 2010-02-11 16:07:20 +0000 (Thu, 11 Feb 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi fix typo in sphere refinement script. ------------------------------------------------------------------------ r2801 | pemsley | 2010-02-11 12:01:01 +0000 (Thu, 11 Feb 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add chi angles note. ------------------------------------------------------------------------ r2800 | pemsley | 2010-02-10 15:47:04 +0000 (Wed, 10 Feb 2010) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-mutate.cc Don't display the "Insufficiently confident..." dialog on a succesful sequence docking. ------------------------------------------------------------------------ r2799 | pemsley | 2010-02-10 15:35:07 +0000 (Wed, 10 Feb 2010) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex Update tutorial-2 to build the B chain from a fit over the B helix. ------------------------------------------------------------------------ r2798 | pemsley | 2010-02-10 15:08:41 +0000 (Wed, 10 Feb 2010) | 12 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/testing.cc Improve the rigid-body refinement by making the size of the rotation corrections depend on the size of the fragment. Change the maximum number of rigid body rounds to 500. Add a output format method for ligand score card. SBase monomers option added to Search Monomer Library GUI. Add regularize-residues function (scheme only). Internally, a use_map flag has been added to generate_molecule_and_refine() and the map and weight arguments removed from the restraints_container_t constructor. scm_to_residue_specs() factored out for use with refine and regularize. --update-self added to --help output. Tidy up the menu item label for docs. ------------------------------------------------------------------------ r2797 | pemsley | 2010-02-10 14:59:14 +0000 (Wed, 10 Feb 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Long-bonded atoms shouldn't have long bonds to hydrogens. ------------------------------------------------------------------------ r2796 | pemsley | 2010-02-10 14:15:57 +0000 (Wed, 10 Feb 2010) | 3 lines Changed paths: M /trunk/doc/user-manual.texi Mention phase shift when using anomalous labels. Document --update-self ------------------------------------------------------------------------ r2795 | pemsley | 2010-02-09 19:20:39 +0000 (Tue, 09 Feb 2010) | 4 lines Changed paths: M /trunk/src/c-interface-network.cc M /trunk/src/coot.in M /trunk/src/testing.cc M /trunk/src/testing.hh Small test for coordinated_waters. Some interesting preliminary results. coot script now moved old binary directories to a revision-specific directory on install. ------------------------------------------------------------------------ r2794 | pemsley | 2010-02-09 19:18:43 +0000 (Tue, 09 Feb 2010) | 5 lines Changed paths: M /trunk/scheme/check-for-updates.scm M /trunk/scheme/coot-utils.scm Allow the progress bar to go to 100%, rather than finishing on 95% or so. pending-install-in-place-func takes an argument (sets the variable to #t or full now). Refactor download-binary-dialog. ------------------------------------------------------------------------ r2793 | pemsley | 2010-02-09 16:50:19 +0000 (Tue, 09 Feb 2010) | 3 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.hh A /trunk/coot-utils/water-coordination.cc Add water coordination search code. Not connected to molecule/graphics classes yet. ------------------------------------------------------------------------ r2792 | pemsley | 2010-02-09 16:49:10 +0000 (Tue, 09 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New prediction mechanism, using to-do list size, weighted. ------------------------------------------------------------------------ r2791 | pemsley | 2010-02-08 18:22:34 +0000 (Mon, 08 Feb 2010) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/libcheck.scm use show-spacegroup rather than (symmetry-operators->xHM (symmetry-operators imol)) for maps for now. ------------------------------------------------------------------------ r2790 | pemsley | 2010-02-08 15:25:34 +0000 (Mon, 08 Feb 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix transform-map with 5 arguments, use show-spacegroup and cell functions. ------------------------------------------------------------------------ r2789 | pemsley | 2010-02-08 14:55:29 +0000 (Mon, 08 Feb 2010) | 5 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/src/c-inner-main.c M /trunk/src/c-interface-network.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Put update-self in a thread so that we can provide a command-line progress bar of sorts. Clean up debugging of downloading. graphics_info_t::update_self added to hold state of command line argument: --update-self. run_update_self_maybe() added to c-inner-main functions. ------------------------------------------------------------------------ r2788 | pemsley | 2010-02-08 13:59:31 +0000 (Mon, 08 Feb 2010) | 7 lines Changed paths: M /trunk/scheme/check-for-updates.scm M /trunk/scheme/coot-utils.scm We want to use the update-self function from the command-line, so promote non-gui download-related functions into coot-utils.scm. run-download-binary-curl now takes functions that set the file-name and the download status (so that they can be used by functions that use curl-info). run-download-binary-curl is (also) run in a thread in update-self. ------------------------------------------------------------------------ r2787 | pemsley | 2010-02-08 01:42:37 +0000 (Mon, 08 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2786 | pemsley | 2010-02-08 01:41:29 +0000 (Mon, 08 Feb 2010) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo todo list was getting too big - cut features. ------------------------------------------------------------------------ r2785 | pemsley | 2010-02-08 01:39:42 +0000 (Mon, 08 Feb 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc HOPE is a SHELX keyword. ------------------------------------------------------------------------ r2784 | pemsley | 2010-02-08 01:39:18 +0000 (Mon, 08 Feb 2010) | 3 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc Enable Esc to interrupt refinement before the dialog is shown. Needed ugly gtk_events_pending()/gtk_main_iteration() usage. ------------------------------------------------------------------------ r2783 | pemsley | 2010-02-07 22:40:09 +0000 (Sun, 07 Feb 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/Makefile.am M /trunk/rel-todo Add a method to build tutorial-2.ps. Update notes. ------------------------------------------------------------------------ r2782 | pemsley | 2010-02-07 22:37:27 +0000 (Sun, 07 Feb 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Symmetry is updated on accepting a modification (replace_coords()). ------------------------------------------------------------------------ r2781 | pemsley | 2010-02-07 22:21:47 +0000 (Sun, 07 Feb 2010) | 4 lines Changed paths: M /trunk/scheme/check-for-updates.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm Move new-molecule-by-smiles-string into coot-utils.scm Check that file-name-for-progress-bar has been set to a file name before stopping the curl download in download-binary-dialog. ------------------------------------------------------------------------ r2780 | pemsley | 2010-02-07 22:15:41 +0000 (Sun, 07 Feb 2010) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc If low resolution limit is not set in the handle_column_label_make_fourier() then presume that it was 999.9. ------------------------------------------------------------------------ r2779 | pemsley | 2010-02-07 22:06:22 +0000 (Sun, 07 Feb 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation.cc M /trunk/src/gtk-manual.cc Remove debugging. ------------------------------------------------------------------------ r2778 | b.lohkamp | 2010-02-07 16:25:13 +0000 (Sun, 07 Feb 2010) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win update windows build to mmdb 1.22 and new clipper ------------------------------------------------------------------------ r2777 | pemsley | 2010-02-07 11:43:49 +0000 (Sun, 07 Feb 2010) | 3 lines Changed paths: M /trunk/src/graphics-info-gui.cc Fix for mis-indexing of molecule in fill_option_menu_with_coordinates_options_internal_3(). ------------------------------------------------------------------------ r2776 | b.lohkamp | 2010-02-06 16:57:53 +0000 (Sat, 06 Feb 2010) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py Fix python hydrogen pdb v3 test ------------------------------------------------------------------------ r2775 | pemsley | 2010-02-05 15:29:16 +0000 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple only download mmdb once. ------------------------------------------------------------------------ r2774 | pemsley | 2010-02-05 15:14:06 +0000 (Fri, 05 Feb 2010) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo Fix the test PDB file in the "Test for mangling of hydrogen names from a PDB v 3.0" test. No "D" atoms now. ------------------------------------------------------------------------ r2773 | pemsley | 2010-02-05 14:24:03 +0000 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Remove silly "L" accelerator. ------------------------------------------------------------------------ r2772 | pemsley | 2010-02-05 14:16:46 +0000 (Fri, 05 Feb 2010) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Add special case of " OXT" for atom names not being in the dictionary (" OXT" should not cause failure). ------------------------------------------------------------------------ r2771 | pemsley | 2010-02-05 13:46:42 +0000 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /trunk/mapview.glade M /trunk/src/interface.c Remove Check waters by difference map menu item from gtk1 interface. ------------------------------------------------------------------------ r2770 | pemsley | 2010-02-05 13:39:38 +0000 (Fri, 05 Feb 2010) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/read-sbase.cc M /trunk/rel-todo M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Enable atom name check before refinement (but not yet regularization). info_dialog_refinement_non_matching_atoms() convenience function introduced. ------------------------------------------------------------------------ r2769 | pemsley | 2010-02-05 12:55:20 +0000 (Fri, 05 Feb 2010) | 14 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc A /trunk/src/c-interface-waters-gui.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Waters with hydrogens now use half-bonds for the hydrogens. add_half_bonds() abstracted out. atom_id_mmdb_expand() moved out of the basic restraints class so that it can be used by the SBase residue reader. matching-compund-names-from-sbase function added. get-sbase-monomer function added. Check waters by difference map has moved into the check waters dialog and the extra "Check Waters by difference map" main menu item has been deleted. open_cif_dictionary_file_selector_dialog() exported to scripting level. standard_deviation_temperature_factor() function created. Various water gui interface functions moved into c-interface-waters-gui.cc fill_option_menu_with_map_options_internal() introducted, it takes a vector of molecule numbers. ------------------------------------------------------------------------ r2768 | b.lohkamp | 2010-02-05 06:55:09 +0000 (Fri, 05 Feb 2010) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-build.cc add python tests for residue type and residue spec generation. in python dont update mac binary fix some python formatting and reference counting ------------------------------------------------------------------------ r2767 | pemsley | 2010-02-05 00:28:45 +0000 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Clear up the MMDB_MAJOR_VERSION usage when calling sort_chains(). ------------------------------------------------------------------------ r2766 | pemsley | 2010-02-05 00:13:51 +0000 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Test that MMDB_VERSION is define before testing it. ------------------------------------------------------------------------ r2765 | pemsley | 2010-02-03 18:06:30 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/molecule-class-info-other.cc Conditionally (on MMDB version) use new mmdb function SortChains(). ------------------------------------------------------------------------ r2764 | pemsley | 2010-02-03 16:56:20 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add snarf-coot-docs chain-id kludge. ------------------------------------------------------------------------ r2763 | pemsley | 2010-02-03 16:55:43 +0000 (Wed, 03 Feb 2010) | 5 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/python/coot_utils.py M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Fixes for mmdb-1.22 const char *chainid; Allow the setting of gap and space penalties for alignment. wgap and wspace now move up into static graphic_info_t variables. Change chain_id() interface to scm and py functions. ------------------------------------------------------------------------ r2762 | pemsley | 2010-02-03 15:46:00 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update clippper version to 20091215. ------------------------------------------------------------------------ r2761 | pemsley | 2010-02-03 15:44:50 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points. ------------------------------------------------------------------------ r2760 | pemsley | 2010-02-03 15:43:48 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Update york ubuntu version. ------------------------------------------------------------------------ r2759 | pemsley | 2010-02-03 14:33:19 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove goosh. ------------------------------------------------------------------------ r2758 | pemsley | 2010-02-03 10:16:41 +0000 (Wed, 03 Feb 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add CPPFLAGS=-P to arguments for guile's configure. ------------------------------------------------------------------------ r2757 | pemsley | 2010-02-02 20:52:40 +0000 (Tue, 02 Feb 2010) | 3 lines Changed paths: M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/read-sbase.cc And add support for atom name checking vs dictionary Add sbase functions matching_sbase_residues_names() and get_sbase_residue(). ------------------------------------------------------------------------ r2756 | pemsley | 2010-02-02 15:26:06 +0000 (Tue, 02 Feb 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc GTK version protection around gtk_labe_set_markup(). ------------------------------------------------------------------------ r2755 | pemsley | 2010-02-01 17:52:49 +0000 (Mon, 01 Feb 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Add protection for a null dialog widget in alignment dialog. ------------------------------------------------------------------------ r2754 | pemsley | 2010-02-01 17:36:41 +0000 (Mon, 01 Feb 2010) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-gui.cc M /trunk/src/coot-align.hh M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc Add a info_dialog_alignment() for the alignment results of align&mutate. ------------------------------------------------------------------------ r2753 | pemsley | 2010-02-01 17:35:13 +0000 (Mon, 01 Feb 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2752 | pemsley | 2010-01-31 03:26:37 +0000 (Sun, 31 Jan 2010) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc Move molecule here by default is for small molecules, add a checkbutton to allow big molecules to move. fill_option_menu_with_coordinates_options_internal_3() made generic by taking a vector of molecule numbers. Add chain-id check for residue name changing. ------------------------------------------------------------------------ r2751 | pemsley | 2010-01-30 00:33:56 +0000 (Sat, 30 Jan 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Trivial formatting change. ------------------------------------------------------------------------ r2750 | pemsley | 2010-01-30 00:33:07 +0000 (Sat, 30 Jan 2010) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Tests added for residue type and residue spec generation. ------------------------------------------------------------------------ r2749 | pemsley | 2010-01-30 00:31:59 +0000 (Sat, 30 Jan 2010) | 2 lines Changed paths: M /trunk/python/coot_gui.py quick-save-as renamed here too. ------------------------------------------------------------------------ r2748 | pemsley | 2010-01-30 00:31:36 +0000 (Sat, 30 Jan 2010) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm Quick-save-as renanmed in keybindings dialog. Fixes for spec generation. Don't update binary if mac. ------------------------------------------------------------------------ r2747 | pemsley | 2010-01-29 23:56:57 +0000 (Fri, 29 Jan 2010) | 2 lines Changed paths: M /trunk/rel-todo New todo list. ------------------------------------------------------------------------ r2746 | pemsley | 2010-01-29 17:21:24 +0000 (Fri, 29 Jan 2010) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Add check buttons for display of Bumps and H-bonds/other bonds in environment distances. ------------------------------------------------------------------------ r2745 | pemsley | 2010-01-29 17:20:26 +0000 (Fri, 29 Jan 2010) | 2 lines Changed paths: M /trunk/rel-todo Empty rel-todo. ------------------------------------------------------------------------ r2744 | pemsley | 2010-01-29 17:18:47 +0000 (Fri, 29 Jan 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/burn-up/process-rel-todo.awk Move to 0.6.2 for the burn-up graph ------------------------------------------------------------------------ r2743 | pemsley | 2010-01-28 18:22:15 +0000 (Thu, 28 Jan 2010) | 2 lines Changed paths: M /trunk/configure.in New pre-release. ------------------------------------------------------------------------ r2742 | pemsley | 2010-01-27 11:17:56 +0000 (Wed, 27 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Notes to release notes. ------------------------------------------------------------------------ r2741 | pemsley | 2010-01-27 01:53:52 +0000 (Wed, 27 Jan 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add some useful debugging for the building the release path. ------------------------------------------------------------------------ r2740 | pemsley | 2010-01-26 23:53:38 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade A /trunk/pixmaps/coot-0.6.1.png A /trunk/pixmaps/coot-0.6.1.xpm M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.6.1 ------------------------------------------------------------------------ r2739 | pemsley | 2010-01-26 23:33:30 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/python/ncs.py M /trunk/python-tests/07_ncs.py skip_to_next_ncs_chain takes an argument, update python interface and test. ------------------------------------------------------------------------ r2738 | pemsley | 2010-01-26 23:19:21 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/07-ncs.scm M /trunk/greg-tests/begin.grg M /trunk/scheme/ncs.scm M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Some support for backwards NCS skipping (does not work yet). ------------------------------------------------------------------------ r2737 | pemsley | 2010-01-26 23:17:03 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New burn points, release prediction display adjustment. ------------------------------------------------------------------------ r2736 | pemsley | 2010-01-26 21:27:28 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/src/coot.in Opps - export GUILE_WARN_DEPRECATED. Should have done that ages ago. ------------------------------------------------------------------------ r2735 | pemsley | 2010-01-26 21:26:45 +0000 (Tue, 26 Jan 2010) | 3 lines Changed paths: M /trunk/scheme/check-for-updates.scm Comment out the format lines because when in a sub-thread the scripting window captures the output and tries to write it, causing a X11 error/crash. ------------------------------------------------------------------------ r2734 | pemsley | 2010-01-26 01:07:53 +0000 (Tue, 26 Jan 2010) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/gtk2-interface.c Add a tooltip for the model_toolbar_rot_trans_toolbutton. ------------------------------------------------------------------------ r2733 | pemsley | 2010-01-25 22:28:12 +0000 (Mon, 25 Jan 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Don't run refinements if there are no restraints for the residues involved. If a residue has a minimal description, detect it and delete it in try_dynamic_add(). ------------------------------------------------------------------------ r2732 | pemsley | 2010-01-25 17:01:20 +0000 (Mon, 25 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/globjects.cc handle some more keyboarding letters when in in_go_to_residue_keyboarding_mode. ------------------------------------------------------------------------ r2731 | pemsley | 2010-01-25 15:35:59 +0000 (Mon, 25 Jan 2010) | 3 lines Changed paths: M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/src/main.cc find_glycosidic_linkage_type() should be called twice because the residue arguments may be the wrong way round the first time. ------------------------------------------------------------------------ r2730 | pemsley | 2010-01-25 14:02:29 +0000 (Mon, 25 Jan 2010) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/high-res/sequence-assignment.cc M /trunk/ligand/ideal-rna.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Rework usage of deep_copy_residue(), normally, we don't want to attach a new chain to resulting residue. Add a chain_id to add_baton_atom(), which finds the chain or creates a new one. ------------------------------------------------------------------------ r2729 | b.lohkamp | 2010-01-24 22:49:39 +0000 (Sun, 24 Jan 2010) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/python/check_for_updates.py M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/fitting.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/python/hello.py M /trunk/python/raster3d.py M /trunk/src/c-interface.cc try to read python cached EDS files python greetings with coot version add pythonic sphere_refinement to fitting (and toolbuttons) make ppm2bmp (for windows) conditional since we dont make ppm screenshots any more reformat pythonic updates download output only use small icons in (pythonic) toolbar manager ------------------------------------------------------------------------ r2728 | b.lohkamp | 2010-01-24 20:13:50 +0000 (Sun, 24 Jan 2010) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/ccp4mg-utils/Makefile.am M /trunk/configure.in A /trunk/macros/libpng.m4 proper usage of (lib)png on windows (no change for other systems) ------------------------------------------------------------------------ r2727 | pemsley | 2010-01-24 16:32:50 +0000 (Sun, 24 Jan 2010) | 2 lines Changed paths: M /trunk/python/coot_gui.py Add DMS to python solvent ligand list. ------------------------------------------------------------------------ r2726 | pemsley | 2010-01-22 20:26:36 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Remove the sort-chains notes. ------------------------------------------------------------------------ r2725 | pemsley | 2010-01-22 20:26:07 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Revert to 2721 for sort_chains() function. ------------------------------------------------------------------------ r2724 | pemsley | 2010-01-22 17:03:48 +0000 (Fri, 22 Jan 2010) | 3 lines Changed paths: M /trunk/src/c-interface.cc another_level() tries to use imol_refinement_map() first, if it can, before using latest map. ------------------------------------------------------------------------ r2723 | pemsley | 2010-01-22 16:11:23 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2722 | pemsley | 2010-01-22 16:10:00 +0000 (Fri, 22 Jan 2010) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Use the utilities sort function, not the implicit one by using a minimol. Headers are preserved. ------------------------------------------------------------------------ r2721 | pemsley | 2010-01-22 16:08:56 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix up the sort_chains() function. ------------------------------------------------------------------------ r2720 | pemsley | 2010-01-22 16:07:58 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/doc/Makefile.am Add a rule to make tutorial.pdf ------------------------------------------------------------------------ r2719 | pemsley | 2010-01-22 16:07:22 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New annotations, burn points. ------------------------------------------------------------------------ r2718 | pemsley | 2010-01-22 12:12:38 +0000 (Fri, 22 Jan 2010) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/globjects.cc Check for go to atom keyboarding mode for B and C key releases. ------------------------------------------------------------------------ r2717 | pemsley | 2010-01-21 22:35:01 +0000 (Thu, 21 Jan 2010) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm Add DMS to solvent ligands. On merging molecules of solvent ligands to protein, unactivate the ligand molecule. ------------------------------------------------------------------------ r2716 | pemsley | 2010-01-20 19:23:12 +0000 (Wed, 20 Jan 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/src/c-inner-main.c M /trunk/src/c-inner-main.h M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc --python (and --no-graphics of course) results in a python prompt at the command line, scm_inner_main() calls start_command_line_python_maybe() instead of scm_shell(). Without USE_PYTHON we just fall out. ------------------------------------------------------------------------ r2715 | pemsley | 2010-01-20 19:02:28 +0000 (Wed, 20 Jan 2010) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Add BLOC to SHELXL non-atom keywords. ------------------------------------------------------------------------ r2714 | pemsley | 2010-01-20 18:23:48 +0000 (Wed, 20 Jan 2010) | 2 lines Changed paths: M /trunk/rel-todo More todo items. ------------------------------------------------------------------------ r2713 | pemsley | 2010-01-20 18:22:17 +0000 (Wed, 20 Jan 2010) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh Set the residue name in the constructor from a PPCAtom atom_selection. ------------------------------------------------------------------------ r2712 | pemsley | 2010-01-20 18:13:45 +0000 (Wed, 20 Jan 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debugging code added to curl build. ------------------------------------------------------------------------ r2711 | pemsley | 2010-01-20 18:03:31 +0000 (Wed, 20 Jan 2010) | 2 lines Changed paths: M /trunk/src/graphics-info-network.cc Add USE_LIBCURL protection to curl_handler_stop_it_flag_set(). ------------------------------------------------------------------------ r2710 | pemsley | 2010-01-19 13:44:47 +0000 (Tue, 19 Jan 2010) | 2 lines Changed paths: M /trunk/python/check_for_updates.py Fix the construction of the binary URL when getting from York (python version). ------------------------------------------------------------------------ r2709 | pemsley | 2010-01-19 13:42:24 +0000 (Tue, 19 Jan 2010) | 2 lines Changed paths: M /trunk/scheme/check-for-updates.scm Fix the construction of the binary URL when getting from York (scheme version). ------------------------------------------------------------------------ r2708 | pemsley | 2010-01-18 16:25:24 +0000 (Mon, 18 Jan 2010) | 3 lines Changed paths: M /trunk/src/graphics-info.h ifdef for curl handlers class. ifdefs for WII_INTERFACE. ------------------------------------------------------------------------ r2707 | pemsley | 2010-01-18 01:24:03 +0000 (Mon, 18 Jan 2010) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/rel-todo M /trunk/src/molecule-class-info-maps.cc Use biased_z_weighted_density_score() to score density fit - upweighting bad scores of fitting into negative density. ------------------------------------------------------------------------ r2705 | b.lohkamp | 2010-01-17 16:12:00 +0000 (Sun, 17 Jan 2010) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/begin.py update python tests and rework skipping mechanism ------------------------------------------------------------------------ r2704 | pemsley | 2010-01-17 16:08:30 +0000 (Sun, 17 Jan 2010) | 3 lines Changed paths: M /trunk/scheme/get-ebi.scm Try to read in the cached/pre-downloaded files when getting an accession code for the EDS (scheme version). ------------------------------------------------------------------------ r2703 | pemsley | 2010-01-17 13:56:06 +0000 (Sun, 17 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/generic-objects.scm After update probe dots, delete the sphere selection molecule, scheme version. ------------------------------------------------------------------------ r2702 | pemsley | 2010-01-17 12:54:33 +0000 (Sun, 17 Jan 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-defines.cc Update the Go To Atom dialog on mutating a base. Add history for base mutation function. Add DA, DC, etc to base names that are nucleotides in is_nucleotide(); ------------------------------------------------------------------------ r2701 | pemsley | 2010-01-17 11:54:03 +0000 (Sun, 17 Jan 2010) | 4 lines Changed paths: M /trunk/python/get_ebi.py M /trunk/scheme/get-ebi.scm When getting the mid-chars for geting eds pdb and mtz, use the downcase string, not the passed accession code id - enables getting EDS accession codes when typed in capitals. ------------------------------------------------------------------------ r2700 | pemsley | 2010-01-16 13:29:19 +0000 (Sat, 16 Jan 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Tweak I bond limit in handle_long_bonded_atom(). ------------------------------------------------------------------------ r2699 | pemsley | 2010-01-16 12:01:27 +0000 (Sat, 16 Jan 2010) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Quick fix for P-backbone mode in Symmetry CA. ------------------------------------------------------------------------ r2698 | pemsley | 2010-01-16 00:36:45 +0000 (Sat, 16 Jan 2010) | 2 lines Changed paths: M /trunk/mini-mol/testminimol.cc Comment out minimol test code because of GetAtomNameA compilation problems. ------------------------------------------------------------------------ r2697 | pemsley | 2010-01-16 00:32:48 +0000 (Sat, 16 Jan 2010) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Add patch to post-gtk2-glade.sh to anti-alias the green fish (go-to-atom toolbar icon). ------------------------------------------------------------------------ r2696 | pemsley | 2010-01-16 00:26:39 +0000 (Sat, 16 Jan 2010) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2695 | pemsley | 2010-01-16 00:26:09 +0000 (Sat, 16 Jan 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.h Add documentation for rigid-body-refine-by-residue-ranges in coot-utils. ------------------------------------------------------------------------ r2694 | pemsley | 2010-01-15 20:06:26 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Add SCM version protection for scm_without_guile() usage. ------------------------------------------------------------------------ r2693 | pemsley | 2010-01-15 20:00:52 +0000 (Fri, 15 Jan 2010) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/molecule-class-info-other.cc Hydrogen environment distances now are synchronised with the display of hydrogens. ------------------------------------------------------------------------ r2692 | pemsley | 2010-01-15 19:27:00 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Update documentation pointers. ------------------------------------------------------------------------ r2691 | pemsley | 2010-01-15 19:19:48 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix typo when testing for shelx molecule in sanitise-alt-confs. ------------------------------------------------------------------------ r2690 | pemsley | 2010-01-15 18:20:54 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/scheme/hello.scm Write out the coot-version info in hello.scm ------------------------------------------------------------------------ r2689 | pemsley | 2010-01-15 18:14:44 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2688 | pemsley | 2010-01-15 18:06:14 +0000 (Fri, 15 Jan 2010) | 7 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/rotamer.cc Remove special MSE rules (mapping to MET) in rotamer.cc. Fix cif tree parser so that it properly parses atom names in the tree (also could be argued that there is a bug in the dictionary - the tree atom names should be quoted). dictionary_residue_restraint_t has a new function: atom_name_for_tree_4c(). Add a test for rotamers for MSE. ------------------------------------------------------------------------ r2687 | pemsley | 2010-01-15 14:45:30 +0000 (Fri, 15 Jan 2010) | 8 lines Changed paths: M /trunk/mini-mol/testminimol.cc M /trunk/rel-todo M /trunk/scheme/check-for-updates.scm M /trunk/src/c-interface-network.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-network.cc M /trunk/src/graphics-info.h Rework binary download again - now it is in a thread, and that thread is long-lived and has to be called from scm_without_guile(). Code added to stop the download thread - we do that by setting a flag in curl_handlers which is examined in write_coot_curl_data_to_file(). And that returns 0 when it sees the stop flag set, hence terminating the download. The user data passed to write_coot_curl_data_to_file() is now a pointer to a pair of a FILE and a CURL handler pointer. ------------------------------------------------------------------------ r2686 | pemsley | 2010-01-15 11:03:54 +0000 (Fri, 15 Jan 2010) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix typo in a reference. ------------------------------------------------------------------------ r2685 | pemsley | 2010-01-13 12:27:53 +0000 (Wed, 13 Jan 2010) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Fix intelligent_previous_atom() when given specs for a recently deleted atom. Add internal test for this. No torsion restraints added for torsion restraints with ESD of 0. ------------------------------------------------------------------------ r2684 | pemsley | 2010-01-13 11:18:43 +0000 (Wed, 13 Jan 2010) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Add #ifdef USE_GUILE for curl_progress_info(). ------------------------------------------------------------------------ r2683 | pemsley | 2010-01-12 20:25:55 +0000 (Tue, 12 Jan 2010) | 5 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/check-for-updates.scm M /trunk/scheme/generic-objects.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-network.cc M /trunk/src/cc-interface.hh A /trunk/src/graphics-info-network.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc Change progress bar updating to use a libcurl function using the CURL handle. Still stall though, so commented out for commit. CURL handles are stored as a graphics_info_t static. Add various function to manipulate the list. ------------------------------------------------------------------------ r2682 | pemsley | 2010-01-12 18:42:48 +0000 (Tue, 12 Jan 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py new burnup points, and annotation. ------------------------------------------------------------------------ r2681 | pemsley | 2010-01-12 17:36:51 +0000 (Tue, 12 Jan 2010) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Delete F10 pre-releases from summary page. ------------------------------------------------------------------------ r2680 | b.lohkamp | 2010-01-11 16:52:51 +0000 (Mon, 11 Jan 2010) | 1 line Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/graphics-info.cc fix reference counting in pythonic user_defined_clicks ------------------------------------------------------------------------ r2679 | pemsley | 2010-01-09 10:50:44 +0000 (Sat, 09 Jan 2010) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/check-for-updates.scm M /trunk/src/c-interface-network.cc M /trunk/src/cc-interface.hh More adjustments to the scheme progress bar. Still not able to update the progress bar by reading the curl progess log without hanging. ------------------------------------------------------------------------ r2678 | pemsley | 2010-01-05 15:29:22 +0000 (Tue, 05 Jan 2010) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/ccp4mg-utils/Makefile.am M /trunk/rel-todo M /trunk/src/callbacks.c Default image type now PNG. ------------------------------------------------------------------------ r2677 | pemsley | 2010-01-05 15:28:04 +0000 (Tue, 05 Jan 2010) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Tidy up continuation markers. ------------------------------------------------------------------------ r2676 | pemsley | 2010-01-05 15:05:21 +0000 (Tue, 05 Jan 2010) | 7 lines Changed paths: M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/utils/coot-utils.cc M /trunk/utils/coot-utils.hh Make the file names for coordinates and PDB files in the stat file be relative if possible. Currently this is done simple-mindedly by checking if cwd string can be found in the file name, and stripping cwd out if it is. Backup and undo/redo function therefore need to take a cwd argument. relativise_file_name() added to utils. Test for relativise_file_name added to internal_tests. ------------------------------------------------------------------------ r2675 | pemsley | 2010-01-05 15:01:36 +0000 (Tue, 05 Jan 2010) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points ------------------------------------------------------------------------ r2674 | b.lohkamp | 2010-01-05 08:18:15 +0000 (Tue, 05 Jan 2010) | 1 line Changed paths: M /trunk/windows/WinCoot_install_masta.nsi fix CRs in WinCoot installer script ------------------------------------------------------------------------ r2673 | pemsley | 2010-01-05 01:44:35 +0000 (Tue, 05 Jan 2010) | 4 lines Changed paths: M /trunk/scheme/check-for-updates.scm M /trunk/scheme/extensions.scm Run the curl processes concurrently to capture the pid (then waitpid). This enables the Cancel button to send a SIGINT to the process when it is pressed. ------------------------------------------------------------------------ r2672 | pemsley | 2010-01-05 01:42:42 +0000 (Tue, 05 Jan 2010) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple When transfering files to biop, send the binary type too. ------------------------------------------------------------------------ r2671 | b.lohkamp | 2010-01-04 19:57:24 +0000 (Mon, 04 Jan 2010) | 1 line Changed paths: M /trunk/python/Makefile.am A /trunk/python/check_for_updates.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/extensions.py D /trunk/update-binary/check_for_updates.py enable (python) updates (only tested for windows as yet) ------------------------------------------------------------------------ r2670 | b.lohkamp | 2010-01-04 07:55:27 +0000 (Mon, 04 Jan 2010) | 1 line Changed paths: M /trunk/windows/WinCoot_install_masta.nsi updated windows installer (update compatible) ------------------------------------------------------------------------ r2669 | b.lohkamp | 2009-12-30 23:18:36 +0000 (Wed, 30 Dec 2009) | 1 line Changed paths: A /trunk/python-tests/09_internal.py M /trunk/python-tests/Makefile.am add python internal tests ------------------------------------------------------------------------ r2668 | pemsley | 2009-12-30 18:35:35 +0000 (Wed, 30 Dec 2009) | 2 lines Changed paths: A /trunk/src/c-interface-wii.cc Add wii interface code - not in build system yet. ------------------------------------------------------------------------ r2667 | b.lohkamp | 2009-12-30 13:27:48 +0000 (Wed, 30 Dec 2009) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/get_ebi.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/update-binary/check_for_updates.py update EDS data directory to new style for python pdb download info dialogs for unsuccessfull python cootaneer results add pythonic auto_weight_for_refinement tutorial data, auto weight and undo symmetry view for python Extensions add python tests for useful refinement results and splitting residues (neg occ) add refinement_results_to_py refine_residues_py returns refinement results now progressbar for python download (still more testing required though) ------------------------------------------------------------------------ r2666 | pemsley | 2009-12-30 10:06:57 +0000 (Wed, 30 Dec 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2665 | pemsley | 2009-12-29 15:11:12 +0000 (Tue, 29 Dec 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ideal/pepflip.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-refine.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc Cannonicalise the argument order of get_residue(). regularize_zone returns an it (were the restraints found flag). ------------------------------------------------------------------------ r2664 | pemsley | 2009-12-29 02:36:51 +0000 (Tue, 29 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update done items. ------------------------------------------------------------------------ r2663 | pemsley | 2009-12-29 02:36:13 +0000 (Tue, 29 Dec 2009) | 4 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-navigation.cc Fixup: check all molecule extents boxes in previous commmit (not just the first one). Add "Undo Symmetry View" to Extensions->Representations. ------------------------------------------------------------------------ r2662 | pemsley | 2009-12-29 02:02:33 +0000 (Tue, 29 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h Add undo_symmetry_view() function. Needs to be bound to a key to be useful. ------------------------------------------------------------------------ r2661 | pemsley | 2009-12-28 19:52:49 +0000 (Mon, 28 Dec 2009) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h Add function to return pkgdatadir, not used yet. Extensions menu item: Load tutorial data if you can find them (based on COOT_PREFIX). ------------------------------------------------------------------------ r2660 | pemsley | 2009-12-28 18:07:37 +0000 (Mon, 28 Dec 2009) | 3 lines Changed paths: M /trunk/doc/coot-faq.texi M /trunk/doc/user-manual.texi M /trunk/src/cc-interface.hh Add sidechain docking documentation. Fix up FAQ so that it formats correctly. ------------------------------------------------------------------------ r2659 | pemsley | 2009-12-28 17:26:41 +0000 (Mon, 28 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Remove a tiny bit of debugging. ------------------------------------------------------------------------ r2658 | pemsley | 2009-12-28 17:26:16 +0000 (Mon, 28 Dec 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/fitting.scm M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Improve GUI on not getting a fitting result in cootaneering. Fix up wolly thinking in fitting functions using with-auto-accept. ------------------------------------------------------------------------ r2657 | pemsley | 2009-12-28 13:50:35 +0000 (Mon, 28 Dec 2009) | 4 lines Changed paths: M /trunk/doc/interface-xml-to-texi.xsl M /trunk/doc/user-manual.texi M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/cc-interface.hh M /trunk/src/coot-dox.cfg Include cc-interface.hh functions in documentation. doxygen config file needed to set PREDEFINED USE_GUILE. cc-interface.hh function docs now in c++-style with sections. ------------------------------------------------------------------------ r2656 | pemsley | 2009-12-28 02:27:41 +0000 (Mon, 28 Dec 2009) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc Bonds to hydrogens are thin (half-width) - less distracting now. Colour enumerations are upper-cased now. ------------------------------------------------------------------------ r2655 | pemsley | 2009-12-27 18:01:55 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Tidy up by using functions. ------------------------------------------------------------------------ r2654 | pemsley | 2009-12-27 17:13:44 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Add release date prediction. ------------------------------------------------------------------------ r2653 | pemsley | 2009-12-27 12:52:00 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2652 | pemsley | 2009-12-27 12:35:49 +0000 (Sun, 27 Dec 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Fix for Takaaki Fukami alt conf problem. Don't set complementary atoms to negative occupancy if this is not a shelx molecule. ------------------------------------------------------------------------ r2651 | pemsley | 2009-12-27 11:25:33 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update done notes. ------------------------------------------------------------------------ r2650 | pemsley | 2009-12-27 11:24:58 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/macros/Makefile.am No need for these variables, automake takes care of the macros. ------------------------------------------------------------------------ r2649 | pemsley | 2009-12-27 11:24:12 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-refine.cc M /trunk/src/graphics-info-modelling.cc Fixes for gtk1 ------------------------------------------------------------------------ r2648 | pemsley | 2009-12-27 11:10:32 +0000 (Sun, 27 Dec 2009) | 2 lines Changed paths: A /trunk/src/c-interface-refine.cc Add needed c-interface-refine.cc. ------------------------------------------------------------------------ r2647 | pemsley | 2009-12-27 04:58:07 +0000 (Sun, 27 Dec 2009) | 7 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h auto-weight-for-refinement function added. Sphere refinement returns a SCM result. refine_residues_vec() returns a refinement_results_t. with-auto-accept macro returns a useful result. graphics_info_t::refinement_results_to_scm() function added. And added menu item to the extensions menu in the Refine sub-menu. ------------------------------------------------------------------------ r2646 | pemsley | 2009-12-24 12:59:16 +0000 (Thu, 24 Dec 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/src/coot-dox.cfg Add cc-interface.hh documentation. ------------------------------------------------------------------------ r2645 | pemsley | 2009-12-23 14:48:36 +0000 (Wed, 23 Dec 2009) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh A /trunk/greg-tests/09-internal.scm M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Add OXT mark test to internal test suite. Add internal tests to test suite. OXT in BCS issue addressed. ------------------------------------------------------------------------ r2644 | pemsley | 2009-12-22 20:32:33 +0000 (Tue, 22 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/get-ebi.scm Move to new-style (pdb-style) EDS data directory scheme. ------------------------------------------------------------------------ r2643 | pemsley | 2009-12-22 13:06:13 +0000 (Tue, 22 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Update the function definintions for snarfing. ------------------------------------------------------------------------ r2642 | pemsley | 2009-12-22 08:16:29 +0000 (Tue, 22 Dec 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/rel-todo Update notes, gleevec from obgen makes a broken PDB file (problem not with Coot). ------------------------------------------------------------------------ r2641 | b.lohkamp | 2009-12-21 15:20:38 +0000 (Mon, 21 Dec 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/update-binary/check_for_updates.py python update updated (more testing required) ------------------------------------------------------------------------ r2640 | pemsley | 2009-12-21 11:23:39 +0000 (Mon, 21 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update done item. ------------------------------------------------------------------------ r2639 | pemsley | 2009-12-21 11:23:13 +0000 (Mon, 21 Dec 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/graphics-info-superpose.cc Fix crash in SSM alignment output. fixes Ed Pozharski's crash. ------------------------------------------------------------------------ r2638 | b.lohkamp | 2009-12-21 10:18:03 +0000 (Mon, 21 Dec 2009) | 1 line Changed paths: M /trunk/windows/WinCoot_install_masta.nsi M /trunk/windows/make_wincoot_installer.bat M /trunk/windows/wincoot-autobuild-all update windows installer, binary type, curl ------------------------------------------------------------------------ r2637 | pemsley | 2009-12-20 18:40:21 +0000 (Sun, 20 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-kk.cc Add includes for compiling c-interface-kk.cc with Python enabled. ------------------------------------------------------------------------ r2636 | pemsley | 2009-12-20 13:42:56 +0000 (Sun, 20 Dec 2009) | 3 lines Changed paths: M /trunk/coot-utils/Makefile.am A /trunk/coot-utils/peak-search-from-list.cc M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/c-interface-kk.cc M /trunk/src/c-interface.h Add code from Kevin Keating to get symmetry equivalent peaks from a list with Python interface. ------------------------------------------------------------------------ r2635 | pemsley | 2009-12-19 10:49:30 +0000 (Sat, 19 Dec 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Use gtk_signal_connect() not g_signal_connect() for GTK1 compatibility. ------------------------------------------------------------------------ r2634 | pemsley | 2009-12-19 01:30:21 +0000 (Sat, 19 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo Update done items in rel-todo. ------------------------------------------------------------------------ r2633 | pemsley | 2009-12-19 01:29:29 +0000 (Sat, 19 Dec 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Move various skeleton gui functions into graphics_info_t. This allows the skeleton dialog OK button to activate the baton dialog if needed. ------------------------------------------------------------------------ r2632 | pemsley | 2009-12-18 22:43:03 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Improved behaviour on enter baton mode when there is no skelton. ------------------------------------------------------------------------ r2631 | pemsley | 2009-12-18 22:15:35 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h Move fill_option_menu_with_skeleton_options() to graphics_info_t. ------------------------------------------------------------------------ r2630 | pemsley | 2009-12-18 22:01:33 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Move wrapped_create_skeleton_dialog int graphics_info_t. ------------------------------------------------------------------------ r2629 | pemsley | 2009-12-18 11:41:54 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/check-for-updates.scm Fix permissions bits test. ------------------------------------------------------------------------ r2628 | pemsley | 2009-12-18 11:01:58 +0000 (Fri, 18 Dec 2009) | 3 lines Changed paths: M /trunk/scheme/check-for-updates.scm Correctly fill directory-is-modifiable? function. Let the binary url depend on host-dir (york test). ------------------------------------------------------------------------ r2627 | pemsley | 2009-12-18 09:28:21 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/check-for-updates.scm Remove http from the york setting of host-dir ------------------------------------------------------------------------ r2626 | pemsley | 2009-12-18 09:27:34 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/check-for-updates.scm make host-dir (e.g. York) depend on binary-type. ------------------------------------------------------------------------ r2625 | pemsley | 2009-12-18 09:16:24 +0000 (Fri, 18 Dec 2009) | 3 lines Changed paths: M /trunk/scheme/check-for-updates.scm Fix the logic of the directory-is-modifiable? test usage. Test needs to be implemented. ------------------------------------------------------------------------ r2624 | pemsley | 2009-12-18 09:04:25 +0000 (Fri, 18 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/check-for-updates.scm new-version was not set for release download (not used used in pre-release). ------------------------------------------------------------------------ r2623 | pemsley | 2009-12-17 17:06:13 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/scheme/check-for-updates.scm Fall back to system curl if coot-prefix/bin/curl is not available. ------------------------------------------------------------------------ r2622 | pemsley | 2009-12-17 16:52:58 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/Makefile.am A /trunk/scheme/check-for-updates.scm (from /trunk/update-binary/check-for-updates.scm:2616) M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm D /trunk/update-binary/check-for-updates.scm Add "Check for updates" into the GUI (scheme). ------------------------------------------------------------------------ r2621 | pemsley | 2009-12-17 16:52:01 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/src/coot.in Add notes about word splitting on args. ------------------------------------------------------------------------ r2620 | pemsley | 2009-12-17 16:51:20 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add report for fed-10 non-python build. ------------------------------------------------------------------------ r2619 | pemsley | 2009-12-17 15:19:02 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/rel-todo Update todo notes. ------------------------------------------------------------------------ r2618 | pemsley | 2009-12-17 15:18:24 +0000 (Thu, 17 Dec 2009) | 3 lines Changed paths: M /trunk/src/post-process-coot-wrap-guile.sh sed out SCM_STRINGP and SCM_STRING_LENGTH from swig output to try to remove some deprecated functions. ------------------------------------------------------------------------ r2617 | pemsley | 2009-12-17 10:47:32 +0000 (Thu, 17 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/rel-todo Fix syntax error in ssh_copy_logs_to_biop. ------------------------------------------------------------------------ r2616 | pemsley | 2009-12-16 15:20:00 +0000 (Wed, 16 Dec 2009) | 6 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/burn-up/burn-up.tab M /trunk/rel-todo M /trunk/src/c-interface-network.cc M /trunk/src/coot.in M /trunk/update-binary/check-for-updates.scm Update binaries now seems to work. The downloading of the files happen in threads and use curl (in the binary package). md5sums are checked and the binary file untared. On startup, bin/coot script checks for pending install, if it exists, it installs the directories before stating coot-real. ------------------------------------------------------------------------ r2615 | pemsley | 2009-12-16 10:25:33 +0000 (Wed, 16 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo ssh_copy_logs_to_biop and ssh_copy_to_biop functions added. ------------------------------------------------------------------------ r2614 | pemsley | 2009-12-16 01:12:00 +0000 (Wed, 16 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update done things. ------------------------------------------------------------------------ r2613 | pemsley | 2009-12-16 01:10:15 +0000 (Wed, 16 Dec 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add 64 bit Ubuntu 9.04. ------------------------------------------------------------------------ r2612 | pemsley | 2009-12-15 16:20:47 +0000 (Tue, 15 Dec 2009) | 2 lines Changed paths: M /trunk/dnotes More things to think about. ------------------------------------------------------------------------ r2611 | pemsley | 2009-12-15 16:20:20 +0000 (Tue, 15 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab Add burn up points ------------------------------------------------------------------------ r2610 | pemsley | 2009-12-15 16:19:53 +0000 (Tue, 15 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple More fixups for building libidn ------------------------------------------------------------------------ r2609 | pemsley | 2009-12-15 16:19:17 +0000 (Tue, 15 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Improve the baton building when the baton runs out of skeleton. ------------------------------------------------------------------------ r2608 | pemsley | 2009-12-14 18:10:54 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Trivial comment change. ------------------------------------------------------------------------ r2607 | pemsley | 2009-12-14 18:10:09 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/pixmaps/go-to-atom.svg Update go to atom icon. Not smooth in toolbar though. ------------------------------------------------------------------------ r2606 | pemsley | 2009-12-14 18:09:21 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/burn-up/process-rel-todo.awk Move to plotting 0.6.1 ------------------------------------------------------------------------ r2605 | pemsley | 2009-12-14 12:16:36 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc Fix logic of isTer() test in check_waters_by_difference_map(). ------------------------------------------------------------------------ r2604 | pemsley | 2009-12-14 11:13:20 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/python/coot_gui.py Similarly, tweak the URL in the python version. ------------------------------------------------------------------------ r2603 | pemsley | 2009-12-14 11:11:28 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/scheme/coot-gui.scm Tweak the RELEASE-NOTES url for Coot News. ------------------------------------------------------------------------ r2602 | pemsley | 2009-12-14 10:45:03 +0000 (Mon, 14 Dec 2009) | 3 lines Changed paths: M /trunk/src/c-interface.cc Tweak the string to "system" function for opening browser window with search results. Remove the quoted quotes. ------------------------------------------------------------------------ r2601 | pemsley | 2009-12-14 09:47:43 +0000 (Mon, 14 Dec 2009) | 2 lines Changed paths: A /trunk/macros/glib.m4 A /trunk/macros/gtk.m4 Add GTK+-1 macros glib.m4 and gtk.m4. Will delete for 0.7 series. ------------------------------------------------------------------------ r2600 | b.lohkamp | 2009-12-13 20:27:18 +0000 (Sun, 13 Dec 2009) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/WinCoot_install_masta.nsi M /trunk/windows/wincoot-autobuild-all updates for windows build ------------------------------------------------------------------------ r2599 | b.lohkamp | 2009-12-13 13:02:22 +0000 (Sun, 13 Dec 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in python tests fail immediately if problem loading modules ------------------------------------------------------------------------ r2598 | pemsley | 2009-12-11 22:47:11 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Quick-Save: bound to Control-S. ------------------------------------------------------------------------ r2597 | pemsley | 2009-12-11 22:03:28 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/python/coot_utils.py Fix recent try/except typo in coot_utils.py ------------------------------------------------------------------------ r2596 | pemsley | 2009-12-11 17:16:02 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi remove ldots from text. ------------------------------------------------------------------------ r2595 | pemsley | 2009-12-11 14:51:10 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/coot.in Add some Coot News. ------------------------------------------------------------------------ r2594 | pemsley | 2009-12-11 14:20:35 +0000 (Fri, 11 Dec 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py Add Bernhard's protection suggestion for conditionally-compiled coot_get_url_as_string ------------------------------------------------------------------------ r2593 | pemsley | 2009-12-11 13:57:21 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/build-it Fix typo in test for greg. ------------------------------------------------------------------------ r2592 | pemsley | 2009-12-11 13:46:18 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/build-it Fix comment typo. ------------------------------------------------------------------------ r2591 | pemsley | 2009-12-11 13:45:15 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/build-it coot_test_python stderr redirection. ------------------------------------------------------------------------ r2590 | pemsley | 2009-12-11 12:35:39 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update todo list. ------------------------------------------------------------------------ r2589 | pemsley | 2009-12-11 12:35:13 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Better document sphere refinement. ------------------------------------------------------------------------ r2588 | pemsley | 2009-12-11 00:23:41 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/build-it add libcurl and libidn to the build. ------------------------------------------------------------------------ r2587 | pemsley | 2009-12-11 00:19:35 +0000 (Fri, 11 Dec 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc get_chi_atom_names() can throw an exception. We should catch it. ------------------------------------------------------------------------ r2586 | pemsley | 2009-12-10 21:48:58 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/coot.in /bin/sh on ubuntu doesn't do functions. Pathetic. Sigh. Use /bin/bash. ------------------------------------------------------------------------ r2585 | pemsley | 2009-12-10 17:24:42 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add check that installation has libidn before building it. ------------------------------------------------------------------------ r2584 | pemsley | 2009-12-10 16:07:36 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add post-process-libcurl logic (for RHEL 4 64 bit). ------------------------------------------------------------------------ r2583 | pemsley | 2009-12-10 15:16:28 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Fix python ifdef. ------------------------------------------------------------------------ r2582 | pemsley | 2009-12-10 13:10:54 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/coot.in Fix typo in apply_pending_install function. ------------------------------------------------------------------------ r2581 | pemsley | 2009-12-10 13:10:12 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/coot.in Fix typo in apply_pending_install function. ------------------------------------------------------------------------ r2580 | pemsley | 2009-12-10 08:59:25 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo ------------------------------------------------------------------------ r2579 | b.lohkamp | 2009-12-10 08:48:25 +0000 (Thu, 10 Dec 2009) | 1 line Changed paths: M /trunk/build-it-win M /trunk/python/coot_utils.py M /trunk/src/c-interface-network.cc M /trunk/src/cc-interface.hh curl for windows and functions for python ------------------------------------------------------------------------ r2578 | pemsley | 2009-12-10 00:08:08 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/rel-todo Update rel-todo. ------------------------------------------------------------------------ r2577 | pemsley | 2009-12-10 00:06:29 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-state.cc Save the chi angles dialog to the state file. ------------------------------------------------------------------------ r2576 | pemsley | 2009-12-10 00:05:22 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/src/coot.in Add function to apply a new pending install before the real executable starts. ------------------------------------------------------------------------ r2575 | pemsley | 2009-12-10 00:02:06 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/update-binary/check-for-updates.scm More tinkering. Add a restart dialog. ------------------------------------------------------------------------ r2574 | pemsley | 2009-12-10 00:01:06 +0000 (Thu, 10 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add extra notes. ------------------------------------------------------------------------ r2573 | pemsley | 2009-12-09 15:51:05 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add LDFLAGS to args for libcurl configure. ------------------------------------------------------------------------ r2572 | pemsley | 2009-12-09 15:20:17 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in build libidn ------------------------------------------------------------------------ r2571 | pemsley | 2009-12-09 14:04:00 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Test for holding dir in making tar file. ------------------------------------------------------------------------ r2570 | pemsley | 2009-12-09 13:56:47 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Trivial comments formatting. ------------------------------------------------------------------------ r2569 | pemsley | 2009-12-09 11:49:44 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add some debugging info for README and RELEASE-NOTES install ------------------------------------------------------------------------ r2568 | pemsley | 2009-12-09 11:34:41 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add libidn to build (for curl). ------------------------------------------------------------------------ r2567 | pemsley | 2009-12-09 10:37:39 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: A /trunk/rel-todo New rel-todo for 0.6.1 ------------------------------------------------------------------------ r2566 | pemsley | 2009-12-09 10:03:08 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in untaring curl tar file. ------------------------------------------------------------------------ r2565 | pemsley | 2009-12-09 09:52:20 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/src/c-interface-network.cc Conditionally include curl/curl.h ------------------------------------------------------------------------ r2564 | pemsley | 2009-12-09 09:49:07 +0000 (Wed, 09 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in building curl test. ------------------------------------------------------------------------ r2563 | pemsley | 2009-12-08 20:20:20 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/update-binary/check-for-updates.scm Stop using phone-home. Still doesn't work. ------------------------------------------------------------------------ r2562 | pemsley | 2009-12-08 20:19:05 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Coot news system now uses coot-get-url-as-string instead of net http. ------------------------------------------------------------------------ r2561 | pemsley | 2009-12-08 20:17:29 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add curl to the build. ------------------------------------------------------------------------ r2560 | pemsley | 2009-12-08 20:12:45 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: D /trunk/rel-todo A /trunk/rel-todo-0.6 (from /trunk/rel-todo:2554) Move out (but save) the old rel-todo. ------------------------------------------------------------------------ r2559 | pemsley | 2009-12-08 19:36:52 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Gtk2 protection around on_go_to_atom_toolbutton_clicked(). ------------------------------------------------------------------------ r2558 | pemsley | 2009-12-08 13:24:33 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add curl to the build system. ------------------------------------------------------------------------ r2557 | pemsley | 2009-12-08 09:51:50 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/update-binary/check-for-updates.scm More update to check-for-updates - better, still not working. ------------------------------------------------------------------------ r2556 | pemsley | 2009-12-08 09:29:51 +0000 (Tue, 08 Dec 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/dnotes A /trunk/macros/guile-lib-guile-gui.m4 (from /trunk/macros/net-http-goosh.m4:2550) M /trunk/macros/libcurl.m4 D /trunk/macros/net-http-goosh.m4 M /trunk/scheme/get-ebi.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc A /trunk/src/c-interface-network.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/update-binary/check-for-updates.scm M /trunk/update-binary/phone-home.scm Start working to get libcurl in use and stop using net http. Updates to the update-binary mechanism. More needed. ------------------------------------------------------------------------ r2555 | pemsley | 2009-12-08 09:27:50 +0000 (Tue, 08 Dec 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Fix up the docs for the old coot reference. ------------------------------------------------------------------------ r2554 | pemsley | 2009-12-07 18:27:38 +0000 (Mon, 07 Dec 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Add tooltip to new toolbutton. ------------------------------------------------------------------------ r2553 | pemsley | 2009-12-07 16:58:43 +0000 (Mon, 07 Dec 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade glade file for Go To Atom toolbutton. ------------------------------------------------------------------------ r2552 | pemsley | 2009-12-07 16:57:44 +0000 (Mon, 07 Dec 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Add Go To Atom toolbutton to the toolbar. ------------------------------------------------------------------------ r2551 | pemsley | 2009-12-07 16:56:40 +0000 (Mon, 07 Dec 2009) | 2 lines Changed paths: M /trunk/configure.in Move on to pre-release (0.6.1-pre-1). ------------------------------------------------------------------------ r2550 | pemsley | 2009-12-04 18:14:07 +0000 (Fri, 04 Dec 2009) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r2549 | pemsley | 2009-12-04 18:13:50 +0000 (Fri, 04 Dec 2009) | 3 lines Changed paths: M /trunk/update-binary/check-for-updates.scm M /trunk/update-binary/download-binary-cmd.scm M /trunk/update-binary/phone-home.scm A few more updates and tweaking of updates mechanism. Waiting for curl/libcurl really. ------------------------------------------------------------------------ r2548 | pemsley | 2009-12-04 15:33:47 +0000 (Fri, 04 Dec 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Update the reference for coot. ------------------------------------------------------------------------ r2547 | pemsley | 2009-12-04 14:56:32 +0000 (Fri, 04 Dec 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Final graph points for 0.6. ------------------------------------------------------------------------ r2546 | pemsley | 2009-12-03 15:34:04 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Update to new refmac monomer-library. ------------------------------------------------------------------------ r2545 | pemsley | 2009-12-03 14:59:19 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple More use of $release_server_dir ------------------------------------------------------------------------ r2544 | pemsley | 2009-12-03 14:54:57 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix typo and get $coot_version.tar.gz from $release_server_dir ------------------------------------------------------------------------ r2543 | pemsley | 2009-12-03 14:37:13 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove several back-ticks. ------------------------------------------------------------------------ r2542 | pemsley | 2009-12-03 14:36:05 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Update the FAQ to Bill's page for Mac Coot. ------------------------------------------------------------------------ r2541 | pemsley | 2009-12-03 14:25:44 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Releases server is now in Oxford. ------------------------------------------------------------------------ r2540 | pemsley | 2009-12-03 13:50:36 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/mapview.glade A /trunk/pixmaps/coot-0.6.xpm M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/src/c-interface-gui.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h M /trunk/update-binary/check-for-updates.scm M /trunk/update-binary/phone-home.scm Release 0.6 ------------------------------------------------------------------------ r2539 | b.lohkamp | 2009-12-03 13:45:29 +0000 (Thu, 03 Dec 2009) | 1 line Changed paths: M /trunk/src/callbacks.c some cleanup of BL DEBUG statements ------------------------------------------------------------------------ r2538 | pemsley | 2009-12-03 13:33:06 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.6.png Update font for reference in splash screen. ------------------------------------------------------------------------ r2537 | pemsley | 2009-12-03 12:11:19 +0000 (Thu, 03 Dec 2009) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.6.png Add new splash screen. ------------------------------------------------------------------------ r2536 | b.lohkamp | 2009-12-03 09:11:42 +0000 (Thu, 03 Dec 2009) | 1 line Changed paths: M /trunk/python/extensions.py disable PISA python interface ------------------------------------------------------------------------ r2535 | b.lohkamp | 2009-12-01 09:39:08 +0000 (Tue, 01 Dec 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py fix label for python stepped refine ------------------------------------------------------------------------ r2534 | pemsley | 2009-11-30 23:32:55 +0000 (Mon, 30 Nov 2009) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r2533 | pemsley | 2009-11-30 23:32:27 +0000 (Mon, 30 Nov 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update release notes (averaging gui). ------------------------------------------------------------------------ r2532 | pemsley | 2009-11-30 23:31:27 +0000 (Mon, 30 Nov 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Renumber residue range activate item uses menu_item_label() now. ------------------------------------------------------------------------ r2531 | pemsley | 2009-11-30 23:27:04 +0000 (Mon, 30 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm fix the label for stepped refine. ------------------------------------------------------------------------ r2530 | pemsley | 2009-11-30 19:55:11 +0000 (Mon, 30 Nov 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/gl-matrix.cc M /trunk/src/gl-matrix.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/junk.cc Add some play/test code for orienting the side-chain up the screen. Doesn't work, the lib functions are in place but the activation code is commented. ------------------------------------------------------------------------ r2529 | pemsley | 2009-11-30 19:51:16 +0000 (Mon, 30 Nov 2009) | 3 lines Changed paths: M /trunk/macros/net-http-goosh.m4 Don't test for goosh, we don't use it any more. Test for guile components using $ac_cv_path_GUILE, not guile. ------------------------------------------------------------------------ r2528 | b.lohkamp | 2009-11-29 17:01:02 +0000 (Sun, 29 Nov 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python-tests/03_ligand.py update python scripts; add most_recently_created_file ------------------------------------------------------------------------ r2527 | b.lohkamp | 2009-11-27 16:11:20 +0000 (Fri, 27 Nov 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py M /trunk/python/parse_pisa_xml.py update python pisa parser, enabled in extensions (for now) ------------------------------------------------------------------------ r2526 | pemsley | 2009-11-27 09:58:10 +0000 (Fri, 27 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Add forgotten n-mav-boxes function for average-map-gui. ------------------------------------------------------------------------ r2525 | b.lohkamp | 2009-11-26 17:14:17 +0000 (Thu, 26 Nov 2009) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py fix typo in python resname_residue_gui and replace with updated function (nicer formatting) add average_map_gui for python ------------------------------------------------------------------------ r2524 | pemsley | 2009-11-26 09:24:24 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo trivial notes updates. ------------------------------------------------------------------------ r2523 | pemsley | 2009-11-26 09:23:47 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py Add resname_residue_gui. ------------------------------------------------------------------------ r2522 | pemsley | 2009-11-26 09:23:06 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add a warning key-sym-code not found in add-key-binding ------------------------------------------------------------------------ r2521 | pemsley | 2009-11-26 09:21:47 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/src/c-inner-main.c Don't run coot-tips if we don't have guile-gtk gui. ------------------------------------------------------------------------ r2520 | pemsley | 2009-11-26 09:20:59 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add a graphics draw in set_residue_name(). ------------------------------------------------------------------------ r2519 | pemsley | 2009-11-26 09:19:35 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Extend description of backrub-rotamers. ------------------------------------------------------------------------ r2518 | pemsley | 2009-11-26 09:19:02 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/configure.in Fix the AM_CONDITIONAL for the GTK2 test. ------------------------------------------------------------------------ r2517 | pemsley | 2009-11-26 08:17:25 +0000 (Thu, 26 Nov 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Use `if USING_GTK2_VERSION' conditional in src/Makefile to generate coot.py. ------------------------------------------------------------------------ r2516 | pemsley | 2009-11-24 15:16:47 +0000 (Tue, 24 Nov 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Fix gtk1 <-> gtk2 typo. ------------------------------------------------------------------------ r2515 | kevin.cowtan | 2009-11-24 14:45:16 +0000 (Tue, 24 Nov 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Add CIS peptide finding to FAQ ------------------------------------------------------------------------ r2514 | pemsley | 2009-11-24 13:44:15 +0000 (Tue, 24 Nov 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Fix typo, .cc not .c. ------------------------------------------------------------------------ r2513 | pemsley | 2009-11-24 13:30:46 +0000 (Tue, 24 Nov 2009) | 3 lines Changed paths: M /trunk/configure.in M /trunk/src/Makefile.am Try to use AM_CONDITIONAL to compile coot_wrap_python_gtk1.cc or coot_wrap_python_gtk2.cc as suggested by Tim Fenn. ------------------------------------------------------------------------ r2512 | pemsley | 2009-11-23 22:02:14 +0000 (Mon, 23 Nov 2009) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/03-ligand.scm M /trunk/src/restraints-editor.cc replace_monomer_restraints in geometry now returns 1 for replaced and 0 for added. "Added" is needed if the user changes the comp_id in the restraints editor (it should not be stored under the old comp_id in the dictionary). ------------------------------------------------------------------------ r2511 | pemsley | 2009-11-23 21:59:32 +0000 (Mon, 23 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm improve documentation string. ------------------------------------------------------------------------ r2510 | pemsley | 2009-11-23 21:58:50 +0000 (Mon, 23 Nov 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points. ------------------------------------------------------------------------ r2509 | pemsley | 2009-11-23 14:35:14 +0000 (Mon, 23 Nov 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add Rename Residue function and GUI and put it in the Modelling sub-menu. ------------------------------------------------------------------------ r2508 | pemsley | 2009-11-23 13:46:05 +0000 (Mon, 23 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add most-recently-created-file to coot-utils. ------------------------------------------------------------------------ r2507 | pemsley | 2009-11-23 13:13:47 +0000 (Mon, 23 Nov 2009) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2506 | pemsley | 2009-11-23 13:13:34 +0000 (Mon, 23 Nov 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk2-interface.c Put a close button on the "Close Molecule" dialog and don't destroy the dialog on pressing "Close marked molecules". Try to fix (crash?) problem of updating the Go To Atom dialog on deleting the go-to-atom molecule. ------------------------------------------------------------------------ r2505 | pemsley | 2009-11-22 16:09:45 +0000 (Sun, 22 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add a gui for average-map gui. Add it into the Map extensions. ------------------------------------------------------------------------ r2504 | pemsley | 2009-11-22 16:06:12 +0000 (Sun, 22 Nov 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc A better error message on not a number for average map scale. Trivial fix. ------------------------------------------------------------------------ r2503 | pemsley | 2009-11-20 15:04:14 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2502 | pemsley | 2009-11-20 15:03:05 +0000 (Fri, 20 Nov 2009) | 3 lines Changed paths: M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh Backrub rotamers now have back-rotation of individual peptides, trying restore to it's original position the O of the peptide, as best as possible. ------------------------------------------------------------------------ r2501 | pemsley | 2009-11-20 14:23:15 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/src/globjects.cc Now cis-peptides are marked as bad by default. ------------------------------------------------------------------------ r2500 | pemsley | 2009-11-20 13:11:15 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Handling coot.py, only move it if the swig was successful. ------------------------------------------------------------------------ r2499 | pemsley | 2009-11-20 13:10:13 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Update geometry graphs on delete_atom(). ------------------------------------------------------------------------ r2498 | pemsley | 2009-11-20 13:08:34 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/autogen.sh Add a new directory for aclocal macros. ------------------------------------------------------------------------ r2497 | pemsley | 2009-11-20 13:08:11 +0000 (Fri, 20 Nov 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/update-binary/download-binary-cmd.scm M /trunk/update-binary/download_binary_cmd.py M /trunk/update-binary/notes Update notes. ------------------------------------------------------------------------ r2496 | pemsley | 2009-11-18 12:23:11 +0000 (Wed, 18 Nov 2009) | 2 lines Changed paths: M /trunk/README M /trunk/TODO M /trunk/dnotes update notes. ------------------------------------------------------------------------ r2495 | pemsley | 2009-11-18 12:22:26 +0000 (Wed, 18 Nov 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo Make the installation of reference structures tar more verbose. ------------------------------------------------------------------------ r2494 | pemsley | 2009-11-18 11:46:56 +0000 (Wed, 18 Nov 2009) | 2 lines Changed paths: M /trunk/macros/Makefile.am M /trunk/macros/clipper.m4 Add some notes to macros. ------------------------------------------------------------------------ r2493 | pemsley | 2009-11-18 11:46:11 +0000 (Wed, 18 Nov 2009) | 3 lines Changed paths: M /trunk/surface/Makefile.am Add FFTW includes, clipper not necessarily in same place as FFTW. This fix will not be needed when cliper-config is used correctly. ------------------------------------------------------------------------ r2492 | pemsley | 2009-11-17 12:39:59 +0000 (Tue, 17 Nov 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple update the version of clipper (090522 had compilation problems on ubuntu 9.10). ------------------------------------------------------------------------ r2491 | b.lohkamp | 2009-11-12 16:56:44 +0000 (Thu, 12 Nov 2009) | 1 line Changed paths: M /trunk/build-it-win update libgnomecanavas version for windows build ------------------------------------------------------------------------ r2490 | pemsley | 2009-11-10 17:36:22 +0000 (Tue, 10 Nov 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi update FAQ. ------------------------------------------------------------------------ r2489 | pemsley | 2009-11-10 11:49:18 +0000 (Tue, 10 Nov 2009) | 2 lines Changed paths: A /trunk/macros/libcurl.m4 Add libcurl.m4, preparing for libcurl usage (killing of net-http). ------------------------------------------------------------------------ r2488 | pemsley | 2009-11-10 11:42:37 +0000 (Tue, 10 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Remove goosh from crash-catcher too (again, use os process). ------------------------------------------------------------------------ r2487 | pemsley | 2009-11-10 11:40:29 +0000 (Tue, 10 Nov 2009) | 2 lines Changed paths: M /trunk/configure.in M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Get rid of goosh dependency - use the one in guile-lib. ------------------------------------------------------------------------ r2486 | pemsley | 2009-11-09 23:42:31 +0000 (Mon, 09 Nov 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi M /trunk/doc/user-manual.texi Add Zalman notes to FAQ. ------------------------------------------------------------------------ r2485 | pemsley | 2009-11-09 12:51:21 +0000 (Mon, 09 Nov 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi update FAQ, old-coot dialog. ------------------------------------------------------------------------ r2484 | pemsley | 2009-11-05 15:34:04 +0000 (Thu, 05 Nov 2009) | 2 lines Changed paths: M /trunk/scheme/coot.scm Fix order of adding shelx-extensions.scm (only if gui has been loaded). ------------------------------------------------------------------------ r2483 | b.lohkamp | 2009-11-05 15:02:00 +0000 (Thu, 05 Nov 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/shelx_extensions.py add python shelx plugin ------------------------------------------------------------------------ r2482 | pemsley | 2009-11-03 23:16:46 +0000 (Tue, 03 Nov 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi update FAQs. ------------------------------------------------------------------------ r2481 | pemsley | 2009-11-02 13:12:17 +0000 (Mon, 02 Nov 2009) | 4 lines Changed paths: M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm M /trunk/scheme/shelx-extensions.scm Change shelx-extensions so that it defines the add-plugin-shelx function. Add an Extensions menu item "Plug-ins" and hang the shelx functions off that. ------------------------------------------------------------------------ r2480 | pemsley | 2009-11-02 00:15:00 +0000 (Mon, 02 Nov 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/rel-todo M /trunk/src/molecule-class-info-maps.cc Add a note - can't make the saving of original_fphidata work for shelx .cif sigmaa maps. ------------------------------------------------------------------------ r2479 | b.lohkamp | 2009-11-01 22:46:42 +0000 (Sun, 01 Nov 2009) | 1 line Changed paths: M /trunk/src/cc-interface.hh fix console float output ------------------------------------------------------------------------ r2478 | pemsley | 2009-11-01 17:45:15 +0000 (Sun, 01 Nov 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add nudge-residue function - and bind it to Ctrl-Arrow-keys. ------------------------------------------------------------------------ r2477 | b.lohkamp | 2009-11-01 16:27:46 +0000 (Sun, 01 Nov 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/fitting.py M /trunk/src/main.cc M /trunk/update-binary/check_for_updates.py A /trunk/update-binary/download_binary_cmd.py M /trunk/update-binary/phone_home.py add and update python update system pass command line args to python fix some python scripts new refmac dictionaries for windows too ------------------------------------------------------------------------ r2476 | pemsley | 2009-11-01 14:38:52 +0000 (Sun, 01 Nov 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2475 | pemsley | 2009-11-01 14:38:29 +0000 (Sun, 01 Nov 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New axes. ------------------------------------------------------------------------ r2474 | pemsley | 2009-11-01 11:43:26 +0000 (Sun, 01 Nov 2009) | 2 lines Changed paths: M /trunk/skeleton/Makefile.am skeleton depends on coords, so include geometry now. ------------------------------------------------------------------------ r2473 | pemsley | 2009-11-01 02:31:08 +0000 (Sun, 01 Nov 2009) | 3 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/src/c-interface-ligands.cc Change shift_range from 1 to 2 in peak_search::move_point_close_to_protein(). Fixes missing neighbouring peak problem (Kevin Keating). ------------------------------------------------------------------------ r2472 | pemsley | 2009-11-01 00:36:45 +0000 (Sun, 01 Nov 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/rel-todo Use the modified refmac monomer library. ------------------------------------------------------------------------ r2471 | pemsley | 2009-11-01 00:31:31 +0000 (Sun, 01 Nov 2009) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/fitting.scm In Fit Protein, check that there are more than 3 atoms in a residue before trying to rotamer-fit and refine it. Fixes "restraints problem" when trying to Fit Protein on a CA-only molecule. ------------------------------------------------------------------------ r2470 | pemsley | 2009-10-31 11:17:26 +0000 (Sat, 31 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Simply adjust formatting of auto_read_make_and_draw_maps(). ------------------------------------------------------------------------ r2469 | pemsley | 2009-10-31 10:40:53 +0000 (Sat, 31 Oct 2009) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h coords now depends on geometry, so that we can ask if 2 residues are linkable (and thus not draw environment distances) (2 phosphates are not linkable thus env distances should be drawn). ------------------------------------------------------------------------ r2468 | pemsley | 2009-10-31 07:35:54 +0000 (Sat, 31 Oct 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-superpose.cc update notes. ------------------------------------------------------------------------ r2467 | pemsley | 2009-10-31 07:33:07 +0000 (Sat, 31 Oct 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-superpose.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/testing.cc Tidy up SSM alignment output. ------------------------------------------------------------------------ r2466 | pemsley | 2009-10-30 23:22:58 +0000 (Fri, 30 Oct 2009) | 4 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Factor out printing function off horizonal SSM alignment printing (so that it can be tested). Update notes. ------------------------------------------------------------------------ r2465 | pemsley | 2009-10-30 23:21:07 +0000 (Fri, 30 Oct 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points. ------------------------------------------------------------------------ r2464 | pemsley | 2009-10-30 18:00:17 +0000 (Fri, 30 Oct 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-rama.hh M /trunk/coot-utils/coot-shelx.hh Add #ifndef protection for these header files. ------------------------------------------------------------------------ r2463 | pemsley | 2009-10-30 02:05:35 +0000 (Fri, 30 Oct 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-superpose.cc Fix alignment output crash bug. No crash now, but alignment not good. ------------------------------------------------------------------------ r2462 | pemsley | 2009-10-29 21:29:46 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Add missing atom assigment in move_waters_around_protein(). ------------------------------------------------------------------------ r2461 | pemsley | 2009-10-29 16:49:00 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-trim.hh M /trunk/coot-utils/trim.cc M /trunk/ligand/find-waters.cc M /trunk/src/molecule-class-info-other.cc coot-utils now does not depend on coords dir. ------------------------------------------------------------------------ r2460 | pemsley | 2009-10-29 16:40:07 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Fix another typo in map_peaks_near_point_py(). ------------------------------------------------------------------------ r2459 | pemsley | 2009-10-29 16:35:59 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Fix typo in map_peaks_near_point_py(). ------------------------------------------------------------------------ r2458 | pemsley | 2009-10-29 15:39:57 +0000 (Thu, 29 Oct 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h Try to add a horizontal sequence alignment. Better. Needs more testing. Fix up the post-ssm-transformation matching CA atom distances. ------------------------------------------------------------------------ r2457 | pemsley | 2009-10-29 15:38:38 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo update todo notes. ------------------------------------------------------------------------ r2456 | pemsley | 2009-10-29 15:38:01 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Factor out the identification of water peaks from their shifting. ------------------------------------------------------------------------ r2455 | pemsley | 2009-10-29 15:36:07 +0000 (Thu, 29 Oct 2009) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc Add cell and symmetry to synthetic molecule (from atom). Fixes Kevin Keating bug? ------------------------------------------------------------------------ r2454 | pemsley | 2009-10-29 15:34:28 +0000 (Thu, 29 Oct 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Factor out draw_these_residue_contacts() for ease of modification later. ------------------------------------------------------------------------ r2453 | pemsley | 2009-10-28 08:24:17 +0000 (Wed, 28 Oct 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-mutate.cc Change the gap penalty and extension penalty when aligning using SetAffineModel(). ------------------------------------------------------------------------ r2452 | pemsley | 2009-10-27 10:28:00 +0000 (Tue, 27 Oct 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/src/align.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc Rearrange todo items. Add in (as yet empty) function to print the SSM alignment sequence horizontally. Prepare to use SetAffineModel in alignment. ------------------------------------------------------------------------ r2451 | pemsley | 2009-10-27 10:24:38 +0000 (Tue, 27 Oct 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py extend data (y axis) range. ------------------------------------------------------------------------ r2450 | pemsley | 2009-10-26 01:48:10 +0000 (Mon, 26 Oct 2009) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/coot-faq.texi M /trunk/ligand/find-ligand.cc M /trunk/rel-todo Fix up several text files. improve --help mode of findligand. New URL for build-it script Fix typo in Aniso atoms Apply buton text. More rel-todo and TODO items. ------------------------------------------------------------------------ r2449 | pemsley | 2009-10-25 04:17:27 +0000 (Sun, 25 Oct 2009) | 3 lines Changed paths: M /trunk/src/command-line.cc M /trunk/src/molecule-class-info-maps.cc Rearrange the args for --help. save the fphidata in map_fill_from_cns_hkl(). ------------------------------------------------------------------------ r2448 | pemsley | 2009-10-24 18:28:55 +0100 (Sat, 24 Oct 2009) | 2 lines Changed paths: M /trunk/doc/coot-faq.texi Update the FAQ. Now looks reasonable. ------------------------------------------------------------------------ r2447 | pemsley | 2009-10-24 05:19:49 +0100 (Sat, 24 Oct 2009) | 2 lines Changed paths: M /trunk/coords/mmdb.cc Further fixes for refmac dictionary atom names (hydrogen names). ------------------------------------------------------------------------ r2446 | pemsley | 2009-10-24 03:51:43 +0100 (Sat, 24 Oct 2009) | 4 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h Convert PDB 3.x format prime name for nucleotide atoms to star names to correspond with the current refmac dictionary. Also change the names of the oxygens on the phophate (e.g. OP1 (new) -> O1P (old)). ------------------------------------------------------------------------ r2445 | b.lohkamp | 2009-10-23 13:12:23 +0100 (Fri, 23 Oct 2009) | 1 line Changed paths: M /trunk/build-it-win fix gzip compression in mmdb for windows (hopefully) ------------------------------------------------------------------------ r2444 | pemsley | 2009-10-22 10:37:36 +0100 (Thu, 22 Oct 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend the x-axis/day range. ------------------------------------------------------------------------ r2443 | pemsley | 2009-10-22 10:35:15 +0100 (Thu, 22 Oct 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Further fix the map sharpening text. ------------------------------------------------------------------------ r2442 | pemsley | 2009-10-22 10:32:32 +0100 (Thu, 22 Oct 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix typo in description of map sharpening. ------------------------------------------------------------------------ r2441 | b.lohkamp | 2009-10-21 08:59:04 +0100 (Wed, 21 Oct 2009) | 1 line Changed paths: M /trunk/python/refmac.py fix refmac log reader to cope with new refmac output ------------------------------------------------------------------------ r2440 | b.lohkamp | 2009-10-20 17:00:24 +0100 (Tue, 20 Oct 2009) | 1 line Changed paths: M /trunk/python/refmac.py fix python refmac module for saving parameters when run with orig mtz file ------------------------------------------------------------------------ r2439 | pemsley | 2009-10-20 01:38:02 +0100 (Tue, 20 Oct 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2438 | pemsley | 2009-10-20 01:35:46 +0100 (Tue, 20 Oct 2009) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Chiral volume string to int and back conversion. Use by restraints editor. ------------------------------------------------------------------------ r2437 | pemsley | 2009-10-20 00:25:45 +0100 (Tue, 20 Oct 2009) | 3 lines Changed paths: M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Fix the encoding of chiral signs, use strings in the restraints editor, not numbers (problem particularly for type "both"). ------------------------------------------------------------------------ r2436 | pemsley | 2009-10-19 19:19:51 +0100 (Mon, 19 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add a history for assign-sequence. ------------------------------------------------------------------------ r2435 | pemsley | 2009-10-19 15:51:31 +0100 (Mon, 19 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add missing imol to history in assign_pir_sequence(). ------------------------------------------------------------------------ r2434 | pemsley | 2009-10-19 14:59:08 +0100 (Mon, 19 Oct 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2433 | pemsley | 2009-10-19 11:32:00 +0100 (Mon, 19 Oct 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Ubuntu build depends on libxmu-dev, it seems. ------------------------------------------------------------------------ r2432 | pemsley | 2009-10-19 11:28:47 +0100 (Mon, 19 Oct 2009) | 3 lines Changed paths: M /trunk/python/Makefile.am The distribution and conditional installation of coot.py is handled in the src directory, it should not be referenced in the python directory. ------------------------------------------------------------------------ r2431 | pemsley | 2009-10-18 16:35:52 +0100 (Sun, 18 Oct 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Update the backrub-rotamer documentation. ------------------------------------------------------------------------ r2430 | pemsley | 2009-10-17 21:47:45 +0100 (Sat, 17 Oct 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in doc sequence function. ------------------------------------------------------------------------ r2429 | pemsley | 2009-10-17 18:22:57 +0100 (Sat, 17 Oct 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix up for add-button-info for views box. ------------------------------------------------------------------------ r2428 | b.lohkamp | 2009-10-16 09:02:44 +0100 (Fri, 16 Oct 2009) | 1 line Changed paths: M /trunk/build-it-win M /trunk/windows/wincoot-autobuild-all update windows build system ------------------------------------------------------------------------ r2427 | pemsley | 2009-10-16 04:51:14 +0100 (Fri, 16 Oct 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Add coot_gtk1.py and coot_gtk2.py to EXTRA_DIST. ------------------------------------------------------------------------ r2426 | b.lohkamp | 2009-10-14 11:57:40 +0100 (Wed, 14 Oct 2009) | 4 lines Changed paths: M /trunk/Makefile.am M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/extensions.py M /trunk/python/libcheck.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/03_ligand.py A /trunk/windows/syminfo.lib python libcheck uses coot-ccp4 dir now too (and update test) add Monomer from Dictionary in python extensions add windows syminfo.lib file, make will install either or ------------------------------------------------------------------------ r2425 | pemsley | 2009-10-12 18:11:43 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/scheme/libcheck.scm Fix up greg test for get monomer to find libcheck output in coot-ccp4. ------------------------------------------------------------------------ r2424 | pemsley | 2009-10-12 18:10:20 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab more burn-up points. ------------------------------------------------------------------------ r2423 | pemsley | 2009-10-12 13:27:04 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am Add rules to make coot_gtk1.py and coot_gtk2.py ------------------------------------------------------------------------ r2422 | pemsley | 2009-10-12 12:05:21 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/rel-todo update release todo. Nothing left. ------------------------------------------------------------------------ r2421 | pemsley | 2009-10-12 11:43:41 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/src/command-line.cc change --test to --self-test in command line arguments. ------------------------------------------------------------------------ r2420 | pemsley | 2009-10-12 11:24:13 +0100 (Mon, 12 Oct 2009) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/build-it-gtk2-simple M /trunk/configure.in A /trunk/data A /trunk/data/Makefile.am A /trunk/data/rnasa-1.8-all_refmac1.mtz A /trunk/data/tutorial-modern.pdb Add data dir, for self-test data (maybe demo later). Add in the build-script a note where to find libcurl. ------------------------------------------------------------------------ r2419 | pemsley | 2009-10-12 10:37:13 +0100 (Mon, 12 Oct 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/configure.in M /trunk/src/Makefile.am Change the rules for making and installing coot.py - now it depends on SWIG_FLAGS and COOT_USE_PYTHON. ------------------------------------------------------------------------ r2418 | pemsley | 2009-10-12 10:35:52 +0100 (Mon, 12 Oct 2009) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/libcheck.scm Put the libcheck files in coot-ccp4 dir. if append-dir-file is called with blank dir, don't do a string-append. ------------------------------------------------------------------------ r2417 | pemsley | 2009-10-12 10:19:04 +0100 (Mon, 12 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Return -1 on molecule not found for get_monomer_from_dictionary(). ------------------------------------------------------------------------ r2416 | b.lohkamp | 2009-10-12 09:45:36 +0100 (Mon, 12 Oct 2009) | 1 line Changed paths: M /trunk/build-it-win M /trunk/python-tests/coot_unittest.py M /trunk/windows/make_wincoot_installer.bat M /trunk/windows/wincoot-autobuild-all update windows build system ------------------------------------------------------------------------ r2415 | pemsley | 2009-10-11 15:58:09 +0100 (Sun, 11 Oct 2009) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Remove debugging. ------------------------------------------------------------------------ r2414 | pemsley | 2009-10-10 14:26:46 +0100 (Sat, 10 Oct 2009) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/burn-up/new-graph.py M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/scheme/extensions.scm Add reading of simple x y z coordinates in cif reader. Add interface to get_monomer_from_dictionary(). update burn-up graph. ------------------------------------------------------------------------ r2413 | pemsley | 2009-10-10 08:35:21 +0100 (Sat, 10 Oct 2009) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc Add protection for usage fo the go to atom window on using sort_chains(). Prevents potential crash [JED]. ------------------------------------------------------------------------ r2412 | pemsley | 2009-10-10 01:06:13 +0100 (Sat, 10 Oct 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Save the resolution limits of the mtz file (if any) to the state file. ------------------------------------------------------------------------ r2411 | pemsley | 2009-10-09 20:23:58 +0100 (Fri, 09 Oct 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/doc/user-manual.texi M /trunk/geometry/protein-geometry.cc Use coot::utils float/int to string converters in dict_torsion_restraint_t::format(). ------------------------------------------------------------------------ r2410 | pemsley | 2009-10-09 15:08:01 +0100 (Fri, 09 Oct 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Add a coordinates file opener in the toolbar. ------------------------------------------------------------------------ r2409 | pemsley | 2009-10-09 14:06:16 +0100 (Fri, 09 Oct 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Updates on graph plotting. Update notes. ------------------------------------------------------------------------ r2408 | pemsley | 2009-10-08 19:32:20 +0100 (Thu, 08 Oct 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add a favicon to the build-info page. ------------------------------------------------------------------------ r2407 | pemsley | 2009-10-08 16:13:17 +0100 (Thu, 08 Oct 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc Remove the exception in get_atom_index_quad because the catch was empty. Use a pair with a bool instead. ------------------------------------------------------------------------ r2406 | pemsley | 2009-10-08 15:08:10 +0100 (Thu, 08 Oct 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Give dict_torsion_restraint a format() function, use this instead of ostringstream in get_atom_index_quad(). Possible fixes a mac crash. ------------------------------------------------------------------------ r2405 | pemsley | 2009-10-08 13:58:33 +0100 (Thu, 08 Oct 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/gtk2-interface.c Put the full GPLv3 licence in the licence box in the about dialog. ------------------------------------------------------------------------ r2404 | pemsley | 2009-10-07 22:23:28 +0100 (Wed, 07 Oct 2009) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/TODO M /trunk/configure.in M /trunk/coords/coot-close.hh M /trunk/dnotes M /trunk/ideal/Makefile.am M /trunk/ligand/rotamer-tables.cc M /trunk/python/Makefile.am M /trunk/rama-data/Makefile.am M /trunk/src/Makefile.am Convert to GPL version 3 the files that had been missed previously. ------------------------------------------------------------------------ r2403 | pemsley | 2009-10-07 11:53:00 +0100 (Wed, 07 Oct 2009) | 2 lines Changed paths: M /trunk/configure.in Remove generation of setup files from configure.in. ------------------------------------------------------------------------ r2402 | b.lohkamp | 2009-10-06 14:04:45 +0100 (Tue, 06 Oct 2009) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/parse_pisa_xml.py update python solvent_ligands_gui and views_panel_gui ------------------------------------------------------------------------ r2401 | kevin.cowtan | 2009-10-06 10:48:27 +0100 (Tue, 06 Oct 2009) | 9 lines Changed paths: M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/main.cc Add internal self-test option. The aim here is to have a set of tests that the user rather than the packager can run. This is needed because there are increasing number of external packagers building the code, who may not be running the existing test suite. Given a bug report, we can ask them to run a self-test and check that the results agree with our builds. So far, this only runs the clipper self tests. Also, interestingly, the clipper-contrib test fails when doing a sigmaa calculation. ------------------------------------------------------------------------ r2400 | pemsley | 2009-10-04 05:59:36 +0100 (Sun, 04 Oct 2009) | 3 lines Changed paths: M /trunk/coot-utils/Makefile.am Re-order lib_LTLIBRARIES so that they are built in the correct order [Tim Fenn]. ------------------------------------------------------------------------ r2399 | pemsley | 2009-10-03 22:53:45 +0100 (Sat, 03 Oct 2009) | 3 lines Changed paths: M /trunk/python/Makefile.am M /trunk/scheme/Makefile.am Use dist_python_DATA, not EXTRA_DIST. Similarly use dist_scheme_DATA, not EXTRA_DIST. ------------------------------------------------------------------------ r2398 | pemsley | 2009-10-03 03:13:33 +0100 (Sat, 03 Oct 2009) | 2 lines Changed paths: M /trunk/python/Makefile.am Remove duplication of coot_load_modules.py ------------------------------------------------------------------------ r2397 | pemsley | 2009-10-03 02:54:15 +0100 (Sat, 03 Oct 2009) | 3 lines Changed paths: M /trunk/src/Makefile.am Use $SHELL not bash to run the post-process script, Windows build does not have bash, it seems. ------------------------------------------------------------------------ r2396 | pemsley | 2009-10-02 07:10:54 +0100 (Fri, 02 Oct 2009) | 2 lines Changed paths: M /trunk/high-res/Makefile.am Fixups for utils in high-res Makefile.am ------------------------------------------------------------------------ r2395 | pemsley | 2009-10-02 06:54:55 +0100 (Fri, 02 Oct 2009) | 2 lines Changed paths: M /trunk/coords/Makefile.am Add utils dir to INCLUDES for coords. ------------------------------------------------------------------------ r2394 | pemsley | 2009-10-02 06:49:16 +0100 (Fri, 02 Oct 2009) | 2 lines Changed paths: M /trunk/compat/Makefile.am Add sleep-fixups.h to Makefile.am for make dist. ------------------------------------------------------------------------ r2393 | b.lohkamp | 2009-10-01 21:43:24 +0100 (Thu, 01 Oct 2009) | 1 line Changed paths: A /trunk/compat/sleep-fixups.h M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/main.cc fix up sleeping for Windows ------------------------------------------------------------------------ r2392 | pemsley | 2009-10-01 19:24:25 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/coot-utils/Makefile.am Add the utils dir to the includes of the coot-utils. ------------------------------------------------------------------------ r2391 | b.lohkamp | 2009-10-01 16:37:51 +0100 (Thu, 01 Oct 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/macros/clipper.m4 M /trunk/macros/coot-windows.m4 M /trunk/macros/glut.m4 M /trunk/macros/with-python.m4 M /trunk/src/c-interface.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/main.cc M /trunk/windows/wincoot-autobuild-all adjustments for windows, esp new MinGW ------------------------------------------------------------------------ r2390 | pemsley | 2009-10-01 14:30:15 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/src/post-process-coot-wrap-guile.sh Remove some debugging. ------------------------------------------------------------------------ r2389 | pemsley | 2009-10-01 14:29:49 +0100 (Thu, 01 Oct 2009) | 6 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/macros/with-guile.m4 M /trunk/src/Makefile.am M /trunk/src/c-interface.cc M /trunk/src/graphics-info-state.cc M /trunk/src/post-process-coot-wrap-guile.sh Don't use AM_CONDITIONAL for COOT_USE_GUILE, use AC_SUBST. Don't use conditionals in Makefile for COOT_USE_GUILE. Some fixups for not compiling with guile or python. Pass guile-config to post-process-coot-wrap-guile.sh not the results of guile-config. ------------------------------------------------------------------------ r2388 | pemsley | 2009-10-01 13:31:00 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix problems of returning a value when not compiled with guile or python. ------------------------------------------------------------------------ r2387 | pemsley | 2009-10-01 10:27:55 +0100 (Thu, 01 Oct 2009) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/post-process-coot-wrap-guile.sh Use bash, not pathetic sh to post-process coot_wrap files. Make sure that the ifdefs are added to the guile 1.6 path too. ------------------------------------------------------------------------ r2386 | pemsley | 2009-10-01 09:55:58 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/Makefile.am Fix incorrect directory build order. ------------------------------------------------------------------------ r2385 | pemsley | 2009-10-01 09:48:52 +0100 (Thu, 01 Oct 2009) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in D /trunk/sequence-view/seq-view-interface.c D /trunk/sequence-view/seq-view-interface.h D /trunk/sequence-view/sequence-view.cc D /trunk/sequence-view/sequence-view.hh M /trunk/src/Makefile.am A /trunk/src/seq-view-interface.c (from /trunk/sequence-view/seq-view-interface.c:2372) A /trunk/src/seq-view-interface.h (from /trunk/sequence-view/seq-view-interface.h:2372) A /trunk/src/sequence-view.cc (from /trunk/sequence-view/sequence-view.cc:2372) A /trunk/src/sequence-view.hh (from /trunk/sequence-view/sequence-view.hh:2372) Move sequence-view code into src/ dir, unconventional dependencies removed and undefined symbols resolved. ------------------------------------------------------------------------ r2384 | pemsley | 2009-10-01 09:32:58 +0100 (Thu, 01 Oct 2009) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/analysis/Makefile.am M /trunk/build/Makefile.am M /trunk/configure.in M /trunk/coords/Makefile.am M /trunk/coot-utils/Makefile.am D /trunk/coot-utils/atomic-numbers.cc D /trunk/coot-utils/coot-fasta.cc D /trunk/coot-utils/coot-fasta.hh D /trunk/coot-utils/coot-utils.cc D /trunk/coot-utils/coot-utils.hh D /trunk/coot-utils/gdk-keysym.awk D /trunk/coot-utils/gdk-keysyms.cc M /trunk/db-main/Makefile.am M /trunk/geometry/Makefile.am M /trunk/ideal/Makefile.am M /trunk/ligand/Makefile.am M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/Makefile.am A /trunk/utils A /trunk/utils/Makefile.am A /trunk/utils/atomic-numbers.cc (from /trunk/coot-utils/atomic-numbers.cc:2372) A /trunk/utils/coot-fasta.cc (from /trunk/coot-utils/coot-fasta.cc:2372) A /trunk/utils/coot-fasta.hh (from /trunk/coot-utils/coot-fasta.hh:2372) A /trunk/utils/coot-utils.cc (from /trunk/coot-utils/coot-utils.cc:2372) A /trunk/utils/coot-utils.hh (from /trunk/coot-utils/coot-utils.hh:2372) A /trunk/utils/gdk-keysym.awk (from /trunk/coot-utils/gdk-keysym.awk:2372) A /trunk/utils/gdk-keysyms.cc (from /trunk/coot-utils/gdk-keysyms.cc:2372) Split trivial utils (utils) from crystallographic utils (still coot-utils). Fix up Makefiles to depend on new utils lib. ------------------------------------------------------------------------ r2383 | pemsley | 2009-10-01 08:22:49 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple comment out the deletion of the coot_wrap files. No longer needed. ------------------------------------------------------------------------ r2382 | pemsley | 2009-10-01 08:20:27 +0100 (Thu, 01 Oct 2009) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/post-process-coot-wrap-guile.sh M /trunk/src/post-process-coot-wrap-python.sh Change the way the coot_wrap files are handled. We no longer make lib_coot_wrap* libraries and now the GTK1 and GTK2 versions are distinguished. ------------------------------------------------------------------------ r2381 | pemsley | 2009-10-01 00:47:28 +0100 (Thu, 01 Oct 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.cc remove remaining atom-utils.h include. ------------------------------------------------------------------------ r2380 | pemsley | 2009-09-30 17:48:36 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo And now typo in rel-todo. ------------------------------------------------------------------------ r2379 | pemsley | 2009-09-30 17:48:05 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab fix burn up point from typo in rel-todo. ------------------------------------------------------------------------ r2378 | pemsley | 2009-09-30 17:41:01 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab More burn-up points. ------------------------------------------------------------------------ r2377 | pemsley | 2009-09-30 15:46:02 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/high-res/Makefile.am M /trunk/surface/Makefile.am LDADDs for surface and high-res. ------------------------------------------------------------------------ r2376 | pemsley | 2009-09-30 15:38:46 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/coot-surface/Makefile.am M /trunk/dnotes LDADD for coot-surface. ------------------------------------------------------------------------ r2375 | pemsley | 2009-09-30 13:39:17 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-lsq.cc Simply wrap a long cout line. ------------------------------------------------------------------------ r2374 | pemsley | 2009-09-30 13:20:34 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: D /trunk/atom-utils Remove atom-utils directory. ------------------------------------------------------------------------ r2373 | pemsley | 2009-09-30 13:19:13 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc Remove atom-utils from coot build. ------------------------------------------------------------------------ r2372 | pemsley | 2009-09-30 13:09:28 +0100 (Wed, 30 Sep 2009) | 3 lines Changed paths: M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am Remove dependency of skeleton on atom-utils. LIBADD the coot-skeleton lib to remove undefined symbols. ------------------------------------------------------------------------ r2371 | b.lohkamp | 2009-09-30 11:38:25 +0100 (Wed, 30 Sep 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/python/ncs.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/user-mods.cc update and fix reference counting in PyLists collect garbage after python tests update CA/P lsq if not nucleotide or amino acid according to mmdb assume nulceotide print warning ------------------------------------------------------------------------ r2370 | pemsley | 2009-09-30 05:44:01 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/sequence-view/Makefile.am LIBADD for sequence_view (not completely resolved (to be expected)). ------------------------------------------------------------------------ r2369 | pemsley | 2009-09-30 05:36:54 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/geometry/Makefile.am M /trunk/ligand/Makefile.am More _LIBADD additions: ligand geometry and coot-utils. ------------------------------------------------------------------------ r2368 | pemsley | 2009-09-30 04:50:21 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/db-main/Makefile.am M /trunk/doc/user-manual.texi coords depends on mini-mol. Build mini-mol first. ------------------------------------------------------------------------ r2367 | pemsley | 2009-09-30 04:24:06 +0100 (Wed, 30 Sep 2009) | 2 lines Changed paths: M /trunk/Makefile.am density-contour depends on coords, build coords before density-contour. ------------------------------------------------------------------------ r2366 | pemsley | 2009-09-29 16:37:24 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/analysis/Makefile.am Fix typo in libcoot_analysis_la_LIBADD. ------------------------------------------------------------------------ r2365 | pemsley | 2009-09-29 16:15:53 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/build/Makefile.am Fix typo in libcoot_cabuild_la_LIBADD. ------------------------------------------------------------------------ r2364 | pemsley | 2009-09-29 14:00:38 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/density-contour/Makefile.am clean up undefined symbols for isosurface lib. ------------------------------------------------------------------------ r2363 | pemsley | 2009-09-29 13:56:12 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/db-main/Makefile.am clean up undefined symbols for db-main lib. ------------------------------------------------------------------------ r2362 | pemsley | 2009-09-29 13:48:34 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/build/Makefile.am clean up undefined symbols for cabuild lib. ------------------------------------------------------------------------ r2361 | pemsley | 2009-09-29 13:45:13 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/cootaneer/Makefile.am clean up undefined symbols for cootaneer lib. ------------------------------------------------------------------------ r2360 | pemsley | 2009-09-29 13:43:00 +0100 (Tue, 29 Sep 2009) | 2 lines Changed paths: M /trunk/analysis/Makefile.am M /trunk/coords/Makefile.am More use of libxxx_la_LIBADD to clean up undefined symbols. ------------------------------------------------------------------------ r2359 | pemsley | 2009-09-29 13:33:14 +0100 (Tue, 29 Sep 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/ideal/Makefile.am M /trunk/mini-mol/Makefile.am Partial implementation of libxxx_la_LIBADD flags to remove undefined symbols. However, there are circular dependencies, so not everything is clean. ------------------------------------------------------------------------ r2358 | pemsley | 2009-09-29 12:36:35 +0100 (Tue, 29 Sep 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc Add a backup for renumber_residue_range() and change_residue_number(). Update notes. ------------------------------------------------------------------------ r2357 | b.lohkamp | 2009-09-29 11:47:13 +0100 (Tue, 29 Sep 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-validate.cc M /trunk/src/user-mods.cc fix pythonic user_mods add python user_mods_gui ------------------------------------------------------------------------ r2356 | pemsley | 2009-09-28 17:25:33 +0100 (Mon, 28 Sep 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/generic-objects.scm Don't show dialogs if we are not using the GUI. ------------------------------------------------------------------------ r2355 | pemsley | 2009-09-28 16:23:37 +0100 (Mon, 28 Sep 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/cc-interface.hh Use coot::util::int_to_string() not clipper's String. Hopefully fix Mac crash on writing history (this should not be necessary, of course). ------------------------------------------------------------------------ r2354 | pemsley | 2009-09-28 15:20:50 +0100 (Mon, 28 Sep 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ideal/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Fixes for drawing ball and stick objects in side-by-side stereo. Needed to make_gl_context_current() for the first context in make_ball_and_stick(). ------------------------------------------------------------------------ r2353 | pemsley | 2009-09-28 14:35:22 +0100 (Mon, 28 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-lsq.cc Delete the atom selections in get_lsq_matrix(). ------------------------------------------------------------------------ r2352 | pemsley | 2009-09-28 14:24:12 +0100 (Mon, 28 Sep 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Throw an exception instead of returning a bad matrix from find_ncs_matrix(). Catch the run-time error. ------------------------------------------------------------------------ r2351 | pemsley | 2009-09-28 14:22:22 +0100 (Mon, 28 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh Use booleans for is_nucleotide_by_dict() functions. ------------------------------------------------------------------------ r2350 | pemsley | 2009-09-28 14:21:45 +0100 (Mon, 28 Sep 2009) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc Remove debugging from pcmmdbmanager() function. ------------------------------------------------------------------------ r2349 | pemsley | 2009-09-28 07:09:36 +0100 (Mon, 28 Sep 2009) | 2 lines Changed paths: M /trunk/python/create_server.py Remove the confusing hash bang. ------------------------------------------------------------------------ r2348 | pemsley | 2009-09-27 19:35:55 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix incorrect function name in do_sequence_view(). ------------------------------------------------------------------------ r2347 | pemsley | 2009-09-27 17:31:17 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface-python.cc Call the graphic_info_t function. ------------------------------------------------------------------------ r2346 | pemsley | 2009-09-27 17:26:03 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Tidy up a bit, remove debugging. ------------------------------------------------------------------------ r2345 | pemsley | 2009-09-27 17:17:29 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/src/user-mods.cc Include guile-fixups.h ------------------------------------------------------------------------ r2344 | pemsley | 2009-09-27 17:13:05 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/src/read-phs.c Fix typo in string index. ------------------------------------------------------------------------ r2343 | pemsley | 2009-09-27 14:39:43 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/user-mods.cc M /trunk/src/user-mods.hh Fix up problems in compiling user-mods with Python. ------------------------------------------------------------------------ r2342 | pemsley | 2009-09-27 14:15:58 +0100 (Sun, 27 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points. ------------------------------------------------------------------------ r2341 | pemsley | 2009-09-27 13:03:29 +0100 (Sun, 27 Sep 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-defines.cc Correctly delete the residue when user clicks on the H of a water in delete water mode. ------------------------------------------------------------------------ r2340 | pemsley | 2009-09-27 12:14:34 +0100 (Sun, 27 Sep 2009) | 6 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh A /trunk/src/user-mods.cc A /trunk/src/user-mods.hh Add in user-mods/flips from the USER MODS card of a pdb file from reduce. Add a SCM and Python interface to output these flips (python interface not finished). Add a GUI to display (in a box of buttons) the SCM representation of the flips. user-mods.cc and user-mods.hh added to the archive. ------------------------------------------------------------------------ r2339 | pemsley | 2009-09-22 17:19:24 +0100 (Tue, 22 Sep 2009) | 7 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gl-bits.hh M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/nsv.cc M /trunk/src/nsv.hh Abstract print_secondary_structure_info to coot-coord-utils. Add IN_STEREO enumerations. Add interface function print_header_secondary_structure_info(). CalcSecStructure() in nsv.cc (new sequence view) and use CResidue colouring. make_ball_and_stick() adjusted, but still doesn't draw twice in side by side stereo. ------------------------------------------------------------------------ r2338 | pemsley | 2009-09-22 15:44:58 +0100 (Tue, 22 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix flatland symmetry molecule generation [JED bug]. ------------------------------------------------------------------------ r2337 | pemsley | 2009-09-22 11:28:56 +0100 (Tue, 22 Sep 2009) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in function that removes residue ranges widgets from the residue-range gui [JED bug]. ------------------------------------------------------------------------ r2336 | pemsley | 2009-09-21 15:41:21 +0100 (Mon, 21 Sep 2009) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm Abstract out *random-jiggle-n-trials* so that it is user-setable. Change the translation jiggle-factor to 1.0, so the ligand doesn't move so far and get sucked into protein density (a temporary hack)). ------------------------------------------------------------------------ r2335 | pemsley | 2009-09-21 13:12:00 +0100 (Mon, 21 Sep 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/pixmaps/go-to-atom.svg M /trunk/rel-todo M /trunk/scheme/coot-gui.scm Update to to atom menu item icon. Fix problem of view name in existing views panel. ------------------------------------------------------------------------ r2334 | b.lohkamp | 2009-09-20 19:56:30 +0100 (Sun, 20 Sep 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py add python test for occupancies after auto-fit rotamer ------------------------------------------------------------------------ r2333 | b.lohkamp | 2009-09-20 17:45:32 +0100 (Sun, 20 Sep 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py python version for adding solvent molecules ------------------------------------------------------------------------ r2332 | pemsley | 2009-09-20 15:32:50 +0100 (Sun, 20 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ncs.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h More consistent use of homology_level, now passed as a parameter. ------------------------------------------------------------------------ r2331 | pemsley | 2009-09-20 12:43:26 +0100 (Sun, 20 Sep 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc Several fixes for running the test suite with incorrect data dir. Mostly problems of testing that the model number is valid. ------------------------------------------------------------------------ r2330 | pemsley | 2009-09-20 11:52:23 +0100 (Sun, 20 Sep 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.h Allow COOT_DATA_DIR env var to override PKGDATADIR for rama-data. ------------------------------------------------------------------------ r2329 | pemsley | 2009-09-20 11:44:18 +0100 (Sun, 20 Sep 2009) | 3 lines Changed paths: M /trunk/greg-tests/begin.grg Add an environment variable (COOT_TEST_DATA_DIR) the check first for the greg-data-dir. ------------------------------------------------------------------------ r2328 | pemsley | 2009-09-20 11:09:32 +0100 (Sun, 20 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Change the y-axis on the burn-up graph ------------------------------------------------------------------------ r2327 | pemsley | 2009-09-19 19:16:32 +0100 (Sat, 19 Sep 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc small clean up and add some comments. ------------------------------------------------------------------------ r2326 | pemsley | 2009-09-19 13:11:33 +0100 (Sat, 19 Sep 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Use the new name for the solvent ligands gui. ------------------------------------------------------------------------ r2325 | pemsley | 2009-09-19 13:11:13 +0100 (Sat, 19 Sep 2009) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm solvent-ligands-gui: add a separator, show the button when an additional one gets added. ------------------------------------------------------------------------ r2324 | pemsley | 2009-09-19 12:20:13 +0100 (Sat, 19 Sep 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Update the extra solvent ligands gui with the ability to add extra TLCs. ------------------------------------------------------------------------ r2323 | pemsley | 2009-09-18 21:07:01 +0100 (Fri, 18 Sep 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Delete hydrogens from the ligand if the targe molecule does not have them. ------------------------------------------------------------------------ r2322 | pemsley | 2009-09-18 18:30:58 +0100 (Fri, 18 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build.cc Fix problem of delete_atom() writing binary to terminal. ------------------------------------------------------------------------ r2321 | pemsley | 2009-09-18 18:05:41 +0100 (Fri, 18 Sep 2009) | 3 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/mini-mol/mini-mol.cc M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/molecule-class-info-maps.cc Add initializers for cell and symmetry in the new minimol molecule constructor. Add solvent addition gui, add add it into the modelling submenu of Extensions. ------------------------------------------------------------------------ r2320 | pemsley | 2009-09-18 16:19:05 +0100 (Fri, 18 Sep 2009) | 2 lines Changed paths: A /trunk/src/gl-bits.hh Add missing gl-bits.hh ------------------------------------------------------------------------ r2319 | pemsley | 2009-09-18 13:50:32 +0100 (Fri, 18 Sep 2009) | 10 lines Changed paths: M /trunk/TODO M /trunk/burn-up/new-graph.py M /trunk/coords/mmdb-crystal.cc M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/db-main/db-main.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/high-res.cc M /trunk/ligand/helix-placement.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/python/coot_utils.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/TODO M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix auto-fit-rotamer on alt-confed residue. minimol atom constructor takes an occupancy argument. Unconst some CResidue args to minimol functions. Add gl_context_info for additional representation manipulation (not finished yet). Add random_jiggle functions - move a residue by a random set of angles and translations then rigid body fit. Useful for small ligand fitting. minimol molecule now has a "synthetic" constructor using a vector of atoms for the atom positions. ------------------------------------------------------------------------ r2318 | pemsley | 2009-09-16 14:10:31 +0100 (Wed, 16 Sep 2009) | 3 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add some jiggle-fit code. Not very useful yet because rigid body fit is not used (that is part of ligand, of course, so some reworking is needed). ------------------------------------------------------------------------ r2317 | b.lohkamp | 2009-09-16 07:28:48 +0100 (Wed, 16 Sep 2009) | 1 line Changed paths: M /trunk/windows/make_wincoot_installer.bat M /trunk/windows/wincoot-autobuild-all update windows autobuild system ------------------------------------------------------------------------ r2316 | pemsley | 2009-09-15 18:30:11 +0100 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /trunk/build-it-win Fix typo in coot_revision. ------------------------------------------------------------------------ r2315 | pemsley | 2009-09-15 17:58:03 +0100 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/go-to-atom.svg M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/support.h Change the go-to-atom icon on the menu item. ------------------------------------------------------------------------ r2314 | pemsley | 2009-09-15 15:47:18 +0100 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c Post-glade edits for previous commit. ------------------------------------------------------------------------ r2313 | pemsley | 2009-09-15 15:27:40 +0100 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Change the entries for distances in find waters dialog to match the labels. ------------------------------------------------------------------------ r2312 | pemsley | 2009-09-15 08:56:44 +0100 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h Clean up the write_state() function. ------------------------------------------------------------------------ r2311 | pemsley | 2009-09-15 08:55:44 +0100 (Tue, 15 Sep 2009) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-win Add extra info to the status lines. Can we get the win build to tell us the revision number? ------------------------------------------------------------------------ r2310 | pemsley | 2009-09-14 19:18:45 +0100 (Mon, 14 Sep 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h Another go at trying to fix the problem reported by Bill. Change to C-style FILE fopen(), fputs(), fclose() for the state scripts. ------------------------------------------------------------------------ r2309 | pemsley | 2009-09-14 16:31:32 +0100 (Mon, 14 Sep 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation.cc Tweak the go to atom dialog() so that the molecule option menu updates better. Remove the date from the build test status file - not needed. ------------------------------------------------------------------------ r2308 | pemsley | 2009-09-14 15:52:48 +0100 (Mon, 14 Sep 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info-state.cc Fixes for state file writing. Don't close the stream before it goes out of scope. Hopefully fixes the problems reported by Bill. ------------------------------------------------------------------------ r2307 | b.lohkamp | 2009-09-13 19:47:32 +0100 (Sun, 13 Sep 2009) | 6 lines Changed paths: M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/08_utils.py M /trunk/src/c-interface.cc add aliased for symmetry_operators_py and ~_to_xHM_py fix pythonic transform_map scripts add python lsq sg change and sg operator/conversion test fix reference counting for python sg functions in c-interface fix printf formatting in ppmutil.cc ------------------------------------------------------------------------ r2306 | pemsley | 2009-09-13 19:25:25 +0100 (Sun, 13 Sep 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-preferences.cc Don't flush the buffer on every line in the preferences file. Maybe this fixes the problem reported by Bill. ------------------------------------------------------------------------ r2305 | pemsley | 2009-09-13 19:22:41 +0100 (Sun, 13 Sep 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Add a date to the fail status message. ------------------------------------------------------------------------ r2304 | pemsley | 2009-09-13 14:12:12 +0100 (Sun, 13 Sep 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/scheme/coot-gui.scm M /trunk/src/coot.in Fix up typo in coot_utils.py for transform_maps(). Don't try to set IFS if the coot shell is not bash. ------------------------------------------------------------------------ r2303 | pemsley | 2009-09-12 23:54:44 +0100 (Sat, 12 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc change function name map_cell_py() to cell_py(). ------------------------------------------------------------------------ r2302 | pemsley | 2009-09-12 23:39:39 +0100 (Sat, 12 Sep 2009) | 4 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h LSQing changes the cell and symm of the moving molecule to that of the reference molecule. More python API fix-ups. ------------------------------------------------------------------------ r2301 | pemsley | 2009-09-12 23:02:04 +0100 (Sat, 12 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/guile-fixups.h fixups for new python code and for old guile. ------------------------------------------------------------------------ r2300 | pemsley | 2009-09-12 22:53:59 +0100 (Sat, 12 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info.h Add the associated sequences to the save state file. ------------------------------------------------------------------------ r2299 | pemsley | 2009-09-12 21:08:10 +0100 (Sat, 12 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo update done items. ------------------------------------------------------------------------ r2298 | pemsley | 2009-09-12 21:07:42 +0100 (Sat, 12 Sep 2009) | 15 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/greg-tests/08-utils.scm M /trunk/python/coot_utils.py M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-defines.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Map transformation by LSQ matrix (and indeed any map transformation) now gets generated into a given/passed unit cell and symmetry - typically the cell and symmetry of the reference coords of the LSQing. set_mmdb_symm() now returns a success value, comparing the set and get values. suggest_grid_sampling() function created. Add a test for spacegroup operators to space group names. Add a utility function generating a clipper::Spacegroup from a list of SCM strings (also python). map_cell_scm is now called simply cell_scm. Likewise python versions of these. Aliases added. Delete water fixed by not using delete_atom_by_atom_index() after delete_residue_hydrogens() (which deletes the atom selections of the atom_sel). Now delete_residue_hydrogen() only deletes the selections if the residue had hydrogens. ------------------------------------------------------------------------ r2297 | pemsley | 2009-09-12 11:04:33 +0100 (Sat, 12 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2296 | pemsley | 2009-09-11 15:59:17 +0100 (Fri, 11 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points. ------------------------------------------------------------------------ r2295 | pemsley | 2009-09-11 12:46:01 +0100 (Fri, 11 Sep 2009) | 2 lines Changed paths: M /trunk/src/coot.in Try setting IFS to stop word splitting of the command line arguments. ------------------------------------------------------------------------ r2294 | pemsley | 2009-09-11 07:49:51 +0100 (Fri, 11 Sep 2009) | 2 lines Changed paths: M /trunk/src/coot.in quote the arguments to coot, stops expansion by the shell. ------------------------------------------------------------------------ r2293 | pemsley | 2009-09-10 00:13:32 +0100 (Thu, 10 Sep 2009) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h separate out the creation of a pointer atom molecule from mearly returning its molecule number (-1 for unset, of course). ------------------------------------------------------------------------ r2292 | pemsley | 2009-09-09 23:50:15 +0100 (Wed, 09 Sep 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.hh Don't display the "Show Additional Representations" check-button if we don't display the frame for the addition representations. ------------------------------------------------------------------------ r2291 | pemsley | 2009-09-09 22:41:41 +0100 (Wed, 09 Sep 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r2290 | pemsley | 2009-09-09 17:47:54 +0100 (Wed, 09 Sep 2009) | 7 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-tree-extras.cc M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc The SeekContacts() in getcontacts() should be liberal, because there is element-type filtering in the contact_info contructor. Change the S radius to 1.1 (S-S bond can be up to 2.2A?). Add print() method for contact_info. Protection for zero-sized contacts in fill_atom_vertex_vec_using_contacts(). Fixes crash. ------------------------------------------------------------------------ r2289 | b.lohkamp | 2009-09-09 16:03:07 +0100 (Wed, 09 Sep 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc update python scripts with repect to alignment_mismatch_gui proper refernce counting in sequence_info_py enable zalman stereo for gtk1 (gtk-glarea) ------------------------------------------------------------------------ r2288 | pemsley | 2009-09-09 00:25:49 +0100 (Wed, 09 Sep 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc And #ifdef the other gtk_widget_set_size_request() usages. ------------------------------------------------------------------------ r2287 | pemsley | 2009-09-09 00:13:24 +0100 (Wed, 09 Sep 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Fixup #ifdef gtk_widget_set_size_request() usage. GTK_MINOR_VERSION > 6 (guess). ------------------------------------------------------------------------ r2286 | pemsley | 2009-09-08 17:47:44 +0100 (Tue, 08 Sep 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Tweak the bond search distance of long_bonded_atom. ------------------------------------------------------------------------ r2285 | pemsley | 2009-09-08 17:36:01 +0100 (Tue, 08 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-gui.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/select-atom-info.hh Add the ability to edit alt-confs in the residue info window. ------------------------------------------------------------------------ r2284 | pemsley | 2009-09-08 17:35:12 +0100 (Tue, 08 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Add extra annotations. ------------------------------------------------------------------------ r2283 | pemsley | 2009-09-08 11:22:36 +0100 (Tue, 08 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab More burn points. ------------------------------------------------------------------------ r2282 | pemsley | 2009-09-08 11:02:36 +0100 (Tue, 08 Sep 2009) | 7 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/rel-todo M /trunk/scheme/extensions.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/rama_plot.cc Put PISA interface into a submenu of Extensions. In PISA interface, check that there are assemblies and inhibit the dialog of the top assembly set if it is "false". If a Ramachandran plot is being displayed, update the active residue (with a green box): update_ramachandran_plot_point_maybe() called from accept_moving_atoms(). ------------------------------------------------------------------------ r2281 | pemsley | 2009-09-08 00:37:42 +0100 (Tue, 08 Sep 2009) | 3 lines Changed paths: M /trunk/python/parse_pisa_xml.py M /trunk/rel-todo M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/graphics-info-graphs.cc Use PISA_WORK_ROOT, not WORK_ROOT (Bernie got it right in the python version). Don't try to get rotamers for HOHs. ------------------------------------------------------------------------ r2280 | pemsley | 2009-09-07 21:15:17 +0100 (Mon, 07 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo Update todo notes. ------------------------------------------------------------------------ r2279 | pemsley | 2009-09-07 18:10:20 +0100 (Mon, 07 Sep 2009) | 10 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc Move tree code into tree-code-extra.cc get_contact_indices_from_restraints() takes an extra arg - should the reverse contacts be added? (they are needed for the contacts-based tree constructor in tree-code-extra.cc. Tree code now uses GetResidue() to make a CResidue * from a minimol residue. wiggly-ligands now falls back to contacts-based tree (using above reverse contacts) when there is no tree in the dictionary. optimize_and_install() factorerd out because of the exception handling of the 2 constructors. ------------------------------------------------------------------------ r2278 | pemsley | 2009-09-07 11:54:18 +0100 (Mon, 07 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-tree-extras.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-other.cc Audit strncpy() usage. Apply fixups and notes. ------------------------------------------------------------------------ r2277 | pemsley | 2009-09-07 11:26:42 +0100 (Mon, 07 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Audit GtkPositionType usage for strings. Make fix-ups. ------------------------------------------------------------------------ r2276 | pemsley | 2009-09-06 11:38:06 +0100 (Sun, 06 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh Add some output formatting for quads and tree_dihedral_info_t. ------------------------------------------------------------------------ r2275 | pemsley | 2009-09-05 18:50:01 +0100 (Sat, 05 Sep 2009) | 2 lines Changed paths: M /trunk/ligand/Makefile.am M /trunk/src/Makefile.am Also here update the order of the minimol lib (problem linking on FC4). ------------------------------------------------------------------------ r2274 | pemsley | 2009-09-05 18:27:26 +0100 (Sat, 05 Sep 2009) | 3 lines Changed paths: M /trunk/ideal/Makefile.am Fix up the order of dependencies now that we are using atom_index_quads in minimol as a dependencies of coot-coord-extras. ------------------------------------------------------------------------ r2273 | pemsley | 2009-09-05 17:55:47 +0100 (Sat, 05 Sep 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc atom_index_quad.torsion takes a CResidue *, not an index. ------------------------------------------------------------------------ r2272 | pemsley | 2009-09-05 16:32:41 +0100 (Sat, 05 Sep 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/mini-mol/Makefile.am A /trunk/mini-mol/atom-quads.cc M /trunk/mini-mol/atom-quads.hh Fix up the current_dihedral calculation in atom_tree_t::set_dihedral(). Now we base it on the passed atom names, not the embedded torsion on i2. atom_index_quad now has a torsion() function which takes a residue and returns a torsion angle. ------------------------------------------------------------------------ r2271 | pemsley | 2009-09-05 15:52:08 +0100 (Sat, 05 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab adjust burn point for missing sampling. ------------------------------------------------------------------------ r2270 | pemsley | 2009-09-05 11:10:38 +0100 (Sat, 05 Sep 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python-tests/01_pdb_mtz.py M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h align_and_mutate() now takes an extra arg: renumber_residues_flag Fix up tests to account for this. ------------------------------------------------------------------------ r2269 | pemsley | 2009-09-04 18:12:47 +0100 (Fri, 04 Sep 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab new burn points ------------------------------------------------------------------------ r2268 | pemsley | 2009-09-04 17:23:13 +0100 (Fri, 04 Sep 2009) | 5 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface.h Attach alignment-mismatches-gui to associate-pir-file when aligning from wrapper-alignment-mismatches-gui. Use sensible atom names in the resulting GUI, which looks at the atom names in a residue, rather than using " CA ". ------------------------------------------------------------------------ r2267 | b.lohkamp | 2009-09-04 16:24:35 +0100 (Fri, 04 Sep 2009) | 8 lines Changed paths: M /trunk/bldnotes M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-nucleotides.cc python tests: - add pucker test - update OXT test python scripts: - fitting observes ins_code and omits HOH - update save dialog positions - add parse_pisa_xml to dist (but dont load, needs more testing) update pucker_info_py ------------------------------------------------------------------------ r2266 | pemsley | 2009-09-04 16:05:36 +0100 (Fri, 04 Sep 2009) | 7 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/fitting.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/coot-align.hh M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Move the fit-chain call into mutate_chain in graphics-info. mutate_chain() now takes a renumber_residue flag, which makes the mutation specs now correspond. On failing mutations, write out the sequence. Change label on the align_and_mutate_autofit_checkbutton. Don't try to rotmaer fit waters in fit-chain. ------------------------------------------------------------------------ r2265 | pemsley | 2009-09-04 11:11:43 +0100 (Fri, 04 Sep 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h Change pukka puckers to use the N1/9-C1* bond to find perpendicular P distance. Critical distance is now 3.0A Add test for phosphate distance in pucker-info. Sequence-info should return #f (False) if there is no sequence assigned. ------------------------------------------------------------------------ r2264 | pemsley | 2009-09-03 20:37:50 +0100 (Thu, 03 Sep 2009) | 2 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Remove some debugging from wiggly ligands. ------------------------------------------------------------------------ r2263 | b.lohkamp | 2009-09-03 11:52:43 +0100 (Thu, 03 Sep 2009) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-python.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-preferences.cc average_map for python (incl. test and fix python_display) ------------------------------------------------------------------------ r2262 | pemsley | 2009-09-03 11:22:01 +0100 (Thu, 03 Sep 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/fitting.scm Don't try to Rama-improve water residues. ------------------------------------------------------------------------ r2261 | pemsley | 2009-09-03 11:03:07 +0100 (Thu, 03 Sep 2009) | 8 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/align.cc M /trunk/src/c-interface-build.cc M /trunk/src/coot-align.cc M /trunk/src/molecule-class-info-mutate.cc Add some warnings when seqnum_from_serial_number() returns an unset seqnum. When making a sequence for an alignment, don't include waters (X) in the sequence. In the generation of the modifications from an alignment, keep a ires_running, so that the insertions are generated +1 from the previous residue in the model - the corrects the error of the insertions being based on the input/target sequence residue numbering. ------------------------------------------------------------------------ r2260 | pemsley | 2009-09-03 10:57:26 +0100 (Thu, 03 Sep 2009) | 7 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/fitting.scm Move associate-pir-file to coot-utils, where it can be used with no-graphics. Rework fit-protein-*-functions to provide protection against refining waters and testing the residue names of residues that have been deleted. When generating the residue specs, don't include residues that have an inscode of #f (in that case, the residue does not exist for some reason). ------------------------------------------------------------------------ r2259 | pemsley | 2009-09-03 07:45:42 +0100 (Thu, 03 Sep 2009) | 4 lines Changed paths: M /trunk/macros/sys-build-type.m4 Fix up COOT_SYS_BUILD_TYPE generation macro. $1 and $2 were being substituted in the awk lines extracting dist_name and dist_ver from /etc/issue. Change to using head, cut and tr. ------------------------------------------------------------------------ r2258 | pemsley | 2009-09-02 18:15:41 +0100 (Wed, 02 Sep 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc Remove debugging from wiggly ligands. ------------------------------------------------------------------------ r2257 | pemsley | 2009-09-02 17:11:07 +0100 (Wed, 02 Sep 2009) | 6 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm Document backrub rotamers. Set Spin Speed in Extensions now in the Settings submenu. Don't do rotamers of HOHs in fit-protein-fit-function. In the coot news, get RELEASE-NOTES, not release-notes (to do with new web server, I guess). ------------------------------------------------------------------------ r2256 | pemsley | 2009-09-02 10:25:53 +0100 (Wed, 02 Sep 2009) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm In save-dialog-positions-to-init-file, fix problem of reading "0-coot.state.scm" when it doesn't exist. ------------------------------------------------------------------------ r2255 | pemsley | 2009-09-02 10:22:59 +0100 (Wed, 02 Sep 2009) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix problem in dump-positions-to-init-file when ~/.coot is not found. ------------------------------------------------------------------------ r2254 | pemsley | 2009-09-02 09:37:15 +0100 (Wed, 02 Sep 2009) | 4 lines Changed paths: M /trunk/auxil/catcheck/Makefile.am M /trunk/auxil/rama/Makefile.am M /trunk/auxil/sec-str/Makefile.am M /trunk/auxil/sec-str/sec-str-dist-check.cc M /trunk/auxil/strand-analysis/Makefile.am M /trunk/auxil/strand-analysis/strand-analysis.cc M /trunk/auxil/vectors/Makefile.am M /trunk/dnotes M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/testdunbrack.cc M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc Various small adjustments to make "make check" compile. Change make_map_from_cif_generic() molecule function to new-style format as suggested by Kevin. ------------------------------------------------------------------------ r2253 | pemsley | 2009-09-01 22:31:50 +0100 (Tue, 01 Sep 2009) | 2 lines Changed paths: M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh Improvements to clash scores for backrub rotamers. ------------------------------------------------------------------------ r2252 | pemsley | 2009-09-01 16:06:58 +0100 (Tue, 01 Sep 2009) | 2 lines Changed paths: M /trunk/src/globjects.cc Restore Ctrl-Z functionality. ------------------------------------------------------------------------ r2251 | pemsley | 2009-09-01 14:22:57 +0100 (Tue, 01 Sep 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface.h Add testing and documentation for average-map. ------------------------------------------------------------------------ r2250 | pemsley | 2009-09-01 13:36:07 +0100 (Tue, 01 Sep 2009) | 4 lines Changed paths: M /trunk/coot-utils/peak-search.cc Rework the peak search so that it discards other points in the same cluster as the peak (cluster being the group of grid coords with density above the cut_off). ------------------------------------------------------------------------ r2249 | pemsley | 2009-09-01 01:00:18 +0100 (Tue, 01 Sep 2009) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/coot.scm M /trunk/scheme/extensions.scm M /trunk/scheme/parse-pisa-xml.scm M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am Trap non-numeric return value from running pisa. Include/load pisa parsing scm file. For PISA menu, only run coot-menubar-menu if it is defined. ------------------------------------------------------------------------ r2248 | pemsley | 2009-09-01 00:03:02 +0100 (Tue, 01 Sep 2009) | 2 lines Changed paths: M /trunk/auxil/catcheck/catcheck.cc M /trunk/auxil/strand-analysis/strand-analysis.cc Add extra includes - problem noted by Justin Lecher. ------------------------------------------------------------------------ r2247 | pemsley | 2009-08-31 21:19:49 +0100 (Mon, 31 Aug 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend number of days.. ------------------------------------------------------------------------ r2246 | pemsley | 2009-08-31 12:50:37 +0100 (Mon, 31 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add include guile-fixups.h. ------------------------------------------------------------------------ r2245 | pemsley | 2009-08-31 12:48:15 +0100 (Mon, 31 Aug 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-gui.scm M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add only one OXT to a residue - extend the OXT/TER test to test for this too. ------------------------------------------------------------------------ r2244 | pemsley | 2009-08-31 00:53:47 +0100 (Mon, 31 Aug 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc Add map averaging function - needs testing. Add protection for crash when getting spacegroup from cif data file where myfsigf.spacegroup() is null. ------------------------------------------------------------------------ r2243 | pemsley | 2009-08-29 07:32:03 +0100 (Sat, 29 Aug 2009) | 2 lines Changed paths: M /trunk/coords/mmdb-extras.cc Tinker with the atom radii table. ------------------------------------------------------------------------ r2242 | pemsley | 2009-08-29 07:22:51 +0100 (Sat, 29 Aug 2009) | 5 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/mmdb-extras.cc Rework the bonding by taking out the star generation and running it only after long_bonds, MSE, CYS have been accounted for. handle_long_bonded_atom() and handle_MET_or_MSE_case() now mark atoms as bonded. ------------------------------------------------------------------------ r2241 | pemsley | 2009-08-29 06:54:23 +0100 (Sat, 29 Aug 2009) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc Rework torsion general so that it works only by contacts. Change the contact generation so that it considers the atom elements of the atoms involved in the (potential) bond. ------------------------------------------------------------------------ r2240 | pemsley | 2009-08-28 20:10:44 +0100 (Fri, 28 Aug 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c Make the Refinement weight entry in the refine_params_dialog work. set_refinemenent_weight_from_entry() for that. Turn off spining on ^Gi Some protection for delete_atom_by_atom_index() and delete_atom(). ------------------------------------------------------------------------ r2239 | pemsley | 2009-08-28 19:02:43 +0100 (Fri, 28 Aug 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/gtk-manual.cc Put the addition representations "all" button outside the frame. ------------------------------------------------------------------------ r2238 | pemsley | 2009-08-28 15:58:09 +0100 (Fri, 28 Aug 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-tree-extras.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/src/c-interface-ligands.cc Use new style atom-tree in wiggly ligands (yay!). Tweak debugging and class documentation. ------------------------------------------------------------------------ r2237 | pemsley | 2009-08-28 13:15:00 +0100 (Fri, 28 Aug 2009) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc Fix up get_rotamer_name_py() to use extra alt_conf arg when constructing a richardson_rotamer(). ------------------------------------------------------------------------ r2236 | pemsley | 2009-08-28 12:52:16 +0100 (Fri, 28 Aug 2009) | 9 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/sequence-assignment.cc M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh M /trunk/ligand/chi-angles.cc M /trunk/ligand/dunbrack.hh M /trunk/ligand/richardson-rotamer.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/python-tests/01_pdb_mtz.py M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-nomenclature.cc M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add clash_score to backrub rotamers. Add alt confs to chi_angle and rotamer code. Add a "Show All Additional Representations" button for each molecule in the Display Manager. get_minimol_pos() moved into minimol::molecule class. Construct a minimol::molecule from a fragment. Update notes. Fix up tests to use alt_conf ("") when using rotamer_score(). ------------------------------------------------------------------------ r2235 | pemsley | 2009-08-28 11:24:20 +0100 (Fri, 28 Aug 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/globjects.cc Remove pick cursor debugging. ------------------------------------------------------------------------ r2234 | pemsley | 2009-08-28 00:27:01 +0100 (Fri, 28 Aug 2009) | 2 lines Changed paths: M /trunk/scheme/Makefile.am Add parse-pisa-xml.scm to the distribution. ------------------------------------------------------------------------ r2233 | pemsley | 2009-08-28 00:25:09 +0100 (Fri, 28 Aug 2009) | 2 lines Changed paths: M /trunk/coords/mmdb-extras.h Add delete_atom_selection() function to atom_selection_container_t ------------------------------------------------------------------------ r2232 | pemsley | 2009-08-28 00:24:14 +0100 (Fri, 28 Aug 2009) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh Add get_pos() function to a minimol. Construct a minimol from a fragment. ------------------------------------------------------------------------ r2231 | kevin.cowtan | 2009-08-27 14:12:01 +0100 (Thu, 27 Aug 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface.cc Cruft removal. The get_spacegroup_from_mmdb_symops (which was the solution we implemented last time this came up and then widely ignored) is redundent. PHS reading code tidied and standardised. ------------------------------------------------------------------------ r2230 | kevin.cowtan | 2009-08-27 12:58:52 +0100 (Thu, 27 Aug 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/molecule-class-info-maps.cc Fixes to transfer symmetry info from MMDB to Clipper via symops, not via symbols. Maps, symm atom picks tested. PHS code not tested. I've been campaigning for everyone to do this for over 3 years now, grrrr. ------------------------------------------------------------------------ r2229 | b.lohkamp | 2009-08-27 11:58:26 +0100 (Thu, 27 Aug 2009) | 1 line Changed paths: M /trunk/src/c-interface.cc fix windows stereo to show maps ------------------------------------------------------------------------ r2228 | pemsley | 2009-08-26 09:34:47 +0100 (Wed, 26 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix typo in hardware-stereo-angle-factor function name. ------------------------------------------------------------------------ r2227 | pemsley | 2009-08-25 10:04:47 +0100 (Tue, 25 Aug 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Convert a clipper::Message_base exception to a std::runtime_error (and that is what we catch in move_waters_around_protein()). ------------------------------------------------------------------------ r2226 | b.lohkamp | 2009-08-24 11:08:04 +0100 (Mon, 24 Aug 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-tree-extras.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/graphics-info-superpose.cc add python test for map sharpening (fix greg test too) include string.h in coot-tree-extras.cc as strncpy not defined otherwise (on FC10 at least) swap SSM output (matrices, rmsd etc last now) ------------------------------------------------------------------------ r2225 | pemsley | 2009-08-23 00:29:53 +0100 (Sun, 23 Aug 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/rel-todo M /trunk/src/c-interface-waters.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Fix crash of sharpening map after reading a map. Add a test for sharpen map. Change to info_dialog() when refinement map not set in go to blob. ------------------------------------------------------------------------ r2224 | pemsley | 2009-08-21 11:28:28 +0100 (Fri, 21 Aug 2009) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh A /trunk/coot-utils/coot-tree-extras.cc M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc Fix the problem of the "wrong" fragment moving in torsion general (do the swap internally, not in rotate_chi_torsion_general()). Add extra constructor for use with a minimol, and an interface to rotate round many bonds. ------------------------------------------------------------------------ r2223 | b.lohkamp | 2009-08-20 15:35:04 +0100 (Thu, 20 Aug 2009) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Zalman stereo mode option in Stereo Dialog ------------------------------------------------------------------------ r2222 | b.lohkamp | 2009-08-20 13:50:24 +0100 (Thu, 20 Aug 2009) | 3 lines Changed paths: M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/parse_pisa_xml.py M /trunk/python-tests/01_pdb_mtz.py updated python parse_pisa and python test TER OXT added python toolbuttons for zalman stereo and swap stereo ------------------------------------------------------------------------ r2221 | pemsley | 2009-08-18 18:20:23 +0100 (Tue, 18 Aug 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc Remove debugging. ------------------------------------------------------------------------ r2220 | pemsley | 2009-08-18 17:51:02 +0100 (Tue, 18 Aug 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh In fill_atom_vertex_vec_using_contacts(), first check that the candidate new forward atom is not already in the forward atom vector. ------------------------------------------------------------------------ r2219 | pemsley | 2009-08-18 16:48:39 +0100 (Tue, 18 Aug 2009) | 3 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/cycle-page-builder.scm Handle "Object not found" (test status file) from new server. Better record writing. ------------------------------------------------------------------------ r2218 | pemsley | 2009-08-18 09:46:37 +0100 (Tue, 18 Aug 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/dnotes Add extra protection when filling the atom_vertex_vec. ------------------------------------------------------------------------ r2217 | pemsley | 2009-08-18 08:40:30 +0100 (Tue, 18 Aug 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add more documentation for finding waters. ------------------------------------------------------------------------ r2216 | pemsley | 2009-08-17 21:18:53 +0100 (Mon, 17 Aug 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/src/graphics-info-modelling.cc Add protection for bad cif tree in constructor of atom_tree_t. Add a contacts-based fall-back for edit-chi angles (for when the dictionary has no tree). ------------------------------------------------------------------------ r2215 | pemsley | 2009-08-17 12:27:48 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/dnotes Minor updates. ------------------------------------------------------------------------ r2214 | pemsley | 2009-08-17 12:21:08 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix a typo. ------------------------------------------------------------------------ r2213 | pemsley | 2009-08-17 12:13:18 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c Fix up typo support.h include file. ------------------------------------------------------------------------ r2212 | pemsley | 2009-08-17 10:17:47 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/rel-todo More done stuff. ------------------------------------------------------------------------ r2211 | pemsley | 2009-08-17 09:28:47 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h GTK1+ and no-canvas fixes. ------------------------------------------------------------------------ r2210 | pemsley | 2009-08-17 09:24:08 +0100 (Mon, 17 Aug 2009) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Remove the removal of the mmdb binaries (they are no longer present/made in new mmdb). ------------------------------------------------------------------------ r2209 | pemsley | 2009-08-17 02:16:09 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Add "Reverse Fragment" to Edit Chi Angles dialog. ------------------------------------------------------------------------ r2208 | pemsley | 2009-08-17 01:11:38 +0100 (Mon, 17 Aug 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Remove the printing of the runtime_error when atom_tree_t constructor fails with no tree in restraint. ------------------------------------------------------------------------ r2207 | pemsley | 2009-08-17 00:14:02 +0100 (Mon, 17 Aug 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo Adjust the rel-todo now that the chi angle code has been committed. ------------------------------------------------------------------------ r2206 | pemsley | 2009-08-16 15:57:46 +0100 (Sun, 16 Aug 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Now rotamers are dictionary based (to get to the atom tree). Lots of functions need to be adjusted to add protein_geometry or dictionary_residue_restraints_t to the arguments. ------------------------------------------------------------------------ r2205 | pemsley | 2009-08-16 11:43:07 +0100 (Sun, 16 Aug 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/ligand/richardson-rotamer.cc Factor out the quad_to_torsion() function in atom_tree_t. Add set_dihedral() function - not used yet. Faster vector usage in richardson-rotamer ------------------------------------------------------------------------ r2204 | pemsley | 2009-08-16 01:30:17 +0100 (Sun, 16 Aug 2009) | 14 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/doc/user-manual.texi M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Add get_contact_indices() function to contact_info class - used in new-style chi-angle code. rotate_about() returns the torsion of the embedded chi-angle in degrees. Replace old-style torsion-general atom moving and chi angle moving (rotate_chi_torsion_general() and update_residue_by_chi_change()). Add a function to return rotation atom names from a residue, restraint and a chi-angle index. Add new statics chi_angle_alt_conf and contact_indices (the latter to store the contatct indices from when the residue is clicked - rather that generate them on the fly - which causes bizarre connectivity when there are clashes). get_non_const_torsions() function added to a residue restraints class. Quite a lot of commented debugging. ------------------------------------------------------------------------ r2203 | pemsley | 2009-08-15 05:10:55 +0100 (Sat, 15 Aug 2009) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix typo in rigid-body function name when snarfing docs. ------------------------------------------------------------------------ r2202 | b.lohkamp | 2009-08-14 17:02:01 +0100 (Fri, 14 Aug 2009) | 3 lines Changed paths: A /trunk/python/parse_pisa_xml.py M /trunk/python-tests/01_pdb_mtz.py add python test for TER OXT add python pisa xml parser (not completely ready) ------------------------------------------------------------------------ r2201 | pemsley | 2009-08-14 13:54:44 +0100 (Fri, 14 Aug 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/rel-todo M /trunk/src/testing.cc M /trunk/src/testing.hh Add more testing of chi-angle code. More debugging in atom_tree, on reverse_flag, change unique_moving_atom_indices not moving_atom_indices. ------------------------------------------------------------------------ r2200 | pemsley | 2009-08-13 18:00:51 +0100 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/molecule-class-info-other.cc Add OXT before TER atom. Include test for this. ------------------------------------------------------------------------ r2199 | pemsley | 2009-08-13 17:19:59 +0100 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /trunk/macros/gtk-canvas.m4 Comment out AM_PATH_IMLIB. ------------------------------------------------------------------------ r2198 | pemsley | 2009-08-13 17:19:03 +0100 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2197 | pemsley | 2009-08-13 09:20:06 +0100 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface-pisa.cc Return a model number for pisa_interaction. ------------------------------------------------------------------------ r2196 | pemsley | 2009-08-13 08:57:27 +0100 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface.h Adjust documentation strings for doxygenation. ------------------------------------------------------------------------ r2195 | pemsley | 2009-08-12 19:28:14 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/rel-todo Update notes, progress. ------------------------------------------------------------------------ r2194 | pemsley | 2009-08-12 19:26:03 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2193 | pemsley | 2009-08-12 19:25:47 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Trivial change. ------------------------------------------------------------------------ r2192 | pemsley | 2009-08-12 19:25:13 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up more syntax errors in user-manual.texi - now works with makeinfo. ------------------------------------------------------------------------ r2191 | pemsley | 2009-08-12 09:34:37 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/doc/Makefile.am Fix the rule to make coot.html ------------------------------------------------------------------------ r2190 | pemsley | 2009-08-12 09:30:55 +0100 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /trunk/doc/Makefile.am Add rule for coot.html ------------------------------------------------------------------------ r2189 | pemsley | 2009-08-11 16:02:07 +0100 (Tue, 11 Aug 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up syntax errors in manual. ------------------------------------------------------------------------ r2188 | pemsley | 2009-08-11 03:37:28 +0100 (Tue, 11 Aug 2009) | 4 lines Changed paths: M /trunk/build/CalphaBuild.cc M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/db-main/db-strands.cc M /trunk/density-contour/CIsoSurface.cpp M /trunk/dnotes M /trunk/ligand/base-pairing.cc M /trunk/macros/glut.m4 M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/pick.cc M /trunk/src/rama_plot.hh Fix various compilation problems with stricter flags on Ubuntu 9.04 g++ (Ubuntu 4.3.3-5ubuntu4) 4.3.3 Autoconf now provides ac_cv_build, not ac_cv_build_alias, it seems. ------------------------------------------------------------------------ r2187 | pemsley | 2009-08-10 16:03:27 +0100 (Mon, 10 Aug 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-utils.cc M /trunk/src/testing.cc M /trunk/src/testing.hh More atom tree code. A constructor from contact indices. Include cstdio in coot-utils.cc. Test for atom_tree atom_vector, a simple derived class. ------------------------------------------------------------------------ r2186 | b.lohkamp | 2009-08-07 16:10:17 +0100 (Fri, 07 Aug 2009) | 16 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/mutate.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/04_cootaneer.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h residue_range_gui and alignment_mismatch_gui for python fix mutate_by_overlap to get return from get_monomer update python coot_util functions add to python extensions: - New mol by symmetry - rigid body fit residue range - arrange water around molecule - alignment vs pir update python associate sequence function update python tests (01_pdb+mtz and 04_cootaneer) fill in python functions (any missing?): - alignment_mismatches_py - add_alt_conf_py - rigid_body_refine_by_residue_ranges_py - origin_pre_shift_py ------------------------------------------------------------------------ r2185 | pemsley | 2009-08-07 13:05:42 +0100 (Fri, 07 Aug 2009) | 2 lines Changed paths: M /trunk/coot-utils/peak-search.cc remove debugging. ------------------------------------------------------------------------ r2184 | pemsley | 2009-08-06 12:47:10 +0100 (Thu, 06 Aug 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add an icon for the burn-up graph. ------------------------------------------------------------------------ r2183 | pemsley | 2009-08-06 11:29:29 +0100 (Thu, 06 Aug 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Use the map sharpening limit in wrapped_create_map_sharpening_dialog(). ------------------------------------------------------------------------ r2182 | pemsley | 2009-08-05 13:55:49 +0100 (Wed, 05 Aug 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.cc Add atom_tree_t::atom_tree_t constructor from indices (not fillled). ------------------------------------------------------------------------ r2181 | pemsley | 2009-08-05 10:34:01 +0100 (Wed, 05 Aug 2009) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am Add mini-mol to the INCLUDES (how did it work without this?). ------------------------------------------------------------------------ r2180 | pemsley | 2009-08-05 10:30:49 +0100 (Wed, 05 Aug 2009) | 3 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm parse-pisa now constructs assembly records and displays the top assemby record set in an info-dialog. ------------------------------------------------------------------------ r2179 | pemsley | 2009-08-05 02:11:22 +0100 (Wed, 05 Aug 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Remove debugging code for update_residue_by_chi_change(). ------------------------------------------------------------------------ r2178 | pemsley | 2009-08-05 01:48:07 +0100 (Wed, 05 Aug 2009) | 3 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm pisa-assemblies function added, running pisa -analyse and then pisa -xml. pisa-assemblies finnishes by runnig pisa-xml. ------------------------------------------------------------------------ r2177 | pemsley | 2009-08-04 18:18:52 +0100 (Tue, 04 Aug 2009) | 2 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Make assembly-sets. ------------------------------------------------------------------------ r2176 | pemsley | 2009-08-04 18:10:53 +0100 (Tue, 04 Aug 2009) | 4 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Progress with PISA xml file handling. Now we make assemblies and handle assembly-sets. [We need to fix it up to make assembly set molecules (not just assembly molecules).] ------------------------------------------------------------------------ r2175 | pemsley | 2009-08-03 17:05:43 +0100 (Mon, 03 Aug 2009) | 10 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ligand/chi-angles.cc M /trunk/rel-todo M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/read-cif.c M /trunk/src/testing.cc M /trunk/src/testing.hh Fix the scroll button settings on reading an mmCIF file with phases. Several blocks of commented/non-running debugging code added (for chi angles). dict_chem_comp_tree_t added to protein-geometry. coot atom tree code added - with testing.cc tests. test for rotation round axis added. --version-full argument added. file_exists() protection on reading mtz file, cif and cns file. Delete the old CMMDBManager molecule and selection in sort_chains(). build-it-gtk2-simple: guile version update to 1.8.7 ------------------------------------------------------------------------ r2174 | pemsley | 2009-08-03 15:51:32 +0100 (Mon, 03 Aug 2009) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc Remove debugging outout of molecule fragments in rigid_body_fit(). ------------------------------------------------------------------------ r2173 | pemsley | 2009-08-03 10:18:54 +0100 (Mon, 03 Aug 2009) | 8 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/burn-up/burn-up.tab M /trunk/scheme/parse-pisa-xml.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh Correct the input matrix type for new_molecule_by_symmetry(). New function new_molecule_by_symmetry_with_atom_selection(). New function new_molecule_by_symmetry_matrix_from_molecule() used by new_molecule_from_symmetry() and new_molecule_by_symmetry_with_atom_selection(). parse-pisa now uses new-molecule-by-symmetry-with-atom-selection. New burn points. ------------------------------------------------------------------------ r2172 | pemsley | 2009-07-30 10:23:31 +0100 (Thu, 30 Jul 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Fix fedora 8 -> typo. ------------------------------------------------------------------------ r2171 | pemsley | 2009-07-30 10:02:27 +0100 (Thu, 30 Jul 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple remove swig from package list tested on ubuntu. ------------------------------------------------------------------------ r2170 | pemsley | 2009-07-28 19:25:30 +0100 (Tue, 28 Jul 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple gtk2 -> $build_type fixups for status ------------------------------------------------------------------------ r2169 | pemsley | 2009-07-28 18:05:10 +0100 (Tue, 28 Jul 2009) | 2 lines Changed paths: M /trunk/src/nsv.cc Fix up X11 problems when using very long canvas (residue number > 5000). ------------------------------------------------------------------------ r2168 | pemsley | 2009-07-27 23:53:21 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo Update done items and TODO. ------------------------------------------------------------------------ r2167 | pemsley | 2009-07-27 23:49:25 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/greg-tests/04-cootaneer.scm M /trunk/src/molecule-class-info-other.cc Assignment of PIR sequence overwrites old assignment for that chain_id. Test added. ------------------------------------------------------------------------ r2166 | pemsley | 2009-07-27 20:30:25 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h Add and document show_pointer_distances_state(). ------------------------------------------------------------------------ r2165 | pemsley | 2009-07-27 19:07:03 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/rel-todo update todo list. ------------------------------------------------------------------------ r2164 | pemsley | 2009-07-27 19:06:45 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Add a source code date - add source code status colouring. ------------------------------------------------------------------------ r2163 | pemsley | 2009-07-27 16:50:15 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New burn points. ------------------------------------------------------------------------ r2162 | pemsley | 2009-07-27 16:49:59 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/scheme/parse-pisa-xml.scm Fix up for name argument of new_molecule_by_symmetry(). ------------------------------------------------------------------------ r2161 | pemsley | 2009-07-27 16:40:31 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add a date for build-in-progress status ------------------------------------------------------------------------ r2160 | pemsley | 2009-07-27 12:41:56 +0100 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.h For WINDOWS_MINGW, set prefer_python in init() not globjects.h ------------------------------------------------------------------------ r2159 | pemsley | 2009-07-25 01:13:56 +0100 (Sat, 25 Jul 2009) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Fix torsion angle difference circular wrapping. ------------------------------------------------------------------------ r2158 | pemsley | 2009-07-25 01:05:40 +0100 (Sat, 25 Jul 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix typo in #defing add_alt_conf_scm(). ------------------------------------------------------------------------ r2157 | pemsley | 2009-07-25 00:55:04 +0100 (Sat, 25 Jul 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add USE_GUILE protection for refine_residues_with_alt_conf_scm() function. ------------------------------------------------------------------------ r2156 | pemsley | 2009-07-24 12:54:40 +0100 (Fri, 24 Jul 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple make compilers_dir depend on build_type (python build logs are split out). ------------------------------------------------------------------------ r2155 | pemsley | 2009-07-24 12:36:35 +0100 (Fri, 24 Jul 2009) | 2 lines Changed paths: A /trunk/scheme/parse-pisa-xml.scm Add parse-pisa-xml. Not loaded - just for development at the moment. ------------------------------------------------------------------------ r2154 | pemsley | 2009-07-23 20:42:56 +0100 (Thu, 23 Jul 2009) | 2 lines Changed paths: M /trunk/rel-todo fix typo in rel-todo. ------------------------------------------------------------------------ r2153 | pemsley | 2009-07-23 20:41:37 +0100 (Thu, 23 Jul 2009) | 7 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/doc/user-manual.texi M /trunk/ideal/Makefile.am M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Put Add Strand Here next to Add Helix Here in Other Tools dialog. Which scripting language to use for that? place_strand_here_dialog() added. prefer_python and set_prefer_python() introduced. Update manual for Replace Residue. Fix preferences_font_size_small_radiobutton typo. ------------------------------------------------------------------------ r2152 | pemsley | 2009-07-23 19:12:18 +0100 (Thu, 23 Jul 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/burn-up/burn-up.tab M /trunk/ideal/Makefile.am M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Environment distances should disappear when the molecule to which they are attached is undisplayed or closed. ------------------------------------------------------------------------ r2151 | pemsley | 2009-07-23 18:41:22 +0100 (Thu, 23 Jul 2009) | 3 lines Changed paths: M /trunk/src/nsv.cc Only move on button release for rect events (c.f. same mod for letter event in rev 2071). ------------------------------------------------------------------------ r2150 | pemsley | 2009-07-22 18:51:08 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/rel-todo Fix typo in build-status for revision number. ------------------------------------------------------------------------ r2149 | pemsley | 2009-07-22 18:17:22 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Use the c-interface texi file that is being generated by xsltproc. ------------------------------------------------------------------------ r2148 | pemsley | 2009-07-22 18:07:13 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab standard burn-up table. ------------------------------------------------------------------------ r2147 | pemsley | 2009-07-22 15:38:17 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Tweak the graph a bit: labels, notes, extend days axis. ------------------------------------------------------------------------ r2146 | pemsley | 2009-07-22 15:37:17 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Extra failure check in Autofit rotamers with ins codes. ------------------------------------------------------------------------ r2145 | pemsley | 2009-07-22 12:40:10 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc do_rotamers() needs use_graphics_interface_flag protection. ------------------------------------------------------------------------ r2144 | pemsley | 2009-07-22 12:27:36 +0100 (Wed, 22 Jul 2009) | 8 lines Changed paths: M /trunk/TODO M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/backrub-rotamer.cc M /trunk/ligand/backrub-rotamer.hh M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Added test for 3 residue in backrub_rotamer::make_test_fragment(). Throw exception on failure. Autofit-rotamer should fall back to conventional mode if backrub_rotamer fails. backrub_rotamer returns a success status too now. graphics-info-modelling: split_residue() needs only split once, give that a suitable atom is found. ------------------------------------------------------------------------ r2143 | pemsley | 2009-07-22 09:54:31 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Use GetAtomTable() (previously forgotten) in split_residue(). ------------------------------------------------------------------------ r2142 | pemsley | 2009-07-22 09:53:34 +0100 (Wed, 22 Jul 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Properly initialise the rtop_orth in move_waters_around_protein(). Don't try to transform atom if the best rtop_orth has not been set. ------------------------------------------------------------------------ r2141 | pemsley | 2009-07-22 01:55:24 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix up the backrub rotamer test. ------------------------------------------------------------------------ r2140 | pemsley | 2009-07-22 01:06:02 +0100 (Wed, 22 Jul 2009) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/rel-todo M /trunk/src/Makefile.am M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-scm.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc M /trunk/src/guile-fixups.h Consient use of guile-fixups.h COOT_WRAP_PYTHON_TEMPLATE is in this directory not $srcdir. ------------------------------------------------------------------------ r2139 | pemsley | 2009-07-22 00:13:46 +0100 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fixup needed for scm_is_string(). ------------------------------------------------------------------------ r2138 | pemsley | 2009-07-21 23:55:07 +0100 (Tue, 21 Jul 2009) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python_pre.cc New wrap code. ------------------------------------------------------------------------ r2137 | pemsley | 2009-07-21 23:18:23 +0100 (Tue, 21 Jul 2009) | 2 lines Changed paths: A /trunk/src/rotamer-search-modes.hh Add missing rotamer-search-modes.hh ------------------------------------------------------------------------ r2136 | pemsley | 2009-07-21 21:50:37 +0100 (Tue, 21 Jul 2009) | 2 lines Changed paths: A /trunk/ligand/backrub-rotamer.cc A /trunk/ligand/backrub-rotamer.hh Add missing backrub-rotamer files. ------------------------------------------------------------------------ r2135 | pemsley | 2009-07-21 21:02:35 +0100 (Tue, 21 Jul 2009) | 70 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/ligand/Makefile.am M /trunk/ligand/ligand.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/torsion-general.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/rotate-translate-modes.hh M /trunk/src/testing.cc M /trunk/src/testing.hh M /trunk/update-binary/notes Add an extra constructor for a minimol residue, taking a vector of atom names, add only atoms with those names. Used to generate the fragment in backrub rotamer. Add backrub-rotamer.cc and backrub-rotamer.hh to ligand source files. Add backrub_rotamer to the scripting interface. Change auto_fit_best_rotamer() to accept a 'mode' argument the defines if this should use backrub mode, conventional mode, or (default, automatic) depend on the resolution of the refinement map. Add a backrub rotamer test. geometry_objects() altered to use a class that contains info about the molecules picked for distances, so that when the molecule is undisplayed, so is the distance. Add "move_waters_to_around_protein() function". Add to extensions. Group water functions together in extensions. Add min_dist_to_points() util helper function. Add get_cell_symm() util helper function. Add shift_to_origin(), median_position() and translate_close_to_origin() util helper functions. Add a test for this. make_sample_protein_coords() has a loop to sample every 4 atoms, not 10. Does not yet select only non-C atoms. Perhaps it should. Add some debugging to torsion-general (which currently does not work (still)) Grr.. Which mmdb functions am I supposed to be using? There are 2 sets and different. In rotamer::GetResidue(), check the the residue atom_selection_container is valid before moving on with the rotamer generation. Add rotamer-search-modes.hh to coot.i so that we have ROTAMERSEARCHAUTOMATIC etc available at the scripting layer. split_residue() now returns the new alt conf string (and a success status). Used in add_add_conf_scm (no python equivalent yet). Added validation test vs input sequence (alignment-mismatches-gui, which uses alignment-mismatches to generate its data). Adds itself to Validation menu. There is a wrapper script (wrapper-alignment-mismatches-gui) that askes for a sequence first if one has not been assigned. Scheme only so far. Added modelling interface "New Molecule by Symop..." an interface to new-molecule-by-symop. Scheme only so far. In sequence-assignment, residue_range_t has been moved out ouf the sequence_assignment namespace as it is a generally useful class (now used in multiple residue range rigid-body refinement). remove (char *) casting on the atom selection on full_atom_spec_to_atom_index() functions (yey!). Added SCM function rigid_body_refine_by_residue_ranges_scm(). Need python version (should be simple). In replace_coords(), in the !change_alt_conf_occ_flags section we need to increment n_atom (otherwise we get "0 atoms updated" message). Some small updates to user-mods.cc (parse_no_adj() function introduced). Use round() not fiddling with floor() in translation components of (shelx) symop card. ------------------------------------------------------------------------ r2134 | b.lohkamp | 2009-07-19 13:07:59 +0100 (Sun, 19 Jul 2009) | 1 line Changed paths: M /trunk/src/globjects.cc fix zalman (no more black lines) ------------------------------------------------------------------------ r2133 | b.lohkamp | 2009-07-14 16:47:03 +0100 (Tue, 14 Jul 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/globjects.cc enable zalman-stereo command line switch fix typo for residues_matching_criteria clean up bldnotes (at least a bit) ------------------------------------------------------------------------ r2132 | b.lohkamp | 2009-07-13 09:10:10 +0100 (Mon, 13 Jul 2009) | 1 line Changed paths: A /trunk/windows A /trunk/windows/WinCoot_install_masta.nsi A /trunk/windows/make_wincoot_installer.bat A /trunk/windows/wincoot-autobuild-all put windows build and installer files in repo ------------------------------------------------------------------------ r2131 | pemsley | 2009-07-11 15:26:39 +0100 (Sat, 11 Jul 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/dnotes M /trunk/rel-todo Add residue_triple class. ------------------------------------------------------------------------ r2130 | b.lohkamp | 2009-07-10 16:49:53 +0100 (Fri, 10 Jul 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/build-it-win update windows installer to python 2.6 ------------------------------------------------------------------------ r2129 | pemsley | 2009-07-09 22:53:23 +0100 (Thu, 09 Jul 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h When clearing dots, don't redraw if dots were not cleared (e.g. they were closed). ------------------------------------------------------------------------ r2128 | pemsley | 2009-07-09 20:24:43 +0100 (Thu, 09 Jul 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Minor note updates. ------------------------------------------------------------------------ r2127 | pemsley | 2009-07-09 20:23:54 +0100 (Thu, 09 Jul 2009) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm remove debugging. ------------------------------------------------------------------------ r2126 | pemsley | 2009-07-09 20:22:47 +0100 (Thu, 09 Jul 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/burn-up/burn-up.tab M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc More burn points. Mark scripting documentation as done. ------------------------------------------------------------------------ r2125 | pemsley | 2009-07-09 20:20:55 +0100 (Thu, 09 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend range to 220 days. ------------------------------------------------------------------------ r2124 | pemsley | 2009-07-09 18:09:27 +0100 (Thu, 09 Jul 2009) | 3 lines Changed paths: M /trunk/doc/Makefile.am Change the directory that the split-by-chapter manual is written (no chapters subdir). ------------------------------------------------------------------------ r2123 | b.lohkamp | 2009-07-09 16:01:30 +0100 (Thu, 09 Jul 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/mutate.py M /trunk/scheme/coot-gui.scm fix keycode extraction for pygtk fix error in key-bindings-gui when using scm AND py key-bindings but still cannot use the callbacks from other scripting language ...and I guess we wont be able to (at least not easily) mutate_nucleotide_range for python update windows buid script ------------------------------------------------------------------------ r2122 | pemsley | 2009-07-08 22:30:35 +0100 (Wed, 08 Jul 2009) | 4 lines Changed paths: M /trunk/src/nsv.cc Fix sequence view canvas problems with a single chain. For some reason we need to cast canvas_y_size as a double (it is an it) when setting scroll_height. ------------------------------------------------------------------------ r2121 | pemsley | 2009-07-08 21:40:46 +0100 (Wed, 08 Jul 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Make links connect with dashed lines - it looks better in most cases. ------------------------------------------------------------------------ r2120 | pemsley | 2009-07-08 18:53:02 +0100 (Wed, 08 Jul 2009) | 3 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/burn-up/burn-up.tab M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/mutate.scm M /trunk/src/c-interface-waters.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h blob_under_pointer_to_screen_centre() now uses an position-searching algorithm that picks the (high point of the) blob at the front. ------------------------------------------------------------------------ r2119 | b.lohkamp | 2009-07-08 15:51:42 +0100 (Wed, 08 Jul 2009) | 1 line Changed paths: M /trunk/src/globjects.cc new Zalman implementation, should work more general now ------------------------------------------------------------------------ r2118 | b.lohkamp | 2009-07-08 15:02:24 +0100 (Wed, 08 Jul 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py update and enable pukka puckers ------------------------------------------------------------------------ r2117 | pemsley | 2009-07-08 14:50:28 +0100 (Wed, 08 Jul 2009) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Add a scripting fuction that mutates a range of nucleotides. ------------------------------------------------------------------------ r2116 | pemsley | 2009-07-06 20:30:16 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple check build dependencies when on ubuntu. ------------------------------------------------------------------------ r2115 | pemsley | 2009-07-06 17:30:55 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Enable pukker-puckers? as a validation menu item. ------------------------------------------------------------------------ r2114 | pemsley | 2009-07-06 17:30:07 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab more burn points. ------------------------------------------------------------------------ r2113 | pemsley | 2009-07-06 13:24:56 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/scheme/snarf-coot-docs.scm Add scheme docuementation to the User Manual. ------------------------------------------------------------------------ r2112 | pemsley | 2009-07-06 13:24:18 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/README M /trunk/bldnotes update notes. ------------------------------------------------------------------------ r2111 | pemsley | 2009-07-06 13:23:23 +0100 (Mon, 06 Jul 2009) | 2 lines Changed paths: M /trunk/src/Makefile.am coot_wrap_python template should be from srcdir, right? ------------------------------------------------------------------------ r2110 | pemsley | 2009-07-04 22:30:45 +0100 (Sat, 04 Jul 2009) | 2 lines Changed paths: M /trunk/cycle-page-builder.scm Bragg3 is on ubuntu-8.04.3 now. ------------------------------------------------------------------------ r2109 | pemsley | 2009-07-04 16:23:23 +0100 (Sat, 04 Jul 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple mmdb from York for the moment (file creation time problems on make). ------------------------------------------------------------------------ r2108 | pemsley | 2009-07-04 15:19:39 +0100 (Sat, 04 Jul 2009) | 2 lines Changed paths: M /trunk/build-it gtk1 prefix for compiler dirs. ------------------------------------------------------------------------ r2107 | pemsley | 2009-07-04 01:42:48 +0100 (Sat, 04 Jul 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Check exit status of wget for coot source tar file. my_exit on non zero. ------------------------------------------------------------------------ r2106 | pemsley | 2009-07-03 19:18:14 +0100 (Fri, 03 Jul 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/cycle-page-builder.scm Add Fed-8 and 10 builds to the build page. ------------------------------------------------------------------------ r2105 | pemsley | 2009-07-03 19:17:36 +0100 (Fri, 03 Jul 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Check for NULL return in get_following_residue(). ------------------------------------------------------------------------ r2104 | pemsley | 2009-07-03 19:16:57 +0100 (Fri, 03 Jul 2009) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Update with new distances/logic for pukka puckers. ------------------------------------------------------------------------ r2103 | pemsley | 2009-07-03 12:51:21 +0100 (Fri, 03 Jul 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc Use GTK1 compatible versions of the wrap code. ------------------------------------------------------------------------ r2102 | pemsley | 2009-07-01 15:52:11 +0100 (Wed, 01 Jul 2009) | 3 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h Rework the pukka puckers. Not fit for public yet. Needs more work. Now the phosphate distance is reported relative to the base. ------------------------------------------------------------------------ r2101 | b.lohkamp | 2009-06-30 21:12:24 +0100 (Tue, 30 Jun 2009) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/coot-utils/coot-coord-utils.cc M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc A /trunk/update-binary/check_for_updates.py A /trunk/update-binary/phone_home.py fix disconnected added atoms bugs (and modify add terminal residue test to test for this; python only) add python modules for binary update (not fully tested, needs more...) update windows build-it add get_torsion_py ------------------------------------------------------------------------ r2100 | pemsley | 2009-06-29 15:02:27 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/torsion-general.hh M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc New/old/previous mgtree.cc - attempting to undo rev 1919 revert. ------------------------------------------------------------------------ r2099 | pemsley | 2009-06-29 14:59:53 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc Gtk1-compatible version of coot_wrap_python. ------------------------------------------------------------------------ r2098 | pemsley | 2009-06-29 14:57:46 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: A /trunk/cycle-page-builder.scm New devel/build-page-maker, cycle-based. ------------------------------------------------------------------------ r2097 | pemsley | 2009-06-29 14:56:39 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: M /trunk/build-it For now, don't use mmdb-mmcif-long-line.patch. This may need to be reviewed. ------------------------------------------------------------------------ r2096 | pemsley | 2009-06-29 14:55:43 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add paragraph describing add alt conf. ------------------------------------------------------------------------ r2095 | pemsley | 2009-06-29 14:54:54 +0100 (Mon, 29 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New table. ------------------------------------------------------------------------ r2094 | pemsley | 2009-06-29 00:15:26 +0100 (Mon, 29 Jun 2009) | 5 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/coot_wrap_python.cc toolbar_multi_refine button functions reworked to compile with guile and python enabled - and to fit the conventional system used for other functions. const some strings in mmdb python interface. ------------------------------------------------------------------------ r2093 | pemsley | 2009-06-28 22:21:11 +0100 (Sun, 28 Jun 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix up defined problems for pre-processor directives. ------------------------------------------------------------------------ r2092 | pemsley | 2009-06-28 22:01:38 +0100 (Sun, 28 Jun 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c Simple tinkering - with set_names for the GUI. ------------------------------------------------------------------------ r2091 | pemsley | 2009-06-28 17:25:12 +0100 (Sun, 28 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Change the GSL version to 1.12 ------------------------------------------------------------------------ r2090 | b.lohkamp | 2009-06-28 15:37:46 +0100 (Sun, 28 Jun 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/macros/sys-build-type.m4 M /trunk/python/cns2coot.py M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/interface.h fix typo to define create_baton_build_params_dialog and protect function for GTK1 version introduce interruptible fit functions for python (using python scripting only) add coot_sys_build_type for python add MinGW to sys-build-types ------------------------------------------------------------------------ r2089 | pemsley | 2009-06-28 14:47:49 +0100 (Sun, 28 Jun 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple On my_exit, remove the test-status file, not the build-status file. ------------------------------------------------------------------------ r2088 | pemsley | 2009-06-27 12:25:49 +0100 (Sat, 27 Jun 2009) | 2 lines Changed paths: M /trunk/build-it Use pre_release_server_dir to set coot_version_pre ------------------------------------------------------------------------ r2087 | pemsley | 2009-06-26 17:48:20 +0100 (Fri, 26 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple And yet further. ------------------------------------------------------------------------ r2086 | pemsley | 2009-06-26 17:44:34 +0100 (Fri, 26 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Change to $pre_release_server_dir later in the script too. ------------------------------------------------------------------------ r2085 | pemsley | 2009-06-25 01:07:12 +0100 (Thu, 25 Jun 2009) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/dnotes M /trunk/rel-todo M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info-other.cc Add a GUI for baton-build params. Add string_to_int and float util functions. Add FinishStructEdit() to mmdb generation from python and scm. ------------------------------------------------------------------------ r2084 | pemsley | 2009-06-24 13:13:40 +0100 (Wed, 24 Jun 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix typo in post-manipulation mode types. ------------------------------------------------------------------------ r2083 | pemsley | 2009-06-24 13:07:20 +0100 (Wed, 24 Jun 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Make pre_release_server_dir be biop.ox. ------------------------------------------------------------------------ r2082 | pemsley | 2009-06-24 06:52:06 +0100 (Wed, 24 Jun 2009) | 3 lines Changed paths: M /trunk/generate-svn-revision-cc.sh Now we use extern "C" in svn-revision.cc, we need to offset the tail by one more (4). ------------------------------------------------------------------------ r2081 | pemsley | 2009-06-22 22:55:11 +0100 (Mon, 22 Jun 2009) | 5 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/mini-mol/mini-mol.cc M /trunk/rel-todo M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Do not copy a TER atom in construction of a minimol molecule from a CMMDBManager. Rotate Translate in the toolbar has a label now. molecule_info's replace_coords() now does not replace a TER atom. ------------------------------------------------------------------------ r2080 | b.lohkamp | 2009-06-22 21:46:16 +0100 (Mon, 22 Jun 2009) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/src/c-interface.h fix args in refine_residues_with_alt_conf_py ------------------------------------------------------------------------ r2079 | b.lohkamp | 2009-06-22 13:57:28 +0100 (Mon, 22 Jun 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_toolbuttons.py M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/coot.in make stand-alone find_waters_dialog and add (main)toolbutton for it (python) ------------------------------------------------------------------------ r2078 | pemsley | 2009-06-22 13:54:01 +0100 (Mon, 22 Jun 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/rel-todo update documentation for post-manipulation-hook. ------------------------------------------------------------------------ r2077 | pemsley | 2009-06-22 12:48:57 +0100 (Mon, 22 Jun 2009) | 13 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/peak-search.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc mmdb-extras.cc's deep_copy_residue() was returning problematic residues when there were no atoms in the returned residue. In such a case, now return a NULL. Now all uses of mmdb-extras.cc's deep_copy_residue() check for NULL. refine_residues (and graphics_info functions thereof) now take an altconf. This is not used yet (e.g. in sphere refinement). So that residues with alt confs in sphere refinement do not get refined currently. deep_copy_residue()s now do not copy the TER atom. Reading in a new PDB now does not change the go_to_atom_molecule. It does not change the Go To Atom dialog. Now using the molecule option menu after reading in a new pdb file works as it should. peak_search max_closeness of peaks is now 2.0 (1.0 was too small). ------------------------------------------------------------------------ r2076 | pemsley | 2009-06-19 18:34:57 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface.h Fix up function documentation. ------------------------------------------------------------------------ r2075 | pemsley | 2009-06-19 14:30:46 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/scheme/fitting.scm M /trunk/src/c-interface-gui.cc Tweak the sensitivities of the refinement buttons for better clarity. ------------------------------------------------------------------------ r2074 | pemsley | 2009-06-19 14:30:11 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab New table. ------------------------------------------------------------------------ r2073 | pemsley | 2009-06-19 14:16:02 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm More protection in residue-alt-confs, atom-ls might be #f from residue-info (if residue not found). ------------------------------------------------------------------------ r2072 | pemsley | 2009-06-19 13:58:56 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New annotation, extend the days. ------------------------------------------------------------------------ r2071 | pemsley | 2009-06-19 11:52:34 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/nsv.cc Actually move to the atom on a GDK_BUTTON_RELEASE, not a motion event. Fixed JED bug. ------------------------------------------------------------------------ r2070 | pemsley | 2009-06-19 00:29:11 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh Fix quoting problems in comment string. ------------------------------------------------------------------------ r2069 | pemsley | 2009-06-19 00:08:18 +0100 (Fri, 19 Jun 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Don't GLADE_HOOKUP_OBJECT() for model_toolbar_rot_trans_toolbutton when GTK_TYPE_MENU_TOOL_BUTTON not defined. Fixes CentOS 4.6 crash. ------------------------------------------------------------------------ r2068 | pemsley | 2009-06-19 00:07:00 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh update teh svn-revision.cc file, now we seem to need extern "C". ------------------------------------------------------------------------ r2067 | pemsley | 2009-06-19 00:05:56 +0100 (Fri, 19 Jun 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Updates for svn_revision() - formatting. ------------------------------------------------------------------------ r2066 | pemsley | 2009-06-18 13:44:03 +0100 (Thu, 18 Jun 2009) | 6 lines Changed paths: A /trunk/update-binary/check-for-updates.scm A /trunk/update-binary/download-binary-cmd.scm M /trunk/update-binary/phone-home.scm Updates for updating binaries. Tested on pre-release. GTK2+ only (because of threads). Now we call the sever and check the type-binary*latest.txt file to find the latest built version. The check-for-updates extension is not added in (as yet). ------------------------------------------------------------------------ r2065 | pemsley | 2009-06-17 12:07:03 +0100 (Wed, 17 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple fix typo. ------------------------------------------------------------------------ r2064 | b.lohkamp | 2009-06-17 11:04:27 +0100 (Wed, 17 Jun 2009) | 3 lines Changed paths: M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex M /trunk/python-tests/02_shelx.py M /trunk/python-tests/07_ncs.py update tutorials add some imol tests/protection to some python tests ------------------------------------------------------------------------ r2063 | pemsley | 2009-06-17 10:19:54 +0100 (Wed, 17 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Experimental latest build for binary type text file added. ------------------------------------------------------------------------ r2062 | pemsley | 2009-06-16 18:51:23 +0100 (Tue, 16 Jun 2009) | 4 lines Changed paths: M /trunk/README M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/gtk2-interface.c Add protection for looking up sequence_view_dialog [Fixes crash]. Also lookup nsv_dialog. Resize the buttons on the preferences dialog. ------------------------------------------------------------------------ r2061 | pemsley | 2009-06-16 18:38:20 +0100 (Tue, 16 Jun 2009) | 2 lines Changed paths: M /trunk/src/nsv.cc Use an int for looping over residue number ticks (not unsigned int). ------------------------------------------------------------------------ r2060 | pemsley | 2009-06-14 23:29:21 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/fitting.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add in coot-sys-build-type function (scheme only so far). Use -DCOOT_SYS_BUILD_TYPE in the src/Makefile.am. ------------------------------------------------------------------------ r2059 | pemsley | 2009-06-14 17:59:10 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: A /trunk/update-binary A /trunk/update-binary/notes A /trunk/update-binary/phone-home.scm Add some test/play code for seeing what binaries are available on the web site. Somehow report back to user for update/download/install. ------------------------------------------------------------------------ r2058 | pemsley | 2009-06-14 01:06:32 +0100 (Sun, 14 Jun 2009) | 2 lines Changed paths: M /trunk/macros/sys-build-type.m4 Tweak the COOT_SYS_BUILD_TYPE into shape. Not yet used in src/Makefile.am ------------------------------------------------------------------------ r2057 | pemsley | 2009-06-14 00:41:36 +0100 (Sun, 14 Jun 2009) | 3 lines Changed paths: M /trunk/configure.in A /trunk/macros/sys-build-type.m4 Start to add sys build type into build system - to be used by updating-binaries mechanism. ------------------------------------------------------------------------ r2056 | pemsley | 2009-06-13 01:11:34 +0100 (Sat, 13 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add coot revision info to build status line. ------------------------------------------------------------------------ r2055 | pemsley | 2009-06-12 08:51:50 +0100 (Fri, 12 Jun 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Delete unused declaration of a GFile in on_coords_filechooserdialog1_response(). ------------------------------------------------------------------------ r2054 | pemsley | 2009-06-12 02:49:22 +0100 (Fri, 12 Jun 2009) | 4 lines Changed paths: M /trunk/src/callbacks.c gtk_file_chooser_get_files() is too modern for old GTK2s. So use gtk_file_chooser_get_filenames(), which returns a GSList of char * filenames (not GFiles). ------------------------------------------------------------------------ r2053 | pemsley | 2009-06-11 17:21:06 +0100 (Thu, 11 Jun 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c GTK1 doesn't have gtk_file_selection_get_selections, so ifdef it out and use the old (singl) file mechanism for GTK1. ------------------------------------------------------------------------ r2052 | pemsley | 2009-06-11 14:18:22 +0100 (Thu, 11 Jun 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc Shift-click and ctrl-click enabled in reading coordinate files by using gtk_file_chooser_get_files() etc. ------------------------------------------------------------------------ r2051 | b.lohkamp | 2009-06-09 22:37:43 +0100 (Tue, 09 Jun 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py add python test for refinement with zero bond esd ------------------------------------------------------------------------ r2050 | pemsley | 2009-06-09 17:50:30 +0100 (Tue, 09 Jun 2009) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Add a Cancel button to multi-refine button set. Pressing the stop button makes the Cancel button visible Pressing the stop button makes the Cancel button sensitive. Pressing the continue button makes the Cancel button insensitive. ------------------------------------------------------------------------ r2049 | pemsley | 2009-06-08 14:19:53 +0100 (Mon, 08 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py New annotation on burn-up graph. ------------------------------------------------------------------------ r2048 | b.lohkamp | 2009-06-08 07:25:30 +0100 (Mon, 08 Jun 2009) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix typo in new TER test ------------------------------------------------------------------------ r2047 | b.lohkamp | 2009-06-07 22:58:31 +0100 (Sun, 07 Jun 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/scheme/extensions.scm add 3D annotations for python update some python tests (TER on water chain...) ------------------------------------------------------------------------ r2046 | pemsley | 2009-06-07 16:20:19 +0100 (Sun, 07 Jun 2009) | 2 lines Changed paths: M /trunk/build/CalphaBuild.cc M /trunk/build/CalphaBuild.hh M /trunk/build/Makefile.am M /trunk/build/testcabuild.cc M /trunk/burn-up/new-graph.py M /trunk/coords/Bond_lines.h M /trunk/coords/Bond_lines_ext.cc M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/coords/Makefile.am M /trunk/coords/coot-close.cc M /trunk/coords/cos-sin.cc M /trunk/coords/cos-sin.h M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-crystal.h M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/coords/utils.cc M /trunk/coords/utils.h M /trunk/coot-surface/Makefile.am M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/atomic-numbers.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-fasta.cc M /trunk/coot-utils/coot-fasta.hh M /trunk/coot-utils/coot-fffear.cc M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx.hh M /trunk/coot-utils/coot-trim.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/coot-utils/test-shelx-reader.cc M /trunk/coot-utils/test-utils.cc M /trunk/coot-utils/trim.cc M /trunk/cootaneer/Makefile.am M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/density-contour/Makefile.am M /trunk/geometry/Makefile.am M /trunk/geometry/Makefile.simple M /trunk/geometry/protein-geometry-mmdb.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/test-geometry.cc M /trunk/high-res/Makefile.am M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/coot-atom-graph.hh M /trunk/high-res/coot-node-info.hh M /trunk/high-res/globularize.cc M /trunk/high-res/high-res.cc M /trunk/high-res/residue-distortions.cc M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/high-res/test-atom-graph.cc M /trunk/high-res/testseqalign.cc M /trunk/high-res/testseqassignment.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/Makefile.simple M /trunk/ideal/lograma.h M /trunk/ideal/molmantest.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/regularize-minimol.hh M /trunk/ideal/test-indexing.cc M /trunk/ideal/test-indexing.hh M /trunk/ideal/with-geometry.cc M /trunk/ligand/Makefile.am M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/ligand/dunbrack.cc M /trunk/ligand/dunbrack.hh M /trunk/ligand/fast-ss-search.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/residue_by_phi_psi.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/test-random.cc M /trunk/ligand/testdunbrack.cc M /trunk/macros/Makefile.am M /trunk/macros/clipper.m4 M /trunk/macros/coot-database.m4 M /trunk/macros/coot-windows.m4 M /trunk/macros/glut.m4 M /trunk/macros/guile-gtk.m4 M /trunk/macros/mmdb-ssm.m4 M /trunk/macros/mmdb.m4 M /trunk/macros/with-guile.m4 M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol-utils.cc M /trunk/mini-mol/mini-mol-utils.hh M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/python/Makefile.am M /trunk/python/coot_lsq.py M /trunk/python/tips.py M /trunk/scheme/coot-lsq.scm M /trunk/scheme/coot.scm M /trunk/scheme/fitting.scm M /trunk/scheme/generic-objects.scm M /trunk/scheme/group-settings.scm M /trunk/scheme/mutate.scm M /trunk/scheme/refmac.scm M /trunk/scheme/tips-gui.scm M /trunk/sequence-view/Makefile.am M /trunk/sequence-view/sequence-view.cc M /trunk/sequence-view/sequence-view.hh M /trunk/setup/coot.csh.in M /trunk/setup/coot.sh.in M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface.h M /trunk/src/callbacks.h M /trunk/src/coot_pythonmodule.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/pick.cc M /trunk/src/positioned-widgets.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/read-phs.c M /trunk/src/read-phs.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh M /trunk/surface/CXXChargeTable.cpp M /trunk/surface/CXXChargeTable.h M /trunk/surface/CXXCircle.cpp M /trunk/surface/CXXCircle.h M /trunk/surface/CXXCircleNode.cpp M /trunk/surface/CXXCircleNode.h M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCoord.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/CXXException.cpp M /trunk/surface/CXXException.h M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXFFTSolventMap.h M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h M /trunk/surface/CXXMatrix4x4.h M /trunk/surface/CXXNewHood.cpp M /trunk/surface/CXXNewHood.h M /trunk/surface/CXXNode.cpp M /trunk/surface/CXXNode.h M /trunk/surface/CXXPointyBit.h M /trunk/surface/CXXQADSurface.cpp M /trunk/surface/CXXQADSurface.h M /trunk/surface/CXXQADSurfaceStaticData.cpp M /trunk/surface/CXXSpace.cpp M /trunk/surface/CXXSpace.h M /trunk/surface/CXXSphereElement.cpp M /trunk/surface/CXXSphereElement.h M /trunk/surface/CXXSphereFlatTriangle.h M /trunk/surface/CXXSphereNode.cpp M /trunk/surface/CXXSphereNode.h M /trunk/surface/CXXSphereTriangle.cpp M /trunk/surface/CXXSphereTriangle.h M /trunk/surface/CXXSphereTriangleEdge.cpp M /trunk/surface/CXXSphereTriangleEdge.h M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXSurfaceVertex.cpp M /trunk/surface/CXXSurfaceVertex.h M /trunk/surface/CXXTorusElement.cpp M /trunk/surface/CXXTorusElement.h M /trunk/surface/CXXTorusNode.cpp M /trunk/surface/CXXTorusNode.h M /trunk/surface/CXXTorusTriangle.cpp M /trunk/surface/CXXTorusTriangle.h M /trunk/surface/CXXTorusTriangle.h.h M /trunk/surface/CXXTriangle.cpp M /trunk/surface/CXXTriangle.h M /trunk/surface/CXXUtils.cpp M /trunk/surface/CXXUtils.h M /trunk/surface/ElectroSurface.cpp M /trunk/surface/TokenIterator.h M /trunk/surface/surface.cpp M /trunk/surface/surface.h M /trunk/tw/Makefile.am M /trunk/tw/coot-tw.hh M /trunk/tw/cootsound.c Make the license clearly version 3. ------------------------------------------------------------------------ r2045 | pemsley | 2009-06-07 13:59:14 +0100 (Sun, 07 Jun 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Move "set spin speed" into setttings in Extensions. ------------------------------------------------------------------------ r2044 | pemsley | 2009-06-06 19:03:41 +0100 (Sat, 06 Jun 2009) | 4 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add the "3D annotations" (just the same as we did on the mailing list several weeks ago). Under Extensions -> Representations. Scheme only so far. Add documentation for this. ------------------------------------------------------------------------ r2043 | pemsley | 2009-06-04 21:25:06 +0100 (Thu, 04 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add protection for NULL residues and chains in construct_from_model_links(). ------------------------------------------------------------------------ r2042 | pemsley | 2009-06-04 16:08:10 +0100 (Thu, 04 Jun 2009) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/ideal/simple-restraint.cc Add long bonds for element AU. Bond limit is 2.4 for AU. Rework debugging of bond restraints - easier for next time. ------------------------------------------------------------------------ r2041 | pemsley | 2009-06-04 01:00:21 +0100 (Thu, 04 Jun 2009) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Additional niceness on the map sharpening slider. ("Sharpen" and "blur" are offset down a line). ------------------------------------------------------------------------ r2040 | pemsley | 2009-06-03 23:32:09 +0100 (Wed, 03 Jun 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/src/c-interface-gui.cc M /trunk/src/gtk2-interface.c Tweak the scale for sharpening, how the marks work properly. ------------------------------------------------------------------------ r2039 | pemsley | 2009-06-03 23:17:16 +0100 (Wed, 03 Jun 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix typo, add extra markup arg for gtk_scale_add_mark(). ------------------------------------------------------------------------ r2038 | pemsley | 2009-06-03 22:39:06 +0100 (Wed, 03 Jun 2009) | 10 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/rotamer.cc M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h TER record on water chain is correctly removed now. Add test for this. On save coords, the active item is from the first molecule with unsaved changes. When refining, check for single HETATM atom in residue, if so, refine with rigid body. Water addtion add HETATMs. Residue names corrected for BR, CA, NA, CL, MG. TER waters are not used in water validation tests. 1 and 999 are added into the residue number entries in the LSQ fit dialog. ------------------------------------------------------------------------ r2037 | pemsley | 2009-06-02 02:28:16 +0100 (Tue, 02 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add TER atom protection for second atom in LINK too. ------------------------------------------------------------------------ r2036 | pemsley | 2009-06-02 02:25:49 +0100 (Tue, 02 Jun 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add TER atom protection in construct_from_model_links(). ------------------------------------------------------------------------ r2035 | pemsley | 2009-06-01 02:08:52 +0100 (Mon, 01 Jun 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New limits for burn-up graph. ------------------------------------------------------------------------ r2034 | pemsley | 2009-06-01 02:06:53 +0100 (Mon, 01 Jun 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fixups for build log redirection. ------------------------------------------------------------------------ r2033 | pemsley | 2009-05-31 15:07:36 +0100 (Sun, 31 May 2009) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build-gui.cc M /trunk/src/cc-interface.hh Handle esd of 0 in restraints. Add a test for esd of 0 in restraints. Reformat for doxygen documentation of monomer functions. ------------------------------------------------------------------------ r2032 | pemsley | 2009-05-30 15:36:55 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info.cc Remove debugging. ------------------------------------------------------------------------ r2031 | pemsley | 2009-05-30 15:36:14 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/scheme/gap.scm Fix for rama restraints usage in fit-gap. ------------------------------------------------------------------------ r2030 | pemsley | 2009-05-30 15:32:09 +0100 (Sat, 30 May 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Add bonds for link entities (construct_from_model_link()). ------------------------------------------------------------------------ r2029 | b.lohkamp | 2009-05-29 15:58:17 +0100 (Fri, 29 May 2009) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h enable Zalman stereo mode (for testing) Add build info to mmdb and clipper logs (windows). ------------------------------------------------------------------------ r2028 | b.lohkamp | 2009-05-27 10:25:34 +0100 (Wed, 27 May 2009) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm remove sharpen map from Extensions (py and scm) ------------------------------------------------------------------------ r2027 | pemsley | 2009-05-26 00:27:58 +0100 (Tue, 26 May 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h Put the Sharpening GUI in the Calculate menu. There it will have tick marks if GTK+ version is recent enough. ------------------------------------------------------------------------ r2026 | pemsley | 2009-05-24 10:12:11 +0100 (Sun, 24 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add build info to mmdb and clipper logs. ------------------------------------------------------------------------ r2025 | pemsley | 2009-05-23 07:46:20 +0100 (Sat, 23 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update to guile-1.8.6 ------------------------------------------------------------------------ r2024 | b.lohkamp | 2009-05-22 18:19:01 +0100 (Fri, 22 May 2009) | 1 line Changed paths: M /trunk/configure.in M /trunk/macros/clipper.m4 M /trunk/src/c-interface-gui.cc check for new clipper in configure ------------------------------------------------------------------------ r2023 | b.lohkamp | 2009-05-22 16:57:40 +0100 (Fri, 22 May 2009) | 4 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc update to new clipper 2.1 090520 fix real exit on windows (with help of new clipper) update sharpen map GUI ------------------------------------------------------------------------ r2022 | pemsley | 2009-05-22 06:46:37 +0100 (Fri, 22 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi The command to return the symmetry is get-symmetry, not show-symmetry. ------------------------------------------------------------------------ r2021 | pemsley | 2009-05-18 13:29:54 +0100 (Mon, 18 May 2009) | 3 lines Changed paths: M /trunk/TODO M /trunk/rel-todo M /trunk/scheme/coot-gui.scm Hack out several items in the todo list for the next release. Adjust the sharpening gui slightly. ------------------------------------------------------------------------ r2020 | b.lohkamp | 2009-05-17 21:39:57 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface.h fix python tests is_shelx_molecule for all (not just GUILE) ------------------------------------------------------------------------ r2019 | b.lohkamp | 2009-05-17 17:27:42 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-preferences.cc add python scripting functions for sharpening maps update python shelx tests ------------------------------------------------------------------------ r2018 | b.lohkamp | 2009-05-17 14:39:02 +0100 (Sun, 17 May 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/shelx.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/begin.py fix startup with toolbuttons (quick hack) add nomenclature errors to python extensions get_atom in python tests take ins-code now add python test for alt conf pepflip ------------------------------------------------------------------------ r2017 | pemsley | 2009-05-17 13:09:48 +0100 (Sun, 17 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove more >&2s. ------------------------------------------------------------------------ r2016 | pemsley | 2009-05-17 12:20:06 +0100 (Sun, 17 May 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Remove addition standard error build logging because bragg3 choked on it (for some reason). ------------------------------------------------------------------------ r2015 | pemsley | 2009-05-15 13:50:46 +0100 (Fri, 15 May 2009) | 7 lines Changed paths: M /trunk/TODO M /trunk/greg-tests/02-shelx.scm M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add Map Sharpening GUI. Add shelx occupancy on terminal residue addition test. Add a optional arg to install_model() and use it to pass shelx molecule state. Rename multi-fit menu items. Add shelx-molecule? to scheme functions Add shelx molecule flag inheritance test. ------------------------------------------------------------------------ r2014 | kevin.cowtan | 2009-05-15 13:50:24 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix CNS code so it actually works. ------------------------------------------------------------------------ r2013 | kevin.cowtan | 2009-05-15 12:20:00 +0100 (Fri, 15 May 2009) | 4 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Actually turn on data of fphidata for some of the input modes. Still expect sharpen() to crash when using other input types. ------------------------------------------------------------------------ r2012 | kevin.cowtan | 2009-05-15 10:41:52 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix up make_map_from_mtz_by_calc_phases. ------------------------------------------------------------------------ r2011 | kevin.cowtan | 2009-05-15 10:38:06 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix sharpen to use clipper2-style HKL_data initialisation. ------------------------------------------------------------------------ r2010 | kevin.cowtan | 2009-05-15 10:33:52 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc [CLIPPER2 CLEANUP] Fix CNS read to work with new sharpen function too. (hopefully) ------------------------------------------------------------------------ r2009 | kevin.cowtan | 2009-05-15 10:22:05 +0100 (Fri, 15 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h [CLIPPER2 CLEANUP] Rewrite calculate_sfs_and_make_map to remove HKL_info from API. ------------------------------------------------------------------------ r2008 | pemsley | 2009-05-14 19:31:33 +0100 (Thu, 14 May 2009) | 4 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Add Kevin's patch so that sharpen() works using the original data. The 2 fft method was scrapped. This method is more complex and invasive to other functions. ------------------------------------------------------------------------ r2007 | pemsley | 2009-05-14 19:25:52 +0100 (Thu, 14 May 2009) | 2 lines Changed paths: M /trunk/src/c-interface.h Fix up function descriptions for better doxygenation. ------------------------------------------------------------------------ r2006 | pemsley | 2009-05-14 15:19:00 +0100 (Thu, 14 May 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix typo in debugging line. ------------------------------------------------------------------------ r2005 | pemsley | 2009-05-14 13:19:55 +0100 (Thu, 14 May 2009) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Rework the sharpen function - now does a 2-way (back and forwards) transform based on the map (not original Fphis). needs more work yet. ------------------------------------------------------------------------ r2004 | pemsley | 2009-05-14 00:51:55 +0100 (Thu, 14 May 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/geometry/protein-geometry.cc M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/gtk2-interface.c Add icon and change text for Display Manager "close" button. check the three-letter-code for restraints in chiral volume analysis. Add the toolbar_multi_refine buttons which seem to have been lost. Remove some debugging. ------------------------------------------------------------------------ r2003 | pemsley | 2009-05-12 16:38:08 +0100 (Tue, 12 May 2009) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Make the "whole molecule" fitting functions interruptible. Introduce Stop and Continue buttons to the toolbar (they don't take focus). on_toolbar_multi_refine_continue_button_clicked() and on_toolbar_multi_refine_stop_button_clicked() callbacks added. ------------------------------------------------------------------------ r2002 | b.lohkamp | 2009-05-11 14:45:48 +0100 (Mon, 11 May 2009) | 1 line Changed paths: M /trunk/src/c-interface-mmdb.cc add the optional argument in python expression (forgot in last commit) ------------------------------------------------------------------------ r2001 | b.lohkamp | 2009-05-11 14:44:50 +0100 (Mon, 11 May 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/python/shelx_extensions.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py add merge_solvent_chains to extensions add test for DNA mutate and merge_solvent_chains fix new test for pepflip (using alt_conf now) Add an optional argument to the occ_b_ele list, in interpretation of a python representation of a molecule that is the segid. python shelx refine work via editable gui with and without given HKL filename ------------------------------------------------------------------------ r2000 | pemsley | 2009-05-11 14:16:22 +0100 (Mon, 11 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/scheme/shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Fix Tim Grune bug - shelx molecules should honour the "don't recentre" option-menu. ------------------------------------------------------------------------ r1999 | pemsley | 2009-05-11 13:29:17 +0100 (Mon, 11 May 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/begin.grg M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/python/fitting.py M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Re-write of pepflip (Ingo Korndoefer bug). pepflip now takes an insertion-code argument. get-atom now takes an insertion-code argument. Fix Nomenclature errors is added to Extensions. next_residue() and previous_residue() util functions introduced. ------------------------------------------------------------------------ r1998 | b.lohkamp | 2009-05-10 22:33:25 +0100 (Sun, 10 May 2009) | 1 line Changed paths: M /trunk/build-it-win update WinCoot to mmdb-1.21 ------------------------------------------------------------------------ r1997 | pemsley | 2009-05-09 12:11:47 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/TODO A /trunk/doc/c-interface_8h.texi M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/callbacks.c Include the doxygen->xml->texi documentation for c-interface functions. ------------------------------------------------------------------------ r1996 | pemsley | 2009-05-09 11:13:27 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi User manual now includes c-interface_8h.texi ------------------------------------------------------------------------ r1995 | pemsley | 2009-05-09 00:32:21 +0100 (Sat, 09 May 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple protect $update_libtool usage. ------------------------------------------------------------------------ r1994 | pemsley | 2009-05-08 17:33:29 +0100 (Fri, 08 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/gtk-manual.cc Don't look for non-existent map_scroll_buttons in get_radio_button_in_scroll_group(). ------------------------------------------------------------------------ r1993 | pemsley | 2009-05-08 14:47:32 +0100 (Fri, 08 May 2009) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/support.c M /trunk/src/support.h Add a destroy callback for the symmetry_controller_dialog. Use it to make just one instance of the symmetry_controller_dialog. Guile version fixes in src/c-interface-mmdb.cc. ------------------------------------------------------------------------ r1992 | pemsley | 2009-05-08 13:56:47 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/graphics-info-state.cc Don't save a state file on exit if started with --nos-state-script. ------------------------------------------------------------------------ r1991 | pemsley | 2009-05-08 08:59:48 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/Makefile.am add density-score-by-residue to dist_bin_SCRIPTS ------------------------------------------------------------------------ r1990 | pemsley | 2009-05-08 08:55:43 +0100 (Fri, 08 May 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix up build-script post-install-slim to account for density-score-by-residue. ------------------------------------------------------------------------ r1989 | pemsley | 2009-05-08 08:53:58 +0100 (Fri, 08 May 2009) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/density-score-by-residue Put density-score-by-residue in the tarball, so we need a density-score-by-residue-real. ------------------------------------------------------------------------ r1988 | pemsley | 2009-05-07 23:22:49 +0100 (Thu, 07 May 2009) | 5 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add an optional argument to the occ_b_ele list, in interpretation of a scheme representation of a molecule that is the segid. Add Torsion general to docs. New Y range for burnup graph. ------------------------------------------------------------------------ r1987 | pemsley | 2009-05-07 20:51:11 +0100 (Thu, 07 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface.cc Reading a CCP4 map no longer leaves the Display Control scroll button in an inconsistent state (JED bug). ------------------------------------------------------------------------ r1986 | pemsley | 2009-05-07 14:20:28 +0100 (Thu, 07 May 2009) | 4 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/rel-todo M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Change seqDist to 0 (work around mmdb bug/strangeness) in SeekContacts() for environment distances - fixes Steven Sheriff bug. Delete the atom selection in make_environment_bonds_box() fixes a memory leak. ------------------------------------------------------------------------ r1985 | pemsley | 2009-05-07 10:27:09 +0100 (Thu, 07 May 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Add a dashed line interface to generic objects. ------------------------------------------------------------------------ r1984 | pemsley | 2009-05-06 23:08:55 +0100 (Wed, 06 May 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/nsv.cc M /trunk/src/nsv.hh Adjustments to the new sequence view. Handle residue number offsets, so that the ticks, axes, letter no longer appear far to the right. ------------------------------------------------------------------------ r1983 | pemsley | 2009-05-06 22:24:52 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Days range to 160 ------------------------------------------------------------------------ r1982 | pemsley | 2009-05-06 18:23:12 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/rel-todo Upgrade build scripts to use mmdb 1.21. ------------------------------------------------------------------------ r1981 | pemsley | 2009-05-06 18:17:00 +0100 (Wed, 06 May 2009) | 2 lines Changed paths: M /trunk/scheme/shelx-extensions.scm Make SHELXL refine work via editable gui with and without given HKL filename. ------------------------------------------------------------------------ r1980 | pemsley | 2009-05-06 17:35:24 +0100 (Wed, 06 May 2009) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/peak-search.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add merge-solvent-chains function, with GUI and test. Add DNA mutation test. add background_is_black_p() to graphics-info class. And use it in draw_anti_aliasing(). More additions to rel-todo and TODO. ------------------------------------------------------------------------ r1979 | b.lohkamp | 2009-05-05 13:09:48 +0100 (Tue, 05 May 2009) | 6 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/generic_objects.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py A /trunk/python/test_internal.py M /trunk/python/tips.py update python scripts: - fix typos and update tips - fix shelxl refine and reading of lst file - add probe_local_sphere - add simple test_internal script ------------------------------------------------------------------------ r1978 | pemsley | 2009-05-05 12:28:44 +0100 (Tue, 05 May 2009) | 3 lines Changed paths: M /trunk/rel-todo A /trunk/scheme/test-internal.scm Add simple test-internal script to run the internal tests and exit appropriately. ------------------------------------------------------------------------ r1977 | pemsley | 2009-05-02 00:01:12 +0100 (Sat, 02 May 2009) | 3 lines Changed paths: M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/rel-todo M /trunk/scheme/remote-control.scm M /trunk/src/testing.cc M /trunk/src/testing.hh Add a function to limit the peak search so that smaller peaks are not listed if a bigger one (absolute) is nearby. ------------------------------------------------------------------------ r1976 | pemsley | 2009-05-01 11:02:37 +0100 (Fri, 01 May 2009) | 4 lines Changed paths: M /trunk/scheme/generic-objects.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/shelx.scm Fix up problem in shelx refine [Tobias Beck]. New molecules by atom selection created as part of probe-local-sphere should not be active. ------------------------------------------------------------------------ r1975 | pemsley | 2009-05-01 10:42:11 +0100 (Fri, 01 May 2009) | 2 lines Changed paths: A /trunk/doc/interface-xml-to-texi.xsl M /trunk/doc/user-manual.texi Add xslt filter for c-interface.h xml doxygen docs to texi. ------------------------------------------------------------------------ r1974 | pemsley | 2009-04-30 17:47:31 +0100 (Thu, 30 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New limits for graph. ------------------------------------------------------------------------ r1973 | pemsley | 2009-04-29 18:28:58 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Make glycosidic bond debugging conditional. ------------------------------------------------------------------------ r1972 | pemsley | 2009-04-29 18:09:57 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1971 | pemsley | 2009-04-29 17:08:19 +0100 (Wed, 29 Apr 2009) | 2 lines Changed paths: M /trunk/src/coot.in unexport LANG, LC_ALL, LC_NUMERIC. ------------------------------------------------------------------------ r1970 | pemsley | 2009-04-28 22:27:41 +0100 (Tue, 28 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/tips.scm Fix some typos, clarify. ------------------------------------------------------------------------ r1969 | pemsley | 2009-04-28 22:27:08 +0100 (Tue, 28 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py new graph annotations. ------------------------------------------------------------------------ r1968 | b.lohkamp | 2009-04-27 15:10:41 +0100 (Mon, 27 Apr 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface.cc M /trunk/src/coot.i M /trunk/src/graphics-info.cc bug fix protein refinemetn options in extensions dont export main_widgets to python (actually should do same for all proper GTK widgets!?) fix reference counting for safe_python_with_return (should fix Ramachandran/ post_manipulation_hook_py problems - finally) add test for post_manipulation_hook_py/Ramachandran ------------------------------------------------------------------------ r1967 | pemsley | 2009-04-27 12:26:25 +0100 (Mon, 27 Apr 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Remove python and its config from bin in slimmed dir. ------------------------------------------------------------------------ r1966 | pemsley | 2009-04-27 11:14:04 +0100 (Mon, 27 Apr 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Convert samplings to ints in reinterp_map_fine_gridding(). ------------------------------------------------------------------------ r1965 | pemsley | 2009-04-25 11:42:12 +0100 (Sat, 25 Apr 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/testing.cc Fix typo in util function canonical_base_name(). Use coot::util::nucleotide_is_DNA(r) in do_base_mutation(). (These 2 together fix bug when trying to mutate DNA). Fix limit check when adding view description (fixes esoteric crash). Fix typo in greg test name. ------------------------------------------------------------------------ r1964 | pemsley | 2009-04-24 14:15:08 +0100 (Fri, 24 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix up typo in snarf-coot-docs ------------------------------------------------------------------------ r1963 | pemsley | 2009-04-24 08:47:55 +0100 (Fri, 24 Apr 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Add PYTHONPATH fix to gtk1 build version. ------------------------------------------------------------------------ r1962 | pemsley | 2009-04-23 11:20:57 +0100 (Thu, 23 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple set up PYTHONPATH when doing greg tests. ------------------------------------------------------------------------ r1961 | pemsley | 2009-04-23 10:33:59 +0100 (Thu, 23 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add diagnostics for test failure. ------------------------------------------------------------------------ r1960 | pemsley | 2009-04-22 23:24:25 +0100 (Wed, 22 Apr 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh Changes for improving the flooding by changing the gridding and giving user control to the atom mask radius and sigma level for a map. ------------------------------------------------------------------------ r1959 | pemsley | 2009-04-22 23:22:51 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1958 | pemsley | 2009-04-22 23:19:23 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New graph. ------------------------------------------------------------------------ r1957 | pemsley | 2009-04-22 19:01:46 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/rel-todo update todo list. ------------------------------------------------------------------------ r1956 | pemsley | 2009-04-22 18:59:47 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/src/coot-render.hh M /trunk/src/graphics-info-render.cc Some updates for renderman output. ------------------------------------------------------------------------ r1955 | pemsley | 2009-04-22 18:22:21 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Pipe std error to python test log too. ------------------------------------------------------------------------ r1954 | pemsley | 2009-04-22 18:20:17 +0100 (Wed, 22 Apr 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Fix typo. ------------------------------------------------------------------------ r1953 | b.lohkamp | 2009-04-22 11:25:41 +0100 (Wed, 22 Apr 2009) | 1 line Changed paths: M /trunk/src/c-interface.cc fix typo in safe_python_command_with_return ------------------------------------------------------------------------ r1952 | b.lohkamp | 2009-04-22 09:44:13 +0100 (Wed, 22 Apr 2009) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-it-win fix python auto-build testing, incl. PYTONHOME and PYTHONPATH ------------------------------------------------------------------------ r1951 | b.lohkamp | 2009-04-21 12:05:57 +0100 (Tue, 21 Apr 2009) | 5 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.in M /trunk/src/main.cc import coot.py now move coot's python dir before global PYTHONPATH make safe_python_command_with_return failsafe if globals are not available (should fix errors related to post_manipulation_hook_py) ------------------------------------------------------------------------ r1947 | b.lohkamp | 2009-04-09 09:02:02 +0100 (Thu, 09 Apr 2009) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/graphics-info.cc fix python post_manipulation_hook and get_refmac_version ------------------------------------------------------------------------ r1946 | pemsley | 2009-04-03 10:51:51 +0100 (Fri, 03 Apr 2009) | 2 lines Changed paths: M /trunk/rel-todo Add new issues. ------------------------------------------------------------------------ r1945 | b.lohkamp | 2009-04-02 13:50:42 +0100 (Thu, 02 Apr 2009) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/scheme/coot-utils.scm M /trunk/src/graphics-info.cc fix run_post_manipulation_hook_py ------------------------------------------------------------------------ r1944 | pemsley | 2009-03-31 08:49:52 +0100 (Tue, 31 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Days to 110 ------------------------------------------------------------------------ r1943 | b.lohkamp | 2009-03-30 12:53:41 +0100 (Mon, 30 Mar 2009) | 1 line Changed paths: M /trunk/python/shelx.py fix import error ------------------------------------------------------------------------ r1942 | pemsley | 2009-03-30 12:25:48 +0100 (Mon, 30 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Tinker with the box placement. ------------------------------------------------------------------------ r1941 | pemsley | 2009-03-27 16:36:51 +0000 (Fri, 27 Mar 2009) | 2 lines Changed paths: M /trunk/dnotes Add ntoes. ------------------------------------------------------------------------ r1940 | b.lohkamp | 2009-03-27 15:36:46 +0000 (Fri, 27 Mar 2009) | 1 line Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/ideal/simple-restraint.cc M /trunk/src/graphics-info-modelling.cc revert alt conf refinement code back to revision 1933 ------------------------------------------------------------------------ r1939 | b.lohkamp | 2009-03-27 13:26:20 +0000 (Fri, 27 Mar 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/python/coot_utils.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py fix and update shelx.py and shelx_extensions.py (now actually working, at least most of it, e.g. reading lst file and project) reading shelx ins file: treats tab as space now (was ignored before) and fix padding problem ------------------------------------------------------------------------ r1938 | pemsley | 2009-03-27 12:12:31 +0000 (Fri, 27 Mar 2009) | 3 lines Changed paths: M /trunk/src/testing.cc Find reference mtz file for test_ligand_fit_from_given_point() in ~/data/greg-data not . ------------------------------------------------------------------------ r1937 | pemsley | 2009-03-27 12:00:17 +0000 (Fri, 27 Mar 2009) | 5 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/rel-todo M /trunk/src/c-interface.h Add a node for scripting functions in user-manual.texi Update doxygen name blocks in c-interface.h so that they do not clash with names from standard documentation. Update notes. ------------------------------------------------------------------------ r1936 | b.lohkamp | 2009-03-25 10:36:18 +0000 (Wed, 25 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c fix question accept dialog order in preferences ------------------------------------------------------------------------ r1935 | b.lohkamp | 2009-03-23 15:32:13 +0000 (Mon, 23 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info-gui.cc fix the reverse button show/hide for docked accept/reject dialog ------------------------------------------------------------------------ r1934 | b.lohkamp | 2009-03-23 15:05:26 +0000 (Mon, 23 Mar 2009) | 9 lines Changed paths: M /trunk/bldnotes M /trunk/coords/mmdb-extras.cc M /trunk/coot-gtk2.glade M /trunk/ideal/simple-restraint.cc M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/remote_control.py M /trunk/src/c-interface.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c enable reuse of python sockets enable refinement of multiple conformations (maybe should have a flag?!) no trafic lights for multiple residue refinement yet (if CA split)!? antialiasing depending on bg colour python GUI to find atoms with zero occ (needs scheme.guile version) reverse button for docked accept/refinement dialog (broken though as for normal accept/reject dialog...) ------------------------------------------------------------------------ r1933 | pemsley | 2009-03-23 10:03:32 +0000 (Mon, 23 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/cc-interface.hh More items in the todo list ------------------------------------------------------------------------ r1932 | pemsley | 2009-03-23 10:02:29 +0000 (Mon, 23 Mar 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm fix formatting of comments. ------------------------------------------------------------------------ r1931 | b.lohkamp | 2009-03-18 16:06:09 +0000 (Wed, 18 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py fixes for python SMILES GUI ------------------------------------------------------------------------ r1930 | b.lohkamp | 2009-03-17 16:56:25 +0000 (Tue, 17 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py fix for overwriting python key bindings ------------------------------------------------------------------------ r1929 | pemsley | 2009-03-17 00:43:07 +0000 (Tue, 17 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py X axis 100 days ------------------------------------------------------------------------ r1928 | pemsley | 2009-03-16 20:58:51 +0000 (Mon, 16 Mar 2009) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in smiles interface. Use label, not text. ------------------------------------------------------------------------ r1927 | pemsley | 2009-03-10 11:55:56 +0000 (Tue, 10 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Extra annotation for burn-up graph. ------------------------------------------------------------------------ r1926 | b.lohkamp | 2009-03-09 14:42:17 +0000 (Mon, 09 Mar 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/create_input_server.py M /trunk/python/create_server.py M /trunk/python/get_ebi.py M /trunk/python/remote_control.py update python scripts add python server control with timeout python threading only runs one timeout function and sleep time can be modified ------------------------------------------------------------------------ r1925 | pemsley | 2009-03-09 11:21:22 +0000 (Mon, 09 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Change day limit and ticks. ------------------------------------------------------------------------ r1924 | pemsley | 2009-03-06 17:59:09 +0000 (Fri, 06 Mar 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/rel-todo M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/get-ebi.scm M /trunk/scheme/remote-control.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/gtk2-interface.c Adjust remote-control a bit, now call pyrun-simple-string (a new function). End Transmission-string spelt correctly. And now ends in a newline char. Add function is-difference-map? Add pyrun_simple_string() scripting function. ------------------------------------------------------------------------ r1923 | pemsley | 2009-03-05 13:59:04 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend graph to 80 days. ------------------------------------------------------------------------ r1922 | pemsley | 2009-03-05 10:49:53 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r1921 | pemsley | 2009-03-05 10:46:31 +0000 (Thu, 05 Mar 2009) | 2 lines Changed paths: M /trunk/rel-todo Update todo list. ------------------------------------------------------------------------ r1920 | pemsley | 2009-03-04 17:19:59 +0000 (Wed, 04 Mar 2009) | 2 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Fix up problem when reverting wiggly-ligand.cc ------------------------------------------------------------------------ r1919 | pemsley | 2009-03-04 14:21:05 +0000 (Wed, 04 Mar 2009) | 4 lines Changed paths: M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/torsion-general.hh M /trunk/src/graphics-info-modelling.cc Revert back chi-angle/rotamer/mgtree code back to before 1877. (1877 to 1917 had broken chi angle code). Now this only has (again) broken wiggly ligand code. ------------------------------------------------------------------------ r1918 | b.lohkamp | 2009-03-04 13:28:19 +0000 (Wed, 04 Mar 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/coords/Bond_lines.cc quick fix for CA + ligand representation ------------------------------------------------------------------------ r1917 | b.lohkamp | 2009-03-03 22:39:41 +0000 (Tue, 03 Mar 2009) | 1 line Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in A /trunk/python/create_input_server.py A /trunk/python/create_server.py M /trunk/python/remote_control.py M /trunk/src/c-interface.cc some fixes and updates for python sockets ------------------------------------------------------------------------ r1916 | kevin.cowtan | 2009-03-03 14:24:50 +0000 (Tue, 03 Mar 2009) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add defines for secondard structure finding templates. Change the default for find_strands() to use latest best parameters. ------------------------------------------------------------------------ r1915 | b.lohkamp | 2009-03-03 11:02:22 +0000 (Tue, 03 Mar 2009) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/src/callbacks.c implement python threading with magic trickery (whats_new_dialog) ------------------------------------------------------------------------ r1914 | pemsley | 2009-03-02 10:55:15 +0000 (Mon, 02 Mar 2009) | 3 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/coot-dox.cfg Fix typo in doc string. Add xml output from doxygen. ------------------------------------------------------------------------ r1913 | pemsley | 2009-03-02 10:53:02 +0000 (Mon, 02 Mar 2009) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.6-pre-1.xpm Fix up missing pixels in splash screen. ------------------------------------------------------------------------ r1912 | b.lohkamp | 2009-03-01 22:10:21 +0000 (Sun, 01 Mar 2009) | 1 line Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/secondary-structure.svg M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h GUI for fast secondary structure search (GTK2) ------------------------------------------------------------------------ r1911 | kevin.cowtan | 2009-02-25 12:45:39 +0000 (Wed, 25 Feb 2009) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h New flexible secondary structure building code. ------------------------------------------------------------------------ r1910 | b.lohkamp | 2009-02-24 11:08:29 +0000 (Tue, 24 Feb 2009) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm add Find Secondary Structure in Extensions ------------------------------------------------------------------------ r1909 | pemsley | 2009-02-23 20:41:57 +0000 (Mon, 23 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Better debugging of sharpen(). ------------------------------------------------------------------------ r1908 | pemsley | 2009-02-23 19:16:47 +0000 (Mon, 23 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Remove debugging from map_fill_from_mtz_with_reso_limits(). ------------------------------------------------------------------------ r1907 | pemsley | 2009-02-23 19:15:34 +0000 (Mon, 23 Feb 2009) | 4 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add the a container original_fphis after reading an MTZ file. Activate its use in sharpen - but that crashes currently. original_fphis have become invalid somehow. ------------------------------------------------------------------------ r1906 | b.lohkamp | 2009-02-23 13:45:06 +0000 (Mon, 23 Feb 2009) | 6 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/begin.py M /trunk/src/molecule-class-info-maps.cc Python Extensions use sort_chains, not reorder_chains python dialog_box_with_buttonss can do HSep between buttons (use in unittest_extensions.py to separate tests belonging to different test classes) set_map_is_difference_map sets difference map colours and contour levels ------------------------------------------------------------------------ r1905 | pemsley | 2009-02-20 18:21:14 +0000 (Fri, 20 Feb 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up guile-gui, post-neil-jerram patch added. ------------------------------------------------------------------------ r1904 | b.lohkamp | 2009-02-20 17:24:00 +0000 (Fri, 20 Feb 2009) | 1 line Changed paths: M /trunk/build-it-win some updates for windows autobuild ------------------------------------------------------------------------ r1903 | pemsley | 2009-02-20 13:04:52 +0000 (Fri, 20 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/extensions.scm Extensions use sort-chains, not reorder-chains. ------------------------------------------------------------------------ r1902 | b.lohkamp | 2009-02-19 15:05:12 +0000 (Thu, 19 Feb 2009) | 1 line Changed paths: M /trunk/python/generic_objects.py fix for pythonic interactive_probe ------------------------------------------------------------------------ r1901 | pemsley | 2009-02-19 14:54:14 +0000 (Thu, 19 Feb 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/c-interface-pisa.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Add more pisa interaction functions. A scripting interface - currently returns nothing. close_residues_from_different_molecules_t is a class because we need to handle the residue vectors before we trash the (combined) molecule. create_mmdbmanager_from_residue_vector() returns something sensible. ------------------------------------------------------------------------ r1900 | pemsley | 2009-02-19 10:16:26 +0000 (Thu, 19 Feb 2009) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/happy-coot-diary.html M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info.cc Add function new_molecule_by_symmetry(), where we give a fractional RTop. To coot-utils/coot-coord-utils.cc add function create_mmdbmanager_from_residue_vector() which will be used for creating models from symmetry/assembly interfaces. ------------------------------------------------------------------------ r1899 | pemsley | 2009-02-19 10:11:52 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix info output when building guile-lib. ------------------------------------------------------------------------ r1898 | pemsley | 2009-02-19 10:10:54 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/macros/glut.m4 Use $acl_libdirstem for glut macro. ------------------------------------------------------------------------ r1897 | pemsley | 2009-02-19 10:10:09 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/build-it Fix typo in outpu info when building guile-lib. ------------------------------------------------------------------------ r1896 | pemsley | 2009-02-19 09:52:54 +0000 (Thu, 19 Feb 2009) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Fix crash when getting links from a CModel that is empty. ------------------------------------------------------------------------ r1895 | pemsley | 2009-02-18 20:44:45 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo Add an item. ------------------------------------------------------------------------ r1894 | pemsley | 2009-02-18 16:19:18 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1893 | pemsley | 2009-02-18 13:59:04 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-gui.cc Fix up shadow variable usage i in fill_chain_option_menu(). ------------------------------------------------------------------------ r1892 | pemsley | 2009-02-18 13:56:49 +0000 (Wed, 18 Feb 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c Fix up initialisation of menu_item in on_model_toolbar_rot_trans_toolbutton_show_menu(). ------------------------------------------------------------------------ r1891 | pemsley | 2009-02-18 13:54:54 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands-gui.cc Fix up small braces issue for niggly compiler. ------------------------------------------------------------------------ r1890 | b.lohkamp | 2009-02-18 12:39:52 +0000 (Wed, 18 Feb 2009) | 1 line Changed paths: M /trunk/src/c-interface-preferences.cc user_defined_click allows only >0 no of clicks ------------------------------------------------------------------------ r1889 | kevin.cowtan | 2009-02-18 08:48:46 +0000 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface.cc Get the normal and difference map the right way round when reading CNS files. ------------------------------------------------------------------------ r1888 | b.lohkamp | 2009-02-17 22:43:57 +0000 (Tue, 17 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/src/graphics-info.cc cleaned up and fixed python user_defined_click ------------------------------------------------------------------------ r1887 | pemsley | 2009-02-17 12:55:23 +0000 (Tue, 17 Feb 2009) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Fix the problem of the scroll buttons all being on (use map_is_displayed() not mol_is_displayed()). ------------------------------------------------------------------------ r1886 | b.lohkamp | 2009-02-16 23:01:01 +0000 (Mon, 16 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/graphics-info.cc python: user_defined_click fixes and merge_solvent_chains funcn ------------------------------------------------------------------------ r1885 | pemsley | 2009-02-16 18:43:14 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build-gui.cc M /trunk/src/graphics-info-gui.cc M /trunk/src/junk.cc Apply potential fix to ChainID transfer-related crash noted by Bob Nolte. ------------------------------------------------------------------------ r1884 | b.lohkamp | 2009-02-16 14:26:01 +0000 (Mon, 16 Feb 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/extensions.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/nsv.cc add 'menu button' to MFR dialog to select rotation mode: this changes the label of the button too and is synchronised with the model toobar ------------------------------------------------------------------------ r1883 | pemsley | 2009-02-16 13:39:29 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Trivial formatting changes. (elipsis) ------------------------------------------------------------------------ r1882 | pemsley | 2009-02-16 13:37:52 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.6-pre-1.xpm Update the pre-release splashscreen. ------------------------------------------------------------------------ r1881 | pemsley | 2009-02-16 12:45:34 +0000 (Mon, 16 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade A /trunk/pixmaps/coot-0.6-pre-1.xpm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c New splash screen for pre-release (long overdue). Add some interferface for renderman output (not useful currently). ------------------------------------------------------------------------ r1880 | pemsley | 2009-02-16 12:43:07 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/rel-todo M /trunk/scheme/ncs.scm Fix up NCS jumping on heterodimers. ------------------------------------------------------------------------ r1879 | pemsley | 2009-02-16 00:40:50 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Adjust the X scale for burn-up graph. ------------------------------------------------------------------------ r1878 | pemsley | 2009-02-16 00:05:07 +0000 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc Remove debugging. ------------------------------------------------------------------------ r1877 | pemsley | 2009-02-15 16:50:08 +0000 (Sun, 15 Feb 2009) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/ligand.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/molecule-class-info-other.cc Include Stuart's new mgtree.cc, which has the forced torsions. Use atom quads in various ligand functions to support this. Adjust logic of cluser_from_point so that it works when we start from within a cluster. ------------------------------------------------------------------------ r1876 | kevin.cowtan | 2009-02-13 14:24:13 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/src/callbacks.c Tidy up the console output slightly when auto-open fails. I don't really understand the fallback path here. ------------------------------------------------------------------------ r1875 | b.lohkamp | 2009-02-13 13:52:00 +0000 (Fri, 13 Feb 2009) | 1 line Changed paths: M /trunk/python-tests/03_ligand.py added python test for dictionary replace ------------------------------------------------------------------------ r1874 | pemsley | 2009-02-13 13:43:12 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/c-interface-validate.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Dynaramas are now labelled with the molecule name. Add ligand Search radiobuttons to gtk1 interface. ------------------------------------------------------------------------ r1873 | pemsley | 2009-02-13 00:44:01 +0000 (Fri, 13 Feb 2009) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/03-ligand.scm M /trunk/rel-todo On chem_comp, delete the previous entry with this comp_id from the restraints dictionary. Test added. ------------------------------------------------------------------------ r1872 | pemsley | 2009-02-13 00:42:10 +0000 (Fri, 13 Feb 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Documentation for overwriting restraints from a mmCIF file. ------------------------------------------------------------------------ r1871 | pemsley | 2009-02-12 14:53:52 +0000 (Thu, 12 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Add Radio buttons for "Search here" in Ligand fitting. Remove remaining GSList scroll group code. ------------------------------------------------------------------------ r1870 | pemsley | 2009-02-12 13:58:42 +0000 (Thu, 12 Feb 2009) | 3 lines Changed paths: M /trunk/configure.in M /trunk/macros/clipper.m4 Test for clipper::CNS_HKLfile now that we depend on it. Improve message when clipper config fails. ------------------------------------------------------------------------ r1869 | pemsley | 2009-02-12 13:08:56 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: M /trunk/configure.in A new version of clipper is required - update configure.in ------------------------------------------------------------------------ r1868 | pemsley | 2009-02-12 10:04:03 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: M /trunk/macros/net-http-goosh.m4 M /trunk/scheme/coot-utils.scm Unfink the goosh usage. ------------------------------------------------------------------------ r1867 | pemsley | 2009-02-12 10:00:09 +0000 (Thu, 12 Feb 2009) | 5 lines Changed paths: M /trunk/libtool M /trunk/macros/net-http-goosh.m4 M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h Fix for the Display Manager scroll group. Now we don't mess with the scroll group - but instead let GTK+ manage the scroll group via widgets. GSList scroll group functions removed. get_radio_butto_in_scroll_group() added. Ligand cluster here flag enabled - no gui to activate thet setting yet. ------------------------------------------------------------------------ r1866 | pemsley | 2009-02-12 09:55:45 +0000 (Thu, 12 Feb 2009) | 2 lines Changed paths: A /trunk/src/canvas-fixes.hh M /trunk/src/nsv.cc Fix up canvas define problems. ------------------------------------------------------------------------ r1865 | kevin.cowtan | 2009-02-11 16:04:39 +0000 (Wed, 11 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Add functions to auto-open CNS-Coot interchange files (new 2009 format from AB) ------------------------------------------------------------------------ r1864 | pemsley | 2009-02-10 22:16:27 +0000 (Tue, 10 Feb 2009) | 4 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc Fix up problem of running Python code in run_user_defined_click_func, where the python function is not defined (because the scm one *is*). Now we check both scm and python against being non-default before running. ------------------------------------------------------------------------ r1863 | pemsley | 2009-02-10 19:59:34 +0000 (Tue, 10 Feb 2009) | 3 lines Changed paths: M /trunk/src/nsv.cc M /trunk/src/nsv.hh Tinker with new sequence view, now highlight in moccasin, rectangle placement adjusted. ------------------------------------------------------------------------ r1862 | pemsley | 2009-02-10 17:01:41 +0000 (Tue, 10 Feb 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Update build it scripts, using new clipper. ------------------------------------------------------------------------ r1861 | b.lohkamp | 2009-02-10 16:24:43 +0000 (Tue, 10 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py add pythonic lsq by atom test ------------------------------------------------------------------------ r1860 | pemsley | 2009-02-09 17:51:29 +0000 (Mon, 09 Feb 2009) | 3 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface.h A /trunk/src/get-residue.cc A /trunk/src/get-residue.hh M /trunk/src/nsv.cc M /trunk/src/nsv.hh Adjustments to the new sequence view, setting up to highlight the block on mouse enter. ------------------------------------------------------------------------ r1859 | pemsley | 2009-02-09 01:52:20 +0000 (Mon, 09 Feb 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface-ligands.cc Move ligand GUI functions into c-interface-ligands-gui.cc ------------------------------------------------------------------------ r1858 | pemsley | 2009-02-09 01:46:37 +0000 (Mon, 09 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1857 | pemsley | 2009-02-08 23:45:32 +0000 (Sun, 08 Feb 2009) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/base-pairing.cc M /trunk/ligand/base-pairing.hh M /trunk/ligand/ideal-rna.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Watson Crick base pairing added. Added watson_crick_pair() to scripting layer. Added to Other Modelling Tools GUI. Test for LSQ by atom added. ------------------------------------------------------------------------ r1856 | b.lohkamp | 2009-02-08 14:36:20 +0000 (Sun, 08 Feb 2009) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h update python tests (seg id tests) add segid to python residue_info add python functions (not tested) and USE_GUILE protection: add_lsq_atom_pair, atom_spec_to_py, user_defined_click... ------------------------------------------------------------------------ r1855 | pemsley | 2009-02-07 21:04:06 +0000 (Sat, 07 Feb 2009) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h Start work on atom-based lsq matching. update (pre) release notes (not done since release). ------------------------------------------------------------------------ r1854 | pemsley | 2009-02-07 15:05:43 +0000 (Sat, 07 Feb 2009) | 6 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/greg-tests/begin.grg M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/nsv.cc Add debugging to Bond_lines.cc, trying to find this stared atom bonding problem. Not fixed yet. get-atom added to coot-utils.scm (from testing begin.grg). Add user-defined-click function. Given params: n-clicks func. New sequence view put in place. ------------------------------------------------------------------------ r1853 | pemsley | 2009-02-06 16:55:38 +0000 (Fri, 06 Feb 2009) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc Test for RNA base mutation name - canonical base name function added. Test for SegIDs on mutation, NCS copy and add terminal residue. A residue-info returns info about segid too now. mutate_base() exposed to scripting layer. ------------------------------------------------------------------------ r1852 | b.lohkamp | 2009-02-06 09:34:37 +0000 (Fri, 06 Feb 2009) | 1 line Changed paths: M /trunk/src/post-process-coot-wrap-guile.sh fix for post processing wrap guile in windows ------------------------------------------------------------------------ r1851 | pemsley | 2009-02-06 08:55:08 +0000 (Fri, 06 Feb 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Fix up rot/trans mode so that residue zone works again. ------------------------------------------------------------------------ r1850 | pemsley | 2009-02-06 07:23:25 +0000 (Fri, 06 Feb 2009) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Use old-style function to get the group from the scroll radio button. Comment out the debugging printfs for the scroll group. ------------------------------------------------------------------------ r1849 | pemsley | 2009-02-06 01:05:13 +0000 (Fri, 06 Feb 2009) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h Apply a fix (hopefully) for the display manager delete molecule bug. save the (new) radio button group by using a "group-changed" callback. ------------------------------------------------------------------------ r1848 | pemsley | 2009-02-05 23:47:36 +0000 (Thu, 05 Feb 2009) | 10 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/Makefile.am D /trunk/ligand/atom-quads.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/mini-mol/Makefile.am A /trunk/mini-mol/atom-quads.hh (from /trunk/ligand/atom-quads.hh:1834) M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Add get_torsion() method to minimols' residue - for testing ligand dihedrals. Move atom-quads.hh to minimol to asist. Add torsioned_atoms_info_t to wligand.hh for testing dihedrals. get_gslist_for_scroll_in_display_manager() method added in attempt to fix display manager delete map bug. (no fix) test_internal_single() exposed to the scripting layer. get_geometry_torsion() split out from display_geometry_torsion(). Don't try to use the GUI when no ligands found in --no-graphics mode. get_atom() from atom spec method added to molecule_class_info_t. ------------------------------------------------------------------------ r1847 | pemsley | 2009-02-05 19:50:20 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Extend x axis to 60 days. ------------------------------------------------------------------------ r1846 | pemsley | 2009-02-05 19:17:13 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1845 | pemsley | 2009-02-05 18:31:43 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/command-line.cc Add in extra flags for --help. ------------------------------------------------------------------------ r1844 | pemsley | 2009-02-05 18:30:48 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/main.cc Add a note about gtk version. ------------------------------------------------------------------------ r1843 | pemsley | 2009-02-05 18:28:22 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo update notes. ------------------------------------------------------------------------ r1842 | pemsley | 2009-02-05 18:27:20 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1841 | pemsley | 2009-02-05 18:26:08 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh map_fill_from_mtz now returns a bool (about the state of the map). ------------------------------------------------------------------------ r1840 | pemsley | 2009-02-05 18:25:12 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add an output operator for dict_torsion_restraint_t. ------------------------------------------------------------------------ r1839 | pemsley | 2009-02-05 18:24:24 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Add some extra text, suggesting making core dump. ------------------------------------------------------------------------ r1838 | pemsley | 2009-02-05 01:46:31 +0000 (Thu, 05 Feb 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Rot/Trans: Set the mmdb_manager properly in the case of ROT_TRANS_TYPE_ZONE. Fixes crash. ------------------------------------------------------------------------ r1837 | pemsley | 2009-02-05 01:30:11 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/fixup-gtk2-interface.sh A /trunk/src/gtk2-interface-rot-trans-fixup.awk M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh More post-processing of the gtk2 interface file, for old GTKs. ------------------------------------------------------------------------ r1836 | pemsley | 2009-02-05 00:40:42 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Fixup: use #ifdef GTK_TYPE_MENU_TOOL_BUTTON ------------------------------------------------------------------------ r1835 | pemsley | 2009-02-05 00:04:22 +0000 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.h More protection of menu tool buttons for old gtks. ------------------------------------------------------------------------ r1834 | b.lohkamp | 2009-02-04 14:09:41 +0000 (Wed, 04 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/libcheck.py fixed libcheck.py, returns imol now ------------------------------------------------------------------------ r1833 | pemsley | 2009-02-04 13:42:50 +0000 (Wed, 04 Feb 2009) | 6 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/coot_pythonmodule.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/main.cc M /trunk/src/post-process-coot-wrap-guile.sh Try again using NEW_COORDS_ADD. Fix problem of rotation atom missing (hence crash) when rotating whole molecule, needed a util function to transfer a whole molecule (with atom index transfer) because the chain-ids of residue selection were mis-applied. Add some includes of cstdios for gmp.h from libguile.h. ------------------------------------------------------------------------ r1832 | pemsley | 2009-02-04 13:32:20 +0000 (Wed, 04 Feb 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add fnction to create an mmdb manager from mmdb manager, with atom index transfer. ------------------------------------------------------------------------ r1831 | pemsley | 2009-02-04 09:22:20 +0000 (Wed, 04 Feb 2009) | 2 lines Changed paths: M /trunk/src/main.cc RHEL 4 (Gtk 2.4.13) does not have gtk_menu_tool_buttons. ------------------------------------------------------------------------ r1830 | b.lohkamp | 2009-02-03 18:57:43 +0000 (Tue, 03 Feb 2009) | 1 line Changed paths: M /trunk/python/coot_gui.py clean up fill_option_menu functions in coot_gui.py ------------------------------------------------------------------------ r1829 | b.lohkamp | 2009-02-03 16:54:44 +0000 (Tue, 03 Feb 2009) | 3 lines Changed paths: M /trunk/ligand/richardson-rotamers.cc M /trunk/src/main.cc fix proline rotamers radio check menus for rotate translate ------------------------------------------------------------------------ r1828 | b.lohkamp | 2009-02-03 14:45:08 +0000 (Tue, 03 Feb 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/libcheck.py M /trunk/python-tests/03_ligand.py M /trunk/scheme/extensions.scm M /trunk/src/callbacks.c M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info.h update libcheck python scripting pythonic replace residue (mutate-by-overlap) fix preferences (and gtk warnings) for new rot-trans toolbutton add -oldpdb to reduce command ------------------------------------------------------------------------ r1827 | pemsley | 2009-02-03 14:20:00 +0000 (Tue, 03 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm Fix up typo in dipole test as per Bernhard's suggestion. ------------------------------------------------------------------------ r1826 | pemsley | 2009-02-03 12:10:37 +0000 (Tue, 03 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/begin.grg remove (turn-on-debugging) - tests fail. ------------------------------------------------------------------------ r1825 | b.lohkamp | 2009-02-03 08:19:50 +0000 (Tue, 03 Feb 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py update python tests ------------------------------------------------------------------------ r1824 | pemsley | 2009-02-02 23:27:23 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/mini-mol/mini-mol.cc Include algorithm, needed for std::sort(). ------------------------------------------------------------------------ r1823 | pemsley | 2009-02-02 23:08:57 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/src/callbacks.c Don't run GtkMenuToolButton for gtk1. ------------------------------------------------------------------------ r1822 | pemsley | 2009-02-02 21:31:24 +0000 (Mon, 02 Feb 2009) | 4 lines Changed paths: M /trunk/rel-todo M /trunk/src/globjects.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc update_map_in_display_control_widget() was being called in initialize_map_things_on_read_molecule(). But we can't do that until xmap_is_filled[0] is set. So move update_map_in_display_control_widget() into the calling function after xmap_is_filled[0] is set. ------------------------------------------------------------------------ r1821 | pemsley | 2009-02-02 19:21:29 +0000 (Mon, 02 Feb 2009) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-gui.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc Add rotate translate mode change to the GUI with a menutoolbar. It gets set up in main.cc ------------------------------------------------------------------------ r1820 | pemsley | 2009-02-02 15:16:10 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/rel-todo M /trunk/scheme/generic-objects.scm Add -oldpdb to the arguments to reduce. ------------------------------------------------------------------------ r1819 | pemsley | 2009-02-02 14:11:58 +0000 (Mon, 02 Feb 2009) | 3 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/residue_by_phi_psi.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc Fix the B-factor test of add-terminal-residue test failure by passing the b-factor to residue_by_phi_psi constructor. ------------------------------------------------------------------------ r1818 | pemsley | 2009-02-02 01:05:11 +0000 (Mon, 02 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm In addition to previous, sort-chains uses a minimol function and a test is added. ------------------------------------------------------------------------ r1817 | pemsley | 2009-02-02 01:04:27 +0000 (Mon, 02 Feb 2009) | 5 lines Changed paths: M /trunk/coords/mmdb-crystal.cc M /trunk/db-main/db-main.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/high-res.cc M /trunk/ideal/regularize-minimol.cc M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/residue_by_phi_psi.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add a b-factor to a minimol atom. Lots of small changes in the use of the constructors then. pcmmdbmanager() no longer takes a bfactor arg, as the atoms have b-factors now. ------------------------------------------------------------------------ r1816 | pemsley | 2009-02-01 17:23:47 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1815 | pemsley | 2009-02-01 17:23:05 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/ligand/dipole.cc M /trunk/rel-todo Add dipole test (and fix up code). ------------------------------------------------------------------------ r1814 | pemsley | 2009-02-01 17:19:33 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Fix syntax error. ------------------------------------------------------------------------ r1813 | pemsley | 2009-02-01 15:58:16 +0000 (Sun, 01 Feb 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/scheme/libcheck.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.h Add function assign_hetatms() and use it after reading a file from libcheck. Introduce function PDB_standard_residue_types() - used in conditionally assigning HETATMs. ------------------------------------------------------------------------ r1812 | pemsley | 2009-02-01 15:46:13 +0000 (Sun, 01 Feb 2009) | 10 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/scheme/coot-gui.scm M /trunk/scheme/libcheck.scm M /trunk/src/Makefile.am A /trunk/src/c-interface-ligands-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c A /trunk/src/guile-fixups.h Better handle the case where libcheck is not found. monomer-molecule-from-3-let-code reworked. Now we check for libcheck in the path and split out the reading of the cif and pdb files from the running of libcheck (those files could already exist and therefore we can just read them even if libcheck is not in path). Also a warning text in the monomer dialog is shown if libcheck is not found (the is tested with a scripting function (not yet implemented for the python path). src/c-interface-ligands-gui.cc added. ------------------------------------------------------------------------ r1811 | pemsley | 2009-02-01 13:50:45 +0000 (Sun, 01 Feb 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-waters.cc M /trunk/src/gtk2-interface.c Add protein->water distance cut offs to the GUI. ------------------------------------------------------------------------ r1810 | pemsley | 2009-01-31 17:27:35 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/rel-todo update todo list and add a picure to diary. ------------------------------------------------------------------------ r1809 | pemsley | 2009-01-31 14:00:23 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm Add a GUI for mutate-by-overlap (Replace residue). Needs a python version. ------------------------------------------------------------------------ r1808 | pemsley | 2009-01-31 09:25:18 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary, fix syntax error. ------------------------------------------------------------------------ r1807 | pemsley | 2009-01-31 08:00:12 +0000 (Sat, 31 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1806 | pemsley | 2009-01-30 17:27:08 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix the RHEL 4 64-bit python build tag. ------------------------------------------------------------------------ r1805 | pemsley | 2009-01-30 16:17:52 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm RHEL 4, 64-bit python-enabled builds. ------------------------------------------------------------------------ r1804 | pemsley | 2009-01-30 09:33:44 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1803 | pemsley | 2009-01-30 09:33:29 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py tinker with burn up graph. ------------------------------------------------------------------------ r1802 | pemsley | 2009-01-30 09:32:03 +0000 (Fri, 30 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/molecule-class-info.cc Add a function to mark atoms as HETATMs and use it in the addition of pointer atoms. ------------------------------------------------------------------------ r1801 | pemsley | 2009-01-30 00:16:09 +0000 (Fri, 30 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo Another item on the TODO list. ------------------------------------------------------------------------ r1800 | pemsley | 2009-01-29 20:36:51 +0000 (Thu, 29 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Add binaries for RHEL 4 64-bit in Oxford. ------------------------------------------------------------------------ r1799 | pemsley | 2009-01-29 00:35:44 +0000 (Thu, 29 Jan 2009) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc small tidy up of formatting. ------------------------------------------------------------------------ r1798 | b.lohkamp | 2009-01-27 20:01:22 +0000 (Tue, 27 Jan 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/gap.py M /trunk/scheme/gap.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc fit-gap: fix python version and make guile to accept assigned sequence various fixes for python functions esp. add_dipole i.e. returns the right result now ------------------------------------------------------------------------ r1797 | pemsley | 2009-01-27 12:14:38 +0000 (Tue, 27 Jan 2009) | 4 lines Changed paths: M /trunk/ligand/dipole.cc A /trunk/pixmaps/coot-favicon.png M /trunk/src/c-interface-ligands.cc Fix up python problem - so that it compiles at least, python code does not give correct result yet for add_dipole(). ------------------------------------------------------------------------ r1796 | pemsley | 2009-01-27 09:30:54 +0000 (Tue, 27 Jan 2009) | 5 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add_dipole functions should return a dipole. SCM version filled. Fails (non-committed) test currently. Add editable shelxl text gui. Pass fixed atom specs in refine from residues vec. ------------------------------------------------------------------------ r1795 | pemsley | 2009-01-27 06:33:00 +0000 (Tue, 27 Jan 2009) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc In generate_molecule_and_refine() add in settings for sec struct and rama restraints. ------------------------------------------------------------------------ r1794 | pemsley | 2009-01-27 05:11:09 +0000 (Tue, 27 Jan 2009) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Tweak tutorial name. ------------------------------------------------------------------------ r1793 | pemsley | 2009-01-26 14:11:08 +0000 (Mon, 26 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py New axes for burn-up graph. ------------------------------------------------------------------------ r1792 | b.lohkamp | 2009-01-20 21:18:46 +0000 (Tue, 20 Jan 2009) | 1 line Changed paths: M /trunk/python/gap.py fit_gap (python) accepts assigned sequence ------------------------------------------------------------------------ r1791 | b.lohkamp | 2009-01-20 15:50:19 +0000 (Tue, 20 Jan 2009) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c update refmac gui (TLS and SAD) to look like new CCP4i GUI side-by-side stereo with anti-aliasing and background colour change ------------------------------------------------------------------------ r1790 | pemsley | 2009-01-20 14:07:44 +0000 (Tue, 20 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Update ubuntu builds to 8.04.2 ------------------------------------------------------------------------ r1789 | b.lohkamp | 2009-01-20 08:21:00 +0000 (Tue, 20 Jan 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/macros/Makefile.am M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h added add_dipole_for_residue in python add lib-prefix.m4 to dist fix set position of 'Go to Atom' dialog refine_residues_py returns True when map found and refinement was executed ------------------------------------------------------------------------ r1788 | pemsley | 2009-01-19 00:16:54 +0000 (Mon, 19 Jan 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/rel-todo M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Add a method to turn off shadows in the file created for raster3d's render. ------------------------------------------------------------------------ r1787 | pemsley | 2009-01-17 16:18:57 +0000 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/ligand/dipole.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info.cc Add some protection and info for dipole construction failure. More protection in residues_near_residue(). ------------------------------------------------------------------------ r1786 | pemsley | 2009-01-17 15:20:34 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Yet more protection in residues_near_residue(). ------------------------------------------------------------------------ r1785 | pemsley | 2009-01-17 15:19:52 +0000 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Make sure that n_res_atoms is sane before proceeding with residues_near_residue(). ------------------------------------------------------------------------ r1784 | pemsley | 2009-01-17 15:10:41 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-ligands.cc #define guile functions for backward compatibility. ------------------------------------------------------------------------ r1783 | pemsley | 2009-01-17 14:17:32 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add interface to add dipole from multiple residues - e.g. an active site. ------------------------------------------------------------------------ r1782 | pemsley | 2009-01-17 12:57:50 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h add_dipole() should return the dipole number. ------------------------------------------------------------------------ r1781 | pemsley | 2009-01-17 02:06:27 +0000 (Sat, 17 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1780 | pemsley | 2009-01-16 21:08:52 +0000 (Fri, 16 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo Add a few more problems to rel-todo. ------------------------------------------------------------------------ r1779 | b.lohkamp | 2009-01-16 16:11:30 +0000 (Fri, 16 Jan 2009) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/pixmaps/torsion-general.svg M /trunk/python-tests/01_pdb_mtz.py fix font for torsion-general.svg update python add terminal residue test (b-factors) ------------------------------------------------------------------------ r1778 | pemsley | 2009-01-16 13:31:53 +0000 (Fri, 16 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info-mutate.cc Remove debugging. ------------------------------------------------------------------------ r1777 | pemsley | 2009-01-16 13:31:35 +0000 (Fri, 16 Jan 2009) | 5 lines Changed paths: M /trunk/burn-up/new-graph.py M /trunk/coot-utils/coot-coord-utils.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/mini-mol/mini-mol.cc M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc Apply default B factor in minimol's pcmmdbmanager(). Apply default B factor in add_side_chain_to_terminal_res(). Add a test for B factors in add terminal residue. Burn up graph extended to 40 days. ------------------------------------------------------------------------ r1776 | b.lohkamp | 2009-01-14 16:58:02 +0000 (Wed, 14 Jan 2009) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.h make_residue_spec and refine_residues for python ------------------------------------------------------------------------ r1775 | pemsley | 2009-01-14 13:49:33 +0000 (Wed, 14 Jan 2009) | 8 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/burn-up/new-graph.py M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc In generate_molecule_and_refine use have_dictionary_for_residue_types() to try to load all the dictionary restraints before making restraints. init_refmac_mon_lib() now returns non-zero when cif contains only links. residue_types_in_residue_vec() utility function added. Tinker with web page builder. Testing to get the python logs correctly linked. ------------------------------------------------------------------------ r1774 | pemsley | 2009-01-13 18:12:07 +0000 (Tue, 13 Jan 2009) | 7 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/doc/user-manual.texi M /trunk/ligand/dipole.cc M /trunk/ligand/dipole.hh M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/Makefile.am Add dipole function, fill_charged_atoms, used in apply_charges in the molecule class. apply_charges sets charges to CXX_UNSET_CHARGE, which gets tested for in CXXCreator. make_surface() now takes a protein_geometry argument. Trap a null chain in sequence-view.cc ------------------------------------------------------------------------ r1773 | b.lohkamp | 2009-01-13 17:53:24 +0000 (Tue, 13 Jan 2009) | 1 line Changed paths: A /trunk/macros/lib-prefix.m4 add lib-prefix.m4 macro to use $acl_libdirstem ------------------------------------------------------------------------ r1772 | b.lohkamp | 2009-01-13 16:37:57 +0000 (Tue, 13 Jan 2009) | 3 lines Changed paths: M /trunk/bldnotes A /trunk/bldnotes-2008 M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c split and update (bl)dnotes combobox for recentre options in coordinates filechooser ------------------------------------------------------------------------ r1771 | b.lohkamp | 2009-01-13 13:19:03 +0000 (Tue, 13 Jan 2009) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/graphics-info.cc updated python tests python functions: residues_near_position_py, run_post_manipulation_hook_py, non_standard_residue_names_py fix python functions: map_peaks_py and map_peaks_near_point_py ------------------------------------------------------------------------ r1770 | pemsley | 2009-01-12 21:01:06 +0000 (Mon, 12 Jan 2009) | 7 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Residue type CL support in refinement. Geometry function added have_dictionary_for_residue_types(). Cif dictionary read success now based on the number of atoms read, not the number of bonds. Switch to rigid body refine uses check_for_no_restraints_object(), not just for waters. ------------------------------------------------------------------------ r1769 | pemsley | 2009-01-12 19:02:03 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/new-graph.py Tinker with the ticks. ------------------------------------------------------------------------ r1768 | pemsley | 2009-01-12 17:48:36 +0000 (Mon, 12 Jan 2009) | 5 lines Changed paths: M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc write_residue_range_to_pdb_file() returns the correct error code and now writes out the the same chain-id as is input. Refactor (almost) duplicated update_refinement_atoms() code. Remove some debugging from residue vector refinement code. ------------------------------------------------------------------------ r1767 | pemsley | 2009-01-12 16:34:34 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/Makefile.am A /trunk/src/graphics-info-gui.cc A /trunk/src/graphics-info-refmac.cc M /trunk/src/graphics-info.cc split graphics-info.cc into better sized chunks, splitting out the refmac functions. ------------------------------------------------------------------------ r1766 | pemsley | 2009-01-12 16:07:02 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/rel-todo M /trunk/src/c-interface-preferences.cc M /trunk/src/gtk2-interface.c Fix up generic_object_clear(). ------------------------------------------------------------------------ r1765 | pemsley | 2009-01-12 16:05:11 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up missing menu items. ------------------------------------------------------------------------ r1764 | pemsley | 2009-01-12 14:29:39 +0000 (Mon, 12 Jan 2009) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/rel-todo M /trunk/src/graphics-info.cc Fix findwaters for use with a map. Fix strange rezooming behaviour of reset view. ------------------------------------------------------------------------ r1763 | pemsley | 2009-01-12 14:12:39 +0000 (Mon, 12 Jan 2009) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/rel-todo M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc Fix up the problem of bonding across gaps in geometry validation (and elsewhere, presumably). ------------------------------------------------------------------------ r1762 | pemsley | 2009-01-12 11:47:23 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update the clipper version in gtk build script. ------------------------------------------------------------------------ r1761 | pemsley | 2009-01-12 11:46:22 +0000 (Mon, 12 Jan 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/dnotes Fix the prefix use in the version of clipper. ------------------------------------------------------------------------ r1760 | pemsley | 2009-01-11 21:29:25 +0000 (Sun, 11 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo update rel-todo. ------------------------------------------------------------------------ r1759 | pemsley | 2009-01-11 10:56:56 +0000 (Sun, 11 Jan 2009) | 2 lines Changed paths: M /trunk/build-it Fix the incorrect use of latest in clipper tar file. ------------------------------------------------------------------------ r1758 | pemsley | 2009-01-10 12:24:29 +0000 (Sat, 10 Jan 2009) | 3 lines Changed paths: M /trunk/rel-todo M /trunk/src/graphics-info-modelling.cc Check for out of ordered residues when no restraints found and add extra info to the dialog in that case. ------------------------------------------------------------------------ r1757 | pemsley | 2009-01-10 11:37:04 +0000 (Sat, 10 Jan 2009) | 3 lines Changed paths: M /trunk/dnotes M /trunk/rel-todo M /trunk/src/molecule-class-info.cc Scale the dipoles. reorder rel-todo. ------------------------------------------------------------------------ r1756 | pemsley | 2009-01-10 11:11:59 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: A /trunk/dnotes M /trunk/rel-todo dnotes added - now with all Release, Fixed and Done items removed. ------------------------------------------------------------------------ r1755 | pemsley | 2009-01-10 10:58:20 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: D /trunk/dnote-2008 A /trunk/dnotes-2008 (from /trunk/dnote-2008:1754) The end of 2008 is when these notes stopped being updated. New notes introduced. ------------------------------------------------------------------------ r1754 | pemsley | 2009-01-10 10:57:16 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: A /trunk/dnote-2008 (from /trunk/dnotes:1751) D /trunk/dnotes Move dnotes. ------------------------------------------------------------------------ r1753 | pemsley | 2009-01-10 10:51:10 +0000 (Sat, 10 Jan 2009) | 4 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/rel-todo M /trunk/src/nsv.cc More update on the sequence viewer, not it seems the right size and does action on click. Reorder the binary builds page. ------------------------------------------------------------------------ r1752 | pemsley | 2009-01-10 10:49:44 +0000 (Sat, 10 Jan 2009) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix the python variable for the installed config file. ------------------------------------------------------------------------ r1751 | pemsley | 2009-01-09 18:31:27 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/scheme/libcheck.scm M /trunk/src/nsv.cc M /trunk/src/nsv.hh More playing with nsv canvas parameter - not right yet. ------------------------------------------------------------------------ r1750 | pemsley | 2009-01-09 18:30:08 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Use scm_is_true() not gh_scm2bool() in get_monomer(). ------------------------------------------------------------------------ r1749 | pemsley | 2009-01-09 16:54:37 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm No more FC6 for setsuko, now we have fedora-8 and fedora-10. ------------------------------------------------------------------------ r1748 | pemsley | 2009-01-09 14:52:41 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up optim/debugging option for compiling on x84_64 (well, Centos5 at least). ------------------------------------------------------------------------ r1747 | pemsley | 2009-01-09 14:51:18 +0000 (Fri, 09 Jan 2009) | 3 lines Changed paths: M /trunk/src/nsv.cc M /trunk/src/nsv.hh Enable go to atom on letter click - using intelligent_this_residue_mmdb_atom(). ------------------------------------------------------------------------ r1746 | pemsley | 2009-01-09 13:33:02 +0000 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py Update burn-up files to reference. ------------------------------------------------------------------------ r1745 | pemsley | 2009-01-09 08:59:49 +0000 (Fri, 09 Jan 2009) | 3 lines Changed paths: M /trunk/build-it M /trunk/burn-up/burn-up.tab M /trunk/burn-up/new-graph.py M /trunk/rel-todo M /trunk/src/geometry-graphs.cc M /trunk/src/nsv.cc M /trunk/src/nsv.hh Updates to nsv. Now we can click on a residues letter, but go to atom/residue not enabled yet. ------------------------------------------------------------------------ r1744 | pemsley | 2009-01-08 21:07:04 +0000 (Thu, 08 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/generic-display-object.hh Add clear method for generic object - needs a test. ------------------------------------------------------------------------ r1743 | pemsley | 2009-01-08 12:24:50 +0000 (Thu, 08 Jan 2009) | 2 lines Changed paths: M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/globjects.cc Fix problem filling map peak points vector. ------------------------------------------------------------------------ r1742 | pemsley | 2009-01-08 01:52:54 +0000 (Thu, 08 Jan 2009) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/rel-todo M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc map-peaks near point function added. In scm and python.o Util function create_mmdbmanager_from_atom() created. peak-search's make_sample_protein_coords() can now take a every_nth arg. ------------------------------------------------------------------------ r1741 | pemsley | 2009-01-07 16:23:58 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/TODO M /trunk/burn-up/new-graph.py M /trunk/dnotes M /trunk/rel-todo M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Add map_peaks functions, Python version is filled, scm version is not. ------------------------------------------------------------------------ r1740 | b.lohkamp | 2009-01-07 13:06:10 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fix python sphere selection test ------------------------------------------------------------------------ r1739 | b.lohkamp | 2009-01-07 12:09:25 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/src/testing.cc windows jiggery fix for testing.cc ------------------------------------------------------------------------ r1738 | b.lohkamp | 2009-01-07 09:02:44 +0000 (Wed, 07 Jan 2009) | 1 line Changed paths: M /trunk/python/generic_objects.py M /trunk/src/molecule-class-info-ribbons.cc fix generic objects gui python bug ------------------------------------------------------------------------ r1737 | pemsley | 2009-01-07 06:19:48 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/ligand/Makefile.am No libccp4mg-pygl_coord.la dependency for findwaters_real. ------------------------------------------------------------------------ r1736 | pemsley | 2009-01-07 00:23:09 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc guile tweaks for 1.6 usage. ------------------------------------------------------------------------ r1735 | pemsley | 2009-01-07 00:13:43 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/src/nsv.cc gtk_canvas_new not gnome_canvas_new (not yet, anyway). ------------------------------------------------------------------------ r1734 | pemsley | 2009-01-07 00:03:18 +0000 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /trunk/autogen.sh M /trunk/src/molecule-class-info-residues.cc M /trunk/src/nsv.cc More tweaks to make a build on gtk1 system. Now we use gettext macros. ------------------------------------------------------------------------ r1733 | pemsley | 2009-01-06 23:59:39 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Fix up python macro that uses $acl_libdirstem. ------------------------------------------------------------------------ r1732 | pemsley | 2009-01-06 23:18:10 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/gtk-manual.cc make GDK_WINDOW_TYPE_HINT_SPLASHSCREEN GTK2 specific. ------------------------------------------------------------------------ r1731 | pemsley | 2009-01-06 23:16:25 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Fix up the python hook function name. ------------------------------------------------------------------------ r1730 | pemsley | 2009-01-06 21:50:55 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Add fixups for old versions of guile. ------------------------------------------------------------------------ r1729 | pemsley | 2009-01-06 21:04:30 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix return typ for python function. ------------------------------------------------------------------------ r1728 | pemsley | 2009-01-06 20:39:58 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: A /trunk/src/nsv.cc A /trunk/src/nsv.hh Add forgotten nsv files. ------------------------------------------------------------------------ r1727 | pemsley | 2009-01-06 19:18:26 +0000 (Tue, 06 Jan 2009) | 42 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb.cc M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/test-utils.cc M /trunk/density-contour/CIsoSurface.cpp M /trunk/dnotes M /trunk/doc/coot-shelx.tex M /trunk/doc/crib-sheet.tex M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/high-res/Makefile.am M /trunk/ideal/test-indexing.cc M /trunk/ligand/Makefile.am A /trunk/ligand/base-pairing.cc A /trunk/ligand/base-pairing.hh A /trunk/ligand/dipole.cc A /trunk/ligand/dipole.hh M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ideal-rna.hh M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/macros/mmdb-ssm.m4 M /trunk/macros/mmdb.m4 M /trunk/macros/with-python.m4 M /trunk/mapview.glade M /trunk/rel-todo M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/generic-objects.scm M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/shelx.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am A /trunk/src/c-interface-build-gui.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot.i M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/main.cc A /trunk/src/manipulation-modes.hh M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc A /trunk/src/molecule-class-info-residues.cc M /trunk/src/molecule-class-info-ribbons.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh A /trunk/src/rotate-translate-modes.hh M /trunk/src/support.c M /trunk/src/testing.cc M /trunk/src/testing.hh Cuba updates: with-no-backups macro fixed. residues-need-position function added (python version needs to be filled) shelx-refine-gui added (Tobias Beck). shelx-extensions use the shelx refine gui. shelx tutorial reworked. Added test for rotamer names and probabilities. Dynamic distances mode uses pick_cursor_maybe(). probe-local-sphere added which uses write-pdb-file-for-molprobity which appends the CON files (not sure that they are needed now, with new probe). molecule-class-info-residues.cc file added. rotamer_score() function filled. Changes for segids, add function last_residue_in_chain returning a pointer to a CResidue. Util functions residue_atoms_segid() and chain_atoms_segid() used to find the segid of a residue before mutation, so that the new residue atoms have the same segid as the old atoms of the mutated residue. Util function copy_segid from residue to residue, used in insert_coords_internal() and copy_residue_range() for similar reasons. set_atom_string_attribute() extended to take a segid attribute. Dipole class and files added (in ligand dir). Functions to add, delete and render dipoles added (currently a problem with the orientation of the arrow object). create_splash_screen_window_for_file() added to work with --splash-screen command line option. Needed enhancements to support.c. cluster_from_point() added to ligand class. Tested in testing.cc, however, it uses hopelessly broken torsion setting code for wiggly ligands. Needs fixing soon - probably a re-write of the atom-tree code. start coding a new sequence view code (exptl::nsv). configure.in and macros now use $acl_libdirstem (and AC_LIB_PREPARE_MULTILIB which sets it up) - after conversation with Tim Fenn. AC_LIB_PREPARE_MULTILIB is defined in lib-prefix.m4 on the system, so that may introduce a gettext dependency for the build system. Keybinding handling changed. Now we are conservative about setting the handled flag, so that more key presses (e.g. A and S) fall through to the scripting layer. post-manipulation-hook, a variable that is check for begin a procedure, and if so, runs it after accepting moving atoms, delete or mutate. Python version needs to be filled [JED]. Added function to set the number of differences shown on the Kleywegt Plot [Clemens]. ------------------------------------------------------------------------ r1726 | pemsley | 2009-01-06 15:05:55 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: A /trunk/ccp4mg-utils/matrix.cc A /trunk/ccp4mg-utils/matrix.h Add ccp4 matrix files - they had been removed from repo. ------------------------------------------------------------------------ r1725 | pemsley | 2009-01-06 14:44:33 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/ccp4mg-utils/Makefile.am M /trunk/configure.in M /trunk/coords/Bond_lines.h M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/high-res/Makefile.am M /trunk/libtool M /trunk/ligand/Makefile.am M /trunk/pixmaps/torsion-general.svg M /trunk/python/coot_utils.py M /trunk/sequence-view/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.py M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.h Revert to 1716 for main trunk. ------------------------------------------------------------------------ r1724 | pemsley | 2009-01-06 14:02:54 +0000 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /trunk/coords/Bond_lines.h trivial diff, the header. ------------------------------------------------------------------------ r1722 | pemsley | 2009-01-06 09:35:05 +0000 (Tue, 06 Jan 2009) | 6 lines Changed paths: M /trunk/ccp4mg-utils/mmut/mman_base.cc M /trunk/ccp4mg-utils/mmut/mman_manager.cc M /trunk/ccp4mg-utils/mmut/mman_manager.h M /trunk/ccp4mg-utils/mmut/mmut_bonds.cc M /trunk/ccp4mg-utils/mmut/mmut_colour.cc M /trunk/ccp4mg-utils/mmut/mmut_colour.h M /trunk/ccp4mg-utils/mmut/mmut_connectivity.cc M /trunk/ccp4mg-utils/mmut/mmut_hbond.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.cc M /trunk/ccp4mg-utils/mmut/mmut_manager.h M /trunk/ccp4mg-utils/mmut/mmut_sasarea.cc M /trunk/ccp4mg-utils/mmut/mmut_sbase.cc M /trunk/ccp4mg-utils/mmut/mmut_sbase.h M /trunk/ccp4mg-utils/pygl/cprimitive.h M /trunk/ccp4mg-utils/util/mgtree.cc M /trunk/ccp4mg-utils/util/redirect.cc Get ccp4mg-utils to compile on GCC 4.3.2 - contains some pretty horrific kludges. It should be fixed by someone who knows the code and uses mmdb-1.19. SBASE code should be careful about const char *s. There is a bug - possibly in ccp4mg-atom_util - which causes a crash on closing Coot. ------------------------------------------------------------------------ r1721 | b.lohkamp | 2008-12-28 15:23:23 +0000 (Sun, 28 Dec 2008) | 5 lines Changed paths: M /trunk/ccp4mg-utils/pygl/texture.cc M /trunk/ligand/Makefile.am M /trunk/pixmaps/torsion-general.svg font fix for torsion-general.svg more ccp4mg include fixes remove all fancy textures in ccp4mg/pygl/textures.cc until we properly test for the GL_VERSION (this should compile on all OS) ------------------------------------------------------------------------ r1720 | b.lohkamp | 2008-12-27 23:01:04 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: M /trunk/ccp4mg-utils/pygl/texture.cc fix opengl ccp4mg texture problem on FC4 (quick fix for now) ------------------------------------------------------------------------ r1719 | b.lohkamp | 2008-12-27 18:05:33 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: M /trunk/ccp4mg-utils/Makefile.am D /trunk/ccp4mg-utils/matrix.cc D /trunk/ccp4mg-utils/matrix.h M /trunk/high-res/Makefile.am M /trunk/ligand/Makefile.am M /trunk/src/Makefile.am fix ccp4mg matrix doublication (hopefully) ------------------------------------------------------------------------ r1718 | b.lohkamp | 2008-12-27 17:04:01 +0000 (Sat, 27 Dec 2008) | 1 line Changed paths: A /trunk/src/molecule-class-info-ribbons.cc add molecule-class-info-ribbons.cc ------------------------------------------------------------------------ r1717 | b.lohkamp | 2008-12-27 16:27:53 +0000 (Sat, 27 Dec 2008) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/bldnotes M /trunk/ccp4mg-utils/Makefile.am A /trunk/ccp4mg-utils/get-all-new-utils.sh A /trunk/ccp4mg-utils/mmut A /trunk/ccp4mg-utils/mmut/Makefile.am A /trunk/ccp4mg-utils/mmut/mman_base.cc A /trunk/ccp4mg-utils/mmut/mman_base.h A /trunk/ccp4mg-utils/mmut/mman_manager.cc A /trunk/ccp4mg-utils/mmut/mman_manager.h A /trunk/ccp4mg-utils/mmut/mmut_basepairs.cc A /trunk/ccp4mg-utils/mmut/mmut_basepairs.h A /trunk/ccp4mg-utils/mmut/mmut_bonds.cc A /trunk/ccp4mg-utils/mmut/mmut_bonds.h A /trunk/ccp4mg-utils/mmut/mmut_colour.cc A /trunk/ccp4mg-utils/mmut/mmut_colour.h A /trunk/ccp4mg-utils/mmut/mmut_connectivity.cc A /trunk/ccp4mg-utils/mmut/mmut_connectivity.h A /trunk/ccp4mg-utils/mmut/mmut_contact.cc A /trunk/ccp4mg-utils/mmut/mmut_contact.h A /trunk/ccp4mg-utils/mmut/mmut_hbond.cc A /trunk/ccp4mg-utils/mmut/mmut_hbond.h A /trunk/ccp4mg-utils/mmut/mmut_lipids.cc A /trunk/ccp4mg-utils/mmut/mmut_lipids.h A /trunk/ccp4mg-utils/mmut/mmut_manager.cc A /trunk/ccp4mg-utils/mmut/mmut_manager.h A /trunk/ccp4mg-utils/mmut/mmut_morph.cc A /trunk/ccp4mg-utils/mmut/mmut_morph.h A /trunk/ccp4mg-utils/mmut/mmut_nma.cc A /trunk/ccp4mg-utils/mmut/mmut_nma.h A /trunk/ccp4mg-utils/mmut/mmut_sasarea.cc A /trunk/ccp4mg-utils/mmut/mmut_sasarea.h A /trunk/ccp4mg-utils/mmut/mmut_sbase.cc A /trunk/ccp4mg-utils/mmut/mmut_sbase.h A /trunk/ccp4mg-utils/mmut/mmut_secstr.cc A /trunk/ccp4mg-utils/mmut/mmut_secstr.h A /trunk/ccp4mg-utils/mmut/mmut_spline.cc A /trunk/ccp4mg-utils/mmut/mmut_util.cc A /trunk/ccp4mg-utils/mmut/mmut_util.h A /trunk/ccp4mg-utils/mmut/splineinfo.h A /trunk/ccp4mg-utils/pygl A /trunk/ccp4mg-utils/pygl/Makefile.am A /trunk/ccp4mg-utils/pygl/atom_util.cc A /trunk/ccp4mg-utils/pygl/atom_util.h A /trunk/ccp4mg-utils/pygl/bezier.cc A /trunk/ccp4mg-utils/pygl/billboard.cc A /trunk/ccp4mg-utils/pygl/build_tree_primitives.cc A /trunk/ccp4mg-utils/pygl/catmull.cc A /trunk/ccp4mg-utils/pygl/catmull.h A /trunk/ccp4mg-utils/pygl/cbuild.h A /trunk/ccp4mg-utils/pygl/cdisplayobject.cc A /trunk/ccp4mg-utils/pygl/cdisplayobject.h A /trunk/ccp4mg-utils/pygl/cprimitive.cc A /trunk/ccp4mg-utils/pygl/cprimitive.h A /trunk/ccp4mg-utils/pygl/font_info.cc A /trunk/ccp4mg-utils/pygl/font_info.h A /trunk/ccp4mg-utils/pygl/font_util.cc A /trunk/ccp4mg-utils/pygl/font_util.h A /trunk/ccp4mg-utils/pygl/freetype_dl.c A /trunk/ccp4mg-utils/pygl/freetype_dl.h A /trunk/ccp4mg-utils/pygl/freetype_font.cc A /trunk/ccp4mg-utils/pygl/freetype_font.h A /trunk/ccp4mg-utils/pygl/help.cc A /trunk/ccp4mg-utils/pygl/help.h A /trunk/ccp4mg-utils/pygl/lincrv.cc A /trunk/ccp4mg-utils/pygl/lincrv.h A /trunk/ccp4mg-utils/pygl/psutil.cc A /trunk/ccp4mg-utils/pygl/psutil.h A /trunk/ccp4mg-utils/pygl/qt-text.cc A /trunk/ccp4mg-utils/pygl/qt-text.cc.orig A /trunk/ccp4mg-utils/pygl/rgbreps.cc A /trunk/ccp4mg-utils/pygl/rgbreps.h A /trunk/ccp4mg-utils/pygl/sphere.cc A /trunk/ccp4mg-utils/pygl/sphere.h A /trunk/ccp4mg-utils/pygl/sphere_0.h A /trunk/ccp4mg-utils/pygl/sphere_1.h A /trunk/ccp4mg-utils/pygl/sphere_2.h A /trunk/ccp4mg-utils/pygl/sphere_3.h A /trunk/ccp4mg-utils/pygl/sphere_4.h A /trunk/ccp4mg-utils/pygl/sphere_arrays.h A /trunk/ccp4mg-utils/pygl/splineset.cc A /trunk/ccp4mg-utils/pygl/subdivide.cc A /trunk/ccp4mg-utils/pygl/subdivide.h A /trunk/ccp4mg-utils/pygl/symmetry.cc A /trunk/ccp4mg-utils/pygl/symmetry.h A /trunk/ccp4mg-utils/pygl/text.cc A /trunk/ccp4mg-utils/pygl/texture.cc A /trunk/ccp4mg-utils/pygl/texture.h A /trunk/ccp4mg-utils/pygl/win_font.cc A /trunk/ccp4mg-utils/pygl/win_font.h A /trunk/ccp4mg-utils/pygl/x11_font.cc A /trunk/ccp4mg-utils/pygl/x11_font.h A /trunk/ccp4mg-utils/pygl/zsortps.cc A /trunk/ccp4mg-utils/util A /trunk/ccp4mg-utils/util/CParamsManager.cc A /trunk/ccp4mg-utils/util/CParamsManager.h A /trunk/ccp4mg-utils/util/Makefile.am A /trunk/ccp4mg-utils/util/cartesian.cc A /trunk/ccp4mg-utils/util/cartesian.h A /trunk/ccp4mg-utils/util/connect.cc A /trunk/ccp4mg-utils/util/connect.h A /trunk/ccp4mg-utils/util/geomutil.cc A /trunk/ccp4mg-utils/util/geomutil.h A /trunk/ccp4mg-utils/util/matrix.cc A /trunk/ccp4mg-utils/util/matrix.h A /trunk/ccp4mg-utils/util/mginterrupt.cc A /trunk/ccp4mg-utils/util/mginterrupt.h A /trunk/ccp4mg-utils/util/mgtree.cc A /trunk/ccp4mg-utils/util/mgtree.h A /trunk/ccp4mg-utils/util/mgutil.cc A /trunk/ccp4mg-utils/util/mgutil.h A /trunk/ccp4mg-utils/util/plane.cc A /trunk/ccp4mg-utils/util/plane.h A /trunk/ccp4mg-utils/util/quat.cc A /trunk/ccp4mg-utils/util/quat.h A /trunk/ccp4mg-utils/util/redirect.cc A /trunk/ccp4mg-utils/util/redirect.h A /trunk/ccp4mg-utils/util/volume.cc A /trunk/ccp4mg-utils/util/volume.h M /trunk/configure.in M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/python/coot_utils.py M /trunk/sequence-view/Makefile.am M /trunk/src/Makefile.am M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.h make_residue_spec for python simple ribbons: added ccp4mg-utils/mmut util pygl ------------------------------------------------------------------------ r1716 | b.lohkamp | 2008-12-24 14:03:39 +0000 (Wed, 24 Dec 2008) | 4 lines Changed paths: M /trunk/python/gap.py M /trunk/src/c-interface-build.cc fix GTK1 refmac (e.g. run_refmac_mtz_file_radiobutton) fix GTK1 fit loop bug (mutate_sequence_use_ramachandran_restraints_checkbutton) fixed python loop GUI bug (GUI only shown if more than 1 loop candidates) ------------------------------------------------------------------------ r1715 | pemsley | 2008-12-19 19:54:47 +0000 (Fri, 19 Dec 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Bye bye F8 builds. ------------------------------------------------------------------------ r1714 | kevin.cowtan | 2008-12-19 16:29:19 +0000 (Fri, 19 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Remove redundent arguments (again) ------------------------------------------------------------------------ r1713 | kevin.cowtan | 2008-12-19 09:59:44 +0000 (Fri, 19 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Update the fragment joining code to extend the fragments before joining, in order to join fragments which don't quite meet. ------------------------------------------------------------------------ r1712 | pemsley | 2008-12-19 09:57:52 +0000 (Fri, 19 Dec 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-modelling.cc M /trunk/src/testing.cc Better restraints (link) searching. glycosidic linkages better now. link_infos_are_glycosidic_p() function added. matching_chem_link() returns a vector. ------------------------------------------------------------------------ r1711 | kevin.cowtan | 2008-12-19 09:36:13 +0000 (Fri, 19 Dec 2008) | 4 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Refactor classes to allow efficient threading of helix and strand searches. (A more aggressive approach to threading would involve splitting the translation search - this would be useful for >2 CPUs. Consider for later.) ------------------------------------------------------------------------ r1710 | pemsley | 2008-12-18 22:52:57 +0000 (Thu, 18 Dec 2008) | 14 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/rel-todo M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Add scm util function to make a residue_spec from a SCM representation. Add new function refine_residues_vec, which calls generate_molecule_and_refine(). Add a make_moving_atoms_asc() function that takes a vector of residues. Add function create_mmdb_manager_from_res_vector(). Add c-interface.h function that exercises these functions. Rewrite closest_approach() so that it uses simple-minded atom by atom test for the residue comparison, not SeekContacts() which gave 0 contacts for reasons I didn't understand. Remove the restraints_container destructor delete [] atom when using a residue vector (it was needed because last_residues does a shallow copy of the restriants). Chop out some features in the rel-todo - now more sane number of items. ------------------------------------------------------------------------ r1709 | kevin.cowtan | 2008-12-17 14:55:28 +0000 (Wed, 17 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Join overlapped secondary structure elements where possible. ------------------------------------------------------------------------ r1708 | kevin.cowtan | 2008-12-16 17:18:49 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Further fast ss find cleanups. ------------------------------------------------------------------------ r1707 | kevin.cowtan | 2008-12-16 16:59:27 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Remove redundent args to SSfind::prep_results ------------------------------------------------------------------------ r1706 | kevin.cowtan | 2008-12-16 15:14:53 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Update fast ss sreach code to allow even faster search within a limited radius of the current rotation centre. ------------------------------------------------------------------------ r1705 | pemsley | 2008-12-16 14:30:31 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/rel-todo Predicates should return booleans. ------------------------------------------------------------------------ r1704 | pemsley | 2008-12-16 13:53:05 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/burn-up/new-graph.py Small formatting tweaks. ------------------------------------------------------------------------ r1703 | pemsley | 2008-12-16 13:39:50 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: A /trunk/burn-up/new-burn-point.sh (from /trunk/burn-up/new-burn.sh:1699) D /trunk/burn-up/new-burn.sh M /trunk/burn-up/new-graph.py Rename to new-burn-point (it simply adds a point to the table) Take off star mark for done data points. ------------------------------------------------------------------------ r1702 | kevin.cowtan | 2008-12-16 13:36:48 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix the name of the 'Strands' molecule. ------------------------------------------------------------------------ r1701 | pemsley | 2008-12-16 13:15:51 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/rel-todo Add release todo notes. ------------------------------------------------------------------------ r1700 | pemsley | 2008-12-16 12:48:49 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/burn-up/new-graph.py Add the PyChart script to make the burn-up png. ------------------------------------------------------------------------ r1699 | pemsley | 2008-12-16 12:23:51 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: A /trunk/burn-up A /trunk/burn-up/burn-up.tab (from /trunk/burn-up.tab:1698) A /trunk/burn-up/new-burn.sh (from /trunk/new-burn.sh:1698) A /trunk/burn-up/process-rel-todo.awk (from /trunk/process-rel-todo.awk:1698) D /trunk/burn-up.tab D /trunk/new-burn.sh D /trunk/process-rel-todo.awk Move burn-up stuff to a new sub-dir. ------------------------------------------------------------------------ r1698 | pemsley | 2008-12-16 11:09:40 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/fast-ss-search.cc A newer compiler picks up syntax errors. ------------------------------------------------------------------------ r1697 | kevin.cowtan | 2008-12-16 10:09:56 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add control files for fast secondary stucture find. ------------------------------------------------------------------------ r1696 | pemsley | 2008-12-16 10:03:52 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: A /trunk/burn-up.tab A /trunk/new-burn.sh A /trunk/process-rel-todo.awk Add files for burnup chart - burn-up.tab is the actual table. Run new-burn.sh to generate a new line. ------------------------------------------------------------------------ r1695 | kevin.cowtan | 2008-12-16 10:02:09 +0000 (Tue, 16 Dec 2008) | 3 lines Changed paths: M /trunk/ligand/Makefile.am M /trunk/ligand/fast-ss-search.cc M /trunk/ligand/fast-ss-search.hh Updated fast secondard structure finding code. Include them in the build again with Makefile.am ------------------------------------------------------------------------ r1694 | pemsley | 2008-12-16 01:20:43 +0000 (Tue, 16 Dec 2008) | 4 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-mutate.cc Change the recentre check button on reading a coordinates file to an option menu (currently of 3 choice, the last and new one being "move molecule here"). Kevin M. ------------------------------------------------------------------------ r1693 | pemsley | 2008-12-16 01:15:46 +0000 (Tue, 16 Dec 2008) | 6 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc M /trunk/src/testing.hh New restraints handling - uses a vector of residues and refactors much restraints code to handle this and conventional/linear residue selection. Add a distance check for peptide linking. Add tests for new restraints constructor. ------------------------------------------------------------------------ r1692 | pemsley | 2008-12-16 01:11:07 +0000 (Tue, 16 Dec 2008) | 2 lines Changed paths: M /trunk/configure.in Convert to 0.6 pre-release ------------------------------------------------------------------------ r1691 | pemsley | 2008-12-15 20:48:44 +0000 (Mon, 15 Dec 2008) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade A /trunk/pixmaps/coot-0.5.1.xpm A /trunk/pixmaps/coot-0.5.2.xpm M /trunk/python/coot_gui.py M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5.2 - fix Shift label atom problem. ------------------------------------------------------------------------ r1690 | pemsley | 2008-12-15 15:29:57 +0000 (Mon, 15 Dec 2008) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5.1. ------------------------------------------------------------------------ r1689 | pemsley | 2008-12-15 13:59:58 +0000 (Mon, 15 Dec 2008) | 7 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ideal-rna.hh M /trunk/src/c-interface-gui.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/main.cc M /trunk/standard-residues.pdb Fix up ideal B form DNA by adding O2*. Change reference nucleotide for ideal B-form DNA. Update documentation for nvidia graphics. Remove some Go To Atom debugging. Dont show citation notice by default. Update dnotes and release notes. ------------------------------------------------------------------------ r1688 | pemsley | 2008-12-15 13:55:43 +0000 (Mon, 15 Dec 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Tidy up superpose ligands dialog, add handling of RTop not found in overlay-my-ligands. ------------------------------------------------------------------------ r1687 | b.lohkamp | 2008-12-15 10:16:53 +0000 (Mon, 15 Dec 2008) | 1 line Changed paths: M /trunk/scheme/extensions.scm fix typo in superpose ligand in extensions ------------------------------------------------------------------------ r1686 | b.lohkamp | 2008-12-15 09:57:29 +0000 (Mon, 15 Dec 2008) | 1 line Changed paths: M /trunk/python/extensions.py M /trunk/scheme/extensions.scm ligand superpose in extensions (py and scm) ------------------------------------------------------------------------ r1685 | kevin.cowtan | 2008-12-13 09:15:19 +0000 (Sat, 13 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Revert changes to Makefile.am until after 0.5.1 ------------------------------------------------------------------------ r1684 | pemsley | 2008-12-12 18:10:16 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/TODO Update TODO. ------------------------------------------------------------------------ r1683 | kevin.cowtan | 2008-12-12 16:37:25 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am A /trunk/ligand/fast-ss-search.cc A /trunk/ligand/fast-ss-search.hh Add files for fast secondary structure search. ------------------------------------------------------------------------ r1682 | b.lohkamp | 2008-12-12 14:26:23 +0000 (Fri, 12 Dec 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/scheme/coot-gui.scm ligand overlay for python incl. GUI (for py and scm) ------------------------------------------------------------------------ r1681 | pemsley | 2008-12-12 13:48:40 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-defines.cc Remove rotamer debugging code. ------------------------------------------------------------------------ r1680 | pemsley | 2008-12-12 13:46:48 +0000 (Fri, 12 Dec 2008) | 2 lines Changed paths: M /trunk/doc/crib-sheet.tex M /trunk/doc/tutorial-2.tex M /trunk/doc/user-manual.texi Update docs for Go To Residue by keyboarding. ------------------------------------------------------------------------ r1679 | pemsley | 2008-12-11 22:03:18 +0000 (Thu, 11 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Remove debugging from Ball and Sticking. ------------------------------------------------------------------------ r1678 | pemsley | 2008-12-11 22:01:57 +0000 (Thu, 11 Dec 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Make ball and stick representations move when the model moves. Stop also making Fat Bonds when making ball and sticks. ------------------------------------------------------------------------ r1677 | pemsley | 2008-12-11 17:24:59 +0000 (Thu, 11 Dec 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Rewrite reset_view(). It works correctly and relative to molecule size now. size_of_molecule() function typo fixed. Go To Atom dialog action reworked when new molecule added/created. On destroy geometry dialog, NULL the stored widget pointer. ------------------------------------------------------------------------ r1676 | pemsley | 2008-12-10 23:31:33 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc Use wrapped_create_geometry_dialog so that we don't crash on trying to open 2 of them. ------------------------------------------------------------------------ r1675 | pemsley | 2008-12-10 23:29:11 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/gap.scm Fix up loop fitting (fit-gap). ------------------------------------------------------------------------ r1674 | pemsley | 2008-12-10 18:18:18 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Document overlay-my-ligands. ------------------------------------------------------------------------ r1673 | pemsley | 2008-12-10 18:15:50 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add overlay-my-ligands function. ------------------------------------------------------------------------ r1672 | pemsley | 2008-12-10 18:08:58 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix up transform-coords-mol. ------------------------------------------------------------------------ r1671 | b.lohkamp | 2008-12-10 13:05:26 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/python/extensions.py M /trunk/python/ncs.py M /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/scheme/extensions.scm extensions: surfaces for python ans fix scheme fix and update manual_ncs_ghosts and ncs tests ------------------------------------------------------------------------ r1670 | pemsley | 2008-12-10 09:58:49 +0000 (Wed, 10 Dec 2008) | 6 lines Changed paths: M /trunk/scheme/fitting.scm The Rama improvement stepped refine was not working properly, it had only one active residue at a time. This is because range-step was being incorrectly calculated. It should be 1 when res-step is 1. I've corrected that now (by fixing the calculation of step-inter) and Rama plot improvement is better. ------------------------------------------------------------------------ r1669 | b.lohkamp | 2008-12-10 09:00:37 +0000 (Wed, 10 Dec 2008) | 1 line Changed paths: M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h more windows jiggery fixes (when using Guile) ------------------------------------------------------------------------ r1668 | pemsley | 2008-12-10 01:39:35 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Simple surfaces gui added to Extensions -> Representations. ------------------------------------------------------------------------ r1667 | pemsley | 2008-12-10 00:53:36 +0000 (Wed, 10 Dec 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Fix up the build-log files for pythonic builds - still needs build-in-progress separated out. ------------------------------------------------------------------------ r1666 | pemsley | 2008-12-10 00:17:15 +0000 (Wed, 10 Dec 2008) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/07-ncs.scm M /trunk/scheme/ncs.scm Fix up manual-ncs-ghosts, no longer hard code in "A" as the master chain id. Add function ncs-master-chain-id. Add a test for correct NCS chain-ids after a manual-ncs-ghosts usage. booleanize the member tests in utils. Update residues_near_residue to work with a radius of 0. ------------------------------------------------------------------------ r1665 | pemsley | 2008-12-10 00:09:23 +0000 (Wed, 10 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc A tidy up of the ncs_ghost_chains() function - nothing new. ------------------------------------------------------------------------ r1664 | b.lohkamp | 2008-12-09 16:49:27 +0000 (Tue, 09 Dec 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ligand/test-ligand.cc M /trunk/python/extensions.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc NCS uses LSQ by default now etxra fast option for LSQ (every 2nd CA) in extensions (guile & python) ------------------------------------------------------------------------ r1663 | b.lohkamp | 2008-12-09 12:42:22 +0000 (Tue, 09 Dec 2008) | 1 line Changed paths: M /trunk/compat/Makefile.am M /trunk/compat/coot-sysdep.h fix windows pokery by including coot-sysdep.h ------------------------------------------------------------------------ r1662 | b.lohkamp | 2008-12-09 10:59:17 +0000 (Tue, 09 Dec 2008) | 1 line Changed paths: A /trunk/compat/coot-sysdep.h M /trunk/coords/Makefile.am M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-utils.cc M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/monomer-utils.cc M /trunk/ligand/rotamer.cc M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc M /trunk/skeleton/Makefile.am M /trunk/src/c-interface-mmdb.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc clean up windows magic jiggery ------------------------------------------------------------------------ r1661 | b.lohkamp | 2008-12-08 13:28:59 +0000 (Mon, 08 Dec 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-ncs.cc LSQ option for NCS matrix detection (in extensions for scheme and python) LSQ matching for poly-nucleotides (CA = P; main chain = P + O & ribose) loading of python modules in extra dirs (COOT_PYTHON_EXTRA_DIRS) fix for preferences font colours ------------------------------------------------------------------------ r1660 | b.lohkamp | 2008-12-08 09:54:29 +0000 (Mon, 08 Dec 2008) | 1 line Changed paths: M /trunk/src/c-interface-info.cc console highlighting and colouring for Windows Dos shell ------------------------------------------------------------------------ r1659 | pemsley | 2008-12-06 17:56:19 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Split make_monomer_restraints() by using make_monomer_restraints_by_residue(). ------------------------------------------------------------------------ r1658 | pemsley | 2008-12-06 17:08:55 +0000 (Sat, 06 Dec 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc M /trunk/src/testing.hh Add a CResidue * vector restraints container constructor. Add the start of a test for refinement using this constructor. ------------------------------------------------------------------------ r1657 | pemsley | 2008-12-06 17:06:43 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/helix-placement.cc comment out debugging. ------------------------------------------------------------------------ r1656 | pemsley | 2008-12-06 15:18:04 +0000 (Sat, 06 Dec 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc The last item in the monomer type chooser is now the active item. (char *) chain_id cleanup. matches_comp_ids_and_groups now returns a flag to say that the residues need to be order swapped to match. Used in find_link_type_rigourous(). ------------------------------------------------------------------------ r1655 | pemsley | 2008-12-06 15:11:27 +0000 (Sat, 06 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex png -> ps. ------------------------------------------------------------------------ r1654 | pemsley | 2008-12-05 14:36:03 +0000 (Fri, 05 Dec 2008) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc Add a bit of protection for rotate_chi, don't do anything if not in rotate_chi mode. ------------------------------------------------------------------------ r1653 | pemsley | 2008-12-05 13:43:05 +0000 (Fri, 05 Dec 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add to the scripting layer rotate_chi() function - to be activated by a PowerMate (for example) in due course. ------------------------------------------------------------------------ r1652 | pemsley | 2008-12-05 00:15:16 +0000 (Fri, 05 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm More elegant formatting of the residue-density-fit-scale-factor text. ------------------------------------------------------------------------ r1651 | b.lohkamp | 2008-12-04 10:15:09 +0000 (Thu, 04 Dec 2008) | 5 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/scheme/extensions.scm buttonize the python key bindings density graph weight GUI in extensions picks up the current weight (scm & py) python tests: moved NCS map test from 01_pdb_mtz.py to 07_ncs.py updated dynamically_transformed maps in tests ------------------------------------------------------------------------ r1650 | pemsley | 2008-12-04 08:44:30 +0000 (Thu, 04 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Remove inadvertent addition of ligand fitting debugging code. ------------------------------------------------------------------------ r1649 | pemsley | 2008-12-03 14:44:39 +0000 (Wed, 03 Dec 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/07-ncs.scm M /trunk/ideal/simple-restraint.cc Move NCS test from 01-pdb+mtz. Better logic for the fixed atom in link restraints. ------------------------------------------------------------------------ r1648 | pemsley | 2008-12-03 12:48:02 +0000 (Wed, 03 Dec 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/07-ncs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h dynamically_transform_maps now takes an extra arg, flag to tell whether or not to try to overwrite existing maps of the same name. Test for dynamically_transform_maps(). ------------------------------------------------------------------------ r1647 | pemsley | 2008-12-03 06:23:21 +0000 (Wed, 03 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm buttonize the scheme+python keybindings (using alignment). ------------------------------------------------------------------------ r1646 | b.lohkamp | 2008-12-02 19:01:31 +0000 (Tue, 02 Dec 2008) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/ncs.py M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h update of python scripts (fix shelx refine extension, ncs, ...) python function for find_terminal_residue_type set_display_maps... for windows stereo (actually previous commit, r1645) ------------------------------------------------------------------------ r1645 | b.lohkamp | 2008-12-02 14:32:55 +0000 (Tue, 02 Dec 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/src/c-interface.cc update Windows build script; fix python shelx refine GUI ------------------------------------------------------------------------ r1644 | pemsley | 2008-12-02 13:45:39 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/main.cc Add Stuart's suggestion for python signal handlers. ------------------------------------------------------------------------ r1643 | pemsley | 2008-12-02 13:44:52 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Remove debugging. ------------------------------------------------------------------------ r1642 | pemsley | 2008-12-02 13:43:55 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex Note to add 4mer-XYS to tutorial-2.tex at some stage. ------------------------------------------------------------------------ r1641 | pemsley | 2008-12-02 13:43:10 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc Reformatting. ------------------------------------------------------------------------ r1640 | pemsley | 2008-12-02 08:16:07 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Use ps files in tutorial, not pngs (which don't work on bubbles). ------------------------------------------------------------------------ r1639 | pemsley | 2008-12-02 07:49:54 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for NCS Ghosts by Residue Range. ------------------------------------------------------------------------ r1638 | pemsley | 2008-12-02 07:40:58 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a GUI for manual-ncs-ghosts - called "NCS Ghosts by Residue Range...". ------------------------------------------------------------------------ r1637 | pemsley | 2008-12-02 01:34:51 +0000 (Tue, 02 Dec 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc Add a operator<< for a chem_link. chem_link should match groups and comp_ids. ------------------------------------------------------------------------ r1636 | pemsley | 2008-12-02 00:53:28 +0000 (Tue, 02 Dec 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc In closest_atom() check the chain_id if set. ------------------------------------------------------------------------ r1635 | pemsley | 2008-12-01 23:11:18 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc In closest_atom() do no to consider molecules that are not displayed. ------------------------------------------------------------------------ r1634 | pemsley | 2008-12-01 19:06:34 +0000 (Mon, 01 Dec 2008) | 9 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Move active_atom_spec() to graphics_info. Adjust closest_atom() to take a chain-id. Add get_atom, which uses closest_atom(). Add internals for for key presses to add to graphics_info_t::go_to_residue_keyboarding_string Add related static bool in_go_to_residue_keyboarding_mode and apply_go_to_residue_keyboading_string(); Utility functions is_number() and is_letter() for given chars. ------------------------------------------------------------------------ r1633 | pemsley | 2008-12-01 15:02:14 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Add a return value to matching_chem_link() and throw an error if not found. ------------------------------------------------------------------------ r1632 | pemsley | 2008-12-01 14:14:57 +0000 (Mon, 01 Dec 2008) | 14 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/scheme/ncs.scm Rename manual-ncs-ghosts as single-manual-ncs-ghost. Introduce new function manual-ncs-ghosts which handles several ghosts chains. closest_approach() function added to utils - function is given 2 residues and returns the closest 2 atoms of those residues. Enhance chem_link class in dictionary. Allow the searching of the chem_links given residue groups. Introduce bonded_pair (of residues) and a container class for them. Add rigourous residue linking - not actived yet, because there is no way to pass a non-linear set of residues to the make_restraints() function. Allow residues that are close in residue index to be bonded (draw). Allow residues that are close in residue index to be restrainted as a peptide bond. ------------------------------------------------------------------------ r1631 | pemsley | 2008-12-01 13:10:48 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-surface.cc Handle the lights better when drawing a surface. ------------------------------------------------------------------------ r1630 | pemsley | 2008-12-01 12:45:53 +0000 (Mon, 01 Dec 2008) | 4 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXSpace.cpp Fixes for G++ 4.3.2 on intrepid. Make the keyboard zoom a bit smooth. Bump the version of GMP in build-it-gtk-simple. ------------------------------------------------------------------------ r1629 | pemsley | 2008-12-01 01:06:38 +0000 (Mon, 01 Dec 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-fasta.cc Protection parentheses around fasta test logical operators. ------------------------------------------------------------------------ r1628 | pemsley | 2008-11-30 18:34:24 +0000 (Sun, 30 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix build_type typo. ------------------------------------------------------------------------ r1627 | pemsley | 2008-11-28 18:37:38 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Trivial formatting. ------------------------------------------------------------------------ r1626 | pemsley | 2008-11-28 15:41:59 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add protection for map_is_displayed(). ------------------------------------------------------------------------ r1625 | pemsley | 2008-11-28 15:29:29 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Restore F8 to the build status page for now. ------------------------------------------------------------------------ r1624 | pemsley | 2008-11-28 12:14:31 +0000 (Fri, 28 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix output log file for gtk2. ------------------------------------------------------------------------ r1623 | pemsley | 2008-11-27 08:08:22 +0000 (Thu, 27 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Make file_list in post_install_slim python-dependent, like the gtk2 version. ------------------------------------------------------------------------ r1622 | pemsley | 2008-11-26 17:56:54 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/python/Makefile.am Remove Makefile.am from EXTRA_DIST. ------------------------------------------------------------------------ r1621 | pemsley | 2008-11-26 13:30:08 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Add some protection to the index in undos. ------------------------------------------------------------------------ r1620 | pemsley | 2008-11-26 13:28:51 +0000 (Wed, 26 Nov 2008) | 3 lines Changed paths: M /trunk/scheme/gap.scm Fix up fit-gap so that the sequence/rama-flag need not be passed - as it used to be. ------------------------------------------------------------------------ r1619 | pemsley | 2008-11-26 13:27:46 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Allow a link restraint between residues that have neighbouring indexes. ------------------------------------------------------------------------ r1618 | pemsley | 2008-11-26 13:26:17 +0000 (Wed, 26 Nov 2008) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc Allow the bonding of close atoms that have residues with neighbouring indexes. ------------------------------------------------------------------------ r1617 | b.lohkamp | 2008-11-26 12:00:54 +0000 (Wed, 26 Nov 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/coords/mmdb-extras.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/monomer-utils.cc M /trunk/ligand/rotamer.cc M /trunk/macros/clipper.m4 M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc make WinCoot clipper 2.1 compliant (incl threading) ------------------------------------------------------------------------ r1616 | pemsley | 2008-11-26 08:37:02 +0000 (Wed, 26 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Quote the argument to info-dialog for the history. ------------------------------------------------------------------------ r1615 | pemsley | 2008-11-24 19:57:37 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1614 | pemsley | 2008-11-24 19:57:14 +0000 (Mon, 24 Nov 2008) | 3 lines Changed paths: A /trunk/geometry/chiral-notes.txt M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc Add dictionary restraints of type "both" - but don't use them to make a restraint. ------------------------------------------------------------------------ r1613 | pemsley | 2008-11-24 19:55:03 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Test for greg using full path to guile. ------------------------------------------------------------------------ r1612 | pemsley | 2008-11-24 18:25:11 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Comment out Pukka Puckers for now. ------------------------------------------------------------------------ r1611 | pemsley | 2008-11-24 15:35:28 +0000 (Mon, 24 Nov 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Remove debugging from restraints editor. Add function size_of_molecule(). Update dnotes. ------------------------------------------------------------------------ r1610 | pemsley | 2008-11-24 13:58:08 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Get ssh and tar file move in the right order. ------------------------------------------------------------------------ r1609 | pemsley | 2008-11-24 13:38:18 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add debugging info for the ssh_copy. ------------------------------------------------------------------------ r1608 | pemsley | 2008-11-24 13:28:03 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Sort out python_version and pver usage in post_install_slim. ------------------------------------------------------------------------ r1607 | pemsley | 2008-11-24 12:58:42 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in gtk2 tar for tar files of gtk2 builds. ------------------------------------------------------------------------ r1606 | pemsley | 2008-11-24 12:23:37 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add find-terminal-residue-type for snarfing. ------------------------------------------------------------------------ r1605 | pemsley | 2008-11-24 12:17:27 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/macros/clipper.m4 Add -lpthread to clipper libs in the macro. ------------------------------------------------------------------------ r1604 | pemsley | 2008-11-24 07:45:36 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix typo in holding tar handling. ------------------------------------------------------------------------ r1603 | pemsley | 2008-11-24 07:13:58 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple link the greg-tests dir in second-test untar dir. ------------------------------------------------------------------------ r1602 | pemsley | 2008-11-24 00:18:15 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix dir for untar/test ------------------------------------------------------------------------ r1601 | pemsley | 2008-11-24 00:13:35 +0000 (Mon, 24 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple fix typo in untaring tar file for test. ------------------------------------------------------------------------ r1600 | pemsley | 2008-11-23 23:56:42 +0000 (Sun, 23 Nov 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Yet more adjustment of the second test - use the holding_tar_file, pipe the test output. ------------------------------------------------------------------------ r1599 | pemsley | 2008-11-23 23:36:04 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple make a holding directory for tar file for pre-release case. ------------------------------------------------------------------------ r1598 | pemsley | 2008-11-23 17:56:39 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Fix the gtk1 vs gtk2 problem for the slim tar file. ------------------------------------------------------------------------ r1597 | pemsley | 2008-11-23 17:35:28 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it make holding dir in gtk1 build. ------------------------------------------------------------------------ r1596 | pemsley | 2008-11-23 16:07:55 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple More typos in build-it scripts for second test. ------------------------------------------------------------------------ r1595 | pemsley | 2008-11-23 15:17:44 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it Fix typo at the end of the script. ------------------------------------------------------------------------ r1594 | pemsley | 2008-11-23 14:14:33 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1593 | pemsley | 2008-11-23 12:29:38 +0000 (Sun, 23 Nov 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Add in a second test - for the tar file. If that fails don't move the binary tar from holding dir. ------------------------------------------------------------------------ r1592 | pemsley | 2008-11-23 11:50:51 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Remove python fedora 8 build report too. ------------------------------------------------------------------------ r1591 | pemsley | 2008-11-23 11:49:18 +0000 (Sun, 23 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Remove Fedora 8 from the build. There is something wrong with the build host. ------------------------------------------------------------------------ r1590 | pemsley | 2008-11-22 19:15:57 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1589 | pemsley | 2008-11-22 07:41:43 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use clipper-2.1, extra tweaks. ------------------------------------------------------------------------ r1588 | pemsley | 2008-11-22 07:19:39 +0000 (Sat, 22 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Try use clipper-2.1 ------------------------------------------------------------------------ r1587 | pemsley | 2008-11-21 12:20:03 +0000 (Fri, 21 Nov 2008) | 4 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Remove l keypress to label atom on click, Add l keypress to label atom closest to screen centre. Rename graphics_info_t::l_is_pressed to graphics_info_t::shift_is_pressed. ------------------------------------------------------------------------ r1586 | pemsley | 2008-11-21 08:14:34 +0000 (Fri, 21 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo. ------------------------------------------------------------------------ r1585 | pemsley | 2008-11-21 08:04:30 +0000 (Fri, 21 Nov 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple swig 1.3.34 is OK for 32 bit systems, I think. Don't halt the build if architecture is not x86_64. ------------------------------------------------------------------------ r1584 | pemsley | 2008-11-20 15:51:09 +0000 (Thu, 20 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r1583 | pemsley | 2008-11-20 15:11:16 +0000 (Thu, 20 Nov 2008) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Add insertion codes into deep_copy_residue() and use SetResID() on copied residues. Fixes problems with rotamers on residues with insertion codes. Add a test for rotamers using 3hfl. ------------------------------------------------------------------------ r1582 | pemsley | 2008-11-19 21:05:42 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add CentOS 64 bit builts. ------------------------------------------------------------------------ r1581 | pemsley | 2008-11-19 21:04:59 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes Tweak for 64 bit builds of coot - Use -O rather rather than -O2. ------------------------------------------------------------------------ r1580 | pemsley | 2008-11-19 21:02:03 +0000 (Wed, 19 Nov 2008) | 3 lines Changed paths: M /trunk/src/graphics-info.cc If the umol does not have modifications, reset undo_molecule regardless of whether or not graphics are being used. ------------------------------------------------------------------------ r1579 | pemsley | 2008-11-19 11:19:58 +0000 (Wed, 19 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1578 | pemsley | 2008-11-18 23:02:44 +0000 (Tue, 18 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use the ccp4 libs underlay. ------------------------------------------------------------------------ r1577 | pemsley | 2008-11-17 20:09:54 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc Fix the re-scaling issue for rotamers on updating the molecule [JED]. Add a flash of the picked atom when in Ctrl-pick vs Ctrl-drag mode. ------------------------------------------------------------------------ r1576 | pemsley | 2008-11-17 12:59:21 +0000 (Mon, 17 Nov 2008) | 3 lines Changed paths: M /trunk/ligand/helix-placement.cc M /trunk/ligand/rotamer-tables.cc Add debugging (for map R 3 2 issue) in helix placement. Remove debugging in rotamer tables (self test). ------------------------------------------------------------------------ r1575 | pemsley | 2008-11-16 02:55:08 +0000 (Sun, 16 Nov 2008) | 3 lines Changed paths: M /trunk/ideal/pepflip.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc Make sure that a pepflip flips the H on the N too - fixed the atom names of the C and the O - how did it ever work before? ------------------------------------------------------------------------ r1574 | pemsley | 2008-11-15 20:34:58 +0000 (Sat, 15 Nov 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Add test for add_atom function. Rename add_cb_to_terminal_res() to add_side_chain_to_terminal_res(), which is more like what it does. ------------------------------------------------------------------------ r1573 | pemsley | 2008-11-15 20:32:42 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Reformatting of long line. ------------------------------------------------------------------------ r1572 | pemsley | 2008-11-15 20:31:56 +0000 (Sat, 15 Nov 2008) | 3 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/positioned-widgets.h set transient geometry dialog in on_distances_and_angles1_activate() by using COOT_UNDEFINED_WINDOW. ------------------------------------------------------------------------ r1571 | pemsley | 2008-11-15 20:29:52 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh Add add_atom function, which adds an atom to a CResidue. ------------------------------------------------------------------------ r1570 | pemsley | 2008-11-15 17:24:30 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/dnotes sync dnotes. ------------------------------------------------------------------------ r1569 | pemsley | 2008-11-15 16:56:02 +0000 (Sat, 15 Nov 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add get_monomer_from_dictionary() function, that gets molecules from the PDB's Chemical Component Library (no restraints). Now uses move_molecule_to_screen_centre_internal. Mostly additions to protein-geometry to add the reading of chem_comp info without using a loop. ------------------------------------------------------------------------ r1568 | pemsley | 2008-11-15 16:52:20 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Add some debugging - but not used. ------------------------------------------------------------------------ r1567 | pemsley | 2008-11-15 16:51:34 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Add some more debugging to with-map.cc. ------------------------------------------------------------------------ r1566 | pemsley | 2008-11-15 16:50:18 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Don't set_transient for store_geometry_dialog(). ------------------------------------------------------------------------ r1565 | pemsley | 2008-11-15 16:48:53 +0000 (Sat, 15 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm define find-aligned-residue-type as find-terminal-residue-type. ------------------------------------------------------------------------ r1564 | b.lohkamp | 2008-11-13 12:03:48 +0000 (Thu, 13 Nov 2008) | 1 line Changed paths: A /trunk/pixmaps/stop.svg M /trunk/python/coot_utils.py M /trunk/python/refmac.py refmac runs 'concurrently' in python now ------------------------------------------------------------------------ r1563 | b.lohkamp | 2008-11-12 09:06:57 +0000 (Wed, 12 Nov 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows autobuild to mmdb 1.19 ------------------------------------------------------------------------ r1562 | b.lohkamp | 2008-11-11 18:58:29 +0000 (Tue, 11 Nov 2008) | 4 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/main.cc rework small-screen detection (not neccessary to use flag any more) added two contour levels for difference maps and map colours in CCP4MG picture file ------------------------------------------------------------------------ r1561 | b.lohkamp | 2008-11-11 09:47:27 +0000 (Tue, 11 Nov 2008) | 3 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/command-line.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/main.cc test for reading/writing gz pdbs (mainly for windows) no-graphics mode protection for toolbar icons ------------------------------------------------------------------------ r1560 | pemsley | 2008-11-10 23:34:50 +0000 (Mon, 10 Nov 2008) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Some debugging of input to fft. ------------------------------------------------------------------------ r1559 | pemsley | 2008-11-10 22:42:57 +0000 (Mon, 10 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Upgrade to mmdb-1.19, get tar file from EBI. ------------------------------------------------------------------------ r1558 | pemsley | 2008-11-10 22:32:28 +0000 (Mon, 10 Nov 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info.cc Change the heuristic fencepost on the number of sensible coloured lines to 512,000. That should be enough even for ribosomes. ------------------------------------------------------------------------ r1557 | b.lohkamp | 2008-11-10 19:35:29 +0000 (Mon, 10 Nov 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc update font colours in preferences small-screen setting automatically detected and applied enable using gzipped files for reading and writing coordinates in windows ------------------------------------------------------------------------ r1556 | pemsley | 2008-11-09 15:29:30 +0000 (Sun, 09 Nov 2008) | 5 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/graphics-info.cc M /trunk/src/pick.h When molecule is in coot::CA_BONDS_PLUS_LIGANDS allow regularize_object_bonds_box to be drawn in with do_Ca_plus_ligands_bonds() args to a bonds_box, rather than do_Ca_bonds(). Allow the torsion of ligands in CA+Ligands mode [Ingo Korndoefer]. ------------------------------------------------------------------------ r1555 | pemsley | 2008-11-09 15:26:57 +0000 (Sun, 09 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Again, don't use clipper-new-ccp4-install.patch or mmdbold. ------------------------------------------------------------------------ r1554 | pemsley | 2008-11-09 15:23:51 +0000 (Sun, 09 Nov 2008) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Fix typo in args to mutate. ------------------------------------------------------------------------ r1553 | pemsley | 2008-11-09 15:22:55 +0000 (Sun, 09 Nov 2008) | 3 lines Changed paths: M /trunk/build-it Don't patch with clipper-new-ccp4-install.patch. Don't enable mmdbold with clipper. ------------------------------------------------------------------------ r1552 | pemsley | 2008-11-08 11:55:07 +0000 (Sat, 08 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Correct the mkdir of the python include dir. ------------------------------------------------------------------------ r1551 | pemsley | 2008-11-08 10:55:26 +0000 (Sat, 08 Nov 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple If no compiler then exit. ------------------------------------------------------------------------ r1550 | pemsley | 2008-11-07 23:35:55 +0000 (Fri, 07 Nov 2008) | 9 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh Fix up find-terminal-residue-type so that it can find the residue type of a residue in the middle of a chain (not just an insertion at the end - mutations are now checked also). define find-aligned-residue-type as find-terminal-residue-type. In coot-align.hh let add_mutation aand add_deletion take the chain_id too. Fix some unassigned variable usage. Yet more tweaking of the build script - don't try to remove the build status file if it is not there. ------------------------------------------------------------------------ r1549 | kevin.cowtan | 2008-11-07 13:34:58 +0000 (Fri, 07 Nov 2008) | 5 lines Changed paths: M /trunk/src/c-interface.cc More radical rewrite of auto-open-mtz. Allows for future expansion, including the use of weights in the list of standard column names. Checks for duplicate column labels, to prevent the same map being opened twice. Code duplication reduced significantly. ------------------------------------------------------------------------ r1548 | pemsley | 2008-11-06 19:28:19 +0000 (Thu, 06 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm tweak the builder info for cycle. ------------------------------------------------------------------------ r1547 | b.lohkamp | 2008-11-06 18:28:44 +0000 (Thu, 06 Nov 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/extensions.py M /trunk/scheme/extensions.scm read refmac log file for outliers in Extension (py and scm) ------------------------------------------------------------------------ r1546 | kevin.cowtan | 2008-11-06 17:16:52 +0000 (Thu, 06 Nov 2008) | 4 lines Changed paths: M /trunk/src/c-interface.cc Make auto-open MTZ open ALL maps from density modification using a list of typical column labels. We should think about what other labels we might add. ------------------------------------------------------------------------ r1545 | b.lohkamp | 2008-11-06 09:47:22 +0000 (Thu, 06 Nov 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/gap.py M /trunk/python/refmac.py M /trunk/python-tests/02_shelx.py M /trunk/scheme/gap.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c added 'Ramachandran Restraints' check button in fit loop GUI (GTK2) fit loop does extra loop build (no res>=6) half from N- and C-terminus (python) python test or shelx aniso U Uij in residue_info are in pdb format order ------------------------------------------------------------------------ r1544 | pemsley | 2008-11-05 10:31:59 +0000 (Wed, 05 Nov 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-info.cc Write out the ansio Us in an atom spec if the atom has them (a list with the b_iso_equiv first). Add a greg test-case for this and previous aniso Us. ------------------------------------------------------------------------ r1543 | pemsley | 2008-11-05 10:29:03 +0000 (Wed, 05 Nov 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Fractionalize the aniso Us before writing them to the output .ins file. ------------------------------------------------------------------------ r1542 | pemsley | 2008-11-02 23:15:39 +0000 (Sun, 02 Nov 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for manual-ncs-ghosts. ------------------------------------------------------------------------ r1541 | pemsley | 2008-11-01 01:14:12 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Make the slim-dir be python-dependent. ------------------------------------------------------------------------ r1540 | pemsley | 2008-11-01 01:10:37 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-it More adjustment of the prefix, now that we have python differentiation. ------------------------------------------------------------------------ r1539 | pemsley | 2008-11-01 01:03:27 +0000 (Sat, 01 Nov 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Adjust settings for setsuko. ------------------------------------------------------------------------ r1538 | pemsley | 2008-10-31 22:10:58 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix typo in ierr. ------------------------------------------------------------------------ r1537 | pemsley | 2008-10-31 17:29:34 +0000 (Fri, 31 Oct 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Make the simple_mon_lib_chewm_comp consistent (re: desc_level) with chem_comp. ------------------------------------------------------------------------ r1536 | pemsley | 2008-10-31 16:59:09 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc If desc_level is in the cif file, extract it, otherwise set it to "None". ------------------------------------------------------------------------ r1535 | b.lohkamp | 2008-10-31 15:41:05 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/scheme/generic-objects.scm M /trunk/src/c-inner-main.c made reduce pdb v3 compliant (i.e. removed -oldpdb flag) ------------------------------------------------------------------------ r1534 | pemsley | 2008-10-31 08:33:28 +0000 (Fri, 31 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Reorder build cells and correct name for cycle. ------------------------------------------------------------------------ r1533 | pemsley | 2008-10-30 18:43:54 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple My python configuration tinkering, this time to coot's configure. ------------------------------------------------------------------------ r1532 | pemsley | 2008-10-30 14:37:30 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc Add Cl and Br to inpected element ids (these are mixed case). ------------------------------------------------------------------------ r1531 | b.lohkamp | 2008-10-30 11:08:56 +0000 (Thu, 30 Oct 2008) | 7 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/ligand/ligand.cc M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Add a python-representation and reorder_chain function + GUI set B-factors for new/mutated atoms to 30 (in ligands.cc as for g.default_new_atoms_b_factor) update the settings of toolbar icons menu selection Add some functions to set b-factors (python only so far) Add reset b-factor after refinement button to refinement options GUI ------------------------------------------------------------------------ r1530 | pemsley | 2008-10-30 00:41:56 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1529 | pemsley | 2008-10-30 00:41:14 +0000 (Thu, 30 Oct 2008) | 2 lines Changed paths: M /trunk/standard-residues.pdb Add Xr residue. Not used yet. ------------------------------------------------------------------------ r1528 | pemsley | 2008-10-30 00:40:39 +0000 (Thu, 30 Oct 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Adjust install_top_dir and generic_prefix so that they are different for python pre-release builds. ------------------------------------------------------------------------ r1527 | b.lohkamp | 2008-10-29 16:12:20 +0000 (Wed, 29 Oct 2008) | 1 line Changed paths: M /trunk/build-it-win update windows build script ------------------------------------------------------------------------ r1526 | pemsley | 2008-10-29 14:46:23 +0000 (Wed, 29 Oct 2008) | 5 lines Changed paths: M /trunk/mapview.glade M /trunk/src/c-interface-superpose.cc M /trunk/src/interface.c least_squares_move_copy_checkbutton was not in gtk1 interface so refering to it crashed coot. Added protection to its use in apply_lsq_matches_by_widget and added it to the gtk1 interface. ------------------------------------------------------------------------ r1525 | b.lohkamp | 2008-10-29 09:51:19 +0000 (Wed, 29 Oct 2008) | 1 line Changed paths: M /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py fixed python 2.6 testing problem ------------------------------------------------------------------------ r1524 | pemsley | 2008-10-29 08:46:15 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple re-work the building of python again. ------------------------------------------------------------------------ r1523 | pemsley | 2008-10-29 08:34:17 +0000 (Wed, 29 Oct 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add scheme-representation and reorder-chains functions (so that chains are now in lexographical order) and add a simple GUI to that function. ------------------------------------------------------------------------ r1522 | pemsley | 2008-10-29 07:36:29 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Better exitting when python not correct. ------------------------------------------------------------------------ r1521 | pemsley | 2008-10-29 07:26:45 +0000 (Wed, 29 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Tinker with python version settings. Now use 2.6 in both. ------------------------------------------------------------------------ r1520 | pemsley | 2008-10-28 18:12:08 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc More reworking of py_to_scm() and py_clean_internal(). If PyObject o is a function, render that as a string. ------------------------------------------------------------------------ r1519 | pemsley | 2008-10-28 18:11:13 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/src/gtk-manual.cc Relabel menu item (CA/backbone, now we do P backbone). Remove debugging. ------------------------------------------------------------------------ r1518 | b.lohkamp | 2008-10-28 16:16:23 +0000 (Tue, 28 Oct 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/cootrc.template M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/command-line.cc M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc synchronised MFR dialog and modelling toolbar moved 'Add Water' to 'Other Modelling Tools' (GTK2) model toolbar defaults to all icons added preferences to change toolbar outline ------------------------------------------------------------------------ r1517 | pemsley | 2008-10-28 07:36:01 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/src/pick.cc Allow the picking of Ps in CA mode. ------------------------------------------------------------------------ r1516 | pemsley | 2008-10-28 07:35:37 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h Allow the P backbone mode in CA display mode. ------------------------------------------------------------------------ r1515 | pemsley | 2008-10-28 03:55:57 +0000 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /trunk/Makefile.am Change cootrc to cootrc.template for EXTRA_DIST. ------------------------------------------------------------------------ r1514 | pemsley | 2008-10-28 03:51:27 +0000 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/callbacks.c M /trunk/src/gtk-manual.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/rama_plot.cc Fix up handling of the scroll group for the "Delete" button in the Display Manager. Fixes JED crash. ------------------------------------------------------------------------ r1513 | pemsley | 2008-10-27 16:52:45 +0000 (Mon, 27 Oct 2008) | 8 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/gtk-manual.cc M /trunk/src/main.cc M /trunk/src/molecule-class-info.cc configure.in sets up commands to build cootrc. Add a command line argument to inhibit splash screen. Add a command line arg to change the splash screen (non-working, as we need to pass the splash screen widget creator the file name to the image.). The "delete molecule" button in the display control crashes coot somehow add some debugging. Start adding SBASE interface into Coot. ------------------------------------------------------------------------ r1512 | pemsley | 2008-10-27 16:48:46 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: D /trunk/cootrc A /trunk/cootrc.template (from /trunk/cootrc:1511) Move cootrc to cootrc.template, now that we can address gtk1 issues. ------------------------------------------------------------------------ r1511 | pemsley | 2008-10-27 16:48:10 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/cootrc Update cootrc - there are diffs, needs a mv to template. ------------------------------------------------------------------------ r1510 | pemsley | 2008-10-27 16:45:09 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Remove debugging. ------------------------------------------------------------------------ r1509 | pemsley | 2008-10-27 16:44:19 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Remove pukka puckers until it works properly. ------------------------------------------------------------------------ r1508 | pemsley | 2008-10-27 16:39:36 +0000 (Mon, 27 Oct 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Don't make test after the python build. Use python version 2.6 ------------------------------------------------------------------------ r1507 | pemsley | 2008-10-27 16:37:30 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex M /trunk/doc/tutorial.tex Update the tutorials. ------------------------------------------------------------------------ r1506 | pemsley | 2008-10-27 02:19:12 +0000 (Mon, 27 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1505 | b.lohkamp | 2008-10-23 22:32:15 +0100 (Thu, 23 Oct 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/cootrc A /trunk/pixmaps/edit-backbone.svg M /trunk/pixmaps/side-chain-180.svg A /trunk/pixmaps/torsion-general.svg M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/gtk2-interface.c new icons for 'Torsion General' and 'Edit Backbone Torsion' modeling toolbar and MFR dialog have same buttons now (although not all shown in toolbar by default) ------------------------------------------------------------------------ r1504 | b.lohkamp | 2008-10-23 14:47:25 +0100 (Thu, 23 Oct 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_toolbuttons.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/testing.cc compiles without GSL now (not sure how usefull and if it is as functional as possible refmac with input mtz file works properly now (?!) updates to refmac.py/scm to work with mtz file input ------------------------------------------------------------------------ r1503 | b.lohkamp | 2008-10-21 19:31:35 +0100 (Tue, 21 Oct 2008) | 8 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/doc/tutorial.tex M /trunk/python/refmac.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/support.h update tutorial with Kevin's images (GTK2) flag and some implementation of resetting of b-factors after refinement copy button for lsq fit GUI re-worked refmac GUI so that you always can take an mtz file as input (needs cleaning up, fixing of phase combination and some implementation in the scheme scripting) ------------------------------------------------------------------------ r1502 | pemsley | 2008-10-17 17:47:45 +0100 (Fri, 17 Oct 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix doc typos. ------------------------------------------------------------------------ r1501 | pemsley | 2008-10-17 13:17:33 +0100 (Fri, 17 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add in non-pythonic centOS 4 gtk2 binary. ------------------------------------------------------------------------ r1500 | b.lohkamp | 2008-10-17 10:27:18 +0100 (Fri, 17 Oct 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/doc/tutorial.tex M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h add GUI/assistent for a user-defined toolbutton in the toolbar menu update the tutorial to be GTK2 compliant (preferences, modeeling toolbar) fixed crash when trying to load images and no appropriate pix-buf loader was available ------------------------------------------------------------------------ r1499 | pemsley | 2008-10-15 15:28:05 +0100 (Wed, 15 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm i686 bins not i386 for ubuntu 8.04. ------------------------------------------------------------------------ r1498 | pemsley | 2008-10-15 11:30:07 +0100 (Wed, 15 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Enable imminent bragg3 build watcher. ------------------------------------------------------------------------ r1497 | pemsley | 2008-10-15 07:46:51 +0100 (Wed, 15 Oct 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Updates to test for patch before continuing. Don't look for bragg3 bins, it can't compile code yet. ------------------------------------------------------------------------ r1496 | b.lohkamp | 2008-10-13 16:13:01 +0100 (Mon, 13 Oct 2008) | 1 line Changed paths: M /trunk/scheme/refmac.scm fixed (guile) run-refmac-for-phases ------------------------------------------------------------------------ r1495 | pemsley | 2008-10-13 14:07:38 +0100 (Mon, 13 Oct 2008) | 2 lines Changed paths: M /trunk/doc/tutorial-2.tex Update tutorial-2.tex ------------------------------------------------------------------------ r1494 | pemsley | 2008-10-10 13:42:24 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update relnotes. ------------------------------------------------------------------------ r1493 | pemsley | 2008-10-10 13:36:03 +0100 (Fri, 10 Oct 2008) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/test-read-components.cc M /trunk/src/c-interface-validate.cc Add mmdb-mmdb-long-line patch to mmdb build. Remove reference to gtk_widget_unref on baddie checked waters - fixes crash [JED]. Enable SBASE in protein geometry. Add is_directory_p() function. ------------------------------------------------------------------------ r1492 | pemsley | 2008-10-10 11:51:02 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo in source code build log file name. ------------------------------------------------------------------------ r1491 | pemsley | 2008-10-10 11:35:04 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add setsuko builds. ------------------------------------------------------------------------ r1490 | pemsley | 2008-10-10 11:32:01 +0100 (Fri, 10 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo in reading source build status. ------------------------------------------------------------------------ r1489 | b.lohkamp | 2008-10-09 15:30:40 +0100 (Thu, 09 Oct 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py conditional import gobject in coot_gui.py ------------------------------------------------------------------------ r1488 | b.lohkamp | 2008-10-09 14:44:00 +0100 (Thu, 09 Oct 2008) | 1 line Changed paths: M /trunk/python/get_ebi.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py python (tests) fixes and updates ------------------------------------------------------------------------ r1487 | pemsley | 2008-10-09 09:58:55 +0100 (Thu, 09 Oct 2008) | 2 lines Changed paths: M /trunk/src/c-interface.h Improve doxygen documentation for Ramachandran angles. ------------------------------------------------------------------------ r1486 | pemsley | 2008-10-09 08:36:51 +0100 (Thu, 09 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Read 2-line status from build-status/status. ------------------------------------------------------------------------ r1485 | pemsley | 2008-10-08 23:46:34 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/ligand/wiggly-ligand.cc Remove some debugging from wiggly ligands. ------------------------------------------------------------------------ r1484 | pemsley | 2008-10-08 17:19:56 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Migrate to CCP4 version 6.0.2 for testing in York. ------------------------------------------------------------------------ r1483 | pemsley | 2008-10-08 17:06:00 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm More debugging for setting of CCP4. ------------------------------------------------------------------------ r1482 | pemsley | 2008-10-08 17:04:44 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add some debugging for setting up of CCP4. ------------------------------------------------------------------------ r1481 | pemsley | 2008-10-08 14:15:49 +0100 (Wed, 08 Oct 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/src/callbacks.c Read a PART card from a shelxl file with a site occupancy factor. Clean up response handling in on_save_restraint_chooserdialog_response(). ------------------------------------------------------------------------ r1480 | pemsley | 2008-10-08 13:57:00 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add NCS residue range edit test. ------------------------------------------------------------------------ r1479 | pemsley | 2008-10-08 13:16:37 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes updat dnotes. ------------------------------------------------------------------------ r1478 | pemsley | 2008-10-08 13:16:06 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES update release notes. ------------------------------------------------------------------------ r1477 | pemsley | 2008-10-08 11:47:26 +0100 (Wed, 08 Oct 2008) | 2 lines Changed paths: M /trunk/build-it Resolve conflict in version number, python fixes. ------------------------------------------------------------------------ r1476 | b.lohkamp | 2008-10-08 09:14:19 +0100 (Wed, 08 Oct 2008) | 1 line Changed paths: M /trunk/src/gtk-manual.cc fixed Display Managers display style menu positions ------------------------------------------------------------------------ r1475 | pemsley | 2008-10-07 18:57:28 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Back to Python 2.5.1, that compiles on bragg3 (tests run). ------------------------------------------------------------------------ r1474 | pemsley | 2008-10-07 17:55:59 +0100 (Tue, 07 Oct 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/radacina_handcuffs-small.svg M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c Use GTK_RESPONSE_CANCEL in destroying a filechooser dialog (restraint_chooserdialog). Add an icons for restraints editor. ------------------------------------------------------------------------ r1473 | b.lohkamp | 2008-10-07 12:51:12 +0100 (Tue, 07 Oct 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python-tests/08_utils.py fixed import gobject for pygtk1 ------------------------------------------------------------------------ r1472 | pemsley | 2008-10-07 09:02:10 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Don't build gobject or pygtk if python is not given as an arg. ------------------------------------------------------------------------ r1471 | pemsley | 2008-10-07 08:48:20 +0100 (Tue, 07 Oct 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Don't build python if it is not passed as an arg. ------------------------------------------------------------------------ r1470 | pemsley | 2008-10-06 23:16:50 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Return a value from the ghost operator<<. ------------------------------------------------------------------------ r1469 | pemsley | 2008-10-06 15:29:03 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix problem of missing NCS residue range operations for more than one peer chain. ------------------------------------------------------------------------ r1468 | pemsley | 2008-10-06 14:18:15 +0100 (Mon, 06 Oct 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Try again with build-web-page builder without pre-release source tar files. ------------------------------------------------------------------------ r1467 | pemsley | 2008-10-06 11:36:40 +0100 (Mon, 06 Oct 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Update web page builder to account for release time, where no pre-release source tar file exists. ------------------------------------------------------------------------ r1466 | b.lohkamp | 2008-10-05 18:05:58 +0100 (Sun, 05 Oct 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py add edit backbone torsion toolbutton ------------------------------------------------------------------------ r1465 | pemsley | 2008-10-05 12:00:15 +0100 (Sun, 05 Oct 2008) | 6 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Remove usage of GTK_BROKEN. Add function atom_index_first_atom_in_residue_with_altconf(), used in show_rotamer_dialog. Now rotamer dialog can be bound to a key. Some debugging added to restraints-editor.hh to help fix the save restraints problem (referencing the wrong residue type). ------------------------------------------------------------------------ r1464 | pemsley | 2008-10-05 11:56:35 +0100 (Sun, 05 Oct 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Fix up writing of cif file (currently from restraints editor). ------------------------------------------------------------------------ r1463 | pemsley | 2008-10-05 11:47:36 +0100 (Sun, 05 Oct 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Comment out debugging for keybinding. ------------------------------------------------------------------------ r1462 | pemsley | 2008-10-01 07:13:54 +0100 (Wed, 01 Oct 2008) | 3 lines Changed paths: M /trunk/coords/mmdb.cc Cleanup with PDBCLEAN_ELEMENT after reading a coordintes file. (Generates elements where they were missing). ------------------------------------------------------------------------ r1461 | b.lohkamp | 2008-09-30 14:55:41 +0100 (Tue, 30 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-preferences.cc fixed clash atoms, updated python extensions ------------------------------------------------------------------------ r1460 | b.lohkamp | 2008-09-30 10:26:58 +0100 (Tue, 30 Sep 2008) | 1 line Changed paths: M /trunk/build-it-win update windows autobuild script ------------------------------------------------------------------------ r1459 | pemsley | 2008-09-29 20:01:28 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Rework the Extensions menu reduce the length and sub-menu the items. ------------------------------------------------------------------------ r1458 | pemsley | 2008-09-29 17:53:01 +0100 (Mon, 29 Sep 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/dnotes M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/junk.cc Move to 0.5.1-pre-1 pre-release. Add a delete molecule button to display manager. Replace the display manager display and active toggle buttons with checkbuttons. ------------------------------------------------------------------------ r1457 | pemsley | 2008-09-29 17:45:11 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Bring back the missing flashing bond (was a typo, commented the wrong line). ------------------------------------------------------------------------ r1456 | pemsley | 2008-09-29 16:44:08 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: A /trunk/doc/tutorial-2.tex Add tutorial-2.tex ------------------------------------------------------------------------ r1455 | pemsley | 2008-09-29 16:41:40 +0100 (Mon, 29 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1454 | pemsley | 2008-09-26 17:19:46 +0100 (Fri, 26 Sep 2008) | 3 lines Changed paths: M /trunk/theor-helix-70.pdb Oops. move theor-helix to new pdb format. Bitten by my own dog-food... or something. ------------------------------------------------------------------------ r1453 | b.lohkamp | 2008-09-26 14:16:47 +0100 (Fri, 26 Sep 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/08_utils.py proper test to import gobject ------------------------------------------------------------------------ r1452 | pemsley | 2008-09-25 17:12:34 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Handle typename in pygobject.h for CentOS4. ------------------------------------------------------------------------ r1451 | pemsley | 2008-09-25 16:33:31 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use the right file name for gobject. ------------------------------------------------------------------------ r1450 | pemsley | 2008-09-25 16:25:34 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use pygobject 2.4 if needed (e.g on CentOS 4). ------------------------------------------------------------------------ r1449 | pemsley | 2008-09-25 16:23:17 +0100 (Thu, 25 Sep 2008) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Add "import gobject" to tests. ------------------------------------------------------------------------ r1448 | pemsley | 2008-09-24 18:54:18 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: A /trunk/DONE M /trunk/TODO Update TODO, Put old TODOs in DONE. ------------------------------------------------------------------------ r1447 | pemsley | 2008-09-24 18:53:03 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/TODO Update todo list. ------------------------------------------------------------------------ r1446 | pemsley | 2008-09-24 14:14:25 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/build-it Tell us what the source tar file was when building coot. ------------------------------------------------------------------------ r1445 | pemsley | 2008-09-24 11:47:16 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Debug test for greg. ------------------------------------------------------------------------ r1444 | pemsley | 2008-09-24 09:10:52 +0100 (Wed, 24 Sep 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Fix formatting of relnotes. ------------------------------------------------------------------------ r1443 | pemsley | 2008-09-24 07:49:29 +0100 (Wed, 24 Sep 2008) | 6 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/pixmaps/add-alt-conf.svg A /trunk/pixmaps/coot-0.5.xpm M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Release 0.5 Change the splash screen Try to build a working version of pygobject on CentOS4 Name the release in the relnotes. Rework the add-alt-conf svg icon. ------------------------------------------------------------------------ r1442 | pemsley | 2008-09-23 14:36:21 +0100 (Tue, 23 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/get-ebi.scm Fix up the URL stub for the OCA server (Dirk Kostrewa). ------------------------------------------------------------------------ r1441 | pemsley | 2008-09-23 09:51:14 +0100 (Tue, 23 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Minor doc update. ------------------------------------------------------------------------ r1440 | pemsley | 2008-09-22 18:10:07 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1439 | pemsley | 2008-09-22 18:09:43 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/density-contour/Makefile.am Tidy up a tiny problem noted by new automake. ------------------------------------------------------------------------ r1438 | pemsley | 2008-09-22 18:07:14 +0100 (Mon, 22 Sep 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1437 | b.lohkamp | 2008-09-22 16:50:28 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py fix for keyboard mapping on some windows systems ------------------------------------------------------------------------ r1436 | b.lohkamp | 2008-09-22 16:44:15 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/src/c-interface-gui.cc fixed file chooser saved size ------------------------------------------------------------------------ r1435 | b.lohkamp | 2008-09-22 11:33:30 +0100 (Mon, 22 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface-gui.cc 'current directory' for filechooser ------------------------------------------------------------------------ r1434 | b.lohkamp | 2008-09-21 21:56:54 +0100 (Sun, 21 Sep 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/src/callbacks.c filechooser resize 'fix' ------------------------------------------------------------------------ r1433 | pemsley | 2008-09-21 12:15:52 +0100 (Sun, 21 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh Use dictionary (where possible) to generate bonds (contacts) for atom tree generation when applying torsions in wiggly ligands. ------------------------------------------------------------------------ r1432 | pemsley | 2008-09-21 00:47:54 +0100 (Sun, 21 Sep 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.hh M /trunk/ligand/chi-angles.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc Fix up crash/failure of ligand search when period caused by torsion period of 0. Add set_debug_wiggly_ligands() function. ------------------------------------------------------------------------ r1431 | pemsley | 2008-09-20 11:22:05 +0100 (Sat, 20 Sep 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c Rework the #ifdefs on file chooser/selector functions. ------------------------------------------------------------------------ r1430 | pemsley | 2008-09-19 16:00:25 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/extensions.scm Enable python code from scheme - for side chain docking and running refmac. ------------------------------------------------------------------------ r1429 | pemsley | 2008-09-19 15:46:39 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Also, similarly protect the _row_actived() function. ------------------------------------------------------------------------ r1428 | pemsley | 2008-09-19 15:44:45 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Add null pointer protection (from intelligent_this_residue_mmdb_atom()) in residue_tree_residue_row_activated(). ------------------------------------------------------------------------ r1427 | pemsley | 2008-09-19 15:11:28 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/coot_pythonmodule.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Remove debugging of erase_last_molecule(). Remove (make invisible) skeleton prune and colour from the GUI. ------------------------------------------------------------------------ r1426 | pemsley | 2008-09-19 13:46:18 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Remove debugging from python (pygtk) macro. ------------------------------------------------------------------------ r1425 | pemsley | 2008-09-19 12:32:10 +0100 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More on NCS ghosts. ------------------------------------------------------------------------ r1424 | pemsley | 2008-09-19 12:31:09 +0100 (Fri, 19 Sep 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple Now GSL is 1.11 we need an exact test for the version number because 1.11 is numerically less than 1.3. ------------------------------------------------------------------------ r1423 | b.lohkamp | 2008-09-19 11:25:40 +0100 (Fri, 19 Sep 2008) | 1 line Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc fixes for model_toolbar ------------------------------------------------------------------------ r1422 | pemsley | 2008-09-18 18:09:39 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove references to glitz, cairo, fontconfig. ------------------------------------------------------------------------ r1421 | pemsley | 2008-09-18 17:00:48 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Add forgotten generic-display-object.hh. ------------------------------------------------------------------------ r1420 | b.lohkamp | 2008-09-18 15:47:30 +0100 (Thu, 18 Sep 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c model_toolbar can dock top and bottom, and has a pop-up menu added model_toolbar function to reattach the toolbar removed handle_read_draw_probe_dots_unformatted_py and reworked handle_read_draw_probe_dots_unformatted to prefer either python or scheme gui ------------------------------------------------------------------------ r1419 | pemsley | 2008-09-18 14:53:51 +0100 (Thu, 18 Sep 2008) | 3 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/globjects.cc Add hybrid_36-reading scan line to probe_dots_unformatted. Needs to be configurable perhaps. ------------------------------------------------------------------------ r1418 | pemsley | 2008-09-18 14:45:11 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1417 | pemsley | 2008-09-18 14:44:21 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/gdk-keysyms.cc Add some comments. ------------------------------------------------------------------------ r1416 | pemsley | 2008-09-18 14:41:54 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Remove telling us that a key was pressed. ------------------------------------------------------------------------ r1415 | pemsley | 2008-09-18 13:01:08 +0100 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-render.cc Fix number format output problem for generic dots. ------------------------------------------------------------------------ r1414 | pemsley | 2008-09-17 18:02:01 +0100 (Wed, 17 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/happy-coot-diary.html M /trunk/src/coot-render.hh A /trunk/src/generic-display-object.hh M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h Add the ability to render (raster3d) generic display objects. ------------------------------------------------------------------------ r1413 | b.lohkamp | 2008-09-17 14:59:59 +0100 (Wed, 17 Sep 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r1412 | pemsley | 2008-09-16 17:09:47 +0100 (Tue, 16 Sep 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 change the version of mmdb that we need. ------------------------------------------------------------------------ r1411 | pemsley | 2008-09-16 13:51:33 +0100 (Tue, 16 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/gdk-keysyms.cc Correct () to [] in key binding codes. ------------------------------------------------------------------------ r1410 | b.lohkamp | 2008-09-16 11:15:22 +0100 (Tue, 16 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/python/mutate.py M /trunk/python/refmac.py M /trunk/python/shelx.py M /trunk/python-tests/08_utils.py M /trunk/src/graphics-info.h fix rama-data for windows ------------------------------------------------------------------------ r1409 | pemsley | 2008-09-15 13:40:32 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/cootrc Fix syntax of small_font, now consistent with others. ------------------------------------------------------------------------ r1408 | pemsley | 2008-09-15 10:27:34 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/src/c-interface-superpose.cc Remove some debugging. ------------------------------------------------------------------------ r1407 | pemsley | 2008-09-15 10:26:21 +0100 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Mark the fc5 python build as python. ------------------------------------------------------------------------ r1406 | b.lohkamp | 2008-09-14 15:18:05 +0100 (Sun, 14 Sep 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade A /trunk/pixmaps/map.svg M /trunk/python/a_rapper_gui.py M /trunk/python/background_demo.py M /trunk/python/bones_reader.py M /trunk/python/brute_lsqman.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/filter.py M /trunk/python/fitting.py M /trunk/python/gap.py M /trunk/python/generic_objects.py M /trunk/python/get_ebi.py M /trunk/python/group_settings.py M /trunk/python/hello.py M /trunk/python/libcheck.py M /trunk/python/mutate.py M /trunk/python/ncs.py M /trunk/python/povray.py M /trunk/python/python_coot_docs.py M /trunk/python/raster3d.py M /trunk/python/refmac.py M /trunk/python/shelx.py M /trunk/python/shelx_extensions.py M /trunk/python/tips_gui.py M /trunk/python/unittest_extensions.py M /trunk/python/what_check.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/05_rna_ghosts.py M /trunk/python-tests/06_ssm.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh updated python(-test) scripts to GPL 3 proper keyboard mapping for keybinding in pygtk 'proper' map icon for preferences ------------------------------------------------------------------------ r1405 | pemsley | 2008-09-14 12:35:00 +0100 (Sun, 14 Sep 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/junk.cc M /trunk/src/support.c M /trunk/src/support.h Change the Undo molecule chooser to the in-build one. Set the active undo molecule correctly. Update the interface files Move refmac button press handler into c-interface-gui.cc ------------------------------------------------------------------------ r1404 | pemsley | 2008-09-14 11:05:17 +0100 (Sun, 14 Sep 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.c M /trunk/src/support.h Change the label on the Search Monomer Library dialog. Update splash screens on gtk1 version. ------------------------------------------------------------------------ r1403 | pemsley | 2008-09-13 19:30:01 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/greg-tests/08-utils.scm M /trunk/scheme/get-ebi.scm M /trunk/src/molecule-class-info-other.cc Remove debugging apparent in the test logs. ------------------------------------------------------------------------ r1402 | pemsley | 2008-09-13 18:53:05 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/ligand-extras.cc Fix short int (0) to std::string ambiguity. Fixes Bernhard's crash. ------------------------------------------------------------------------ r1401 | pemsley | 2008-09-13 18:13:31 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix typo in previous debugging comment removal. ------------------------------------------------------------------------ r1400 | pemsley | 2008-09-13 15:57:24 +0100 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Remove cispep debugging. ------------------------------------------------------------------------ r1399 | pemsley | 2008-09-13 14:13:07 +0100 (Sat, 13 Sep 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Check that chain pointer is valid before using it in cis_peptides_info_from_coords(). Fixes baton build crash. ------------------------------------------------------------------------ r1398 | pemsley | 2008-09-11 09:00:36 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/ligand/ligand-extras.cc M /trunk/ligand/test-fffear-in-coot.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh when in flood mode, make the output residue name and atom name be DUM. ------------------------------------------------------------------------ r1397 | pemsley | 2008-09-11 07:44:17 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: D /trunk/pixmaps/arashiyama-park-bevelled.jpg D /trunk/pixmaps/arashiyama-park.xcf D /trunk/pixmaps/coot-0.2.xpm D /trunk/pixmaps/coot-0.3.xpm D /trunk/pixmaps/coot-0.4-alternate.xpm D /trunk/pixmaps/coot-0.4-pre.xpm D /trunk/pixmaps/coot-0.4.xpm D /trunk/pixmaps/coot-16-bevel.xpm Remove unneeded xpm pixmaps and other images to make the tar ball smaller. ------------------------------------------------------------------------ r1396 | pemsley | 2008-09-11 07:15:34 +0100 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Chnage the source of gtkglext to software/extras. ------------------------------------------------------------------------ r1395 | pemsley | 2008-09-10 22:14:40 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: A /trunk/coot-utils/xmap-stats.cc A /trunk/coot-utils/xmap-stats.hh Add forgotten xmap-stats files. ------------------------------------------------------------------------ r1394 | pemsley | 2008-09-10 19:40:07 +0100 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc Adjust the output filenames, use water_molecule, to be writen out to the file name given to findwaters. ------------------------------------------------------------------------ r1393 | pemsley | 2008-09-10 19:25:35 +0100 (Wed, 10 Sep 2008) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/dnotes M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/xmap-utils.cc M /trunk/src/xmap-utils.h Improve the flooding mechanism. Not too hard, as it turns out, use peaksearch, not clusters and move the xmap-utils (mean_and_variance) into coot-utils, from src dir. ------------------------------------------------------------------------ r1392 | pemsley | 2008-09-10 15:51:19 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1391 | pemsley | 2008-09-10 13:23:45 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc Fix problem of recentering when there are no coordinates molecules displayed. ------------------------------------------------------------------------ r1390 | pemsley | 2008-09-10 13:09:57 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/find-waters.cc Add a check that the mtz file is properly read before using the map. ------------------------------------------------------------------------ r1389 | pemsley | 2008-09-10 10:05:16 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/ligand/ligand-extras.cc Remove debugging output for flood mode. ------------------------------------------------------------------------ r1388 | pemsley | 2008-09-10 10:04:01 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/configure.in Remove HAVE_SYS_STDTYPES_H debugging from configure. ------------------------------------------------------------------------ r1387 | pemsley | 2008-09-10 09:58:56 +0100 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc Tidy up find waters output - leave it for there now. I think findwaters needs a new algorithm in flood mode. Now is not the time. ------------------------------------------------------------------------ r1386 | pemsley | 2008-09-10 09:50:43 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh Improvements to find-waters --flood mode. ------------------------------------------------------------------------ r1385 | pemsley | 2008-09-10 08:25:16 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r1384 | pemsley | 2008-09-10 08:21:32 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/autogen.sh A bit of feedback when using Darwin. ------------------------------------------------------------------------ r1383 | pemsley | 2008-09-10 08:20:36 +0100 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /trunk/cootaneer/Makefile.am Don't install cootaneer_demo. ------------------------------------------------------------------------ r1382 | pemsley | 2008-09-09 19:28:45 +0100 (Tue, 09 Sep 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c Correctly type the new togglebutton when looking up the dialog. ------------------------------------------------------------------------ r1381 | pemsley | 2008-09-09 19:24:45 +0100 (Tue, 09 Sep 2008) | 6 lines Changed paths: M /trunk/README M /trunk/RELEASE-NOTES M /trunk/autogen.sh M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Refactor the chi angles dialog filling, add a check button to add hydrogen torsions/chi angles. Add a c-interface function used by the check button callback, the dialog need to know its own residue type. clear_out_container() utility function added. ------------------------------------------------------------------------ r1380 | b.lohkamp | 2008-09-09 15:50:25 +0100 (Tue, 09 Sep 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/libcheck.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/03_ligand.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c updated python tests refine-toolbar show/hide & left/right in preferences ------------------------------------------------------------------------ r1379 | b.lohkamp | 2008-09-09 07:55:10 +0100 (Tue, 09 Sep 2008) | 1 line Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/src/c-interface.cc M /trunk/src/command-line.cc fixed test fail on python keybinding ------------------------------------------------------------------------ r1378 | b.lohkamp | 2008-09-08 20:41:39 +0100 (Mon, 08 Sep 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/libcheck.py M /trunk/src/command-line.cc M /trunk/src/main.cc stepped rama refine for python key bindings for python small-screen command line option (replaces eee) fix gdb crash on windows on loading icons ------------------------------------------------------------------------ r1377 | pemsley | 2008-09-08 14:20:24 +0100 (Mon, 08 Sep 2008) | 4 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/ligand/ligand.cc M /trunk/mapview.glade M /trunk/scheme/coot-gui.scm M /trunk/src/Makefile.am M /trunk/src/graphics-info-defines.cc M /trunk/src/interface.c Add a setting of HAVE_SYS_TYPES_H, needed for loading a guile header. Fix button label for Ramachandran Restraints in Gtk1 version (TS). Update notes. ------------------------------------------------------------------------ r1376 | pemsley | 2008-09-07 18:35:34 +0100 (Sun, 07 Sep 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Use $PYTHON, not python to get python variables, for CFLAGS and linking. ------------------------------------------------------------------------ r1375 | pemsley | 2008-09-07 17:51:31 +0100 (Sun, 07 Sep 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add a definition for set-find-hydrogen-torsions for doc snarfing. ------------------------------------------------------------------------ r1374 | pemsley | 2008-09-01 15:41:01 +0100 (Mon, 01 Sep 2008) | 4 lines Changed paths: M /trunk/doc/tutorial.tex Update tutorial. Fixes from Kevin, except the use of png instead of ps for figures (bounding box problems). ps remain. More NCS text. ------------------------------------------------------------------------ r1373 | pemsley | 2008-08-31 15:35:49 +0100 (Sun, 31 Aug 2008) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/pixmaps/edit-chi.svg M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Changes from Osaka (and Tokyo a bit): Create function make_mols_from_atom_selection, which makes a selected and masked molecule for use in rigid body fitting. Add internal test for this. Refactor rigid body fitting, so that we can script it and pass an mmdb atom selection. This is a feature for Catherine Lawson. Remove some casting from mmdb char * args (now const). ------------------------------------------------------------------------ r1372 | pemsley | 2008-08-26 16:57:22 +0100 (Tue, 26 Aug 2008) | 2 lines Changed paths: M /trunk/cootaneer/cootaneer-demo.cpp uncast the call to ReadPDBASCII now that we are using the new mmdb. ------------------------------------------------------------------------ r1371 | pemsley | 2008-08-23 13:50:28 +0100 (Sat, 23 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add a test for mangling hydrogen names from a 3.0 file. Fails if Coot not linked with mmdb-1.12 or better. ------------------------------------------------------------------------ r1370 | pemsley | 2008-08-22 18:26:42 +0100 (Fri, 22 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add some documentation for mutate-by-overlap. ------------------------------------------------------------------------ r1369 | b.lohkamp | 2008-08-21 17:51:57 +0100 (Thu, 21 Aug 2008) | 1 line Changed paths: M /trunk/src/command-line.cc M /trunk/src/command-line.hh M /trunk/src/globjects.cc M /trunk/src/main.cc eee command line option for small screens ------------------------------------------------------------------------ r1368 | b.lohkamp | 2008-08-20 19:51:52 +0100 (Wed, 20 Aug 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/what_check.py what_check.py functional ------------------------------------------------------------------------ r1367 | pemsley | 2008-08-20 17:26:21 +0100 (Wed, 20 Aug 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes ------------------------------------------------------------------------ r1366 | pemsley | 2008-08-20 17:24:18 +0100 (Wed, 20 Aug 2008) | 2 lines Changed paths: M /trunk/src/pick.cc M /trunk/src/pick.h Add some more debugging for atom picking. ------------------------------------------------------------------------ r1365 | b.lohkamp | 2008-08-20 11:18:54 +0100 (Wed, 20 Aug 2008) | 1 line Changed paths: M /trunk/python/a_rapper_gui.py A /trunk/python/what_check.py updated python rapper gui, added what_check.py (both need testing) ------------------------------------------------------------------------ r1364 | pemsley | 2008-08-19 14:49:42 +0100 (Tue, 19 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Add forgotten get-refmac-sad-atom-info-scm for doc snarfing. ------------------------------------------------------------------------ r1363 | b.lohkamp | 2008-08-19 14:08:22 +0100 (Tue, 19 Aug 2008) | 5 lines Changed paths: M /trunk/bldnotes M /trunk/build-it-win M /trunk/coot-gtk2.glade M /trunk/cootrc M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc mmdb 1.12 for windows build scheme refmac for SAD, TWIN, NCS, TLS, rigid body etc. all toolbar (and button) icons are set to 16x16 model/fit/refine dialog has svgs instead of pngs ------------------------------------------------------------------------ r1362 | pemsley | 2008-08-18 17:04:42 +0100 (Mon, 18 Aug 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm M /trunk/dnotes Use mmdb version 1.12 Put link to source build log and dir of program builds in binary cells. ------------------------------------------------------------------------ r1361 | pemsley | 2008-08-18 14:07:53 +0100 (Mon, 18 Aug 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Put the build dir into the links. ------------------------------------------------------------------------ r1360 | pemsley | 2008-08-17 20:13:19 +0100 (Sun, 17 Aug 2008) | 4 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm Fix syntax error in coot-has-pygtk?. Add Extensions menu item to refine a protein with Rama restraints. Re-works stepped-refine to allow the use of Ramachandran restraints. ------------------------------------------------------------------------ r1359 | pemsley | 2008-08-17 00:48:51 +0100 (Sun, 17 Aug 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/scheme/libcheck.scm M /trunk/src/restraints-editor.cc Add some -b-D extras to libcheck interface - doesn't seem to work though. In the restraints editor, if the tlc is missing, make the tlc be a copy of the comp_id. ------------------------------------------------------------------------ r1358 | pemsley | 2008-08-15 16:00:36 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Correct a few syntax errors in the user manual. ------------------------------------------------------------------------ r1357 | b.lohkamp | 2008-08-15 14:38:54 +0100 (Fri, 15 Aug 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info.cc fixes for refmac SAD refinement connected most new refmac function in guile ------------------------------------------------------------------------ r1356 | pemsley | 2008-08-15 13:20:04 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/coords/mmdb.cc Ooops - remove the debugging code (commented out fix_wrapped_names()). ------------------------------------------------------------------------ r1355 | pemsley | 2008-08-15 11:53:51 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/dnotes M /trunk/happy-coot-diary.html Add a if (0) round the atom name debugging. I could be coming back to it. ------------------------------------------------------------------------ r1354 | pemsley | 2008-08-15 11:52:51 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi document --code for accession codes. ------------------------------------------------------------------------ r1353 | pemsley | 2008-08-15 11:49:37 +0100 (Fri, 15 Aug 2008) | 5 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/command-line.cc D /trunk/src/command-line.h A /trunk/src/command-line.hh (from /trunk/src/command-line.h:1351) M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/interface.h M /trunk/src/main.cc M /trunk/src/support.h Add the reading of accesion code files from the command line (slow). add-c-extern.sh condition now GTK_MAJOR_VERSION > 1, not dependent on the GTK_MINOR_VERSION. Works better for CentOS build. commanand-line.h renamed to command-line.hh. ------------------------------------------------------------------------ r1352 | pemsley | 2008-08-15 11:30:16 +0100 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /trunk/build-it Fix test info syntax error. ------------------------------------------------------------------------ r1351 | pemsley | 2008-08-14 16:18:28 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1350 | pemsley | 2008-08-14 16:00:52 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/interface.c M /trunk/src/interface.h Add chi squared values for gtk1 accept/reject dialog. ------------------------------------------------------------------------ r1349 | b.lohkamp | 2008-08-14 14:58:01 +0100 (Thu, 14 Aug 2008) | 4 lines Changed paths: M /trunk/bldnotes M /trunk/python/coot_utils.py M /trunk/python/povray.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/refmac.scm coot-has-pygtk? for scheme: run cootaneering and read_refmac_log if we have pygtk povray name change for 64bit windows ------------------------------------------------------------------------ r1348 | pemsley | 2008-08-14 14:27:47 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Remove debugging from resdiue editor creator. ------------------------------------------------------------------------ r1347 | pemsley | 2008-08-14 14:22:57 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Some debugging on the residue editor creator. ------------------------------------------------------------------------ r1346 | pemsley | 2008-08-14 13:36:26 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c Support code for restraints editor without gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r1345 | b.lohkamp | 2008-08-14 12:42:32 +0100 (Thu, 14 Aug 2008) | 3 lines Changed paths: M /trunk/bldnotes M /trunk/pixmaps/phenixed.svg M /trunk/pixmaps/residue-info.svg M /trunk/pixmaps/sequence-view.svg M /trunk/python/gap.py M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h add terminal residue mutates if associated sequence (no autofit!?) more changes to pixmap svg fonts ------------------------------------------------------------------------ r1344 | pemsley | 2008-08-14 11:29:41 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi update docs (command line args). ------------------------------------------------------------------------ r1343 | pemsley | 2008-08-14 11:12:13 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Enable -c direct commands from the command line. ------------------------------------------------------------------------ r1342 | pemsley | 2008-08-14 10:37:28 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/command-line.cc M /trunk/src/command-line.h partly enable executable commands from the command line. ------------------------------------------------------------------------ r1341 | pemsley | 2008-08-14 09:49:52 +0100 (Thu, 14 Aug 2008) | 2 lines Changed paths: M /trunk/src/pick.cc Add displayed info into atom picking debug info. ------------------------------------------------------------------------ r1340 | pemsley | 2008-08-14 09:23:06 +0100 (Thu, 14 Aug 2008) | 8 lines Changed paths: M /trunk/autogen.sh M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/pick.cc Add code to output number of links (will use them for bonding/refinement later). Fix NCS chain documentation. A bit better build output when not running tests. Add a debug_atom_picking setting. Remove char * casting from a graphics-info-navigation.cc atom selection function. ------------------------------------------------------------------------ r1339 | b.lohkamp | 2008-08-13 11:26:53 +0100 (Wed, 13 Aug 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/gap.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h gap/loop fitting will fit both directions and fire up a GUI to select (python) fix for no-graphics ------------------------------------------------------------------------ r1338 | pemsley | 2008-08-12 14:52:48 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py Update cis peptide python test. ------------------------------------------------------------------------ r1337 | pemsley | 2008-08-12 13:59:39 +0100 (Tue, 12 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Cispep test is now expected to pass (note that an unexpected pass causes an overall fail - and the tar file is not built). ------------------------------------------------------------------------ r1336 | pemsley | 2008-08-12 12:14:50 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/src/align.cc Tweak the arg to Get1LetterCode(rn, r). Not sure how this works... ------------------------------------------------------------------------ r1335 | b.lohkamp | 2008-08-12 12:13:59 +0100 (Tue, 12 Aug 2008) | 4 lines Changed paths: A /trunk/bldnotes M /trunk/build-it-win M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-utils.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc added EDS references notebook tab Windows adjustments for icon size change on small screens added bldnotes ------------------------------------------------------------------------ r1334 | pemsley | 2008-08-12 07:30:50 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 Fix up the mmdb test so that is it consistemt with the code (using cpstr). ------------------------------------------------------------------------ r1333 | pemsley | 2008-08-12 01:20:23 +0100 (Tue, 12 Aug 2008) | 2 lines Changed paths: M /trunk/build-it Use mmdb version 1.11. ------------------------------------------------------------------------ r1332 | pemsley | 2008-08-11 20:59:25 +0100 (Mon, 11 Aug 2008) | 5 lines Changed paths: M /trunk/autogen.sh M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/db-main/db-strands.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/high-res/globularize.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/with-map.cc M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-helix-placement.cc M /trunk/sequence-view/sequence-view.cc M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/command-line.cc M /trunk/src/density-score-by-residue.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/post-process-coot-wrap-guile.sh A /trunk/src/post-process-coot-wrap-python.sh M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h Changes for mmdb 1.11 and GCC 4.3 Clean up char * vs const char * usage. More diagnostics in ligand tests. Tweak the post-processing of the guile wrap files for char * -> const char *. ------------------------------------------------------------------------ r1331 | pemsley | 2008-08-11 19:47:49 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/macros/mmdb.m4 Add in test for CISPEP support to mmdb. ------------------------------------------------------------------------ r1330 | b.lohkamp | 2008-08-11 15:30:58 +0100 (Mon, 11 Aug 2008) | 4 lines Changed paths: M /trunk/python/extensions.py M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/post-gtk2-glade.sh ncs submenu in python extensions antialiased gtk+-2.0 icons refinement toolbar icons shrink automatically on small screens ------------------------------------------------------------------------ r1329 | pemsley | 2008-08-11 13:30:55 +0100 (Mon, 11 Aug 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Properly set the scroll wheel map in the state file. Add documentation for moving zero occupancy atoms. Add an option not to move atoms with zero occupancy in refinement. ------------------------------------------------------------------------ r1328 | pemsley | 2008-08-11 09:34:40 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/src/c-inner-main.c Update documentation (NCS chain). ------------------------------------------------------------------------ r1327 | pemsley | 2008-08-11 01:00:20 +0100 (Mon, 11 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Add a GUI for NCS chain. ------------------------------------------------------------------------ r1326 | pemsley | 2008-08-09 06:44:42 +0100 (Sat, 09 Aug 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm We need a GUI to associate the sequence, even if python is available. ------------------------------------------------------------------------ r1325 | b.lohkamp | 2008-08-08 14:20:14 +0100 (Fri, 08 Aug 2008) | 4 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/gap.py M /trunk/python/mutate.py M /trunk/python/shelx_extensions.py M /trunk/scheme/gap.scm file selector/chooser switch in python scripts toolbuttons can have a suggested icon fit loop works backwards for python AND scheme now ------------------------------------------------------------------------ r1324 | b.lohkamp | 2008-08-07 17:01:50 +0100 (Thu, 07 Aug 2008) | 6 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/azerbaijan.svg A /trunk/pixmaps/azerbaijan2.svg M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/extensions.py M /trunk/python/refmac.py M /trunk/scheme/refmac.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c fixed refmac dialog (gtk2, python) hide/show for docked accept/reject refinement toolbar (incl. preferences) associate sequence in py extensions py extension have accelerator added garib pixmaps... ------------------------------------------------------------------------ r1323 | pemsley | 2008-08-05 04:19:09 +0100 (Tue, 05 Aug 2008) | 3 lines Changed paths: M /trunk/src/graphics-info.cc Make the traffic light distortion for Rama follow the scale of restraints geometry distortion. ------------------------------------------------------------------------ r1322 | pemsley | 2008-08-05 04:09:35 +0100 (Tue, 05 Aug 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Tweak the scale of the Ramachandran plot distortion. ------------------------------------------------------------------------ r1321 | pemsley | 2008-08-05 04:08:30 +0100 (Tue, 05 Aug 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/interface.h Some forgotten things on Rama updates? (Don't know how they got lost). ------------------------------------------------------------------------ r1320 | b.lohkamp | 2008-08-03 12:42:20 +0100 (Sun, 03 Aug 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc refmac twin option implemented ------------------------------------------------------------------------ r1319 | pemsley | 2008-08-01 17:52:00 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1318 | pemsley | 2008-08-01 17:00:13 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Tweak the colour scheme for Ramachandran geometry box. ------------------------------------------------------------------------ r1317 | pemsley | 2008-08-01 16:24:32 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h M /trunk/src/testing.cc Add GUI check button for Ramachandran restraints. ------------------------------------------------------------------------ r1316 | pemsley | 2008-08-01 15:25:31 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Fix up the setting of fixed atom in the Ramachandran restraints. By Jove, I think it's working now! ------------------------------------------------------------------------ r1315 | pemsley | 2008-08-01 13:19:37 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/pixmaps/change-chain-id.svg Make a test update of change-chain-id.svg with Inkscape. test font testings are preserved. ------------------------------------------------------------------------ r1314 | pemsley | 2008-08-01 13:10:41 +0100 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /trunk/greg-tests/08-utils.scm M /trunk/src/c-interface.cc Add test python command for unknown python command. Fix up safe_python_command_with_return to handle unknown python command. ------------------------------------------------------------------------ r1313 | pemsley | 2008-08-01 10:58:19 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /trunk/src/fix-filechooser-sentinels.awk M /trunk/src/gtk2-interface.c Also fix sentinels of new (refmac) file choosers. ------------------------------------------------------------------------ r1312 | pemsley | 2008-08-01 10:33:27 +0100 (Fri, 01 Aug 2008) | 2 lines Changed paths: A /trunk/src/fix-filechooser-sentinels.awk M /trunk/src/fixup-gtk2-interface.sh M /trunk/src/gtk2-interface.c Add script to fix sentinels in file_chooser_dialog_new. ------------------------------------------------------------------------ r1311 | b.lohkamp | 2008-08-01 08:36:52 +0100 (Fri, 01 Aug 2008) | 1 line Changed paths: M /trunk/pixmaps/change-chain-id.svg M /trunk/pixmaps/chiral.svg M /trunk/pixmaps/connect-to-usf.svg M /trunk/pixmaps/density-fit.svg M /trunk/pixmaps/edit-chi.svg M /trunk/pixmaps/geom.svg M /trunk/pixmaps/gln-asn-b-factors.svg M /trunk/pixmaps/gln-asn-b-factorssvg.svg M /trunk/pixmaps/renumber-residues.svg M /trunk/pixmaps/side-chain-180.svg font lists for svgs with text ------------------------------------------------------------------------ r1310 | pemsley | 2008-07-31 12:39:29 +0100 (Thu, 31 Jul 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc Add in correct scale factor for phi and psi torsion gradients. Factor out multiplications in torsion gradients. ------------------------------------------------------------------------ r1309 | pemsley | 2008-07-31 12:01:27 +0100 (Thu, 31 Jul 2008) | 3 lines Changed paths: M /trunk/src/testing.cc Apply dx the other direction to get a better estimate of the numerical gradient. kdc_torsion_test() passes now. ------------------------------------------------------------------------ r1308 | pemsley | 2008-07-31 11:54:48 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Clean up kdc_torsion_test(). ------------------------------------------------------------------------ r1307 | pemsley | 2008-07-31 11:46:46 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Add in scale factor to convert dD/dx1 to dtheta/dx1 in kdc_torsion_test(). ------------------------------------------------------------------------ r1306 | b.lohkamp | 2008-07-31 08:16:22 +0100 (Thu, 31 Jul 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c atom_spec fix, some refmac additions & fixes ------------------------------------------------------------------------ r1305 | pemsley | 2008-07-31 00:22:26 +0100 (Thu, 31 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add Diagnosis for applying guile-gtk patch. ------------------------------------------------------------------------ r1304 | pemsley | 2008-07-30 18:57:26 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix typo in temp factor for *atom_info_string_py. ------------------------------------------------------------------------ r1303 | pemsley | 2008-07-30 18:22:13 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Updates relnotes. ------------------------------------------------------------------------ r1302 | pemsley | 2008-07-30 18:21:02 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix long-standing crash on opening cell and symmetry with no molecules read. ------------------------------------------------------------------------ r1301 | pemsley | 2008-07-30 17:53:36 +0100 (Wed, 30 Jul 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc Change atom-info-string to return a SCM and atom_info_string_py to return a PyObject *. Add function to strip spaces from a string. Add some debugging to retraints editor startup (from callback.c) code. ------------------------------------------------------------------------ r1300 | b.lohkamp | 2008-07-30 15:57:18 +0100 (Wed, 30 Jul 2008) | 1 line Changed paths: M /trunk/python/clear_backup.py M /trunk/python/coot_gui.py M /trunk/src/molecule-class-info-maps.cc windows and python script fixes ------------------------------------------------------------------------ r1299 | pemsley | 2008-07-30 15:31:41 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html Test for gtk minor version, use that to apply guile-gtk patches. ------------------------------------------------------------------------ r1298 | pemsley | 2008-07-30 13:39:01 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use old version of pyobject if pkg-config is not new enough. ------------------------------------------------------------------------ r1297 | pemsley | 2008-07-30 12:34:27 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c GtkMenuToolButton does not exist for GTK 2.4. #ifdef it out. ------------------------------------------------------------------------ r1296 | pemsley | 2008-07-30 12:10:51 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust test for up to date python. ------------------------------------------------------------------------ r1295 | pemsley | 2008-07-30 10:24:45 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c More fiddling with ifdefs to try to compile on Gtk 2.4 ------------------------------------------------------------------------ r1294 | pemsley | 2008-07-30 01:13:55 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/happy-coot-diary.html M /trunk/ifdef-for-create-aboutdialog.awk M /trunk/src/add-c-extern.sh M /trunk/src/fixup-gtk2-interface.sh M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Hand apply the edits to comment out the aboutdialog function when needed. ------------------------------------------------------------------------ r1293 | pemsley | 2008-07-30 00:38:30 +0100 (Wed, 30 Jul 2008) | 2 lines Changed paths: A /trunk/ifdef-for-create-aboutdialog.awk Add awk to to #ifdef out the create_aboutdialog() function. ------------------------------------------------------------------------ r1292 | pemsley | 2008-07-29 22:10:52 +0100 (Tue, 29 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/reference.tex M /trunk/happy-coot-diary.html M /trunk/high-res/sequence-assignment.cc M /trunk/src/callbacks.c M /trunk/src/testing.cc M /trunk/src/testing.hh Add in Kevin's torsion derivatives test. Some possible fixes for using Gtk version 2.4. ------------------------------------------------------------------------ r1291 | pemsley | 2008-07-29 22:03:24 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust test for build_guile_gtk. ------------------------------------------------------------------------ r1290 | pemsley | 2008-07-29 21:41:07 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Correctly test the up to date python version. ------------------------------------------------------------------------ r1289 | pemsley | 2008-07-29 20:03:31 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1288 | pemsley | 2008-07-29 19:17:49 +0100 (Tue, 29 Jul 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add centos build info to web build status page. ------------------------------------------------------------------------ r1287 | b.lohkamp | 2008-07-29 12:03:42 +0100 (Tue, 29 Jul 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/begin.py update python scripting and python tests added "add alt conf" to coot_toolbuttons ------------------------------------------------------------------------ r1286 | pemsley | 2008-07-28 15:34:39 +0100 (Mon, 28 Jul 2008) | 9 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/geometry/Makefile.am M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/happy-coot-diary.html M /trunk/ideal/Makefile.am M /trunk/macros/gtk-canvas.m4 M /trunk/scheme/coot-gui.scm A /trunk/scheme/what-check.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Changes from Nijmegen. Add what-check check.db parser what-check.scm Added dict_link_chiral_t to dictionary. Added chem_link to dictionary. Add data_mods to dictionary - stub/code in progress. Fixed geometry's Makefile so that parallel make works. Update key bindings in the User Manual. Updates to compile without GTK_CANVAS. ------------------------------------------------------------------------ r1285 | pemsley | 2008-07-28 13:11:57 +0100 (Mon, 28 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/molecule-class-info.h Updates to make side by side stereo work with display lists. We need first and second display lists when using side by side stereo. ------------------------------------------------------------------------ r1284 | pemsley | 2008-07-26 16:01:29 +0100 (Sat, 26 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1283 | pemsley | 2008-07-26 01:16:52 +0100 (Sat, 26 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1282 | pemsley | 2008-07-21 13:48:12 +0100 (Mon, 21 Jul 2008) | 2 lines Changed paths: A /trunk/ideal/logparse.awk Add logparse.awk ------------------------------------------------------------------------ r1281 | pemsley | 2008-07-21 10:23:34 +0100 (Mon, 21 Jul 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/tips-gui.scm M /trunk/src/c-interface-gui.cc Spell check user manual. Update notes. Remove debugging. ------------------------------------------------------------------------ r1280 | pemsley | 2008-07-19 00:19:35 +0100 (Sat, 19 Jul 2008) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/tips-gui.scm Remove bang directives, recommendation from Bill Scott (strange but true, it seems). Fiddle with the next release date. ------------------------------------------------------------------------ r1279 | pemsley | 2008-07-18 22:19:11 +0100 (Fri, 18 Jul 2008) | 6 lines Changed paths: M /trunk/coords/Cartesian.cc M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/surface/CXXQADSurface.cpp Enable Rama restraints colour box in refinement accept/reject dialog Return a GdkColor from a distortion, not a pointer. Scripting function set_numerical_gradients(int istate). Add a new release time for old-coot. Some small compilation clean-ups. ------------------------------------------------------------------------ r1278 | pemsley | 2008-07-18 02:16:24 +0100 (Fri, 18 Jul 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-rama.cc M /trunk/dnotes M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc update other files (committed from wrong directory). ------------------------------------------------------------------------ r1277 | pemsley | 2008-07-18 01:01:31 +0100 (Fri, 18 Jul 2008) | 8 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/testing.cc M /trunk/src/testing.hh Tidy up the peptide torsion and rama refinement interface. fill_distortion_torsion_gradients() factored out and used in torsion restraints too. Flanking rama restraints added. However the Rama refinement still fails - no progress. Disappointing. But, if you don't turn on ramachandran refinement (not documented) , users can't the the failure. Needs more work (obviously). ------------------------------------------------------------------------ r1276 | pemsley | 2008-07-16 22:52:35 +0100 (Wed, 16 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1275 | pemsley | 2008-07-15 23:30:31 +0100 (Tue, 15 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1274 | pemsley | 2008-07-14 15:22:57 +0100 (Mon, 14 Jul 2008) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ideal/lograma.cpp M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/testing.cc Remove debugging from lograma. Introduce my_df_torsions_internal - may be removed later. scale R the same in f and df. ------------------------------------------------------------------------ r1273 | pemsley | 2008-07-14 02:12:56 +0100 (Mon, 14 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/ligand.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h More tidying. More initialization of initialized variables. ------------------------------------------------------------------------ r1272 | pemsley | 2008-07-13 17:38:05 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.h Remove unneeded std::string in assignment of column labels in setup_internal(). ------------------------------------------------------------------------ r1271 | pemsley | 2008-07-13 16:29:38 +0100 (Sun, 13 Jul 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/db-main/db-main.cc M /trunk/geometry/protein-geometry.cc M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/sequence-assignment.cc M /trunk/ideal/Makefile.am M /trunk/ideal/lograma.cpp M /trunk/ideal/logramatest.cpp M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/ligand.hh M /trunk/mini-mol/mini-mol-utils.cc M /trunk/skeleton/BuildCas.cc M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Minor fixes, uninitialized variables etc found when using 4.3 with more checking options enabled. Some debugging added to simple-restraint.cc ------------------------------------------------------------------------ r1270 | pemsley | 2008-07-13 13:12:11 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Clean up the tests, more info on failures. ------------------------------------------------------------------------ r1269 | pemsley | 2008-07-13 12:35:54 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc M /trunk/src/gtk-manual.cc Some fixes for uninitalized variables. ------------------------------------------------------------------------ r1268 | pemsley | 2008-07-13 12:35:18 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/testing.cc Add some debugging for the setting of rama restraints. ------------------------------------------------------------------------ r1267 | pemsley | 2008-07-13 12:13:43 +0100 (Sun, 13 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add a function to hide and show the vertical modelling toolbar (its frame, really). ------------------------------------------------------------------------ r1266 | pemsley | 2008-07-12 16:23:45 +0100 (Sat, 12 Jul 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/testing.cc M /trunk/src/testing.hh More test code for Ramachandran refinement. ------------------------------------------------------------------------ r1265 | pemsley | 2008-07-12 16:23:01 +0100 (Sat, 12 Jul 2008) | 2 lines Changed paths: M /trunk/libtool autogen.sh hardy makes new libtool. ------------------------------------------------------------------------ r1264 | pemsley | 2008-07-12 10:54:08 +0100 (Sat, 12 Jul 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-rama.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/src/testing.cc Remove ramachandran_probability from coot-coord-utils. Update documentations. ------------------------------------------------------------------------ r1263 | pemsley | 2008-07-11 17:28:42 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More formatting updates for the user manual. ------------------------------------------------------------------------ r1262 | pemsley | 2008-07-11 17:00:47 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/Makefile.am Add some info to doc Makfiles. ------------------------------------------------------------------------ r1261 | pemsley | 2008-07-11 16:50:57 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi More formatting updates for user manual. ------------------------------------------------------------------------ r1260 | pemsley | 2008-07-11 16:41:56 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Now the user manual compiles cleanly with texi2html 1.76. ------------------------------------------------------------------------ r1259 | pemsley | 2008-07-11 16:29:17 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi update user-manual. ------------------------------------------------------------------------ r1258 | pemsley | 2008-07-11 16:28:06 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: A /trunk/doc/coot-plain-2.jpg Add/update coot-plain-2.jpg for web version of manual. ------------------------------------------------------------------------ r1257 | pemsley | 2008-07-11 12:52:41 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: A /trunk/coot-utils/coot-rama.cc A /trunk/coot-utils/coot-rama.hh Add coot-rama files, where the moved phi/psi code now resides. ------------------------------------------------------------------------ r1256 | pemsley | 2008-07-11 12:51:55 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/AUTHORS M /trunk/TODO M /trunk/coot-utils/Makefile.am M /trunk/dnotes M /trunk/src/graphics-info.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/testing.cc Add internal test for ramachandran angles. Move phi_psi_t to utils. ------------------------------------------------------------------------ r1255 | pemsley | 2008-07-11 12:49:19 +0100 (Fri, 11 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add a macro for using active residue. ------------------------------------------------------------------------ r1254 | pemsley | 2008-07-11 00:45:38 +0100 (Fri, 11 Jul 2008) | 7 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc Rotate/translate and rotate around fragment centre works with the sliders. Ca Zone -> mainchain now pops up a dialog when then range is too short. set-matrix is saved to the status file. peptide plane restraints state is saved in state file if off. Plane restraints button in Refinement Control now behaves properly. Document the variable refmac-extra-params. ------------------------------------------------------------------------ r1253 | b.lohkamp | 2008-07-10 22:50:31 +0100 (Thu, 10 Jul 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-interface-build.cc M /trunk/src/callbacks.c M /trunk/src/cmtz-interface.cc more refmac gui functions (TWIN no working still) ------------------------------------------------------------------------ r1252 | pemsley | 2008-07-10 15:04:16 +0100 (Thu, 10 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add update_maps() function to the scripting layer. ------------------------------------------------------------------------ r1251 | pemsley | 2008-07-10 15:03:43 +0100 (Thu, 10 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes ------------------------------------------------------------------------ r1250 | b.lohkamp | 2008-07-10 13:57:37 +0100 (Thu, 10 Jul 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info.h updated refmac gui (gtk2) and made SAD functional (TWIN option needs some more testing) ------------------------------------------------------------------------ r1249 | pemsley | 2008-07-10 11:08:01 +0100 (Thu, 10 Jul 2008) | 4 lines Changed paths: M /trunk/coords/mmdb-extras.h M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/testing.cc M /trunk/src/testing.hh Make atom_selection_container_t a class - at last. Use a vector of functions in testing. Add part of a test for ramachandran probabilities. ------------------------------------------------------------------------ r1248 | pemsley | 2008-07-09 18:53:00 +0100 (Wed, 09 Jul 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/scheme/extensions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/testing.cc Add some testing features to install_simple_wiggly_ligands(). Throw an excetion now. ------------------------------------------------------------------------ r1247 | pemsley | 2008-07-09 14:36:20 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc A bit more tidying up in the monomer restraints scm code. ------------------------------------------------------------------------ r1246 | pemsley | 2008-07-09 13:48:00 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/tw/tw.cc Use SCM_CAR not scm_car and SCM_CDR nto scm_cdr, for 1.6 compatibility. ------------------------------------------------------------------------ r1245 | pemsley | 2008-07-09 12:31:33 +0100 (Wed, 09 Jul 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-info.cc Add a stream output of a plane restraints. Correct addition of plane restraints from scm objects. Update test to test for correct plane restraint. ------------------------------------------------------------------------ r1244 | pemsley | 2008-07-09 08:52:29 +0100 (Wed, 09 Jul 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-info.cc Change monomer bond restraint test to use regularize, not refine. Adjustments in reading SCM restraints. ------------------------------------------------------------------------ r1243 | pemsley | 2008-07-09 01:57:03 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/begin.grg M /trunk/src/c-interface-info.cc Oops - revert previous change (set-monomer and test had not been likewise adjusted). ------------------------------------------------------------------------ r1242 | pemsley | 2008-07-09 01:26:38 +0100 (Wed, 09 Jul 2008) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-info.cc Remove the extra list encapsulting the key in the monomer-restraints alists. So now (assoc-ref restraints key) returns a simple list, not a list within a list. ------------------------------------------------------------------------ r1241 | pemsley | 2008-07-09 01:00:00 +0100 (Wed, 09 Jul 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes update dnotes an rel notes. ------------------------------------------------------------------------ r1240 | pemsley | 2008-07-08 21:37:12 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1239 | pemsley | 2008-07-08 18:30:57 +0100 (Tue, 08 Jul 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add Coot News to About dialog. Make better names for new molecules from map-transformation using lsq gui. ------------------------------------------------------------------------ r1238 | pemsley | 2008-07-08 16:55:31 +0100 (Tue, 08 Jul 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/ligand/rotamer.hh M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-references.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Change the probability tables so that they are loaded when needed, not at startup. Add a reference tab for the Uppsala Electron Density Server. Note: This may mess badly with src/gtk2-interface.c, so some rebuilding of the interface source may be needed. ------------------------------------------------------------------------ r1237 | pemsley | 2008-07-08 16:52:55 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Make a coot-gtk2.glade that works with glade-2.10.0. ------------------------------------------------------------------------ r1236 | pemsley | 2008-07-08 15:13:53 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1235 | pemsley | 2008-07-08 13:07:26 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/snarf-coot-docs.scm Fix up coot-has-python-p for snarfing docs. ------------------------------------------------------------------------ r1234 | pemsley | 2008-07-08 13:03:13 +0100 (Tue, 08 Jul 2008) | 3 lines Changed paths: M /trunk/ligand/primitive-chi-angles.hh M /trunk/src/c-interface-info.cc M /trunk/src/testing.cc M /trunk/src/testing.hh Fix chi angle problem on using residue info on a GLY or ALA. Some initial code for testing wiggly ligands. ------------------------------------------------------------------------ r1233 | b.lohkamp | 2008-07-08 08:17:15 +0100 (Tue, 08 Jul 2008) | 1 line Changed paths: M /trunk/src/c-interface.h more fixes for test_internal ------------------------------------------------------------------------ r1232 | b.lohkamp | 2008-07-08 07:45:05 +0100 (Tue, 08 Jul 2008) | 1 line Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h fixed test_internal_xx ------------------------------------------------------------------------ r1231 | pemsley | 2008-07-08 00:23:19 +0100 (Tue, 08 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Some adjustments for stringification. Maybe more portable now? ------------------------------------------------------------------------ r1230 | pemsley | 2008-07-07 21:33:02 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1229 | pemsley | 2008-07-07 21:17:21 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1228 | pemsley | 2008-07-07 21:10:52 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/src/testing.cc Add stringify for size_t. ------------------------------------------------------------------------ r1227 | pemsley | 2008-07-07 20:34:53 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/Makefile.am Put atom-quads.hh in the Makefile.am so that it gets added to the source tar. ------------------------------------------------------------------------ r1226 | pemsley | 2008-07-07 19:53:07 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1225 | pemsley | 2008-07-07 16:34:24 +0100 (Mon, 07 Jul 2008) | 3 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface-info.cc Correctly output all the chi angles of the first alt conf set in Residue Info dialog. ------------------------------------------------------------------------ r1224 | pemsley | 2008-07-07 16:15:33 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/primitive-chi-angles.cc M /trunk/ligand/rotamer-tables.cc Clean up the debugging of rotamers. ------------------------------------------------------------------------ r1223 | pemsley | 2008-07-07 16:08:22 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: A /trunk/ligand/atom-quads.hh Add atom-quads.hh ------------------------------------------------------------------------ r1222 | pemsley | 2008-07-07 16:07:48 +0100 (Mon, 07 Jul 2008) | 9 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/happy-coot-diary.html M /trunk/ligand/Makefile.am M /trunk/ligand/monomer-utils.hh M /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.hh M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc A /trunk/src/testing.cc A /trunk/src/testing.hh Rework the chi-angle code. Now we don't use monomer-utils or chi-angles when getting the chi angles in probability_tables. We use primitive_chi_angles. This is so that the architecture of primitive_chi_angles and monomer_utils do not collide. Some of monomer_utils is in primitive_chi_angles now. The whole rotamer/chi-angles code needs reworking/cleaning up, but probability_tables and primitive_chi_angles are good. Added rudimentary internal testing, accessible from the scripting layer. ------------------------------------------------------------------------ r1221 | pemsley | 2008-07-07 16:01:01 +0100 (Mon, 07 Jul 2008) | 2 lines Changed paths: A /trunk/ligand/primitive-chi-angles.cc A /trunk/ligand/primitive-chi-angles.hh Add new chi angle code. ------------------------------------------------------------------------ r1220 | pemsley | 2008-07-07 11:01:11 +0100 (Mon, 07 Jul 2008) | 3 lines Changed paths: A /trunk/clean-changes.sh Simple utility to remove files that were changed, but we want to discard the changes. Follow by svn update, typically. ------------------------------------------------------------------------ r1219 | pemsley | 2008-07-04 23:10:05 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.hh include math.h for lrint(). ------------------------------------------------------------------------ r1218 | b.lohkamp | 2008-07-04 18:57:12 +0100 (Fri, 04 Jul 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/Makefile.am A /trunk/python/bones_reader.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/cmtz-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h added python bones_reader added set rotamer python unittest updated glade refmac gui to incorporate TLS, SAD and TWIN refinement (not all properly functional yet) ------------------------------------------------------------------------ r1217 | pemsley | 2008-07-04 15:13:34 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add source build info to page. ------------------------------------------------------------------------ r1216 | pemsley | 2008-07-04 14:13:54 +0100 (Fri, 04 Jul 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add a function to return the rotamer name give a residue spec. Needs a python version too. ------------------------------------------------------------------------ r1215 | pemsley | 2008-07-04 12:17:16 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/molecule-class-info-other.cc Add test for set-rotamer functions. ------------------------------------------------------------------------ r1214 | pemsley | 2008-07-04 11:40:46 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add functions n_rotamers() and set_residue_to_rotamer_number(). ------------------------------------------------------------------------ r1213 | pemsley | 2008-07-04 02:07:12 +0100 (Fri, 04 Jul 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple post-hoc documentation and bump the version number now that we do guile-lib build. ------------------------------------------------------------------------ r1212 | pemsley | 2008-07-03 19:38:16 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Remove the set_display_lists_for_maps(1) in mono_mode(). ------------------------------------------------------------------------ r1211 | pemsley | 2008-07-03 17:32:40 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1210 | pemsley | 2008-07-03 14:44:19 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/src/c-interface-mmdb.cc Add string.h for memcpy() usage. ------------------------------------------------------------------------ r1209 | pemsley | 2008-07-03 14:10:21 +0100 (Thu, 03 Jul 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/ligand/monomer-utils.cc M /trunk/src/graphics-info-modelling.cc When there are alt confs in the residue, then get_chi_angles results in an inconsistency in probability_this_rotamer() in rotamer_probability_tables. Some investigation code added. ------------------------------------------------------------------------ r1208 | pemsley | 2008-07-03 13:55:25 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer-tables.cc Add string.h include file for strncmp() usage. GCC 4.3 ------------------------------------------------------------------------ r1207 | pemsley | 2008-07-03 12:48:50 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c Make the "draw hydrogens" in bond parameters work immediately too. ------------------------------------------------------------------------ r1206 | pemsley | 2008-07-03 12:40:26 +0100 (Thu, 03 Jul 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info.cc Make the bond width activate apply immediately (not just after "Apply" button hit). ------------------------------------------------------------------------ r1205 | pemsley | 2008-07-03 12:30:58 +0100 (Thu, 03 Jul 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Set g.bond_parameters_molecule correctly when it has not been set in wrapped_create_bond_parameters_dialog. Fixes Bill Scott bug. ------------------------------------------------------------------------ r1204 | pemsley | 2008-07-03 12:19:25 +0100 (Thu, 03 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add a function to query the state of the peptide plane restraints. ------------------------------------------------------------------------ r1203 | b.lohkamp | 2008-07-03 10:36:00 +0100 (Thu, 03 Jul 2008) | 5 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py A /trunk/python/shelx_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/08_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h added python shelx extensions refinement options dialog in extensions (py) probe dots for rotamers (if do_probe_dots_on_chis_and_rotamers) option to RSR after auto-fit-rotamer ------------------------------------------------------------------------ r1202 | pemsley | 2008-07-02 19:15:32 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1201 | b.lohkamp | 2008-07-02 18:25:18 +0100 (Wed, 02 Jul 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py updated rotamer outlier test ------------------------------------------------------------------------ r1200 | pemsley | 2008-07-02 15:05:11 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Update rotamer probability test now that we have new probability tables. ------------------------------------------------------------------------ r1199 | pemsley | 2008-07-02 14:43:18 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Fix typos. ------------------------------------------------------------------------ r1198 | pemsley | 2008-07-02 14:15:48 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1197 | pemsley | 2008-07-02 14:06:48 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Make the multi-chicken colours a touch brighter. ------------------------------------------------------------------------ r1196 | pemsley | 2008-07-02 14:01:03 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add multi-chicken (lots of maps with chickenwire representation). ------------------------------------------------------------------------ r1195 | pemsley | 2008-07-02 13:32:55 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer-tables.cc More cleanups of debugging rotamer-tables usage. ------------------------------------------------------------------------ r1194 | pemsley | 2008-07-02 13:27:56 +0100 (Wed, 02 Jul 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1193 | pemsley | 2008-07-02 13:24:34 +0100 (Wed, 02 Jul 2008) | 4 lines Changed paths: M /trunk/AUTHORS M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/ligand/Makefile.am M /trunk/ligand/monomer-utils.cc A /trunk/ligand/rotamer-tables.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Several changes to add rotamer probability plots. There is a self-test of the probabilities that is run as on construction. New codes goes into rotamer-tables.cc, rather than rotamer.cc ------------------------------------------------------------------------ r1192 | pemsley | 2008-07-01 19:55:09 +0100 (Tue, 01 Jul 2008) | 2 lines Changed paths: M /trunk/ligand/chi-angles.cc Fix typo in for OD1 in chi angle definition. ------------------------------------------------------------------------ r1191 | b.lohkamp | 2008-07-01 13:27:50 +0100 (Tue, 01 Jul 2008) | 4 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/python/coot_utils.py A /trunk/python/unittest_extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/Makefile.am A /trunk/python-tests/begin.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc updated python unittests reorganisation of python unittest, added unittest_extension to run one python test, a whole set of tests or all tests ------------------------------------------------------------------------ r1190 | pemsley | 2008-07-01 00:35:15 +0100 (Tue, 01 Jul 2008) | 2 lines Changed paths: A /trunk/rama-data/Makefile.am Add the Makefile.am for rama-data (sigh). ------------------------------------------------------------------------ r1189 | pemsley | 2008-06-30 15:55:58 +0100 (Mon, 30 Jun 2008) | 6 lines Changed paths: M /trunk/Makefile.am M /trunk/atom-utils/Makefile.am M /trunk/atom-utils/atom-utils.cc M /trunk/configure.in M /trunk/dnotes M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/sequence-view/Makefile.am M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.h More updates to rotamer probability. We now read them into Coot on start-up. Rotamer probabilites added to dist tar file. Canonicalize include in atom-utils and sequence-view (hopefully now it will not try to use *installed* include files when it should be reading local ones. ------------------------------------------------------------------------ r1188 | pemsley | 2008-06-30 15:41:11 +0100 (Mon, 30 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1187 | pemsley | 2008-06-30 14:29:51 +0100 (Mon, 30 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ideal/simple-restraint.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Throw exception on reading the rotamer probability tables. ------------------------------------------------------------------------ r1186 | pemsley | 2008-06-30 14:00:34 +0100 (Mon, 30 Jun 2008) | 3 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h Change fix_hydrogen_names() to fix_wrapped_names() so we can fix atoms other than Hs (e.g. Os). ------------------------------------------------------------------------ r1185 | b.lohkamp | 2008-06-27 12:39:25 +0100 (Fri, 27 Jun 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/mutate.py M /trunk/python/tips.py M /trunk/python/tips_gui.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h lots of new python functions (build in and script); all scripts up to date!? fixed memory (reference counting) problem for Py_False and Py_True (hopefully) ------------------------------------------------------------------------ r1184 | pemsley | 2008-06-26 17:37:59 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/restraints-editor.cc M /trunk/src/restraints-editor.hh Add function write_restraints_cif_dictinary(). ------------------------------------------------------------------------ r1183 | pemsley | 2008-06-26 16:23:43 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm D /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot.scm loop fitting updates. ------------------------------------------------------------------------ r1182 | pemsley | 2008-06-26 16:10:12 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm more updates to a-rapper-gui ------------------------------------------------------------------------ r1181 | kevin.cowtan | 2008-06-26 12:41:53 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/src/xmap-utils.cc Fix for map sigma level calculation (use doubles for summation) ------------------------------------------------------------------------ r1180 | pemsley | 2008-06-26 09:27:36 +0100 (Thu, 26 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Read all the rotamer tables and add them to rotamer_probability_tables tables. ------------------------------------------------------------------------ r1179 | pemsley | 2008-06-26 07:44:02 +0100 (Thu, 26 Jun 2008) | 3 lines Changed paths: M /trunk/ligand/rotamer.cc Add stub functions for fill_chi_1_2_3 and fill_chi_1_2_3_4, so that this compiles with GCC 3.2. ------------------------------------------------------------------------ r1178 | pemsley | 2008-06-25 23:19:02 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/ligand/test-ligand.cc Partial updates for adding Molprobity rotamer probability tables. ------------------------------------------------------------------------ r1177 | pemsley | 2008-06-25 23:15:26 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/03-ligand.scm trivial typo fix. ------------------------------------------------------------------------ r1176 | pemsley | 2008-06-25 21:52:50 +0100 (Wed, 25 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/arp-warp-xml.scm M /trunk/src/c-interface-build.cc GUI for ARP/wARP loopy improved. replace_fragment() now correctly quotes its string in the history. ------------------------------------------------------------------------ r1175 | pemsley | 2008-06-25 17:28:29 +0100 (Wed, 25 Jun 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/refmac.scm M /trunk/src/c-interface-info.cc Add SCM and scheme code (get-refmac-version) needed to get no-labels Refmac to work. ------------------------------------------------------------------------ r1174 | pemsley | 2008-06-25 14:14:27 +0100 (Wed, 25 Jun 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add carbohdrate refinement info. ------------------------------------------------------------------------ r1173 | pemsley | 2008-06-24 19:45:26 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/ligand/rotamer.hh Tinker with some code for rotamer probabilites. ------------------------------------------------------------------------ r1172 | pemsley | 2008-06-24 18:15:05 +0100 (Tue, 24 Jun 2008) | 3 lines Changed paths: M /trunk/configure.in M /trunk/macros/net-http-goosh.m4 Guile-lib is added as an extra dependency (sorry Bill :). Add a macro to test for it at configure time. ------------------------------------------------------------------------ r1171 | b.lohkamp | 2008-06-24 14:59:26 +0100 (Tue, 24 Jun 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c display skipped tests update references for About dialog clean callback.c (GTK_MAJOR_VERSION around each function) ------------------------------------------------------------------------ r1170 | pemsley | 2008-06-24 14:26:41 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/scheme/arp-warp-xml.scm Fix more types in loops-to-build line. Still loopy does not like it though. ------------------------------------------------------------------------ r1169 | pemsley | 2008-06-24 13:58:47 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/arp-warp-xml.scm Fix type in loops-to-build arg. ------------------------------------------------------------------------ r1168 | pemsley | 2008-06-24 13:56:21 +0100 (Tue, 24 Jun 2008) | 11 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils-nucleotides.cc M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/ideal-rna.cc M /trunk/ligand/test-ligand.cc M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/coot.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc If user specifies t in RNA, skip that residue (I will come back to make this better later). Add some starting code to test-ligand.cc to read rotamer probabilities. Add and execute test and build for guile-lib to build-its. Add a function to return the ccp4i projects to the SCM level. Add the loading of arp-warp-xml.scm, this will fail if guile-lib is not in place. Move nucleotide functions into the correct c-interfaces files. Correct map_cell_scm(), and its molecule-class-info function. Update diary. ------------------------------------------------------------------------ r1167 | pemsley | 2008-06-24 01:36:44 +0100 (Tue, 24 Jun 2008) | 7 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c fill_references_notebook argument corrected, together with GTK2 interface usage. map_parameters_scm() and map_cell_scm() function introduced initially for ARP/wARP inteface usage. Add guile-lib to build-it-gtk2-simple. Update diary. ------------------------------------------------------------------------ r1166 | pemsley | 2008-06-24 01:33:52 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am Add arp-warp interface to XML file. ------------------------------------------------------------------------ r1165 | pemsley | 2008-06-24 01:32:56 +0100 (Tue, 24 Jun 2008) | 2 lines Changed paths: A /trunk/scheme/arp-warp-xml.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Add ARP/wARP XML interface - first draft. ------------------------------------------------------------------------ r1164 | pemsley | 2008-06-23 17:34:58 +0100 (Mon, 23 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1163 | pemsley | 2008-06-23 17:34:37 +0100 (Mon, 23 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add map transformation by LSQ model fit to the Extensions menu. Tidy it up a bit. ------------------------------------------------------------------------ r1162 | pemsley | 2008-06-23 15:23:08 +0100 (Mon, 23 Jun 2008) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Move functions for alignment/mutate into GUI and mutate source files (from build). Fix up align_on_chain() function. ------------------------------------------------------------------------ r1161 | pemsley | 2008-06-23 15:20:08 +0100 (Mon, 23 Jun 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/04-cootaneer.scm M /trunk/greg-tests/begin.grg factor out file->string function. Add test for align and mutate. ------------------------------------------------------------------------ r1160 | b.lohkamp | 2008-06-21 14:40:38 +0100 (Sat, 21 Jun 2008) | 1 line Changed paths: M /trunk/build-it-win fixes for windows build ------------------------------------------------------------------------ r1159 | pemsley | 2008-06-21 02:12:17 +0100 (Sat, 21 Jun 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/scheme/coot-utils.scm Update dnotes and todo. Move Centos build to 0.6. ------------------------------------------------------------------------ r1158 | pemsley | 2008-06-21 01:57:20 +0100 (Sat, 21 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.h Update theMapContours display list when the map is not displayed. ------------------------------------------------------------------------ r1157 | pemsley | 2008-06-20 23:44:33 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Don't do 2 backups for an eigen flip. ------------------------------------------------------------------------ r1156 | b.lohkamp | 2008-06-20 23:06:43 +0100 (Fri, 20 Jun 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h A /trunk/src/coot-references.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/post-glade M /trunk/src/support-gtk2-extras.c M /trunk/src/support.c python gui: protect build-in functions from being overwritten add References dialog to About dialog (and fixed icon) ------------------------------------------------------------------------ r1155 | pemsley | 2008-06-20 22:16:25 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple One more go at getting the logic of testing/prerelease correct. ------------------------------------------------------------------------ r1154 | b.lohkamp | 2008-06-20 19:10:49 +0100 (Fri, 20 Jun 2008) | 1 line Changed paths: M /trunk/src/density-score-by-residue.cc move stdlib.h (Windows compile error) ------------------------------------------------------------------------ r1153 | pemsley | 2008-06-20 17:16:06 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1152 | pemsley | 2008-06-20 16:50:18 +0100 (Fri, 20 Jun 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2-simple M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add display on/off functionality for Ball and Stick additional reps. Changed display list handle container from a list to a vector. ------------------------------------------------------------------------ r1151 | pemsley | 2008-06-20 13:53:08 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Adjust the settings of running the tests again. ------------------------------------------------------------------------ r1150 | pemsley | 2008-06-20 02:13:20 +0100 (Fri, 20 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes Don't run the tests if not in york or biop. ------------------------------------------------------------------------ r1149 | pemsley | 2008-06-19 23:33:08 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/coot-close.cc M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/find-waters.cc M /trunk/ligand/ligand.cc M /trunk/ligand/rotamer.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/mol-hierachy.cc Add the ability to rotamer MSEs, by adding a function that adds extra contacts if the residue type is MSE (mmdb-extras.cc). ------------------------------------------------------------------------ r1148 | pemsley | 2008-06-19 17:19:32 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc Add use_graphics_interface_flag protection to graphics_draw() in set_display_lists_for_maps(). ------------------------------------------------------------------------ r1147 | pemsley | 2008-06-19 13:44:38 +0100 (Thu, 19 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/density-score-by-residue.cc M /trunk/src/fix-nomenclature.cc M /trunk/src/gtk-manual.cc Further updates for 4.3, use of stdlib.h and string.h ------------------------------------------------------------------------ r1146 | pemsley | 2008-06-19 13:42:19 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/mutate.scm Updates to rapper GUI. Export 3 letter-code -> char for use by rapper gui. ------------------------------------------------------------------------ r1145 | pemsley | 2008-06-19 13:01:00 +0100 (Thu, 19 Jun 2008) | 3 lines Changed paths: M /trunk/src/c-inner-main.c M /trunk/src/c-interface.cc From JED valgrind log, add an extra char for null termination of strings added to the preferences dir string. ------------------------------------------------------------------------ r1144 | b.lohkamp | 2008-06-19 09:45:38 +0100 (Thu, 19 Jun 2008) | 1 line Changed paths: M /trunk/scheme/ncs.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/post-gtk2-glade.sh revision in About dialog ------------------------------------------------------------------------ r1143 | pemsley | 2008-06-18 18:39:21 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple As per JED request, number the build logs in a more sensible way. ------------------------------------------------------------------------ r1142 | b.lohkamp | 2008-06-18 16:41:23 +0100 (Wed, 18 Jun 2008) | 4 lines Changed paths: M /trunk/python/ncs.py M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/post-gtk2-glade.sh fixed 'o' button in python builds include revision (and python) in About dialog (GTK2) removed bug on windows' backup_maybe() ------------------------------------------------------------------------ r1141 | pemsley | 2008-06-18 16:22:48 +0100 (Wed, 18 Jun 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Update dnotes (comment out debugging). ------------------------------------------------------------------------ r1140 | pemsley | 2008-06-18 16:21:42 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add links to python test log files. ------------------------------------------------------------------------ r1139 | b.lohkamp | 2008-06-18 12:07:17 +0100 (Wed, 18 Jun 2008) | 1 line Changed paths: M /trunk/python-tests/01_pdb_mtz.py fixed CIS pep test for missing pdb file ------------------------------------------------------------------------ r1138 | pemsley | 2008-06-18 08:59:15 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh Fix up typo, USE_PYTHON not USE_GUILE. ------------------------------------------------------------------------ r1137 | pemsley | 2008-06-18 03:00:53 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes rearrange todo list for 0.5 ------------------------------------------------------------------------ r1136 | pemsley | 2008-06-18 02:44:14 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc own_molecule_number() should also check for valid map molecule. ------------------------------------------------------------------------ r1135 | pemsley | 2008-06-18 02:42:26 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm Active the molecule number test. ------------------------------------------------------------------------ r1134 | pemsley | 2008-06-18 02:38:37 +0100 (Wed, 18 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update the distribution of readline. ------------------------------------------------------------------------ r1133 | b.lohkamp | 2008-06-17 22:29:49 +0100 (Tue, 17 Jun 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh more python functions, e.g. residues_near_residue_py ------------------------------------------------------------------------ r1132 | pemsley | 2008-06-17 17:47:22 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/AUTHORS Add Bernhard to the Authors. ------------------------------------------------------------------------ r1131 | b.lohkamp | 2008-06-17 15:40:05 +0100 (Tue, 17 Jun 2008) | 5 lines Changed paths: M /trunk/python/generic_objects.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc all python unittest output to stdout pygtk button to show/hide all generic objects bug fix in generic_object_name_py (PYTHON BUG, not mine) side-by-side stereo -> mono resizes window to half width (GTK2) ------------------------------------------------------------------------ r1130 | pemsley | 2008-06-17 14:11:45 +0100 (Tue, 17 Jun 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Fix up hydrogens/glycosidic test typo. Throw fail if no monomer restraints in update monomer restraints test. ------------------------------------------------------------------------ r1129 | pemsley | 2008-06-17 13:55:09 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix glycosidic link test. ------------------------------------------------------------------------ r1128 | pemsley | 2008-06-17 05:14:37 +0100 (Tue, 17 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update to guile-1.8.5 ------------------------------------------------------------------------ r1127 | pemsley | 2008-06-16 08:49:43 +0100 (Mon, 16 Jun 2008) | 4 lines Changed paths: M /trunk/greg-tests/08-utils.scm Add begin round extra python command tests (funny, this didn't fail on some other machines). ------------------------------------------------------------------------ r1126 | pemsley | 2008-06-16 01:43:17 +0100 (Mon, 16 Jun 2008) | 10 lines Changed paths: M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/begin.grg M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/src/graphics-info.cc Tinkerings with a-rapper-gui.scm - it runs rapper now at least and reads in output pdb file. Add python key bindings to the key bindings GUI. Add atom-match? to begin.grg. Add a tuple test to run-python-command. Add a replace-fragement test. Do not display hydrogen atoms in the intermediate atoms in refinement if they are not displayed in the "static" atoms. Update dnotes. ------------------------------------------------------------------------ r1125 | b.lohkamp | 2008-06-15 13:41:13 +0100 (Sun, 15 Jun 2008) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/08_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc fixed skip in unittest ------------------------------------------------------------------------ r1124 | pemsley | 2008-06-15 12:36:11 +0100 (Sun, 15 Jun 2008) | 4 lines Changed paths: M /trunk/src/c-interface.cc py_clean_internal() could return NULL, resulting in run_python_command() receiving a NULL, thus crashing. Fixed (converted to Py_None). Test added. ------------------------------------------------------------------------ r1123 | pemsley | 2008-06-15 01:41:10 +0100 (Sun, 15 Jun 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm do_colour_by_molecule_bonds() updated to add zero occupancy spots. Document flip ligand. Add "ca-trace" to rapper args. Add coot-news-info. ------------------------------------------------------------------------ r1122 | pemsley | 2008-06-13 15:48:55 +0100 (Fri, 13 Jun 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-defines.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Fix up add-c-extern.sh to add semicolons. Fixed atom click handling checks for a fixed atom dialog before using it. Fixed atoms added for Gtk1. Release notes, diary, TODO updated. ------------------------------------------------------------------------ r1121 | pemsley | 2008-06-13 09:58:16 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1120 | pemsley | 2008-06-13 09:56:41 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Test for SHELXL waters being added to a new chain. ------------------------------------------------------------------------ r1119 | pemsley | 2008-06-13 09:54:27 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/src/globjects.cc Make the initial bond parameters molecule number invalid, so that wrapped_create_bond_parameters_dialog() no longer fails at start. ------------------------------------------------------------------------ r1118 | pemsley | 2008-06-13 09:32:06 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Rename the residue if the residue names don't match in copy_residue_range() for ncs fragments. ------------------------------------------------------------------------ r1117 | pemsley | 2008-06-13 09:30:38 +0100 (Fri, 13 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add mutate residue test to NCS copy region test. ------------------------------------------------------------------------ r1116 | b.lohkamp | 2008-06-13 09:30:35 +0100 (Fri, 13 Jun 2008) | 3 lines Changed paths: M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/Makefile.am M /trunk/python-tests/coot_unittest.py M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-render.cc more unittests, add coot_unittest to Makefile.am some improvements to povray ------------------------------------------------------------------------ r1115 | pemsley | 2008-06-12 23:10:58 +0100 (Thu, 12 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/ncs.scm M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix the the apply_ncs_to_view_orientation function in the case of NCS with a heterodimer (fixes Phil's problem?) ------------------------------------------------------------------------ r1114 | pemsley | 2008-06-12 21:35:35 +0100 (Thu, 12 Jun 2008) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/gdk-keysym.awk M /trunk/coot-utils/gdk-keysyms.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/begin.grg M /trunk/scheme/ncs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-nucleotides.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Add draw_ncs_ghost_state() function. Add has-term-atom? function to begin.grg, used to test if a residue has a TER record. TER records are removed from C-terminii on adding a terminal residue. Need to update terminal residue addition test pdb. Add non-alpha-numeric key codes. Extra key code tests. Add test for residues near residue. ------------------------------------------------------------------------ r1113 | pemsley | 2008-06-12 00:51:24 +0100 (Thu, 12 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add "pukka puckers?" gui to the validation menu. ------------------------------------------------------------------------ r1112 | b.lohkamp | 2008-06-11 17:12:35 +0100 (Wed, 11 Jun 2008) | 1 line Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple python test only run if build with python ------------------------------------------------------------------------ r1111 | b.lohkamp | 2008-06-11 17:02:54 +0100 (Wed, 11 Jun 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/graphics-info-render.cc better povray clipping and avoid view angles > 180 python testing in build-it and build-it-gtk2-simple ------------------------------------------------------------------------ r1110 | b.lohkamp | 2008-06-11 15:07:43 +0100 (Wed, 11 Jun 2008) | 4 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python/coot_utils.py M /trunk/python/generic_objects.py M /trunk/python/group_settings.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc python molprobity fixes fix empty residue type selection returning valid imol, but not valid molecule test for empty residue type selection (python/scheme) ------------------------------------------------------------------------ r1109 | b.lohkamp | 2008-06-10 12:38:51 +0100 (Tue, 10 Jun 2008) | 1 line Changed paths: M /trunk/build-it-win M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info.h fix for font in sequence view and CCP4 directory in file selection ------------------------------------------------------------------------ r1108 | pemsley | 2008-06-10 08:20:14 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Adjust these closing of maps in the shelx tests. ------------------------------------------------------------------------ r1107 | pemsley | 2008-06-10 08:14:58 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-waters.cc Add bad model and map protection. ------------------------------------------------------------------------ r1106 | pemsley | 2008-06-10 02:00:15 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: A /trunk/coot-utils/coot-coord-utils-nucleotides.cc A /trunk/src/c-interface-nucleotides.cc Add missing files. ------------------------------------------------------------------------ r1105 | pemsley | 2008-06-10 01:58:47 +0100 (Tue, 10 Jun 2008) | 9 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot-align.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add pucker analysis (at a deep level, scripting but not GUI). Add function to convert to a residue_spec_t from a SCM object. Start throwing exceptions. c-interface-nucleotides.cc coot-coord-utils-nucleotides.cc introduced. On addition of waters (find-waters) to a shelx molecule, set the atom occupancy to 11.0 Make a function get_following_residue() (c.f. get_residue()). utils lsq_plane_deviation now returns the rms deviation of the plane too. ------------------------------------------------------------------------ r1104 | pemsley | 2008-06-10 01:52:44 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-waters.cc Add no graphics protection. ------------------------------------------------------------------------ r1103 | pemsley | 2008-06-10 01:51:45 +0100 (Tue, 10 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/begin.grg Add test for adding waters to shelx molecule. Factor out shelxl water test. ------------------------------------------------------------------------ r1102 | pemsley | 2008-06-09 17:35:12 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc Move reset_view(). ------------------------------------------------------------------------ r1101 | b.lohkamp | 2008-06-09 17:32:35 +0100 (Mon, 09 Jun 2008) | 1 line Changed paths: M /trunk/python/coot_utils.py M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h removable glob extensions; fix font width in seq view fixed?! ------------------------------------------------------------------------ r1100 | pemsley | 2008-06-09 17:27:45 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Add restraint updating test. ------------------------------------------------------------------------ r1099 | pemsley | 2008-06-09 17:25:01 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update release notes. ------------------------------------------------------------------------ r1098 | pemsley | 2008-06-09 17:24:00 +0100 (Mon, 09 Jun 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Fix typo. ------------------------------------------------------------------------ r1097 | b.lohkamp | 2008-06-09 14:52:14 +0100 (Mon, 09 Jun 2008) | 6 lines Changed paths: M /trunk/build-it-win M /trunk/ligand/test-helix-placement.cc M /trunk/python/refmac.py M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c ligand/test-helix-placement.cc src/c-interface.cc src/c-interface-validate.cc src/callbacks.c build-it-win ------------------------------------------------------------------------ r1096 | pemsley | 2008-06-08 23:46:50 +0100 (Sun, 08 Jun 2008) | 3 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for applying sequence info in Add Terminal Residue and reading in the pdb file after it has had hydrogens added. ------------------------------------------------------------------------ r1095 | pemsley | 2008-06-07 14:20:19 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add hilighting function - using residues-near-residue. ------------------------------------------------------------------------ r1094 | pemsley | 2008-06-07 14:19:24 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r1093 | pemsley | 2008-06-07 14:18:55 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Notes for simple build-it. ------------------------------------------------------------------------ r1092 | pemsley | 2008-06-07 14:17:33 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add show hydrogens state function. ------------------------------------------------------------------------ r1091 | pemsley | 2008-06-07 14:15:12 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Update smooth recentering documentation. ------------------------------------------------------------------------ r1090 | pemsley | 2008-06-07 09:41:44 +0100 (Sat, 07 Jun 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Bump up the version of Python to 2.5.2 ------------------------------------------------------------------------ r1089 | pemsley | 2008-06-06 23:07:51 +0100 (Fri, 06 Jun 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h In active_atom_spec(), pick only atoms that are pickable. ------------------------------------------------------------------------ r1088 | pemsley | 2008-06-06 21:21:25 +0100 (Fri, 06 Jun 2008) | 2 lines Changed paths: A /trunk/rama-data A /trunk/rama-data/rama500-general.data A /trunk/rama-data/rama500-gly-sym.data A /trunk/rama-data/rama500-prepro.data A /trunk/rama-data/rama500-pro.data A /trunk/rama-data/rota500-arg.data A /trunk/rama-data/rota500-asn.data A /trunk/rama-data/rota500-asp.data A /trunk/rama-data/rota500-cys.data A /trunk/rama-data/rota500-gln.data A /trunk/rama-data/rota500-glu.data A /trunk/rama-data/rota500-his.data A /trunk/rama-data/rota500-ile.data A /trunk/rama-data/rota500-leu.data A /trunk/rama-data/rota500-lys.data A /trunk/rama-data/rota500-met.data A /trunk/rama-data/rota500-phetyr.data A /trunk/rama-data/rota500-pro.data A /trunk/rama-data/rota500-ser.data A /trunk/rama-data/rota500-thr.data A /trunk/rama-data/rota500-trp.data A /trunk/rama-data/rota500-val.data Add rotamer probabilities from Molprobity. ------------------------------------------------------------------------ r1087 | pemsley | 2008-06-05 17:41:57 +0100 (Thu, 05 Jun 2008) | 3 lines Changed paths: M /trunk/scheme/shelx-extensions.scm Update, by adding a filter function the use of generic-chooser-and-file-selection in shelx-extensions.scm. ------------------------------------------------------------------------ r1086 | pemsley | 2008-06-05 14:14:03 +0100 (Thu, 05 Jun 2008) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-extras.cc M /trunk/coot-surface/rgbreps.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/test-utils.cc M /trunk/cootaneer/buccaneer-prot.cpp M /trunk/cootaneer/cootaneer-sequence.cpp M /trunk/db-main/db-main.cc M /trunk/db-main/testdbmain.cc M /trunk/db-main/train-pepflip.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/test-geometry.cc M /trunk/high-res/globularize.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/test-ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/skeleton/BuildCas.cc M /trunk/surface/CXXFortranFile.cpp Small fixes from porting to GCC 4.3. Fixes sort(),reverse()/algorithm, abs() no longer returns an int - now use stdlib.h and labs(). atof()/stdlib, strcp and other string functions in string.h, ------------------------------------------------------------------------ r1085 | pemsley | 2008-06-05 12:33:58 +0100 (Thu, 05 Jun 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Change default number of step on smooth scrolling from 80 to 40. ------------------------------------------------------------------------ r1084 | pemsley | 2008-06-05 04:11:40 +0100 (Thu, 05 Jun 2008) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/test-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Sort chains function added coot util, but deleting chain causes crash. Sort chains test added but not used yet. Residues near residue function added. Add c-interface.h documentation for delete_checked_waters_baddies(). Documentation for raster3d bones. ------------------------------------------------------------------------ r1083 | pemsley | 2008-06-02 10:31:19 +0100 (Mon, 02 Jun 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Properly pad the UNIT line with 0s to the size of the SFAC line. ------------------------------------------------------------------------ r1082 | pemsley | 2008-06-01 18:00:28 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-build.cc Go To Atom dialog is properly updated on merging molecules. ------------------------------------------------------------------------ r1081 | pemsley | 2008-06-01 17:16:28 +0100 (Sun, 01 Jun 2008) | 4 lines Changed paths: M /trunk/scheme/generic-objects.scm M /trunk/src/molecule-class-info-mutate.cc Add a user variable reduce-molecule-updates-current, that when set makes the output of reduce overwrite the probed molecule (not create a new one). ------------------------------------------------------------------------ r1080 | pemsley | 2008-06-01 17:13:55 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Put the SFAC line before the UNIT line in shelxl output. ------------------------------------------------------------------------ r1079 | pemsley | 2008-06-01 12:36:11 +0100 (Sun, 01 Jun 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-mutate.cc Remember the scroll wheel map in the state file. Don't monkey with the alignment score (now back to defaults and alignment gets both (test) N an C term alignment correct). ------------------------------------------------------------------------ r1078 | pemsley | 2008-06-01 11:34:08 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Add to the state file, the setting for the refinement map. ------------------------------------------------------------------------ r1077 | pemsley | 2008-06-01 03:57:41 +0100 (Sun, 01 Jun 2008) | 10 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/coot-align.cc M /trunk/src/coot-align.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Add function to set the scroll wheel map. Add functions to print a residue spec, and to compare residue specs. Extend alignment class to add insertions at the C terminus. Add code to get the terminal residue type by sequence alignment. Change from char *get_pkgdatadir() to PyObject *get_pkgdatadir_py(), fixes a bug. Added find_terminal_residue_type() function used for testing. Change the default graphics_info_t::add_terminal_residue_type from "ALA" to "auto". ------------------------------------------------------------------------ r1076 | pemsley | 2008-06-01 03:52:08 +0100 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm add shelx-extensions.scm to installed files. ------------------------------------------------------------------------ r1075 | pemsley | 2008-06-01 03:51:10 +0100 (Sun, 01 Jun 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py Take out verbiage on key pressing, but not found in python list. add get_pkgdatadir() redefinition. ------------------------------------------------------------------------ r1074 | pemsley | 2008-05-29 22:57:08 +0100 (Thu, 29 May 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Enable double clicking to label for symmetry atoms. ------------------------------------------------------------------------ r1073 | pemsley | 2008-05-28 19:48:00 +0100 (Wed, 28 May 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Fix change of drawing style on modifying a molecule in CA+ligs representation. ------------------------------------------------------------------------ r1072 | pemsley | 2008-05-28 19:04:20 +0100 (Wed, 28 May 2008) | 7 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/03-ligand.scm M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add flip-ligand function. Should be bound to a key. Added test for above. Fixed extra parameters to additional represenations in the state file. Fix up the GUI reading for ball and stick add reps. molecule-number-list updated to use range. update dnotes and TODO. ------------------------------------------------------------------------ r1071 | pemsley | 2008-05-28 14:29:05 +0100 (Wed, 28 May 2008) | 3 lines Changed paths: M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/08-utils.scm skip the molecule number test for now - Hmm.. In the ligand test, don't make 50 copies any more - make 5. ------------------------------------------------------------------------ r1070 | pemsley | 2008-05-27 18:40:58 +0100 (Tue, 27 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h own_molecule_number() introduced for testing consistency of internal and external molecule numbers. ------------------------------------------------------------------------ r1069 | pemsley | 2008-05-27 18:39:49 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Some notes for baton building. ------------------------------------------------------------------------ r1068 | pemsley | 2008-05-27 18:39:13 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Tidy up SCM usage. ------------------------------------------------------------------------ r1067 | pemsley | 2008-05-27 18:36:56 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/TODO More TODOs. ------------------------------------------------------------------------ r1066 | pemsley | 2008-05-27 18:36:03 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/dnotes upate dnotes. ------------------------------------------------------------------------ r1065 | pemsley | 2008-05-27 17:53:58 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/08-utils.scm Add molecule number consistency test at teh end of utils section. ------------------------------------------------------------------------ r1064 | pemsley | 2008-05-27 16:27:17 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Increase the vertical size of the atoms window in residue info dialog. ------------------------------------------------------------------------ r1063 | pemsley | 2008-05-27 16:15:26 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/graphics-info-superpose.cc Re-order TODO list. ------------------------------------------------------------------------ r1062 | pemsley | 2008-05-27 16:14:16 +0100 (Tue, 27 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface-superpose.cc Add a menu to the chain option menu in superpose dialog, so that we don't get "gtk_menu_get_active: assertion `GTK_IS_MENU (menu)' failed" ------------------------------------------------------------------------ r1061 | pemsley | 2008-05-27 16:12:22 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add flying hydrogens post-undo test. ------------------------------------------------------------------------ r1060 | pemsley | 2008-05-27 16:10:55 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm Some more progress on rapper gui. Doesn't work yet - problem with params.xml ------------------------------------------------------------------------ r1059 | pemsley | 2008-05-27 16:10:06 +0100 (Tue, 27 May 2008) | 2 lines Changed paths: M /trunk/doc/tutorial.tex Fix typo in skeletonization docs. ------------------------------------------------------------------------ r1058 | pemsley | 2008-05-26 11:19:34 +0100 (Mon, 26 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/geometry-graphs.cc Punt the smooth icon rendering. ------------------------------------------------------------------------ r1057 | b.lohkamp | 2008-05-25 17:32:40 +0100 (Sun, 25 May 2008) | 1 line Changed paths: M /trunk/src/graphics-info-superpose.cc fixed doublication of imol in SSM superpose ------------------------------------------------------------------------ r1056 | pemsley | 2008-05-22 17:15:02 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm New glycosidic bond test (new test pdb file). ------------------------------------------------------------------------ r1055 | pemsley | 2008-05-22 17:14:30 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Correct fix for A-L.cif (etc) file reading from monomer library. ------------------------------------------------------------------------ r1054 | pemsley | 2008-05-22 16:10:18 +0100 (Thu, 22 May 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.cc Try to read A-L.cif if a-L.cif fails. Same for B-D.cif and b-D.cif. Does this fix the glyosidic bond test? ------------------------------------------------------------------------ r1053 | pemsley | 2008-05-22 11:24:47 +0100 (Thu, 22 May 2008) | 3 lines Changed paths: M /trunk/src/restraints-editor.cc Fix up error reading plane restraints when there are plane restraints with different number of atoms. ------------------------------------------------------------------------ r1052 | pemsley | 2008-05-22 00:13:42 +0100 (Thu, 22 May 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix typo in status file name. ------------------------------------------------------------------------ r1051 | pemsley | 2008-05-21 15:58:55 +0100 (Wed, 21 May 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Update build analysis page to get correct tar files (fixes bug on introduction of bins links from WinCoot build). ------------------------------------------------------------------------ r1050 | pemsley | 2008-05-21 14:34:59 +0100 (Wed, 21 May 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add representation_type arg to addition_representation_args (so that we can specify ball and stick, simple lines, etc). ------------------------------------------------------------------------ r1049 | pemsley | 2008-05-20 20:39:28 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r1048 | pemsley | 2008-05-20 20:33:51 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r1047 | pemsley | 2008-05-20 17:25:20 +0100 (Tue, 20 May 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/src/molecule-class-info.cc Use write_atom_selection_file() not atom_sel.mol->WritePDBASCII() in make_backup(). Fixes problem of renaming hydrogens on undo. ------------------------------------------------------------------------ r1046 | pemsley | 2008-05-20 10:03:22 +0100 (Tue, 20 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Add bond length test for glycosidic linkage. ------------------------------------------------------------------------ r1045 | pemsley | 2008-05-19 14:29:58 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Change the distance for finding glycosidic linkage to 3.0A. ------------------------------------------------------------------------ r1044 | b.lohkamp | 2008-05-19 13:29:54 +0100 (Mon, 19 May 2008) | 1 line Changed paths: M /trunk/python/refmac.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.cc python scripting for refmac NCS and rigid body groups ------------------------------------------------------------------------ r1043 | pemsley | 2008-05-19 12:19:41 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm Revert coot-crash-catcher.scm to how it used to be. ------------------------------------------------------------------------ r1042 | pemsley | 2008-05-19 08:06:37 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/dnotes Resolve updates. ------------------------------------------------------------------------ r1041 | pemsley | 2008-05-19 07:40:33 +0100 (Mon, 19 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Markup in progress build-result in grey. ------------------------------------------------------------------------ r1040 | pemsley | 2008-05-19 07:19:05 +0100 (Mon, 19 May 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info.cc Additional representations frame is not shown if there are no add reps. Additional representations frame dynamically updated and shown on addition of a add rep. Fix crash on pressing space with no molecules shown. Recentre on reading a shelx molecule. ------------------------------------------------------------------------ r1039 | pemsley | 2008-05-19 06:23:28 +0100 (Mon, 19 May 2008) | 3 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-gui.scm Add ARP/wARP interface to the loop builder (not filled yet). Add transform-map-using-lsq-matrix-gui. ------------------------------------------------------------------------ r1038 | pemsley | 2008-05-18 13:16:28 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Update the build and test status, so that we can tell the difference between an in-progress build and a failed build. ------------------------------------------------------------------------ r1037 | pemsley | 2008-05-18 09:50:45 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/callbacks.c M /trunk/src/molecule-class-info.cc Don't delete the menu in fill_place_atom_molecule_option_menu() if the menu is null (as it always is for GTK2, I think). ------------------------------------------------------------------------ r1036 | pemsley | 2008-05-18 09:39:51 +0100 (Sun, 18 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r1035 | pemsley | 2008-05-18 09:38:00 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info.cc Updates to get the correct residue number and SFAC when a new atom is added to a shelx molecule. ------------------------------------------------------------------------ r1034 | pemsley | 2008-05-18 09:36:24 +0100 (Sun, 18 May 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Updates for handling SFAC updates when a new atom type is introduced into a shelx molecule. ------------------------------------------------------------------------ r1033 | b.lohkamp | 2008-05-15 16:32:15 +0100 (Thu, 15 May 2008) | 8 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/refmac.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc M /trunk/src/cmtz-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h added some new python extensions fixed selection of molecules in python coot_gui fixed crash if HOME had "/" at the end new refmac GUI (for gtk2): - refinement options - phase combination with phi&fom and hl (only works for python currently) - NCS button (needs to made functional...) ------------------------------------------------------------------------ r1032 | pemsley | 2008-05-14 23:16:09 +0100 (Wed, 14 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add no-graphics protection to set_display_lists_for_maps(). ------------------------------------------------------------------------ r1031 | pemsley | 2008-05-14 05:11:28 +0100 (Wed, 14 May 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/simple-restraint.cc M /trunk/ligand/chi-angles.cc M /trunk/ligand/ideal-rna.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h The torsion angles are better handled now, incorporating the correct handling of const angles in edit chi. And maybe wiggly ligands too. Investigation/debugging add to ideal nucleic acids. Clear Ball&Stick added to Extensions. Update validation graphs on delete water and residue. ------------------------------------------------------------------------ r1030 | pemsley | 2008-05-13 07:17:07 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm map-sigma wrapper. ------------------------------------------------------------------------ r1029 | pemsley | 2008-05-13 07:12:57 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/generic-objects.scm Use -oldbpdb arg when running reduce. ------------------------------------------------------------------------ r1028 | pemsley | 2008-05-13 07:11:40 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/scheme/povray.scm update to povray 3.6 (actually, make it user-setable now). ------------------------------------------------------------------------ r1027 | pemsley | 2008-05-13 06:55:36 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add map sigma test. ------------------------------------------------------------------------ r1026 | pemsley | 2008-05-13 06:31:05 +0100 (Tue, 13 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix problem of messing with display lists when not using graphics (found from running tests on a mac). ------------------------------------------------------------------------ r1025 | pemsley | 2008-05-13 05:37:44 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.h Add map_sigma() function (combined with previous commit). ------------------------------------------------------------------------ r1024 | pemsley | 2008-05-13 05:36:52 +0100 (Tue, 13 May 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add no graphics protection to set_background_colour(). ------------------------------------------------------------------------ r1023 | pemsley | 2008-05-12 21:12:01 +0100 (Mon, 12 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix ups to get the url of the WinCoot binary correct. ------------------------------------------------------------------------ r1022 | pemsley | 2008-05-12 01:15:10 +0100 (Mon, 12 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Updates to find bernhard's WinCoot binary builds. ------------------------------------------------------------------------ r1021 | b.lohkamp | 2008-05-09 10:24:37 +0100 (Fri, 09 May 2008) | 1 line Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc more windows directory/backup fixes ------------------------------------------------------------------------ r1020 | b.lohkamp | 2008-05-08 10:03:14 +0100 (Thu, 08 May 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r1019 | b.lohkamp | 2008-05-06 20:17:46 +0100 (Tue, 06 May 2008) | 3 lines Changed paths: M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc more windows directory fixes, esp. for backup and recover session. recover session checks if COOT_BACKUP_DIR exists now. ------------------------------------------------------------------------ r1018 | b.lohkamp | 2008-05-06 15:29:19 +0100 (Tue, 06 May 2008) | 1 line Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/python/coot_utils.py M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info.cc M /trunk/src/main.cc Windows directory fixes ------------------------------------------------------------------------ r1017 | pemsley | 2008-05-04 12:57:47 +0100 (Sun, 04 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Enable the display of WinCoot build. ------------------------------------------------------------------------ r1016 | pemsley | 2008-05-03 23:55:00 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use guile version 1.8.4 ------------------------------------------------------------------------ r1015 | pemsley | 2008-05-03 23:36:32 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Apply -ne -> != fix from Joseph Moran. ------------------------------------------------------------------------ r1014 | pemsley | 2008-05-03 23:31:46 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/build-it-win Make the win coot build test output to gtk2-test.log (with optional guile). ------------------------------------------------------------------------ r1013 | pemsley | 2008-05-03 18:10:35 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-info.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Minor adjustments to get gtk1 version to compile. ------------------------------------------------------------------------ r1012 | b.lohkamp | 2008-05-03 17:08:24 +0100 (Sat, 03 May 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py A /trunk/python/remote_control.py M /trunk/src/c-interface.cc M /trunk/src/c-interface.h remote control for python (not properly working yet) ------------------------------------------------------------------------ r1011 | pemsley | 2008-05-03 14:07:15 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/rama_plot.cc M /trunk/src/restraints-editor.cc Fix resizing of the other GL context in side by side stereo mode. ------------------------------------------------------------------------ r1010 | pemsley | 2008-05-03 14:03:02 +0100 (Sat, 03 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm Rework the key binding GUI, to display already-existing key bindings. ------------------------------------------------------------------------ r1009 | pemsley | 2008-05-02 11:27:17 +0100 (Fri, 02 May 2008) | 2 lines Changed paths: M /trunk/python/coot_toolbuttons.py Add pixmaps to pixbuf_dir. ------------------------------------------------------------------------ r1008 | pemsley | 2008-05-01 23:47:56 +0100 (Thu, 01 May 2008) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm Couple of fixes to key bindings. Fix error when key not found. Improve display of keybindings in dialog. ------------------------------------------------------------------------ r1007 | pemsley | 2008-05-01 09:48:01 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add back the format line which makes the key bindings work again. ------------------------------------------------------------------------ r1006 | pemsley | 2008-05-01 08:57:18 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1005 | pemsley | 2008-05-01 08:47:24 +0100 (Thu, 01 May 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/happy-coot-diary.html Dragon is doing the F8 builds currently. ------------------------------------------------------------------------ r1004 | b.lohkamp | 2008-04-29 13:34:52 +0100 (Tue, 29 Apr 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/refmac.py M /trunk/python-tests/08_utils.py M /trunk/scheme/refmac.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h refmac can be run without setting column labels ------------------------------------------------------------------------ r1003 | pemsley | 2008-04-28 20:23:39 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r1002 | pemsley | 2008-04-28 17:16:24 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/src/restraints-editor.cc Fix make_tree_store_for_planes in the case of 24 (not 14) atoms. ------------------------------------------------------------------------ r1001 | pemsley | 2008-04-28 15:57:16 +0100 (Mon, 28 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Apply Joseph Moran's fix correctly. ------------------------------------------------------------------------ r1000 | pemsley | 2008-04-28 14:51:18 +0100 (Mon, 28 Apr 2008) | 5 lines Changed paths: M /trunk/README M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2 M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/greg-tests/08-utils.scm M /trunk/happy-coot-diary.html M /trunk/ligand/dunbrack.cc M /trunk/mapview.glade M /trunk/python/extensions.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-defines.cc M /trunk/src/main.cc Add a function coot_has_python_p() and schemey version. Cootaneer renamed and will use the python version, if available. Fix gtk1 add reps group for checkbuttons. Trivial clean ups. ------------------------------------------------------------------------ r999 | b.lohkamp | 2008-04-28 10:24:11 +0100 (Mon, 28 Apr 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py fixed cootaneer tree path problem ------------------------------------------------------------------------ r998 | b.lohkamp | 2008-04-28 09:49:26 +0100 (Mon, 28 Apr 2008) | 6 lines Changed paths: M /trunk/python/Makefile.am A /trunk/python/brute_lsqman.py A /trunk/python/clear_backup.py M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/main.cc avoid loading toolbutton preferences when no-graphics coot_toolbuttons picks up pkgdatadir if COOT_PIX_BUFFER is not defined improved file handling in coot_unittest.py clear_backup.py in again add brute_lsqman.py ------------------------------------------------------------------------ r997 | pemsley | 2008-04-27 09:30:02 +0100 (Sun, 27 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/08-utils.scm Update key bindings test, now that we pass a binding name. ------------------------------------------------------------------------ r996 | pemsley | 2008-04-25 22:28:46 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. first for a long time. ------------------------------------------------------------------------ r995 | pemsley | 2008-04-25 22:01:09 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/happy-coot-diary.html New Oxfordian Happy Coot diary. ------------------------------------------------------------------------ r994 | pemsley | 2008-04-25 21:26:49 +0100 (Fri, 25 Apr 2008) | 2 lines Changed paths: M /trunk/python-tests/Makefile.am Fix 07_ncs.py typo. ------------------------------------------------------------------------ r993 | pemsley | 2008-04-25 17:18:18 +0100 (Fri, 25 Apr 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Rework the web page builder, accounting for pythonic builds and rearranging build hosts. ------------------------------------------------------------------------ r992 | pemsley | 2008-04-25 16:56:23 +0100 (Fri, 25 Apr 2008) | 5 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm Add a name to the key binding mechanism. Add New molecule by sphere to gui. Change the name of Cootaneer. Add primitive gui to show key bindings. ------------------------------------------------------------------------ r991 | b.lohkamp | 2008-04-25 08:56:57 +0100 (Fri, 25 Apr 2008) | 1 line Changed paths: M /trunk/python/Makefile.am remove clear_backup.py from makefile ------------------------------------------------------------------------ r990 | pemsley | 2008-04-24 11:32:04 +0100 (Thu, 24 Apr 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Test python against the installation version, not the system version. ------------------------------------------------------------------------ r989 | b.lohkamp | 2008-04-24 08:53:46 +0100 (Thu, 24 Apr 2008) | 3 lines Changed paths: M /trunk/python/Makefile.am M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/python/exercise_python_mol.py M /trunk/python-tests/01_pdb_mtz.py A /trunk/python-tests/08_utils.py M /trunk/python-tests/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/main.cc added python module clear_backup.py and test 08_utils.py various python fixes ------------------------------------------------------------------------ r988 | pemsley | 2008-04-23 23:04:37 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm No longer build for FC6 on bragg1. ------------------------------------------------------------------------ r987 | pemsley | 2008-04-23 22:01:27 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-it diagnose build_type problems. ------------------------------------------------------------------------ r986 | pemsley | 2008-04-23 20:45:35 +0100 (Wed, 23 Apr 2008) | 3 lines Changed paths: M /trunk/build-it More tinkering with the build and test status files for gtk1 build to separate out the python build statuses. ------------------------------------------------------------------------ r985 | pemsley | 2008-04-23 20:20:27 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/build-it Change the file name target for the build and test log file. ------------------------------------------------------------------------ r984 | pemsley | 2008-04-23 19:51:45 +0100 (Wed, 23 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/interface.c remove some debugging. ------------------------------------------------------------------------ r983 | b.lohkamp | 2008-04-23 11:44:45 +0100 (Wed, 23 Apr 2008) | 1 line Changed paths: A /trunk/python/example_python_mol_representation.py A /trunk/python/exercise_python_mol.py add python modules ------------------------------------------------------------------------ r982 | b.lohkamp | 2008-04-22 09:40:22 +0100 (Tue, 22 Apr 2008) | 1 line Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh py_to_scm (and scm_to_py) fixed ------------------------------------------------------------------------ r981 | b.lohkamp | 2008-04-22 08:39:56 +0100 (Tue, 22 Apr 2008) | 1 line Changed paths: M /trunk/build-it-win updated windows build script ------------------------------------------------------------------------ r980 | pemsley | 2008-04-21 21:28:19 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/fascinating-things.scm Fix up the fascintating things. Test junk has been left lying around. ------------------------------------------------------------------------ r979 | pemsley | 2008-04-21 21:23:41 +0100 (Mon, 21 Apr 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/geometry/protein-geometry.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/restraints-editor-c.h M /trunk/src/restraints-editor.cc Add a save restraints option to the residue editor. Remove some debugging output. ------------------------------------------------------------------------ r978 | pemsley | 2008-04-21 14:15:54 +0100 (Mon, 21 Apr 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Only set the active text item if we have get_active text for a combo box. (ifdef outs on Gtk1 build). ------------------------------------------------------------------------ r977 | pemsley | 2008-04-21 14:08:03 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc Set the active item for the additional representation bond width. ------------------------------------------------------------------------ r976 | pemsley | 2008-04-21 13:51:35 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Set the first entry in the restraints editor type selector (ALA, typically). ------------------------------------------------------------------------ r975 | pemsley | 2008-04-21 10:10:36 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes D /trunk/restraints-editor/src/restraints-editor.cc D /trunk/restraints-editor/src/restraints-editor.hh M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.cc M /trunk/src/interface.h A /trunk/src/restraints-editor-c.h A /trunk/src/restraints-editor.cc (from /trunk/restraints-editor/src/restraints-editor.cc:966) A /trunk/src/restraints-editor.hh (from /trunk/restraints-editor/src/restraints-editor.hh:970) Big updates to the restraints editor. Merge it into the main line. ------------------------------------------------------------------------ r974 | pemsley | 2008-04-21 10:08:04 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c New gtk2 interface - residue editor and with names. ------------------------------------------------------------------------ r973 | pemsley | 2008-04-21 05:46:50 +0100 (Mon, 21 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add monomer_types function. ------------------------------------------------------------------------ r972 | pemsley | 2008-04-20 23:06:19 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix typo. ------------------------------------------------------------------------ r971 | pemsley | 2008-04-20 22:48:52 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot.scm M /trunk/scheme/fascinating-things.scm Add fascintating-things to the loaded files. ------------------------------------------------------------------------ r970 | pemsley | 2008-04-20 22:30:23 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/restraints-editor/src/restraints-editor.hh updates to restraints-editor.hh. It will be moved shortly. ------------------------------------------------------------------------ r969 | pemsley | 2008-04-20 20:18:03 +0100 (Sun, 20 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Put a limit to the size of the red bars. ------------------------------------------------------------------------ r968 | b.lohkamp | 2008-04-18 21:32:49 +0100 (Fri, 18 Apr 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/c-interface-preferences.cc some Windows directory fixes python scripting function to start widgets in threads (used in read_refmac_log) ------------------------------------------------------------------------ r967 | pemsley | 2008-04-18 08:48:01 +0100 (Fri, 18 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Don't test on the 0th element of a python list in py_to_scm(). ------------------------------------------------------------------------ r966 | pemsley | 2008-04-17 23:20:57 +0100 (Thu, 17 Apr 2008) | 6 lines Changed paths: M /trunk/autogen.sh M /trunk/config.guess M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh Add scm_to_py and py_to_scm. They are broken though when used with run_scheme_command and run_python_command(). run_scheme_command fails when there is a parenetheses mismatch. run_python_command fails when given a python list. However, run_scheme_command works with a scheme list. ------------------------------------------------------------------------ r965 | pemsley | 2008-04-17 21:09:26 +0100 (Thu, 17 Apr 2008) | 2 lines Changed paths: A /trunk/restraints-editor/Makefile.am M /trunk/restraints-editor/src/Makefile.am A /trunk/restraints-editor/src/callbacks.c A /trunk/restraints-editor/src/callbacks.h A /trunk/restraints-editor/src/post-glade A /trunk/restraints-editor/src/post-gtk2-glade.sh A /trunk/restraints-editor/src/restraints-editor-c.h A /trunk/restraints-editor/src/restraints-editor.cc A /trunk/restraints-editor/src/restraints-editor.hh Add the restraints editor (0.5) to the repo. ------------------------------------------------------------------------ r964 | b.lohkamp | 2008-04-17 17:56:01 +0100 (Thu, 17 Apr 2008) | 5 lines Changed paths: A /trunk/python/a_rapper_gui.py M /trunk/python/coot_utils.py M /trunk/python/libcheck.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/06_ssm.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc added run_python_command and run_scheme_command added missing Py_DECREF (maybe too many...) fix libcheck.py and some unittests added a_rapper_gui.py (not fully functional yet, hence not in Makefile.am yet) ------------------------------------------------------------------------ r963 | kevin.cowtan | 2008-04-17 17:04:15 +0100 (Thu, 17 Apr 2008) | 4 lines Changed paths: M /trunk/src/molecule-class-info.cc Add Polar and Euler representations (+ translation) when transforming a molecule. Useful for SSM and NCS - e.g. can get operators for another program. ------------------------------------------------------------------------ r962 | pemsley | 2008-04-17 12:23:35 +0100 (Thu, 17 Apr 2008) | 4 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add the ability to write a cif restraints to a dictionary_residue_resetraint. Not quite working because the MMCIFData DataName is getting overwritten. Perhaps I need a cif category or some such. ------------------------------------------------------------------------ r961 | pemsley | 2008-04-16 18:40:19 +0100 (Wed, 16 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add a write_cif() stub function to dictionary_residue_restraints_t class. ------------------------------------------------------------------------ r960 | b.lohkamp | 2008-04-14 11:25:15 +0100 (Mon, 14 Apr 2008) | 3 lines Changed paths: M /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/tips.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh pythonized goto_next/prev_atom_maybe some bug fixes in python unittest and python modules ------------------------------------------------------------------------ r959 | pemsley | 2008-04-13 11:00:16 +0100 (Sun, 13 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add line tellling us where the std output has been redirected. ------------------------------------------------------------------------ r958 | pemsley | 2008-04-12 15:38:47 +0100 (Sat, 12 Apr 2008) | 5 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc stop echoing rsync lines in build log. clean build and test status before starting. Rework the saving of the worst satisfied restraint in a residue. Rework switching of stereo modes. ------------------------------------------------------------------------ r957 | pemsley | 2008-04-09 13:04:56 +0100 (Wed, 09 Apr 2008) | 4 lines Changed paths: M /trunk/greg-tests/03-ligand.scm If CCP4 is not available, let's get the monomer files from greg data dir. monomer-molecule-from-3-let-code still needs to provide a valid molecule for the test to pass. ------------------------------------------------------------------------ r956 | pemsley | 2008-04-09 12:40:16 +0100 (Wed, 09 Apr 2008) | 4 lines Changed paths: M /trunk/greg-tests/03-ligand.scm Change test to throw untested on invalid molecule, not lack of CCP4. Which makes "Get monomer test" pass if monomer-3GP.pdb and libcheck_3GP.cif exist in the current directory. ------------------------------------------------------------------------ r955 | pemsley | 2008-04-09 12:30:08 +0100 (Wed, 09 Apr 2008) | 3 lines Changed paths: M /trunk/src/c-interface-gui.cc Add graphics_info_t::use_graphics_interface_flag protection to set_model_toolbar_style(). ------------------------------------------------------------------------ r954 | pemsley | 2008-04-09 10:40:26 +0100 (Wed, 09 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm do better at getting a build result when the web page is not there. ------------------------------------------------------------------------ r953 | pemsley | 2008-04-09 09:07:09 +0100 (Wed, 09 Apr 2008) | 2 lines Changed paths: M /trunk/build-it Remove the test status file of this run, not a gtk2 one. ------------------------------------------------------------------------ r952 | pemsley | 2008-04-08 19:31:35 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/python-tests/Makefile.am Fix up the python tests, so that the source tar gets made correctly. ------------------------------------------------------------------------ r951 | pemsley | 2008-04-08 17:15:42 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it Update build-it placement of log files to match gtk2 version. ------------------------------------------------------------------------ r950 | pemsley | 2008-04-08 17:14:58 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix a typo in write-pdb. ------------------------------------------------------------------------ r949 | pemsley | 2008-04-08 14:20:13 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add protection in case the test status does not exist. ------------------------------------------------------------------------ r948 | pemsley | 2008-04-08 14:19:15 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Update build test results. Better results from Ubuntu now? ------------------------------------------------------------------------ r947 | pemsley | 2008-04-08 14:05:48 +0100 (Tue, 08 Apr 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc use gtk_window_set_default_size() not gtk_window_resize() for gtk1. ------------------------------------------------------------------------ r946 | pemsley | 2008-04-08 13:42:48 +0100 (Tue, 08 Apr 2008) | 4 lines Changed paths: M /trunk/build-it M /trunk/build-web-page-builder.scm M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/restraints-editor/restraints-editor.glade M /trunk/restraints-editor/src/main.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-state.cc M /trunk/src/main.cc Change build-it to put logs in more standard place. More tinkering with web page builder, spacing reordering. Change graphics window/glarea size usage. [Ethan Merritt bug] ------------------------------------------------------------------------ r945 | b.lohkamp | 2008-04-07 19:13:00 +0100 (Mon, 07 Apr 2008) | 3 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade A /trunk/python-tests/Makefile.am M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c move smooth scroll preferences from maps to general put python-test into distribution ------------------------------------------------------------------------ r944 | pemsley | 2008-04-06 16:05:56 +0100 (Sun, 06 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm handle entities with a macro. ------------------------------------------------------------------------ r943 | b.lohkamp | 2008-04-05 21:38:05 +0100 (Sat, 05 Apr 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_toolbuttons.py toolbutton connection fix ------------------------------------------------------------------------ r942 | pemsley | 2008-04-05 20:20:30 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Fix the test pass text from the remote log. ------------------------------------------------------------------------ r941 | pemsley | 2008-04-05 12:32:34 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Add links to summary page. ------------------------------------------------------------------------ r940 | pemsley | 2008-04-05 12:07:43 +0100 (Sat, 05 Apr 2008) | 3 lines Changed paths: M /trunk/greg-tests/06-ssm.scm M /trunk/src/graphics-info-superpose.cc Fix superpose-with-atom-selection bug (hopefully). Added another test (new test data needed). ------------------------------------------------------------------------ r939 | pemsley | 2008-04-05 12:06:46 +0100 (Sat, 05 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc remove debugging. ------------------------------------------------------------------------ r938 | pemsley | 2008-04-04 17:32:50 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add build results from foreign build hosts. ------------------------------------------------------------------------ r937 | pemsley | 2008-04-04 17:28:15 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/group-settings.scm M /trunk/scheme/tips.scm Fix up typo in the setting of rapper-dir. ------------------------------------------------------------------------ r936 | pemsley | 2008-04-04 16:05:10 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Change test for guile-gtk ------------------------------------------------------------------------ r935 | pemsley | 2008-04-04 12:30:18 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm adjust the output files names. ------------------------------------------------------------------------ r934 | pemsley | 2008-04-04 12:22:36 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a bit of bolding. ------------------------------------------------------------------------ r933 | b.lohkamp | 2008-04-04 11:20:04 +0100 (Fri, 04 Apr 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/Makefile.am M /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in A /trunk/python/coot_toolbuttons.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc M /trunk/src/molecule-class-info.h added python toolbar buttons with 'manager' moved .coot*preferences.* to dir ~/.preferences/coot*preferences.* ------------------------------------------------------------------------ r932 | pemsley | 2008-04-04 11:10:48 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add status of last build. ------------------------------------------------------------------------ r931 | pemsley | 2008-04-04 10:35:40 +0100 (Fri, 04 Apr 2008) | 2 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple Write build/test status more consistently. ------------------------------------------------------------------------ r930 | pemsley | 2008-04-04 00:35:30 +0100 (Fri, 04 Apr 2008) | 3 lines Changed paths: M /trunk/build-it M /trunk/build-it-gtk2-simple echo to a file the build and test status. To be picked up by the web page builder. ------------------------------------------------------------------------ r929 | pemsley | 2008-04-03 14:44:46 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/db-main/db-strands.cc Now that reference structures have strand info, we can use them. ------------------------------------------------------------------------ r928 | pemsley | 2008-04-03 14:44:03 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add chem_comp to dict_chem_comp constructor. ------------------------------------------------------------------------ r927 | pemsley | 2008-04-03 14:42:49 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix up the info about environment variables. ------------------------------------------------------------------------ r926 | pemsley | 2008-04-03 13:33:16 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Tabularise the results. ------------------------------------------------------------------------ r925 | pemsley | 2008-04-03 09:14:04 +0100 (Thu, 03 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a title. Add a link for the svn log. ------------------------------------------------------------------------ r924 | pemsley | 2008-04-02 16:47:56 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Copy over binary file to York if we are in biop. ------------------------------------------------------------------------ r923 | pemsley | 2008-04-02 16:46:47 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/group-settings.scm Trivial changes for rapper support. ------------------------------------------------------------------------ r922 | pemsley | 2008-04-02 16:46:02 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More updates, now to handle build log links from outside York. ------------------------------------------------------------------------ r921 | pemsley | 2008-04-02 15:29:23 +0100 (Wed, 02 Apr 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh Add the operator<< for various classes. They had only been friends before. Reported by Morten. ------------------------------------------------------------------------ r920 | pemsley | 2008-04-02 15:12:48 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Add use_graphics_interface_flag around create_no_restraints_info_dialog(). ------------------------------------------------------------------------ r919 | pemsley | 2008-04-02 14:18:08 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add horne test for refinement with no graphics and no dictionary. ------------------------------------------------------------------------ r918 | pemsley | 2008-04-02 14:10:45 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Don't create dialogs about refinement when there is no graphics. ------------------------------------------------------------------------ r917 | pemsley | 2008-04-02 14:08:34 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Set up ccp4 on cycle in test. ------------------------------------------------------------------------ r916 | pemsley | 2008-04-02 14:08:03 +0100 (Wed, 02 Apr 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm Take out Gtk2 build on FC2 for the moment (guile-gtk does not compile there). Add logs for ubuntu build. ------------------------------------------------------------------------ r915 | pemsley | 2008-04-02 14:06:59 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Change the name from NCS Loop to something more sensible. ------------------------------------------------------------------------ r914 | pemsley | 2008-04-02 14:06:20 +0100 (Wed, 02 Apr 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Correctly save the type of bond restraints (e.g. coval). ------------------------------------------------------------------------ r913 | pemsley | 2008-04-01 12:13:23 +0100 (Tue, 01 Apr 2008) | 2 lines Changed paths: M /trunk/greg-tests/07-ncs.scm Add NCS Residue Range copy test. ------------------------------------------------------------------------ r912 | pemsley | 2008-04-01 12:09:37 +0100 (Tue, 01 Apr 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Also redirect std err for building guile extras. ------------------------------------------------------------------------ r911 | pemsley | 2008-04-01 11:45:19 +0100 (Tue, 01 Apr 2008) | 7 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/callbacks.c M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/support-gtk2-extras.c Fix range function in coot-utils. Use gtk_image_new_from_stock not gtk_image_new_from_icon_name for the clear icon in the toolbar (gtk 2.4, FC3). Change to InsResidue not AddResidue where we can for NCS residue range copy. #ifdef out each toolbar function. I was getting confused. Simplify test for guile-gtk. ------------------------------------------------------------------------ r910 | pemsley | 2008-03-31 14:18:32 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes update notes from impala. ------------------------------------------------------------------------ r909 | pemsley | 2008-03-31 10:46:10 +0100 (Mon, 31 Mar 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/build-web-page-builder.scm Put the tar file name into 16-coot.txt log Change text for svn revision output. ------------------------------------------------------------------------ r908 | pemsley | 2008-03-31 10:45:11 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix typo in logic of compiling conditional gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r907 | pemsley | 2008-03-31 10:31:50 +0100 (Mon, 31 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Find svn code revision. ------------------------------------------------------------------------ r906 | pemsley | 2008-03-30 21:31:09 +0100 (Sun, 30 Mar 2008) | 3 lines Changed paths: M /trunk/build-web-page-builder.scm M /trunk/dnotes Output the page generation time/date. Update notes. ------------------------------------------------------------------------ r905 | pemsley | 2008-03-30 21:29:09 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/coords/mmdb-crystal.h uncommented the include of Cartesian.h so that r899 compiles for Bill. Strange. ------------------------------------------------------------------------ r904 | pemsley | 2008-03-30 21:26:03 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.hh operator[] for atom ids should be/have been const. ------------------------------------------------------------------------ r903 | pemsley | 2008-03-30 19:07:03 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc #if tests for gtk version around gtk_combo_box_get_active_text(). ------------------------------------------------------------------------ r902 | pemsley | 2008-03-30 10:34:07 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a refresh of 10 minutes. ------------------------------------------------------------------------ r901 | pemsley | 2008-03-30 02:37:30 +0100 (Sun, 30 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add python fc3 version. ------------------------------------------------------------------------ r900 | pemsley | 2008-03-29 20:05:33 +0000 (Sat, 29 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More build targets. ------------------------------------------------------------------------ r899 | pemsley | 2008-03-29 12:25:06 +0000 (Sat, 29 Mar 2008) | 3 lines Changed paths: M /trunk/atom-utils/Makefile.am Add -I $(top_srcdir)/ccp4mg-utils to INCLUDES so that atom-utils can fit mgtree.h from a clean install. ------------------------------------------------------------------------ r898 | pemsley | 2008-03-29 07:48:17 +0000 (Sat, 29 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm More sober colours. ------------------------------------------------------------------------ r897 | pemsley | 2008-03-28 22:07:36 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Add a limit to the bar size. ------------------------------------------------------------------------ r896 | pemsley | 2008-03-28 22:04:38 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Update web page builder to output coloured bars. ------------------------------------------------------------------------ r895 | pemsley | 2008-03-28 17:40:14 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/build-web-page-builder.scm Change the title. ------------------------------------------------------------------------ r894 | pemsley | 2008-03-28 16:12:43 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/sequence-view/Makefile.am Add ccp4mg-utils to INCLUDES for mgtree.h ------------------------------------------------------------------------ r893 | b.lohkamp | 2008-03-28 15:06:00 +0000 (Fri, 28 Mar 2008) | 1 line Changed paths: M /trunk/src/callbacks.c M /trunk/src/callbacks.h gtk1 fixes ------------------------------------------------------------------------ r892 | pemsley | 2008-03-28 12:35:47 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info-maps.cc Fix error checking of maps (again). Now the function can actually read a map. ------------------------------------------------------------------------ r891 | pemsley | 2008-03-28 12:26:10 +0000 (Fri, 28 Mar 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-info.cc M /trunk/src/gtk-manual.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add torsion id to torsion restrain info. Fix addional representations and undo bug. ------------------------------------------------------------------------ r890 | pemsley | 2008-03-28 10:57:49 +0000 (Fri, 28 Mar 2008) | 2 lines Changed paths: A /trunk/restraints-editor A /trunk/restraints-editor/restraints-editor.glade A /trunk/restraints-editor/src A /trunk/restraints-editor/src/Makefile.am A /trunk/restraints-editor/src/main.cc Add code for restraints editor - not in main app yep - just creating/storage/testing. ------------------------------------------------------------------------ r889 | b.lohkamp | 2008-03-28 10:57:35 +0000 (Fri, 28 Mar 2008) | 9 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-glue-gtk2.c A /trunk/src/coot-gtk2.defs M /trunk/src/coot-preferences.h M /trunk/src/coot_pythonmodule.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c add toolbar style to preferences removed the following from the menu (actually hidden for easy recovery): HID-> Virtual trackball Edit-> Font size & Pink Pointer size Draw-> Recentre, dragged map, smooth recentre & antialias added glue code (python and guile) for the toolbar changed toolbar items (Reset View etc) to toolbuttons Python function for adding toolbar buttons ------------------------------------------------------------------------ r888 | pemsley | 2008-03-26 15:52:15 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am gtk-manual.c to gtk-manual.cc in src/Makefile.am ------------------------------------------------------------------------ r887 | pemsley | 2008-03-26 15:36:37 +0000 (Wed, 26 Mar 2008) | 4 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc Fix valgrind-found bug in reading bogus map. Remove some debugging. Make the Mitch Miller test rotate less. ------------------------------------------------------------------------ r886 | b.lohkamp | 2008-03-26 15:20:31 +0000 (Wed, 26 Mar 2008) | 5 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/fitting.py M /trunk/python/ncs.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/src/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-render.cc more python functions (ncs_ligand, ncs_ghost... and guis) some more unittest functions (not tested yet) 'fixed' zoom/angle for povray images (not perfect but reasonable) backwards building in loop fitting (was actually there already...) ------------------------------------------------------------------------ r885 | pemsley | 2008-03-26 14:26:06 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: A /trunk/build-web-page-builder.scm (from /trunk/pe-test.scm:884) D /trunk/pe-test.scm Rename to build-web-page-builder.scm ------------------------------------------------------------------------ r884 | pemsley | 2008-03-26 14:24:53 +0000 (Wed, 26 Mar 2008) | 2 lines Changed paths: A /trunk/pe-test.scm web page builder added. Needs a name change. ------------------------------------------------------------------------ r883 | pemsley | 2008-03-25 14:10:23 +0000 (Tue, 25 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-python.cc Add string checking in key_sym_code_py(). ------------------------------------------------------------------------ r882 | pemsley | 2008-03-25 14:05:28 +0000 (Tue, 25 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-python.cc Add "coot-utils.hh" include for key sym decoding from python. ------------------------------------------------------------------------ r881 | pemsley | 2008-03-25 13:50:16 +0000 (Tue, 25 Mar 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/scheme/a-rapper-gui.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/scheme/ncs.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-maps.cc Add NCS ligands function and GUI. Add inverse-rtop function (calling clipper function across scripting layer). transform-coord-molecule renamed transform-coords-molecule. set-molecule-name now updates the name in the Display Control Window. Add command line to rapper gui - needs testing. ------------------------------------------------------------------------ r880 | pemsley | 2008-03-24 21:48:44 +0000 (Mon, 24 Mar 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/ncs.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Changes so that we transform the screen centre on NCS jumping - no longer go to the related CA. Cuter, especially for ligands. ------------------------------------------------------------------------ r879 | pemsley | 2008-03-24 21:10:51 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r878 | pemsley | 2008-03-24 14:00:56 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/08-utils.scm M /trunk/ideal/lograma.h M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Export NCS ghost info to the scripting layer. ------------------------------------------------------------------------ r877 | pemsley | 2008-03-24 05:41:10 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: A /trunk/greg-tests/08-utils.scm M /trunk/greg-tests/Makefile.am M /trunk/greg-tests/begin.grg M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-scm.cc Add more testing for the key symms. ------------------------------------------------------------------------ r876 | pemsley | 2008-03-24 05:04:26 +0000 (Mon, 24 Mar 2008) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-utils.hh A /trunk/coot-utils/gdk-keysym.awk A /trunk/coot-utils/gdk-keysyms.cc M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-python.cc M /trunk/src/c-interface-scm.cc M /trunk/src/cc-interface.hh Add function to decode a string to a key index - for use in key bindings. ------------------------------------------------------------------------ r875 | pemsley | 2008-03-23 23:37:51 +0000 (Sun, 23 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Fix up NCS maps test - 5 extra molecules. ------------------------------------------------------------------------ r874 | pemsley | 2008-03-23 12:36:44 +0000 (Sun, 23 Mar 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Fix typo in NCS map test. ------------------------------------------------------------------------ r873 | pemsley | 2008-03-22 23:07:34 +0000 (Sat, 22 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/snarf-coot-docs.scm Fix up water chain define for doc snarfing. ------------------------------------------------------------------------ r872 | pemsley | 2008-03-22 22:20:29 +0000 (Sat, 22 Mar 2008) | 6 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ligand/test-ligand.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/torsion-general.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h The change_by() function of torsion_general now takes a tree pointer. (that is the initial tree on startup - so that the tree is not calculated and changed on every mouse motion - thus causing a bug). Utility get_first_res_of_moving_atoms() function added. ------------------------------------------------------------------------ r871 | pemsley | 2008-03-22 21:03:22 +0000 (Sat, 22 Mar 2008) | 6 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Document "Make a difference map". "Apply NCS loop..." function added to extensions. make-difference-map-gui added to coot-gui.scm Fixed lighting of display list objects. Works better now for me. Fixed colouring of Ball and Stick atoms. ------------------------------------------------------------------------ r870 | pemsley | 2008-03-22 18:13:13 +0000 (Sat, 22 Mar 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Cartesian.cc M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.cc Adjust the picking algorithm, so that atoms at the back of the slab score worse. Make set_graphics_window_size() work properly. ------------------------------------------------------------------------ r869 | pemsley | 2008-03-22 17:02:10 +0000 (Sat, 22 Mar 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/graphics-info-pick.cc M /trunk/src/gtk-manual.cc Reorder header files so that gtk-manual.cc compiles on bubbles. ------------------------------------------------------------------------ r868 | pemsley | 2008-03-22 16:31:52 +0000 (Sat, 22 Mar 2008) | 4 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.cc M /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h More additional representation code. Now they are displayed in the Display Control dialog. And saved into the state file. ------------------------------------------------------------------------ r867 | pemsley | 2008-03-22 09:16:39 +0000 (Sat, 22 Mar 2008) | 8 lines Changed paths: M /trunk/TODO M /trunk/configure.in M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h D /trunk/src/gtk-manual.c A /trunk/src/gtk-manual.cc (from /trunk/src/gtk-manual.c:859) M /trunk/src/gtk-manual.h A /trunk/src/gtk-manual.hh M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Remove LINGUAS code from configure.in Add dynamically-tranformed map test. gtk-manual.c ->gtk-manual.cc Add gtk-manual.hh - for C++ interface. Add set_show_additional_representation(). Fix dynamically-tranformed map bug. Document set-default-temperature-factor-for-new-atoms ------------------------------------------------------------------------ r866 | b.lohkamp | 2008-03-15 16:25:10 +0000 (Sat, 15 Mar 2008) | 1 line Changed paths: M /trunk/src/graphics-info-render.cc fixed povray camera position (zoom still a bit out) ------------------------------------------------------------------------ r865 | b.lohkamp | 2008-03-14 20:10:57 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/python/povray.py M /trunk/python/raster3d.py M /trunk/scheme/hello.scm M /trunk/scheme/povray.scm M /trunk/scheme/raster3d.scm M /trunk/src/graphics-info-render.cc some povray fixes (sadly still not properly working... the camera position...) ------------------------------------------------------------------------ r864 | pemsley | 2008-03-14 13:00:15 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/src/globjects.cc Don't allow translation drag of intermediate atoms when they are a rotamer. ------------------------------------------------------------------------ r863 | pemsley | 2008-03-14 12:54:31 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/scheme/mutate.scm Fix typo error in delete-sidechain-range. ------------------------------------------------------------------------ r862 | pemsley | 2008-03-14 12:53:22 +0000 (Fri, 14 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes A template for additional representations. Not sure if I like it. ------------------------------------------------------------------------ r861 | pemsley | 2008-03-14 09:43:03 +0000 (Fri, 14 Mar 2008) | 3 lines Changed paths: M /trunk/ligand/wiggly-ligand.cc Fix problem of not working ligand search when Flexible ligand is used with e.g. SO4. ------------------------------------------------------------------------ r860 | pemsley | 2008-03-13 19:32:54 +0000 (Thu, 13 Mar 2008) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/src/c-interface-info.cc Sidestep bug coot_gui.py in handling string for history. In restraints code, use unsigned int where needed for cleanness. ------------------------------------------------------------------------ r859 | pemsley | 2008-03-13 17:37:59 +0000 (Thu, 13 Mar 2008) | 2 lines Changed paths: M /trunk/mapview.glade M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/interface.c Correct widget names in add_rep_dialog for gtk1. ------------------------------------------------------------------------ r858 | pemsley | 2008-03-13 16:36:51 +0000 (Thu, 13 Mar 2008) | 9 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/scheme/tips.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a scheme Missing Atoms gui to Extensions. Fill wrapped_create_add_additional_representation_gui(). And add_additional_representation_by_widget(). Works now except: ball and stick, needs to get bond width from combobox in gtk1. Add home on the range (a menu item) for additional representations. Skeleton alignment_results_scm() and alignment_results_py() added. ------------------------------------------------------------------------ r857 | pemsley | 2008-03-13 13:37:27 +0000 (Thu, 13 Mar 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot.in M /trunk/src/interface.c M /trunk/src/interface.h Add gtk1 add_reps_dialog. Make source. ------------------------------------------------------------------------ r856 | b.lohkamp | 2008-03-12 10:26:45 +0000 (Wed, 12 Mar 2008) | 4 lines Changed paths: M /trunk/build-it-win M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/coot-gtk2.glade M /trunk/cootrc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/main.cc changed size of gtk's icons in refinement toolbar (avoids elongated window) fixed docked accept_reject_dialog (key binding and crash when changing modes) some MinGW windows fixes ------------------------------------------------------------------------ r855 | pemsley | 2008-03-11 12:09:47 +0000 (Tue, 11 Mar 2008) | 2 lines Changed paths: A /trunk/scheme/a-rapper-gui.scm Add a Rapper GUI. ------------------------------------------------------------------------ r854 | pemsley | 2008-03-11 12:07:34 +0000 (Tue, 11 Mar 2008) | 3 lines Changed paths: M /trunk/src/coot.in Kludge in 1.8 to GUILE_LOAD_PATH - addresses Kevin's Ubuntu build/install problem? ------------------------------------------------------------------------ r853 | pemsley | 2008-03-10 11:09:15 +0000 (Mon, 10 Mar 2008) | 2 lines Changed paths: M /trunk/mapview.glade Add a gtk1 version of the additional representation dialog. ------------------------------------------------------------------------ r852 | pemsley | 2008-03-07 19:46:16 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix the typo in the python output of chem_comp_bond - spotted by Nigel M. ------------------------------------------------------------------------ r851 | pemsley | 2008-03-07 15:04:18 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade Name the widgets in add_reps_dialog. ------------------------------------------------------------------------ r850 | pemsley | 2008-03-07 14:18:13 +0000 (Fri, 07 Mar 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Change the key binding mechanism. Now we have add-key-binding function. Much cleaner. ------------------------------------------------------------------------ r849 | pemsley | 2008-03-07 12:54:13 +0000 (Fri, 07 Mar 2008) | 5 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Remove cruffty get_text_for_go_to_atom_chain_xxx() functions. Add bond width arg to additional_representation scripting functions. Fix up problems with creating/reading restraints in python scripting. It can eat its own dog food now, I think. ------------------------------------------------------------------------ r848 | pemsley | 2008-03-07 11:53:49 +0000 (Fri, 07 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Add use_graphics_interface protection in post_go_to_atom_window(). ------------------------------------------------------------------------ r847 | pemsley | 2008-03-07 01:41:15 +0000 (Fri, 07 Mar 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/gtk2-interface.c Use new style partial charge info. Add a Addition Representation gui to glade. Not used or properly filled. ------------------------------------------------------------------------ r846 | pemsley | 2008-03-07 00:01:29 +0000 (Fri, 07 Mar 2008) | 13 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/command-line.h Add function save-dialog-positions-to-init-file Add a hook for it in the extensions menu. Add a greg test case "Post Go To Atom no molecules". Rework the partial charge info in the dictionary. Now it carries a flag. This is how it will be for xyz positions too (i.e. pairs, one of which is a bool saying if this is a valid field or not). Add the reading of model coords into dictionary. Not finish yet. Or tested. Add function additional_representation_info_scm() Add command line option -c - but not activated yet - when shall the command line string be evaluated? Urgency hints removed from coot-gt2.glade. Hmm... ------------------------------------------------------------------------ r845 | pemsley | 2008-03-06 15:39:18 +0000 (Thu, 06 Mar 2008) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h More additional representation code. Now new bonds can be generated from the scripting layer. And cleared. We need a GUI. ------------------------------------------------------------------------ r844 | pemsley | 2008-03-06 12:24:13 +0000 (Thu, 06 Mar 2008) | 2 lines Changed paths: M /trunk/db-main/db-main.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info.cc Add tweaks from Francois. ------------------------------------------------------------------------ r843 | b.lohkamp | 2008-03-06 09:26:36 +0000 (Thu, 06 Mar 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py fix coot_gui.py for use with coot commands in assignments ------------------------------------------------------------------------ r842 | pemsley | 2008-03-05 23:14:50 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: A /trunk/geometry/test-read-components.cc A /trunk/geometry/test-read-components.hh Add test-read-components files. ------------------------------------------------------------------------ r841 | pemsley | 2008-03-05 23:10:31 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc More pythonization of restraints code. ------------------------------------------------------------------------ r840 | pemsley | 2008-03-05 19:30:19 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-info.cc Clean up pythonization of restraints interface. ------------------------------------------------------------------------ r839 | pemsley | 2008-03-05 18:54:46 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Continuing pythonization of restraints input/output. ------------------------------------------------------------------------ r838 | pemsley | 2008-03-05 18:53:04 +0000 (Wed, 05 Mar 2008) | 9 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/dnotes M /trunk/geometry/Makefile.am M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/Makefile.am M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-navigation.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Rework the intelligent_goto_next/previous atom function. Now we can "next" over insertion codes and gaps. SCM goto_next_atom_maybe() function created for testing. atom_to_atom_index() function created to quickly get atom index. Add greg-test for this. Start on addition represenations: display_bonds() split to allow for addtional representations. Add the mitch miller test for NPD atoms from shelx files. ------------------------------------------------------------------------ r837 | pemsley | 2008-03-05 08:42:14 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c update splash screen. ------------------------------------------------------------------------ r836 | pemsley | 2008-03-05 08:40:52 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.5-pre.xpm Add a new splash screen ------------------------------------------------------------------------ r835 | pemsley | 2008-03-05 08:39:18 +0000 (Wed, 05 Mar 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/main.cc update the splash screen. ------------------------------------------------------------------------ r834 | b.lohkamp | 2008-03-04 15:11:45 +0000 (Tue, 04 Mar 2008) | 1 line Changed paths: M /trunk/build-it-win updated MinGW autobuild script ------------------------------------------------------------------------ r833 | pemsley | 2008-03-04 14:47:23 +0000 (Tue, 04 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix syntax errors of adding Refinement map protection to add_terminal_residue(). ------------------------------------------------------------------------ r832 | pemsley | 2008-03-04 08:34:32 +0000 (Tue, 04 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add refinement map test to add_terminal_residue() [like BL suggested]. ------------------------------------------------------------------------ r831 | pemsley | 2008-03-03 19:39:13 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/gtk2-interface.c More pythonization of restraints code. ------------------------------------------------------------------------ r830 | b.lohkamp | 2008-03-03 17:11:57 +0000 (Mon, 03 Mar 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py M /trunk/python/extensions.py M /trunk/python/generic_objects.py M /trunk/python/povray.py M /trunk/python/raster3d.py M /trunk/python/shelx.py M /trunk/python-tests/01_pdb_mtz.py M /trunk/python-tests/02_shelx.py M /trunk/python-tests/03_ligand.py M /trunk/python-tests/04_cootaneer.py M /trunk/python-tests/07_ncs.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h python unittest functions complete and functional (as of today) added and fixed some python (scripting) functions ------------------------------------------------------------------------ r829 | pemsley | 2008-03-03 15:41:22 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/gl-matrix.cc M /trunk/src/gl-matrix.h Change the gl error handler, useful for NPD anisotropic atom matrices. ------------------------------------------------------------------------ r828 | pemsley | 2008-03-03 15:08:00 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/graphics-info-navigation-gtk2.cc Add protection for invalid go_to_atom_molecule. ------------------------------------------------------------------------ r827 | pemsley | 2008-03-03 13:56:20 +0000 (Mon, 03 Mar 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/globjects.cc A bit of Pythonization of restraints import/export code. ------------------------------------------------------------------------ r826 | b.lohkamp | 2008-03-01 22:37:19 +0000 (Sat, 01 Mar 2008) | 1 line Changed paths: A /trunk/build-it-win autobuild script for MinGW ------------------------------------------------------------------------ r825 | b.lohkamp | 2008-03-01 17:17:32 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/python/coot_utils.py D /trunk/python-tests/01-pdb+mtz.py A /trunk/python-tests/01_pdb_mtz.py A /trunk/python-tests/02_shelx.py D /trunk/python-tests/03-ligand.py A /trunk/python-tests/03_ligand.py A /trunk/python-tests/04_cootaneer.py A /trunk/python-tests/05_rna_ghosts.py A /trunk/python-tests/06_ssm.py A /trunk/python-tests/07_ncs.py M /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-build.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc added more python unittest functions ------------------------------------------------------------------------ r824 | pemsley | 2008-03-01 13:05:07 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r823 | pemsley | 2008-03-01 13:03:37 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc Improve error reporting. ------------------------------------------------------------------------ r822 | pemsley | 2008-03-01 13:02:49 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Handle EQIV card better. ------------------------------------------------------------------------ r821 | pemsley | 2008-03-01 13:02:12 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/autogen.sh Fix up code block spacing. ------------------------------------------------------------------------ r820 | pemsley | 2008-03-01 13:01:50 +0000 (Sat, 01 Mar 2008) | 2 lines Changed paths: M /trunk/src/junk.cc Add mmcif reading code test case for Eugene, to junk.cc ------------------------------------------------------------------------ r819 | pemsley | 2008-02-29 11:04:35 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix problem of not running tests when build_coot_prerelease not set. ------------------------------------------------------------------------ r818 | pemsley | 2008-02-29 10:31:10 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Add guile-1.6.x fix ups ------------------------------------------------------------------------ r817 | pemsley | 2008-02-29 01:32:22 +0000 (Fri, 29 Feb 2008) | 2 lines Changed paths: M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh More monomer restraints parsing. Now we go both ways. ------------------------------------------------------------------------ r816 | pemsley | 2008-02-28 14:17:18 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/geometry/protein-geometry.hh Add operator[] for plane restraints (needed for previous restraints using code). ------------------------------------------------------------------------ r815 | pemsley | 2008-02-28 14:06:50 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fill monomer_restraints() function. ------------------------------------------------------------------------ r814 | pemsley | 2008-02-28 12:45:21 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc update notes, tidy formatting. ------------------------------------------------------------------------ r813 | pemsley | 2008-02-28 12:43:51 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/src/graphics-info-superpose.cc Fix problem of fitting over wrong molecle, when using copy in superpose_with_atom_selection(). Fixes crash. ------------------------------------------------------------------------ r812 | pemsley | 2008-02-28 12:22:59 +0000 (Thu, 28 Feb 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm don't use run-gtk-pending-events, it is not defined when no graphics. ------------------------------------------------------------------------ r811 | pemsley | 2008-02-28 11:14:13 +0000 (Thu, 28 Feb 2008) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh Ooops. I'd forgotten to add fixed atom flags to chiral volume restraints. Fixes crash on bubbles - and errors elsewhere, I suspect. ------------------------------------------------------------------------ r810 | pemsley | 2008-02-27 14:18:08 +0000 (Wed, 27 Feb 2008) | 10 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc Move GTk functios from c-interface.cc into c-interface-gui.cc setup_python_window_entry() setup_guile_window_entry() python_window_enter_callback() guile_window_enter_callback() fill_option_menu_with_map_options() fill_option_menu_with_skeleton_options() set_contour_sigma_button_and_entry() set_contour_by_sigma_step_maybe() ------------------------------------------------------------------------ r809 | pemsley | 2008-02-27 14:12:34 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix up char * usage in PyRunSimpleString in python_window_enter_callback(). ------------------------------------------------------------------------ r808 | b.lohkamp | 2008-02-27 14:10:55 +0000 (Wed, 27 Feb 2008) | 1 line Changed paths: M /trunk/src/c-interface.cc fixed python scripting gtk version issue ------------------------------------------------------------------------ r807 | pemsley | 2008-02-27 12:59:30 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple If build_coot_prerelease by line 942, don't touch it or $run_tests. ------------------------------------------------------------------------ r806 | pemsley | 2008-02-27 12:49:32 +0000 (Wed, 27 Feb 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/06-ssm.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-other.cc Add a return value to try_assign_cell() in coot-shelx-ins.cc Remove some debugging. Add run-gtk-pending-events function. ------------------------------------------------------------------------ r805 | pemsley | 2008-02-27 11:37:02 +0000 (Wed, 27 Feb 2008) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx.hh M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Set the filled_flag for a ShelxIns in the constructor. Add some debugging. ------------------------------------------------------------------------ r804 | pemsley | 2008-02-27 11:34:53 +0000 (Wed, 27 Feb 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Reorder tests. Allow a little wriggle room in 0 values from differnce map on a different grid. ------------------------------------------------------------------------ r803 | pemsley | 2008-02-27 09:33:19 +0000 (Wed, 27 Feb 2008) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Fix isTer() test for closest_atom(). Fixes crash. ------------------------------------------------------------------------ r802 | b.lohkamp | 2008-02-26 23:17:09 +0000 (Tue, 26 Feb 2008) | 3 lines Changed paths: M /trunk/python/coot_utils.py A /trunk/python-tests A /trunk/python-tests/01-pdb+mtz.py A /trunk/python-tests/03-ligand.py A /trunk/python-tests/coot_unittest.py M /trunk/src/c-interface-mmdb.cc M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc some fixes for MINGW compilation add python-tests and some python unittest functions (more to come) ------------------------------------------------------------------------ r801 | pemsley | 2008-02-26 14:44:09 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: A /trunk/ideal/lograma.cpp A /trunk/ideal/lograma.h A /trunk/ideal/logramatest.cpp Add Kevin's LogRama class and test program ------------------------------------------------------------------------ r800 | pemsley | 2008-02-26 13:58:00 +0000 (Tue, 26 Feb 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/greg-tests/01-pdb+mtz.scm Add the alt conf residue deletion test - JED bug. Pretty up the report of the test result. ------------------------------------------------------------------------ r799 | pemsley | 2008-02-26 12:54:01 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple More adjustments to building guile-gtk ------------------------------------------------------------------------ r798 | pemsley | 2008-02-26 12:47:08 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Fix up guile_gtk build variable usage. ------------------------------------------------------------------------ r797 | pemsley | 2008-02-26 08:33:02 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-map.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc Commit for previous commit notes (was wrong dir). ------------------------------------------------------------------------ r796 | pemsley | 2008-02-26 08:28:05 +0000 (Tue, 26 Feb 2008) | 23 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/group-settings.scm M /trunk/scheme/snarf-coot-docs.scm Add another dummy function for snarfing. Add function first-n. Abstract interesting-residue-gui. Add commented mitch miller aniso test. Add "mask and difference map" greg test. Remove the commands to save the moving of the window from the history (too noisy). save_symmetry_coords_from_fileselection moved to c-interface-gui.cc quote arg of atom-info history. Same for save_coordinates(). Add function difference_map() and coot-map-utils code for that. install_map() renamed to install_ghost_map(). Check atom->isTer() for NCS differences and in atom button list returned to Go To Atom dialog. Added several debuggings. Reorder args to save_symmetry_coords() In molecule_info_class_t::delete_residue_with_altconf() check that an atoms are suitable for deletion before deleting the atom selection [JED]. Check for atom->isTer() in atom_pick(). Add Ramachandran restraints support in simple-restraints.cc/hh Add lograma class from Kevin (first "flat 0" version). Add args to with-map to test torsion and rama restraints. ------------------------------------------------------------------------ r795 | pemsley | 2008-02-26 07:52:23 +0000 (Tue, 26 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Try new guile-gtk build variables. ------------------------------------------------------------------------ r794 | b.lohkamp | 2008-02-18 19:53:43 +0000 (Mon, 18 Feb 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/tips.py M /trunk/scheme/tips.scm M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Fix automatic file sorting and filtering in gtk2 fileselection ------------------------------------------------------------------------ r793 | b.lohkamp | 2008-02-17 16:31:12 +0000 (Sun, 17 Feb 2008) | 1 line Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c option to automatically set file filter for file chooser ------------------------------------------------------------------------ r792 | b.lohkamp | 2008-02-16 13:30:54 +0000 (Sat, 16 Feb 2008) | 1 line Changed paths: M /trunk/src/c-inner-main.c M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-preferences.cc M /trunk/src/main.cc fixes for gtk1 compilation ------------------------------------------------------------------------ r791 | b.lohkamp | 2008-02-15 20:31:32 +0000 (Fri, 15 Feb 2008) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot-preferences.h M /trunk/src/globjects.cc A /trunk/src/graphics-info-preferences.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc implemented Preferences dialog (writes either or both, guile and python files) on the way added some extra bitmap glut atom label fonts, possibly obsolete menu items are not removed yet preferences are trumped by state files and .coot files python preferences are trumped by scm references ------------------------------------------------------------------------ r790 | pemsley | 2008-02-15 01:05:12 +0000 (Fri, 15 Feb 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Add generic-object-name from scm function) ------------------------------------------------------------------------ r789 | pemsley | 2008-02-14 14:07:38 +0000 (Thu, 14 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/ncs.scm M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Fix occassional "flatlanding" when ncs chain skipping [JED]. ------------------------------------------------------------------------ r788 | pemsley | 2008-02-14 12:56:28 +0000 (Thu, 14 Feb 2008) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h symm_colour changed to symmetry_colour and symmetry_colour_merge_weight is made a single variable, not an array. set symmetry colour and colour merge is added to the state file [fixes Doug Kuntz request]. ------------------------------------------------------------------------ r787 | pemsley | 2008-02-14 09:40:54 +0000 (Thu, 14 Feb 2008) | 5 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c add_ccp4i_projects_to_optionmenu() now takes the file_selection_type as an argument so that we can encode it in position passed to option_menu_refmac_ccp4i_project_signal_func(). Save python from the rsync filter. ------------------------------------------------------------------------ r786 | pemsley | 2008-02-13 16:56:51 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/c-interface-build.cc remove extra erase_last_molecule() calls in new_molecule functions. ------------------------------------------------------------------------ r785 | pemsley | 2008-02-13 12:29:38 +0000 (Wed, 13 Feb 2008) | 5 lines Changed paths: M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc Fix up the NCS differences geometry graph. It should be more robust now. Add water_chain_from_shelx_ins to scripting layer. Add start of partial charges code. ------------------------------------------------------------------------ r784 | pemsley | 2008-02-13 12:25:34 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm Add shelx test and non-happy path tests. ------------------------------------------------------------------------ r783 | pemsley | 2008-02-13 12:24:15 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Add functions for snarfing. ------------------------------------------------------------------------ r782 | pemsley | 2008-02-13 12:23:20 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/pixmaps/add-water.svg M /trunk/pixmaps/side-chain-180.svg Tinker with icons. ------------------------------------------------------------------------ r781 | pemsley | 2008-02-13 12:22:40 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it Add Joseph Moran's CC fix. ------------------------------------------------------------------------ r780 | pemsley | 2008-02-13 09:04:54 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use --strip 1 for python patch, not -p0. ------------------------------------------------------------------------ r779 | pemsley | 2008-02-13 08:45:47 +0000 (Wed, 13 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in cci patches when building Python (from Nigel Moriarty). ------------------------------------------------------------------------ r778 | pemsley | 2008-02-12 17:53:37 +0000 (Tue, 12 Feb 2008) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info-ncs.cc ncs_residue_info_t is not to be used if filled is not 1. Fixes mad max residue number and problem creating graph x axis [JED]. ------------------------------------------------------------------------ r777 | pemsley | 2008-02-12 16:52:47 +0000 (Tue, 12 Feb 2008) | 4 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/positioned-widgets.h More work on fixed atom dialog. Now it behaves sensibly when an atom is picked - a wrapper for the dialog is used and stored as a static. ------------------------------------------------------------------------ r776 | pemsley | 2008-02-12 15:28:04 +0000 (Tue, 12 Feb 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade A /trunk/pixmaps/anchor.svg M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/support-gtk2-extras.c Add Fixed atom Toolbar icon. Add destroy callback to fixed atom dialog. ------------------------------------------------------------------------ r775 | pemsley | 2008-02-12 08:56:02 +0000 (Tue, 12 Feb 2008) | 4 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Remove GUILE_VERSION debugging from configure.in Change to toolbarbutton for fixed atoms in model_toolbar. Add fixup-gtk2-interface.sh for old gtk2 file choosers. ------------------------------------------------------------------------ r774 | pemsley | 2008-02-12 08:36:02 +0000 (Tue, 12 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add in the Neil Jerram guile-gui patch. ------------------------------------------------------------------------ r773 | pemsley | 2008-02-11 23:02:29 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Remove pycairo build and fix up test for build for guile_gtk ------------------------------------------------------------------------ r772 | pemsley | 2008-02-11 22:44:43 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple remove freetype etc dependencies of pycairo. ------------------------------------------------------------------------ r771 | pemsley | 2008-02-11 22:42:23 +0000 (Mon, 11 Feb 2008) | 2 lines Changed paths: M /trunk/src/coot.in set PYTHONHOME in coot, because of relocatability. ------------------------------------------------------------------------ r770 | pemsley | 2008-02-11 18:21:18 +0000 (Mon, 11 Feb 2008) | 3 lines Changed paths: M /trunk/configure.in D /trunk/src/coot A /trunk/src/coot.in (from /trunk/src/coot:769) configure.in sets GUILE_VERSION and that macro is exanded in coot.in to make coot, so that coot loads guile modules correctly. ------------------------------------------------------------------------ r769 | pemsley | 2008-02-11 18:10:59 +0000 (Mon, 11 Feb 2008) | 3 lines Changed paths: M /trunk/src/coot Add setting for GUILE_VERSION so that guile loads properly from coot with version 1.8 guile. ------------------------------------------------------------------------ r768 | b.lohkamp | 2008-02-11 10:14:03 +0000 (Mon, 11 Feb 2008) | 1 line Changed paths: M /trunk/src/c-interface-preferences.cc filled generic_object_name_py ------------------------------------------------------------------------ r767 | pemsley | 2008-02-10 21:34:33 +0000 (Sun, 10 Feb 2008) | 3 lines Changed paths: M /trunk/python/coot_load_modules.py.in M /trunk/python/extensions.py Comment out pygtk.require("2.0") in coot_load_modules.py. Comment out sep.props.sensitive = False in extension.py. ------------------------------------------------------------------------ r766 | pemsley | 2008-02-10 03:11:10 +0000 (Sun, 10 Feb 2008) | 10 lines Changed paths: M /trunk/build-it-gtk2-simple M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/pixmaps/refine-1.svg M /trunk/src/c-interface-gui.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h A /trunk/src/fixup-gtk2-interface.sh M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c In configure.in change to 2.4.12 for GTK version check. Add (GTK_MINOR_VERSION < 10) to gtk2_file_chooser_selector/chooser usage. Similarly #def out GtkFileChooserConfirmation usage in callbacks.c and callbacks.h Add fixup-gtk2-interface.sh to remove 2.8 dependencies. Currently we need to run this by hand. That should be automated later. Add fixed atom check in graphics-info-defines.cc Add pkg-config test for gtk in build-it-gtk-simple so that we can know if we need to fix up guile-gtk's gtk-glue.c ------------------------------------------------------------------------ r765 | pemsley | 2008-02-09 23:25:49 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface-preferences.cc Fix typo in iobj. ------------------------------------------------------------------------ r764 | pemsley | 2008-02-09 23:15:02 +0000 (Sat, 09 Feb 2008) | 3 lines Changed paths: M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h Pass back a SCM for generic_object_name() and generic_object_index() checks for closed generic objects and ignore them. ------------------------------------------------------------------------ r763 | pemsley | 2008-02-09 15:48:45 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Use pygtk 2.8.6 for simple build too. ------------------------------------------------------------------------ r762 | pemsley | 2008-02-09 15:46:53 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Us pygtk version 2.8.6 not 2.12.1, can we now build pygtk on FC5 machine? ------------------------------------------------------------------------ r761 | pemsley | 2008-02-09 11:15:35 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2-simple Add back building of gtkglext. ------------------------------------------------------------------------ r760 | pemsley | 2008-02-09 00:13:57 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: A /trunk/build-it-gtk2-simple Remove gtk2 and pkg-config building. Test for Fedora core 5. ------------------------------------------------------------------------ r759 | pemsley | 2008-02-09 00:11:01 +0000 (Sat, 09 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix logic of atk installation. ------------------------------------------------------------------------ r758 | pemsley | 2008-02-08 19:27:50 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 version testing. ------------------------------------------------------------------------ r757 | pemsley | 2008-02-08 18:28:03 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Try requiring gtk 2.10 ------------------------------------------------------------------------ r756 | pemsley | 2008-02-08 17:42:36 +0000 (Fri, 08 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 lib cleaning problems, add debugging. ------------------------------------------------------------------------ r755 | pemsley | 2008-02-07 14:59:14 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/pixmaps/rigid-body.svg M /trunk/pixmaps/side-chain-180.png M /trunk/pixmaps/side-chain-180.svg Update a couple of icons. ------------------------------------------------------------------------ r754 | pemsley | 2008-02-07 13:46:05 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Tinker with build_gmp logic. ------------------------------------------------------------------------ r753 | pemsley | 2008-02-07 13:44:15 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Add coot-preferences.h to Makefile.am ------------------------------------------------------------------------ r752 | pemsley | 2008-02-07 13:12:31 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Grr... Spell validation-graphs correctly. Sigh. ------------------------------------------------------------------------ r751 | pemsley | 2008-02-07 12:48:14 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/src/Makefile.am Oops. Add validation-graphs.hh to the Makefile.am too. ------------------------------------------------------------------------ r750 | pemsley | 2008-02-07 12:41:21 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add test and build of ATK, needed for gtk+2.10.x ------------------------------------------------------------------------ r749 | pemsley | 2008-02-07 09:19:32 +0000 (Thu, 07 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/scheme/snarf-coot-docs.scm Fix ncs-chain-ids-scm for correct snarfing. ------------------------------------------------------------------------ r748 | pemsley | 2008-02-07 08:52:25 +0000 (Thu, 07 Feb 2008) | 6 lines Changed paths: M /trunk/atom-utils/Makefile.am M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/happy-coot-diary.html M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c The other major part of the molecule array -> vector changes. These are to move the validation graphs, the ramachandran plots and sequence view into the molecules. set_validation_graph() and get_validation_graph() functions created. erase_last_molecule()s have been matched to create_molecule()s. ------------------------------------------------------------------------ r747 | pemsley | 2008-02-06 19:09:40 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: A /trunk/src/validation-graphs.hh Oops. Add validation-graphs header. ------------------------------------------------------------------------ r746 | b.lohkamp | 2008-02-06 18:10:11 +0000 (Wed, 06 Feb 2008) | 7 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/Makefile.am D /trunk/src/add-coot-i-extern.sh M /trunk/src/coot.i M /trunk/src/coot.py D /trunk/src/coot_pre.i changed interesting_things_gui back to gtk.window (uses nested gtk mainloop now) changed coot.i back (apparently do not need any extern statements...) cosmetic changes to read_refmac_log ------------------------------------------------------------------------ r745 | pemsley | 2008-02-06 17:53:07 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/molecule-class-info.h match create_molecules() with erase_last_molecule() in c-interface-build.cc ------------------------------------------------------------------------ r744 | pemsley | 2008-02-06 17:51:21 +0000 (Wed, 06 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 More tinkering with tests for pango, cairo etc. Change to the version Bernhard recommends. ------------------------------------------------------------------------ r743 | b.lohkamp | 2008-02-06 14:18:03 +0000 (Wed, 06 Feb 2008) | 6 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py M /trunk/src/Makefile.am A /trunk/src/add-coot-i-extern.sh M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-python.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot M /trunk/src/coot.i A /trunk/src/coot_pre.i M /trunk/src/main.cc tooltip for interesting_things_gui (required change from gtk.window to gtk.dialog); used in read_refmac_log coot.i can be generated from coot_pre.i with src/add-coot-i-extern.sh (auto- matically adds extern to PyObjects from c-interface.h etc.). Remember to run when additional py functions are avaliable!! ------------------------------------------------------------------------ r742 | pemsley | 2008-02-04 11:37:43 +0000 (Mon, 04 Feb 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc Add the ability to turn off DTI stereo (thanks Hartmut Luecke). ------------------------------------------------------------------------ r741 | b.lohkamp | 2008-02-02 16:18:41 +0000 (Sat, 02 Feb 2008) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/python/coot_gui.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot A /trunk/src/coot-preferences.h M /trunk/src/coot.i M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c include COOT_PYTHON_DIR in coot some python functions tollbars and variable notebook tabs for preferences, add coot-preferences.h fixed python scripting window for non-pygtk (including memory issue) ------------------------------------------------------------------------ r740 | pemsley | 2008-02-01 14:18:05 +0000 (Fri, 01 Feb 2008) | 4 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-maps.cc Make tests pass - fix return value of handle-read-ccp4-map. Remove some debugging from simple-restraint.cc. Add fixed atom dialog - gtk1 version. ------------------------------------------------------------------------ r739 | pemsley | 2008-02-01 13:20:47 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Add fixed atom dialog. ------------------------------------------------------------------------ r738 | pemsley | 2008-02-01 13:10:01 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/src/c-interface.cc Remove "force redraw" debugging line. ------------------------------------------------------------------------ r737 | pemsley | 2008-02-01 13:05:14 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.h Fix up fixed atom in refinement. They work now (but from scripting, not gui) ------------------------------------------------------------------------ r736 | pemsley | 2008-02-01 02:36:26 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix up test for pygobject and pygtk. ------------------------------------------------------------------------ r735 | pemsley | 2008-02-01 02:29:06 +0000 (Fri, 01 Feb 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix problem in scripting args to coot's configure. ------------------------------------------------------------------------ r734 | pemsley | 2008-01-31 18:55:28 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/gtk2-interface.c further improvements on the fixed atoms in refinement. ------------------------------------------------------------------------ r733 | pemsley | 2008-01-31 15:37:19 +0000 (Thu, 31 Jan 2008) | 6 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/happy-coot-diary.html M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Changed fixed atom to be specs that are passed to simple_restraint. simple_restraint needs to properly handle the fixed atoms when generating the restraints. build-it-gtk2: Change HOSTLOGDIR to include gtk2 to separate it from gtk1 build logs. ------------------------------------------------------------------------ r732 | pemsley | 2008-01-31 14:00:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/junk.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Update code for fixing atoms. Not transfered to GUI or refinement code yet. ------------------------------------------------------------------------ r731 | pemsley | 2008-01-31 12:41:13 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-maps.cc M /trunk/src/molecule-class-info.cc Move lots of molecule_class_info_t map functions to molecule-class-info-maps.cc. ------------------------------------------------------------------------ r730 | pemsley | 2008-01-31 08:40:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add extra tests for reading bogus mtz/maps. ------------------------------------------------------------------------ r729 | pemsley | 2008-01-31 08:39:26 +0000 (Thu, 31 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Make the log files be gtk2-build.log, to separate them out from gtk1 build. ------------------------------------------------------------------------ r728 | pemsley | 2008-01-30 17:23:23 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes rearrange cairo and librsvg. ------------------------------------------------------------------------ r727 | pemsley | 2008-01-30 16:26:51 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fontonfig added. ------------------------------------------------------------------------ r726 | pemsley | 2008-01-30 15:53:27 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Freetype2 building updates. ------------------------------------------------------------------------ r725 | pemsley | 2008-01-30 15:19:10 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Remove static patch (for sgi). Add test/build for freetype2 ------------------------------------------------------------------------ r724 | pemsley | 2008-01-30 09:36:48 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in pkg-configure build. ------------------------------------------------------------------------ r723 | pemsley | 2008-01-30 09:27:40 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in building of pkg-config. ------------------------------------------------------------------------ r722 | pemsley | 2008-01-30 09:25:54 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add --pygtk to configure for coot. ------------------------------------------------------------------------ r721 | pemsley | 2008-01-30 02:54:51 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 librsvg depends on cairo apparently - reorder. ------------------------------------------------------------------------ r720 | pemsley | 2008-01-30 02:48:16 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix typo in gtk2 set test for failure. ------------------------------------------------------------------------ r719 | pemsley | 2008-01-30 02:40:03 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix pkg-config typo. ------------------------------------------------------------------------ r718 | pemsley | 2008-01-30 02:39:07 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix syntax error. ------------------------------------------------------------------------ r717 | pemsley | 2008-01-30 02:37:37 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 pycairo needs cairo 1.4.12 - so test for cairo, setting build_gtk=1 on failure. ------------------------------------------------------------------------ r716 | pemsley | 2008-01-30 00:34:11 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add test for pycairo ------------------------------------------------------------------------ r715 | pemsley | 2008-01-30 00:08:19 +0000 (Wed, 30 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add pycairo. ------------------------------------------------------------------------ r714 | pemsley | 2008-01-29 18:56:06 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 pygobject typos. ------------------------------------------------------------------------ r713 | pemsley | 2008-01-29 18:52:34 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 more pygobject typos fixed. ------------------------------------------------------------------------ r712 | pemsley | 2008-01-29 18:49:47 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 fix typos. ------------------------------------------------------------------------ r711 | pemsley | 2008-01-29 18:46:31 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typos in build-it-gtk2 ------------------------------------------------------------------------ r710 | pemsley | 2008-01-29 18:37:59 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/Makefile.am Add ncs greg tests to tar file. ------------------------------------------------------------------------ r709 | pemsley | 2008-01-29 18:31:28 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes Add pkg-config and pygobject builds. ------------------------------------------------------------------------ r708 | pemsley | 2008-01-29 16:30:56 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 M /trunk/src/c-interface-build.cc more debugging in the pygkt macro. ------------------------------------------------------------------------ r707 | b.lohkamp | 2008-01-29 16:20:54 +0000 (Tue, 29 Jan 2008) | 1 line Changed paths: M /trunk/python/extensions.py Fix Cootaneer-gui in extensions.py ------------------------------------------------------------------------ r706 | b.lohkamp | 2008-01-29 16:11:11 +0000 (Tue, 29 Jan 2008) | 1 line Changed paths: M /trunk/python/coot_gui.py M /trunk/python/refmac.py refmac log file reader for python ------------------------------------------------------------------------ r705 | pemsley | 2008-01-29 15:44:23 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 M /trunk/src/c-interface-build.cc Remove ambiguity of double from python variable in constructing atom attributes. ------------------------------------------------------------------------ r704 | pemsley | 2008-01-29 15:22:02 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 pygtk settings, improved. ------------------------------------------------------------------------ r703 | pemsley | 2008-01-29 15:12:38 +0000 (Tue, 29 Jan 2008) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Adjust pygtk settings so that it compiles in only if specified. ------------------------------------------------------------------------ r702 | pemsley | 2008-01-29 10:06:58 +0000 (Tue, 29 Jan 2008) | 4 lines Changed paths: M /trunk/build-it-gtk2 M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a SCM function refmac_params_scm(). Add function erase_last_molecule() for when we create a molecule, but fail to fill it. ------------------------------------------------------------------------ r701 | pemsley | 2008-01-28 19:46:54 +0000 (Mon, 28 Jan 2008) | 4 lines Changed paths: M /trunk/atom-utils/atom-utils.cc M /trunk/doc/Makefile.am M /trunk/doc/functions.tex M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/libtool M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/coot M /trunk/src/coot.py M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc Move from graphics::molecules begin an array to being a vector. Tests pass. Validation graphs need to be moved in to molecules. expand_molecule_space() needs some thought. ------------------------------------------------------------------------ r700 | pemsley | 2008-01-28 17:54:03 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add lib/python2.5 to the rsynced files. ------------------------------------------------------------------------ r699 | pemsley | 2008-01-28 17:45:18 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 more python debugging. ------------------------------------------------------------------------ r698 | pemsley | 2008-01-28 17:44:05 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Further python/pygtk tinkering. ------------------------------------------------------------------------ r697 | pemsley | 2008-01-28 17:30:46 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add a test for the existance of pygtk ------------------------------------------------------------------------ r696 | pemsley | 2008-01-28 16:57:04 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging/fixes. ------------------------------------------------------------------------ r695 | pemsley | 2008-01-28 16:54:13 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging. ------------------------------------------------------------------------ r694 | pemsley | 2008-01-28 16:50:33 +0000 (Mon, 28 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 add debugging. ------------------------------------------------------------------------ r693 | pemsley | 2008-01-26 15:44:29 +0000 (Sat, 26 Jan 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/python/coot_load_modules.py.in M /trunk/scheme/mutate.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-mutate.cc Fix GTK Warning on using CCP4i option menu in a map file selector. Add test for atom order after mutation. Change order of arguments to mutate function. ------------------------------------------------------------------------ r692 | pemsley | 2008-01-25 23:35:02 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/TODO M /trunk/build-it-gtk2 M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes Fix up write_ins_file_internal to return a good status on correct write. So that test passes. ------------------------------------------------------------------------ r691 | pemsley | 2008-01-25 23:14:56 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/07-ncs.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h A better name for NCS chains. Update greg test. ------------------------------------------------------------------------ r690 | pemsley | 2008-01-25 18:08:47 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Update the pepflip test, now that we have changed the arguments to the scripting function. ------------------------------------------------------------------------ r689 | pemsley | 2008-01-25 16:40:20 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm extra error messages from shelx greg test. ------------------------------------------------------------------------ r688 | pemsley | 2008-01-25 14:45:00 +0000 (Fri, 25 Jan 2008) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/snarf-coot-docs.scm Need to define scm commands in snarf-coot-docs.scm so that coot-utils.scm can be loaded OK. ------------------------------------------------------------------------ r687 | pemsley | 2008-01-25 14:13:31 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Fix refmac arg construction when using python. Should fix Bill Scott's bug. ------------------------------------------------------------------------ r686 | pemsley | 2008-01-25 12:44:27 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/macros/net-http-goosh.m4 Fix up macro test for guile-gui so that it doesn't try to use $DISPLAY. ------------------------------------------------------------------------ r685 | pemsley | 2008-01-25 11:50:49 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/train-pepflip.cc Update pepflip code. ------------------------------------------------------------------------ r684 | pemsley | 2008-01-25 00:45:35 +0000 (Fri, 25 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc Fill validation graph for NCS differences. ------------------------------------------------------------------------ r683 | pemsley | 2008-01-24 20:52:57 +0000 (Thu, 24 Jan 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-graphs.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.h Add NCS differences to Validation menu on the GUI. Fix up (on penelope) accession button problems. ------------------------------------------------------------------------ r682 | pemsley | 2008-01-24 18:45:32 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 build-it-gtk extra notes. ------------------------------------------------------------------------ r681 | b.lohkamp | 2008-01-24 17:21:16 +0000 (Thu, 24 Jan 2008) | 7 lines Changed paths: M /trunk/configure.in M /trunk/macros/with-guile.m4 M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ncs.cc A /trunk/src/c-interface-python.cc A /trunk/src/c-interface-python.hh M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/graphics-info.cc M /trunk/src/main.cc docked accept/reject toolbar shows distorsion chi2 as tooltip and extra information for chiral outliers (in the Chirals box) and introduced CIS petides (extra box). new python functions and file (c-interface-python.cc) configure with no --with-guile (or with --without-guile) ignores all guile configuring ------------------------------------------------------------------------ r680 | pemsley | 2008-01-24 12:55:43 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Further work on the NCS differences graph. ------------------------------------------------------------------------ r679 | pemsley | 2008-01-24 12:06:43 +0000 (Thu, 24 Jan 2008) | 3 lines Changed paths: M /trunk/src/gtk-manual.c M /trunk/src/gtk-manual.h M /trunk/src/molecule-class-info.cc Use GINT_TO_POINTER and GPOINTER_TO_INT not casting int * for display control window control. ------------------------------------------------------------------------ r678 | pemsley | 2008-01-24 01:01:22 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 adjustments. ------------------------------------------------------------------------ r677 | pemsley | 2008-01-24 00:56:22 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 gtk2 adjustments. ------------------------------------------------------------------------ r676 | pemsley | 2008-01-24 00:51:43 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Gtk2 adjustments. ------------------------------------------------------------------------ r675 | pemsley | 2008-01-24 00:49:58 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Adjust build-it-gtk2, gtk2 dependencies. ------------------------------------------------------------------------ r674 | pemsley | 2008-01-24 00:45:03 +0000 (Thu, 24 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Build GTK2 from scratch: librsvg, cairo, pango, glitz. glib, gtk+-2 ------------------------------------------------------------------------ r673 | pemsley | 2008-01-23 14:07:36 +0000 (Wed, 23 Jan 2008) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/train-pepflip.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ideal/pepflip.cc M /trunk/python/extensions.py M /trunk/scheme/coot-gui.scm M /trunk/scheme/fitting.scm M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc Add pepfip-active-residue. Add test-for-pepflip code into db-main. Trying to find a good metrix now. Eigen value filtering of fragments to speed things up. ------------------------------------------------------------------------ r672 | pemsley | 2008-01-23 09:30:00 +0000 (Wed, 23 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Fix typo in guile test. ------------------------------------------------------------------------ r671 | pemsley | 2008-01-23 09:25:37 +0000 (Wed, 23 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Change the tests for gtk, and try to build guile with optimization. ------------------------------------------------------------------------ r670 | pemsley | 2008-01-22 18:29:48 +0000 (Tue, 22 Jan 2008) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/dnotes M /trunk/greg-tests/02-shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Add a test for INS file from PDB. Make refinement button label configurable. If cell not found, add a cell from a mmdb manager in shelx writer. ------------------------------------------------------------------------ r669 | pemsley | 2008-01-22 18:26:53 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/configure.in A /trunk/macros/net-http-goosh.m4 Test for net http, goosh and gui if guile is to be used. ------------------------------------------------------------------------ r668 | pemsley | 2008-01-22 14:48:32 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/post-gtk2-glade.sh Add a button to the accession code window. ------------------------------------------------------------------------ r667 | pemsley | 2008-01-22 12:35:59 +0000 (Tue, 22 Jan 2008) | 2 lines Changed paths: M /trunk/src/callbacks.c Fix typo in GTK version test. ------------------------------------------------------------------------ r666 | b.lohkamp | 2008-01-22 11:28:36 +0000 (Tue, 22 Jan 2008) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c smaller toolbar style chooser button accept_reject dialog can be docked (set_accept_reject_dialog) ------------------------------------------------------------------------ r665 | pemsley | 2008-01-21 21:27:33 +0000 (Mon, 21 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes update notes. ------------------------------------------------------------------------ r664 | b.lohkamp | 2008-01-21 14:29:02 +0000 (Mon, 21 Jan 2008) | 1 line Changed paths: M /trunk/configure.in Check for gtk2 version 2.8 ------------------------------------------------------------------------ r663 | b.lohkamp | 2008-01-21 09:43:58 +0000 (Mon, 21 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/add-c-extern.sh M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Changes to model/refine toolbar. Has style chooser and handle now. ------------------------------------------------------------------------ r662 | pemsley | 2008-01-19 23:32:26 +0000 (Sat, 19 Jan 2008) | 2 lines Changed paths: M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/train-pepflip.cc More progress on the matching of pentapeptides. ------------------------------------------------------------------------ r661 | pemsley | 2008-01-18 21:00:43 +0000 (Fri, 18 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add pkgconfig support to find gtkglext ------------------------------------------------------------------------ r660 | pemsley | 2008-01-18 18:34:37 +0000 (Fri, 18 Jan 2008) | 2 lines Changed paths: M /trunk/build-it-gtk2 Add the building of gtkglext. ------------------------------------------------------------------------ r659 | pemsley | 2008-01-18 16:01:14 +0000 (Fri, 18 Jan 2008) | 3 lines Changed paths: M /trunk/build-it-gtk2 Lots of trials on build-it-gtk2, guile, guile-gtk, python dependences updated. ------------------------------------------------------------------------ r658 | b.lohkamp | 2008-01-18 09:24:41 +0000 (Fri, 18 Jan 2008) | 1 line Changed paths: M /trunk/src/coot setting COOT_PYTHON_PATH ------------------------------------------------------------------------ r657 | pemsley | 2008-01-17 17:29:53 +0000 (Thu, 17 Jan 2008) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it-gtk2 M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c Verticalize the refinement traffic lights. ------------------------------------------------------------------------ r656 | b.lohkamp | 2008-01-17 12:56:21 +0000 (Thu, 17 Jan 2008) | 1 line Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-scm.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc implement gtk2's overwrite protection when saving files in file_ chooser mode ------------------------------------------------------------------------ r655 | pemsley | 2008-01-17 11:39:22 +0000 (Thu, 17 Jan 2008) | 2 lines Changed paths: A /trunk/src/molecule-class-info-maps.cc Add molecule-class-info-maps.cc ------------------------------------------------------------------------ r654 | pemsley | 2008-01-17 11:37:58 +0000 (Thu, 17 Jan 2008) | 3 lines Changed paths: M /trunk/src/c-interface-scm.cc include guile/gh.h for guile-1.6.7, so that gh_scm2int is defined. Perhaps not the best fix. ------------------------------------------------------------------------ r653 | pemsley | 2008-01-17 11:09:35 +0000 (Thu, 17 Jan 2008) | 2 lines Changed paths: M /trunk/src/c-interface-ncs.cc Use SCM_CDR not scm_cdr for guile-1.6.7 ------------------------------------------------------------------------ r652 | pemsley | 2008-01-17 10:37:36 +0000 (Thu, 17 Jan 2008) | 65 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/db-main/Makefile.am M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/testdbmain.cc A /trunk/db-main/train-pepflip.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm A /trunk/greg-tests/07-ncs.scm M /trunk/high-res/sequence-assignment.cc M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/test-ligand.cc M /trunk/ligand/torsion-general.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/process-greg-log.awk M /trunk/scheme/Makefile.am M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/coot.scm M /trunk/scheme/get-ebi.scm M /trunk/scheme/greg-extensions.scm A /trunk/scheme/matrices.scm M /trunk/scheme/ncs.scm M /trunk/sequence-view/sequence-view.cc M /trunk/src/Makefile.am M /trunk/src/align.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/cmtz-interface.cc M /trunk/src/command-line.cc M /trunk/src/coot-align.cc M /trunk/src/coot-nomenclature.cc M /trunk/src/density-score-by-residue.cc M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/mol-hierachy.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info-widget-work.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc M /trunk/src/pick.h M /trunk/src/rama_mousey.cc M /trunk/src/rama_plot.cc M /trunk/src/read-phs.c Changes from Chennia Trip: Many and various fixes because I turned on -Wall Updated copyright notices test-ligand expanded to test torsion general. db_main extended to support pepflip testing (not completed). Add code to "train" pepflip by getting best values for cuttoffs (not complete). Function added from Chart, to transpose a matrix. Used in nudge view to move the axes relative to screen orientation (like Bernhard had done in the python version). pick_atom() updated to take account of what is being displayed. If in CA mode, only CAs can be picked. map_sampling_rate is passed to the fill_map_from_mtz etc functions, rather than using a static in the class. A small step. SCM ncs_chains function added. Used in ncs chain skipping. A test added for this. Also SCM ncs_chain_differences_scm() - returns a SCM variable, but needs to be made into a graph at some stage soon. A test added for this. coot-gtk2.glade was a massive (but simple) conflict. There were ^Ms in the glade file. make_atom_spec(SCM spec) function created. map_rate_sampling not used as a static variable, but is now passed to function. For mtz and phs reading. A sharpen() function introduced - but only a stub. There is a problem with storing the data. mark_atom_as_fixed() function added - for use in marking atom as "fixed" during refinement. This feature addition stalled. Needs completing. Tricky. After seeing several screenshots from Coot at the meeting in Chennai (all with hard-to-see skinny bonds), the default bond width is changed to 5. Add a SHELXL test from Fredrick Hollander .ins file. Fixes the problem of reading lowercased symm ops. Add a SHELXL test reading insulin .ins and .fcf data. Spacegroups tested. Add a test for libraries using problem data from Seth Horne. Added infrastructure for Ramachandran plot refinement. drag_intermediate_atom() function added which can simulate the user dragging atoms with the mouse. This should be added to the history at some stage. Dragged atom "rubber sheet" changed so that atoms close to the dragged atom are not distorted (from the dragged atom) so much - not sure if I like this new way. ------------------------------------------------------------------------ r651 | b.lohkamp | 2008-01-16 09:16:20 +0000 (Wed, 16 Jan 2008) | 12 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/coot.i M /trunk/src/coot.py M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h new 'cootaneer' gui for python imol.apply_sequence will offset unsequenced residues too to avoid residue doublications cootaneer_internal wont change chain_ids any more (BL & KC) new functions: assign_sequence_from_file (using clipper) assign_sequence_from_string delete_all_sequences_from_molecule delete_sequence_by_chain_id change_chain_id_with_result_py (scm function missing...) ------------------------------------------------------------------------ r650 | pemsley | 2008-01-11 17:28:02 +0000 (Fri, 11 Jan 2008) | 2 lines Changed paths: M /trunk/configure.in Move configure.in to 0.5-pre-1 ------------------------------------------------------------------------ r649 | pemsley | 2008-01-11 14:00:05 +0000 (Fri, 11 Jan 2008) | 2 lines Changed paths: A /trunk/build-it-gtk2 Add build-it-gtk2. ------------------------------------------------------------------------ r648 | b.lohkamp | 2008-01-10 09:21:43 +0000 (Thu, 10 Jan 2008) | 6 lines Changed paths: M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/python/generic_objects.py M /trunk/python/ncs.py M /trunk/python/raster3d.py M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot.py M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/post-gtk2-glade.sh decided on version 0.4.2-pre-1 for now. Fixed some python scripts. Some fixes for unusual Windows paths. Introduce GTK2's filechooser for GTK2 build with a flag to selected between the fileslector and filechooser. ------------------------------------------------------------------------ r647 | pemsley | 2008-01-03 07:15:32 +0000 (Thu, 03 Jan 2008) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.4-alternate.xpm M /trunk/pixmaps/coot-0.4.xpm Update splash screens to 0.4.1. ------------------------------------------------------------------------ r646 | pemsley | 2008-01-03 00:42:15 +0000 (Thu, 03 Jan 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES Release 0.4.1 Update release notes. ------------------------------------------------------------------------ r645 | pemsley | 2008-01-02 23:51:21 +0000 (Wed, 02 Jan 2008) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/dnotes M /trunk/src/globjects.cc Fix problem of referencing scroll map, with no map loaded (causing crash). configure.in to 0.4.1 ------------------------------------------------------------------------ r644 | pemsley | 2008-01-02 14:32:35 +0000 (Wed, 02 Jan 2008) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Fix typo in test. ------------------------------------------------------------------------ r643 | pemsley | 2008-01-02 14:32:05 +0000 (Wed, 02 Jan 2008) | 3 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Hmm... The greg test failed for the insulin.res file. Add some debugging. ------------------------------------------------------------------------ r642 | pemsley | 2008-01-02 12:58:40 +0000 (Wed, 02 Jan 2008) | 4 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/main.cc Release 0.4 Add alternate splash screen. Update About dialog. ------------------------------------------------------------------------ r641 | pemsley | 2008-01-02 00:26:48 +0000 (Wed, 02 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade A /trunk/pixmaps/coot-0.4-alternate.xpm A /trunk/pixmaps/coot-0.4.xpm M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/main.cc New splash screen for gtk2. ------------------------------------------------------------------------ r640 | pemsley | 2008-01-01 21:34:31 +0000 (Tue, 01 Jan 2008) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Run post glade script, so that it compiles. ------------------------------------------------------------------------ r639 | pemsley | 2008-01-01 20:56:14 +0000 (Tue, 01 Jan 2008) | 2 lines Changed paths: M /trunk/TODO Update 0.5's todo list. ------------------------------------------------------------------------ r638 | pemsley | 2008-01-01 19:16:44 +0000 (Tue, 01 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Add Martin Noble to the credits. ------------------------------------------------------------------------ r637 | pemsley | 2008-01-01 19:04:27 +0000 (Tue, 01 Jan 2008) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc Move handle_get_accession_code() to c-interface-gui.cc ------------------------------------------------------------------------ r636 | pemsley | 2008-01-01 18:55:28 +0000 (Tue, 01 Jan 2008) | 11 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-map.cc M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h Add torsions to the accept/reject dialog text (if they are turned on). Fix problem of torsions box not being set in the refinement parameters dialog when activated from the toolbar. Fix up do_torsions_toggle(). Create and use wrapped_create_refine_params_dialog() Move set_refine_params_toggle_buttons() to c-interface-gui.cc Move fill_chiral_volume_molecule_option_menu to c-interface-gui.cc When torsion refinement had been turned on, chirals had been turned off. This is fixed now. Refinement lights code tided up using a vector of pairs of strings. ------------------------------------------------------------------------ r635 | pemsley | 2008-01-01 15:23:17 +0000 (Tue, 01 Jan 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h Remove the colourselection pickers and replace them with frames that contain event boxes. In the Gtk2 version, set the background colour of these event boxes on refinement updates. ------------------------------------------------------------------------ r634 | pemsley | 2008-01-01 01:52:37 +0000 (Tue, 01 Jan 2008) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Fix up the refinement lights. Now they are updated on interactive refinement. They are insensitive and greyed out now (I don't like the colours much). ------------------------------------------------------------------------ r633 | pemsley | 2008-01-01 00:01:39 +0000 (Tue, 01 Jan 2008) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/mapview.glade M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc Add code to display coloured lights on refinement. In progress. ------------------------------------------------------------------------ r632 | pemsley | 2007-12-31 22:04:06 +0000 (Mon, 31 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Fix typo in previous commit. Silly - tired. ------------------------------------------------------------------------ r631 | pemsley | 2007-12-31 22:01:34 +0000 (Mon, 31 Dec 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc Add valid map protection to skeletonize_map_by_optionmenu(). ------------------------------------------------------------------------ r630 | pemsley | 2007-12-31 21:55:19 +0000 (Mon, 31 Dec 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/molecule-class-info.cc Add has_map() protection to update_clipper_skeleton(). Might fix a crash. ------------------------------------------------------------------------ r629 | pemsley | 2007-12-31 21:17:06 +0000 (Mon, 31 Dec 2007) | 3 lines Changed paths: M /trunk/macros/with-python.m4 Put a test for Python.h in the with-python macro, if it not found, then we don't compile with python. ------------------------------------------------------------------------ r628 | pemsley | 2007-12-31 20:32:24 +0000 (Mon, 31 Dec 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-navigation-gtk2.cc Move add_sort_button to fileselection to c-interface-gui.cc Fix the problem of unrefing the atom_tree in the Gtk2 Go To Atom window. ------------------------------------------------------------------------ r627 | pemsley | 2007-12-31 20:09:50 +0000 (Mon, 31 Dec 2007) | 6 lines Changed paths: M /trunk/dnotes M /trunk/scheme/clear-backup.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc More fixing of clear-backup code, bug found in gtk1 version. Some more cleaning up of fileselections and the ccp4i project optionmenu therein. add_ccp4i_project_optionmenu() now takes an extra arg, which is the file selection type. ------------------------------------------------------------------------ r626 | pemsley | 2007-12-31 18:32:43 +0000 (Mon, 31 Dec 2007) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/ligand/ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc A /trunk/src/testing-scm.cc A /trunk/src/testing-scm.hh Clean up some debugging. Add testing-scm files - for use after 0.4 is released. No need to set pointer to imol in is_difference_map checkbutton on map read. ------------------------------------------------------------------------ r625 | pemsley | 2007-12-30 18:26:35 +0000 (Sun, 30 Dec 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in dialog-box-of-buttons function. ------------------------------------------------------------------------ r624 | pemsley | 2007-12-30 17:48:49 +0000 (Sun, 30 Dec 2007) | 2 lines Changed paths: M /trunk/scheme/Makefile.am Add bones-reader.scm to the Makefile.am so that it gets installed. ------------------------------------------------------------------------ r623 | pemsley | 2007-12-30 17:35:57 +0000 (Sun, 30 Dec 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/src/c-interface-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.h Chi Angles now get written to the Residue Info screen. Reworked monomer_utils and chi_angles classes. ------------------------------------------------------------------------ r622 | pemsley | 2007-12-30 11:29:26 +0000 (Sun, 30 Dec 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Restore the mysteriously-disappeared menu items in the nucleotide builder dialog. ------------------------------------------------------------------------ r621 | pemsley | 2007-12-30 03:28:09 +0000 (Sun, 30 Dec 2007) | 2 lines Changed paths: A /trunk/src/support-gtk2-extras.c Add missing src/support-gtk2-extras.c ------------------------------------------------------------------------ r620 | pemsley | 2007-12-30 02:13:27 +0000 (Sun, 30 Dec 2007) | 8 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/greg-tests/02-shelx.scm M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/mapview.glade M /trunk/scheme/greg-extensions.scm M /trunk/src/Makefile.am M /trunk/src/add-c-extern.sh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/pick.cc M /trunk/src/pick.h M /trunk/src/support.c M /trunk/src/support.h Add shelx insulin to greg tests. Add reverse button to accept/reject dialog. Add dynamic distances, with togglebutton in Geometry. Extra conditional in graphics-info-defines.cc check_if_in_geometry_range_defines support-gtk2-extra.c added which contains pixbuf functions. Tinker with starting support for RAMA targets in idealization. ------------------------------------------------------------------------ r619 | pemsley | 2007-12-28 22:15:11 +0000 (Fri, 28 Dec 2007) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/cootrc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ligand/torsion-general.cc M /trunk/macros/libglade.m4 M /trunk/mapview.glade M /trunk/pixmaps/connect-to-usf.svg M /trunk/scheme/clear-backup.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cmtz-interface.cc A /trunk/src/coot-fileselections.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.c M /trunk/src/support.h Fix up the contact indices generator for torsion_general. Add a Reverse button to the accept_reject dialog. Add a static reverse flag for this. Document Clear Backups. Make delete-coot-backup-files behave more elegantly when it can't write a file. Improve macro for libglade. Move some GUI functions into c-interface-gui.cc Use DEFINES for dialog fileselection lookups. ------------------------------------------------------------------------ r618 | pemsley | 2007-12-27 18:40:45 +0000 (Thu, 27 Dec 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Fix problem of missing file. ------------------------------------------------------------------------ r617 | pemsley | 2007-12-27 17:40:33 +0000 (Thu, 27 Dec 2007) | 2 lines Changed paths: M /trunk/src/rama_plot.cc Fix fabs on diff. ------------------------------------------------------------------------ r616 | pemsley | 2007-12-27 17:33:01 +0000 (Thu, 27 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc Remove debugging line for file chooser. ------------------------------------------------------------------------ r615 | pemsley | 2007-12-27 17:23:39 +0000 (Thu, 27 Dec 2007) | 2 lines Changed paths: A /trunk/ligand/test-ligand.cc Add test-ligand.cc ------------------------------------------------------------------------ r614 | pemsley | 2007-12-27 16:54:28 +0000 (Thu, 27 Dec 2007) | 3 lines Changed paths: M /trunk/ligand/Makefile.am A /trunk/ligand/torsion-general.cc A /trunk/ligand/torsion-general.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Implement torsion_general. Not too painful as it turns out. Seems to work OK, but currently needs a widget to setup_torsion_general(). ------------------------------------------------------------------------ r613 | pemsley | 2007-12-26 23:30:28 +0000 (Wed, 26 Dec 2007) | 19 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/05-rna-ghosts.scm M /trunk/greg-tests/06-ssm.scm M /trunk/greg-tests/begin.grg M /trunk/macros/with-python.m4 M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/Makefile.am M /trunk/src/TODO M /trunk/src/add-c-extern.sh M /trunk/src/c-interface-build.cc A /trunk/src/c-interface-database.cc A /trunk/src/c-interface-database.hh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/coot.i M /trunk/src/gl-matrix.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/rama_plot.cc M /trunk/src/support.h Add scheme function sanitize-alt-confs-in-residue. Make the greg tests run faster on a machine with slow graphics by determining the number of frames to rotate using roate-n-frames Overhaul tweak alt confs test case to account for the fact that the active residue is not always in imol-rnase Adjust conditionals in interface.h Exit should be the door icon. Create globularize_dialog(). Not attached to anything yet. Move add_filename_filter_button to c-interface-gui.cc Use an enum var for chooser_selector_flag. Add torsion_general infrastructure - not working yet. Create c-interface-database.cc for database interaction code. Add c-interface-database.hh to coot.i. Display list objects now only get drawn when drawit is true. Kleywegt plots now draw lines to the edges of the plot, rather than right across the plot when going over the border. Check that a menu from an option menu returns a valid pointer before using (destroying) it. ------------------------------------------------------------------------ r612 | pemsley | 2007-12-23 00:43:03 +0000 (Sun, 23 Dec 2007) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/add-c-extern.sh M /trunk/src/callbacks.c M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.c M /trunk/src/support.h Fix greg-test tweaking alt confs. Clean up interface.c Hack in a create_coords_filechooserdialog1() to gtk-manual.c. Remove duplication in interface.h Fix up add-c-extern for extra Gtk2 functions. ------------------------------------------------------------------------ r611 | pemsley | 2007-12-21 15:43:47 +0000 (Fri, 21 Dec 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/python/coot_utils.py No more MET disulfide bonds. ------------------------------------------------------------------------ r610 | pemsley | 2007-12-21 14:02:43 +0000 (Fri, 21 Dec 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add function shelx-molecule? and associated raw function. Also residue-info-dialog-is-displayed(). Alos density_at_point() to the scripting layer. Added sanitise alt confs function and greg test. ------------------------------------------------------------------------ r609 | pemsley | 2007-12-20 23:43:26 +0000 (Thu, 20 Dec 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/05-rna-ghosts.scm M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-defines.cc Update greg test rna-ghosts to use new set-atom-attributes. Much faster. Add function residue_info_dialog(). Rename other residue_info functions. ------------------------------------------------------------------------ r608 | pemsley | 2007-12-20 19:38:55 +0000 (Thu, 20 Dec 2007) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/sequence-view/seq-view-interface.c M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc Use GPOINTER_TO_INT when dereferencing sequence_view molecule. Add multiple atoms attributes test. Remove debugging from setting attributes code. ------------------------------------------------------------------------ r607 | pemsley | 2007-12-19 23:21:29 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/molecule-class-info-other.cc Fix atom selection of setting atom attributes. ------------------------------------------------------------------------ r606 | pemsley | 2007-12-19 20:54:33 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add set_atom_attributes() function which takes a list of attributes.:Wq ------------------------------------------------------------------------ r605 | pemsley | 2007-12-19 19:03:56 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/generate-svn-revision-cc.sh Echo the revision number. ------------------------------------------------------------------------ r604 | pemsley | 2007-12-19 13:34:14 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Fix syntax error in setup_ccp4 ------------------------------------------------------------------------ r603 | pemsley | 2007-12-19 10:12:56 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Remove ccp4_onlylibs code from build-it. ------------------------------------------------------------------------ r602 | pemsley | 2007-12-19 10:05:40 +0000 (Wed, 19 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Setup for testing and tars on biop too. ------------------------------------------------------------------------ r601 | pemsley | 2007-12-18 17:28:41 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h More Gtk1 vs gtk2 fixes. ------------------------------------------------------------------------ r600 | pemsley | 2007-12-18 16:45:45 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.h More Gtk1 vs Gtk2 fixes. ------------------------------------------------------------------------ r599 | pemsley | 2007-12-18 16:34:32 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc More Gtk1 vs Gtk2 fixes. ------------------------------------------------------------------------ r598 | pemsley | 2007-12-18 16:32:53 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc More Gtk1 vs Gtk2 fixes. ------------------------------------------------------------------------ r597 | pemsley | 2007-12-18 16:18:42 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc More Gtk1 fixes. ------------------------------------------------------------------------ r596 | pemsley | 2007-12-18 16:14:36 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/callbacks.c Fix up some of Bernhard's Gtk2-specific changes to work with Gtk1. ------------------------------------------------------------------------ r595 | pemsley | 2007-12-18 15:09:11 +0000 (Tue, 18 Dec 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/callbacks.c M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h multi-read-pdb should not recentre on every pdb file. Be more rigourous when getting atom indexes in replace_coords(). Uses moving_atom_matches(). Fixes JED water crash. Clear up model toolbar togglebutton untoggling. ------------------------------------------------------------------------ r594 | pemsley | 2007-12-18 12:31:51 +0000 (Tue, 18 Dec 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/generate-svn-revision-cc.sh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/ideal/Makefile.am M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/ideal/with-map.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/molecule-class-info-other.cc Add verbose mode to geometry_protein. Add a map utility function to debug with-map. Don't draw display list objects when the displayit is not set in a molecule. Add note about ncs edits to user-manual. ------------------------------------------------------------------------ r593 | pemsley | 2007-12-18 10:19:37 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Python settings outside the subshell. ------------------------------------------------------------------------ r592 | pemsley | 2007-12-18 09:19:25 +0000 (Tue, 18 Dec 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Kevin fixes sigmaA from cif problem, I had been using wrong parameters. ------------------------------------------------------------------------ r591 | b.lohkamp | 2007-12-17 23:01:21 +0000 (Mon, 17 Dec 2007) | 1 line Changed paths: M /trunk/src/globjects.cc src/globjects.ss disable glEnable(GL_MULTISAMPLE_ARB) for windows ------------------------------------------------------------------------ r590 | pemsley | 2007-12-17 19:33:53 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it More python tweaking. ------------------------------------------------------------------------ r589 | pemsley | 2007-12-17 15:59:34 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Tell us some info re: building pythonized version. ------------------------------------------------------------------------ r588 | b.lohkamp | 2007-12-17 14:02:07 +0000 (Mon, 17 Dec 2007) | 16 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.h M /trunk/src/post-gtk2-glade.sh src/c-interface-gui.cc src/interface.h src/gtk2-interface.c src/globjects.cc src/c-interface.cc src/graphics-info.h src/callbacks.c src/callbacks.h src/post-gtk2-glade.sh src/c-interface.h use file_chooser for coordinates gui if gtk2_chooser_selector_flag is 1 introduce gtk2_chooser_selector_flag with functions set_gtk2_chooser_selector_flag(int) to set and gtk2_chooser_selector_flag_state() to query so far works only for coordinate file chooser... ------------------------------------------------------------------------ r587 | pemsley | 2007-12-17 13:43:26 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it More info about python version. ------------------------------------------------------------------------ r586 | pemsley | 2007-12-17 08:49:03 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Python setting fixes. ------------------------------------------------------------------------ r585 | pemsley | 2007-12-17 08:44:03 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Fix typo in python settings. ------------------------------------------------------------------------ r584 | pemsley | 2007-12-17 01:10:16 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Tag the python tar files (again) with -python ------------------------------------------------------------------------ r583 | pemsley | 2007-12-17 01:05:50 +0000 (Mon, 17 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Pythonize only sometimes. ------------------------------------------------------------------------ r582 | b.lohkamp | 2007-12-15 17:05:21 +0000 (Sat, 15 Dec 2007) | 12 lines Changed paths: M /trunk/autogen.sh M /trunk/macros/gtk-canvas.m4 M /trunk/python/coot_gui.py M /trunk/python/coot_utils.py M /trunk/python/extensions.py python/extensions.py updated with new functions and shuffled python/coot_gui.py updated and added functions python/coot_utils.py updated and added functions macros/gtk-canvas.m4 doesnt look for imlib on windows (probably should be for gtk2 builds in general) autogen.sh set directories for my windows machine ------------------------------------------------------------------------ r581 | pemsley | 2007-12-15 12:50:11 +0000 (Sat, 15 Dec 2007) | 3 lines Changed paths: M /trunk/scheme/ncs.scm Speed up the wrapping of the NCS chains jumping by not considering atoms in solvent chains. ------------------------------------------------------------------------ r580 | pemsley | 2007-12-15 09:00:38 +0000 (Sat, 15 Dec 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Add some MODE_MULTISAMPLE comments to the GL routines. ------------------------------------------------------------------------ r579 | pemsley | 2007-12-15 08:56:45 +0000 (Sat, 15 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-validate.cc Add Occ to the button string [Wendy Offen]. ------------------------------------------------------------------------ r578 | pemsley | 2007-12-14 10:52:10 +0000 (Fri, 14 Dec 2007) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Remove menu debugging. ------------------------------------------------------------------------ r577 | pemsley | 2007-12-14 10:51:49 +0000 (Fri, 14 Dec 2007) | 3 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/src/c-interface-gui.cc M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info.cc Fix up more cases of option menus without menus for Gtk2 version (including show_select_map_dialog()). ------------------------------------------------------------------------ r576 | pemsley | 2007-12-13 17:45:55 +0000 (Thu, 13 Dec 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh Add torsion angle filtering and sorting before they are added to the GUI. ------------------------------------------------------------------------ r575 | pemsley | 2007-12-13 12:11:01 +0000 (Thu, 13 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface-scm.hh M /trunk/src/graphics-info-state.cc Add USE_GUILE protection for schemize_command_strings(). ------------------------------------------------------------------------ r574 | pemsley | 2007-12-13 12:06:04 +0000 (Thu, 13 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Copy over the ChangeLog, README and RELEASE-NOTES on good test. ------------------------------------------------------------------------ r573 | pemsley | 2007-12-12 19:04:20 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-ligands.cc M /trunk/src/graphics-info.cc Add no graphics protection to ligand GUIs. ------------------------------------------------------------------------ r572 | pemsley | 2007-12-12 19:02:54 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Update greg test for occs, giving more info on failure. ------------------------------------------------------------------------ r571 | pemsley | 2007-12-12 18:29:09 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Redirect testing output to $LOGS/$HOST-testing.log ------------------------------------------------------------------------ r570 | pemsley | 2007-12-12 14:34:37 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/python/coot_gui.py Match greenness on the python scripting window. ------------------------------------------------------------------------ r569 | pemsley | 2007-12-12 13:56:33 +0000 (Wed, 12 Dec 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc Add many stock buttons to GUI dialogs. Fix problem of bad menu (for Gtk2?) from an option_menu in graphics_info_t::fill_option_menu_with_coordinates_option Now can close the new About dialog. ------------------------------------------------------------------------ r568 | pemsley | 2007-12-12 03:05:40 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Apply static map_sampling rate to maps created by cif sigmaa and phs maps. ------------------------------------------------------------------------ r567 | pemsley | 2007-12-12 02:53:21 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm M /trunk/src/coot M /trunk/src/coot_pythonmodule.cc More fiddling with python/gtk2 and getting to building on a gtk1 system. ------------------------------------------------------------------------ r566 | pemsley | 2007-12-12 02:31:28 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/coot-glue.hh D /trunk/src/coot_pythonmodule.c M /trunk/src/coot_pythonmodule.cc M /trunk/src/main.cc Tidy up pything/gtk2 mods. ------------------------------------------------------------------------ r565 | pemsley | 2007-12-12 01:46:47 +0000 (Wed, 12 Dec 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix typo in setting the release timer. ------------------------------------------------------------------------ r564 | pemsley | 2007-12-11 22:57:43 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: A /trunk/src/coot-glue-gtk2-python.cc Add coot-glue-gtk2-python.cc ------------------------------------------------------------------------ r563 | pemsley | 2007-12-11 22:43:51 +0000 (Tue, 11 Dec 2007) | 6 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-inner-main.h M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-glue-gtk2.c A /trunk/src/coot-glue.hh A /trunk/src/coot_pythonmodule.cc M /trunk/src/main.cc M /trunk/src/support.c M /trunk/src/support.h Add many fixes to get Coot to compile with Gtk2 and guile and python. Let's not enable_broken for anything. Let's use C++ rather than C. Lots of rearranging src/coot_pythonmodule.cc. Add coot-glue.hh. ------------------------------------------------------------------------ r562 | pemsley | 2007-12-11 17:16:53 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/gtk2-interface.c Re-work the new about dialog. ------------------------------------------------------------------------ r561 | pemsley | 2007-12-11 17:01:39 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: M /trunk/src/coot-glue-gtk2.c M /trunk/src/coot_pythonmodule.c Fix up problems with GTK1 and python. ------------------------------------------------------------------------ r560 | pemsley | 2007-12-11 16:38:52 +0000 (Tue, 11 Dec 2007) | 3 lines Changed paths: M /trunk/src/c-interface-mutate.cc M /trunk/src/support.c Fix up GTk2 protection in support.c Re-order header includes in c-interface-mutate.cc. Fixes Python #define horrors? ------------------------------------------------------------------------ r559 | pemsley | 2007-12-11 14:22:07 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: M /trunk/src/support.c M /trunk/src/support.h Add Gtk2 protection for pixbuf functions. ------------------------------------------------------------------------ r558 | pemsley | 2007-12-11 14:06:59 +0000 (Tue, 11 Dec 2007) | 11 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it M /trunk/coot-gtk2.glade M /trunk/dnotes A /trunk/generate-svn-revision-cc.sh M /trunk/greg-tests/03-ligand.scm M /trunk/ideal/simple-restraint.cc M /trunk/macros/libglade.m4 M /trunk/pixmaps/side-chain-180.svg M /trunk/python/coot_load_modules.py.in M /trunk/scheme/coot-gui.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/support.c M /trunk/src/support.h Fix the test for 64 bits in build-it. Get GSL from mirrorservice.org Comment out foolish thinking in handling libglade configure args. generate-svn-revision-cc.sh function added. should be added to the script that produces the tar file for the web. Tidy up greg tests a bit. Add aboutdialog for Gtk2. Needs work. Added extra functions to support.c and support.h to handle pixbuf in the aboutdialog. svn-revision.cc added to src/Makefile.am, (but not the svn repo). ------------------------------------------------------------------------ r557 | pemsley | 2007-12-11 13:57:46 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: M /trunk/src/main.cc Try to get the correct setting of use_gui_qm for Gtk1 interface. ------------------------------------------------------------------------ r556 | pemsley | 2007-12-11 11:41:05 +0000 (Tue, 11 Dec 2007) | 2 lines Changed paths: M /trunk/TODO resolve conflict ------------------------------------------------------------------------ r555 | pemsley | 2007-12-10 21:46:55 +0000 (Mon, 10 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Dewinter's ccp4 for testing. ------------------------------------------------------------------------ r554 | pemsley | 2007-12-10 17:48:05 +0000 (Mon, 10 Dec 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/rama_plot.cc Fix problem (crash) when clearing canvas on edit backbone torsions. Python protection on python commands. ------------------------------------------------------------------------ r553 | b.lohkamp | 2007-12-10 17:15:23 +0000 (Mon, 10 Dec 2007) | 14 lines Changed paths: M /trunk/python/coot_gui.py M /trunk/python/extensions.py M /trunk/src/c-interface.cc src/c-interface.cc fix cis_peptides_py and py_residue python/coot_gui.py introduce cis_peptide_gui python/extensions.py add cis_peptide_gui and reshuffle a bit more to reshuffle and add... ------------------------------------------------------------------------ r552 | pemsley | 2007-12-10 15:32:17 +0000 (Mon, 10 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix the python #define for safe_python_command_with_return (again). ------------------------------------------------------------------------ r551 | pemsley | 2007-12-10 15:31:16 +0000 (Mon, 10 Dec 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix the order of the python #define test. ------------------------------------------------------------------------ r550 | b.lohkamp | 2007-12-10 10:03:17 +0000 (Mon, 10 Dec 2007) | 106 lines Changed paths: M /trunk/python/coot_load_modules.py.in M /trunk/python/coot_utils.py M /trunk/src/Makefile.am M /trunk/src/c-inner-main.h M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/coot-glue-gtk2.c M /trunk/src/coot.i A /trunk/src/coot_pythonmodule.c M /trunk/src/coot_wrap_python.cc M /trunk/src/geometry-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info-render.cc M /trunk/src/main.cc src/cc-interface.hh define python equivalents to SCM functions new funcn: safe_python_command_with_return runs a python command and retrieves a return value src/c-inner-main.h define initcoot_python (for extensions) src/c-interface-build.cc add some debackslashing for windows python equivalent functions to SCM functions make new funcn: show_set_undo_molecule_chooser_py() (Paul: we should have these in scheme too?) src/c-interface.cc more python functions make new funcns: centre_of_mass_string_py make_image_raster3d_py make_image_povray_py run_state_file_py wrapped_create_run_state_file_dialog_py raster_screen_shot_py (Paul: we should have these in scheme too?) src/c-interface-gui.cc some windows fixes and introduce suck_model_fit_dialog_bl (a variant of pauls function) src/c-interface.h more python definitions src/c-interface-info.cc more python functions src/c-interface-ligands.cc even more python functions src/c-interface-mmdb.cc more python funtions src/c-interface-mutate.cc more python functions graphics-info.h is moved up, because of Mac python problems src/c-interface-preferences.cc more python functions and python/pygtk things new function: handle_read_draw_probe_dots_unformatted_py (Paul: we should have that in scheme too?) src/c-interface-superpose.cc more python functions src/c-interface-validate.cc more pythonizing new funcn: probe_available_p_py gln_asn_b_factor_outliers_py (Paul: we should have that in scheme too?) src/command-line.cc move __GNU_LIBRARY__ up graphics-info.h is moved up, because of Mac python problems src/coot-glue-gtk2.c include python glue code src/coot.i include python functions for coot.py src/geometry-graphs.cc increase label size for GNOME_CANVAS and canvas size for Windows src/graphics-info-modelling.cc windows magic jiggery pokery src/graphics-info-navigation.cc disable GTK_ENABLE_BROKEN for MINGW src/main.cc some adjustments for python usage, esp with graphics (GTK2/PYGTK) graphics-info.h is moved up, because of Mac python problems src/Makefile.am include coot_pythonmodule.c for glue code and corresponding flags use actually GUILE_GTK_CFLAGS src/graphics-info-render.cc make a sphere if cylinder has no length (happens for maps a lot and causes povray errors) src/coot_pythonmodule.cc new! For coot glue code src/c-interface-widgets.cc graphics-info.h is moved up, because of Mac python problems ------------------------------------------------------------------------ r549 | pemsley | 2007-12-08 08:29:00 +0000 (Sat, 08 Dec 2007) | 2 lines Changed paths: M /trunk/build-it etup CCP4 and use it to test coot before making binaries. ------------------------------------------------------------------------ r548 | pemsley | 2007-12-08 08:13:20 +0000 (Sat, 08 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Add setup_ccp4. ------------------------------------------------------------------------ r547 | pemsley | 2007-12-07 18:25:18 +0000 (Fri, 07 Dec 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/doc/coot-shelx.tex M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/04-cootaneer.scm M /trunk/greg-tests/05-rna-ghosts.scm M /trunk/src/graphics-info-graphs.cc Fix tests - tidy up output and fix cispep test to properly fail when it can't get the residue type. ------------------------------------------------------------------------ r546 | pemsley | 2007-12-07 15:00:50 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Try coot-real-exit, not plain exit. ------------------------------------------------------------------------ r545 | pemsley | 2007-12-07 14:57:08 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/02-shelx.scm Fix typo in data files for shelxl testing. ------------------------------------------------------------------------ r544 | pemsley | 2007-12-07 14:50:28 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Fix errors in build-it ------------------------------------------------------------------------ r543 | pemsley | 2007-12-07 13:28:34 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm M /trunk/greg-tests/04-cootaneer.scm Move references to greg test data to cannonical directory. ------------------------------------------------------------------------ r542 | pemsley | 2007-12-07 13:16:52 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/begin.grg The correct greg-data-dir for york. ------------------------------------------------------------------------ r541 | pemsley | 2007-12-07 13:13:12 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Use the right coot for testing. ------------------------------------------------------------------------ r540 | pemsley | 2007-12-07 12:34:12 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/begin.grg M /trunk/src/c-interface-build.cc Add valid molecule test to pepflip function. ------------------------------------------------------------------------ r539 | pemsley | 2007-12-07 12:25:53 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/begin.grg Make a more general place to find greg-data. ------------------------------------------------------------------------ r538 | pemsley | 2007-12-07 12:19:05 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it update build-it. ------------------------------------------------------------------------ r537 | pemsley | 2007-12-07 12:14:51 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/Makefile.am Add begin.grg to Makefile.am. ------------------------------------------------------------------------ r536 | pemsley | 2007-12-07 11:59:18 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: A /trunk/greg-tests/Makefile.am Add forgotten greg-test Makefile.am ------------------------------------------------------------------------ r535 | pemsley | 2007-12-07 11:55:56 +0000 (Fri, 07 Dec 2007) | 9 lines Changed paths: M /trunk/Makefile.am M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/build-it M /trunk/configure.in M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/coot-shelx.tex M /trunk/scheme/coot-gui.scm M /trunk/scheme/greg-extensions.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Add greg-tests to the dist tar file. Tidy up coot-shelx doc. Use force-output at the end of greg-tests in greg-extensions.scm Add Mutate icons. Don't try to render graphs if we don't have a gui (greg tests now work on the command line). history strings should come before the actual operation - changed handle-read-draw-molecule-with-recentre and make-and-draw-map. ------------------------------------------------------------------------ r534 | pemsley | 2007-12-07 11:43:24 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it testing debugging. ------------------------------------------------------------------------ r533 | pemsley | 2007-12-07 11:39:07 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Add a test_coot function. To be tested. ------------------------------------------------------------------------ r532 | pemsley | 2007-12-07 11:22:16 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/06-ssm.scm Update greg tests, CISPEP test is expected failure now. ------------------------------------------------------------------------ r531 | pemsley | 2007-12-07 10:45:17 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Fix test for bulding greg. ------------------------------------------------------------------------ r530 | pemsley | 2007-12-07 10:42:08 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it set DYLD_LIBRARY_PATH. ------------------------------------------------------------------------ r529 | pemsley | 2007-12-07 10:31:54 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Fix typo in greg addition. ------------------------------------------------------------------------ r528 | pemsley | 2007-12-07 10:30:24 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Add greg to build system (not used yet). ------------------------------------------------------------------------ r527 | b.lohkamp | 2007-12-07 09:33:40 +0000 (Fri, 07 Dec 2007) | 1 line Changed paths: M /trunk/python/hello.py Fix hello.py for mac ------------------------------------------------------------------------ r526 | pemsley | 2007-12-07 01:07:58 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/pixmaps/add-peptide-1.svg M /trunk/pixmaps/add-water.svg M /trunk/pixmaps/flip-peptide.svg A /trunk/pixmaps/mutate-auto-fit.svg A /trunk/pixmaps/mutate.svg More icon svg updates - icons for mutate added. ------------------------------------------------------------------------ r525 | pemsley | 2007-12-07 00:38:58 +0000 (Fri, 07 Dec 2007) | 2 lines Changed paths: M /trunk/build-it Update python dependency. ------------------------------------------------------------------------ r524 | pemsley | 2007-12-06 16:23:17 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Use $ac_cv_build_alias not `uname`. ------------------------------------------------------------------------ r523 | pemsley | 2007-12-06 16:16:19 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/macros/with-python.m4 remove dangling break; typ from last edit. ------------------------------------------------------------------------ r522 | pemsley | 2007-12-06 16:12:27 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/macros/with-python.m4 Use cannonical test for windows, not in-place test. ------------------------------------------------------------------------ r521 | pemsley | 2007-12-06 15:30:02 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/src/main.cc Just a tidy up of the indentation. ------------------------------------------------------------------------ r520 | pemsley | 2007-12-06 15:27:33 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc update coot_wraps to use 1.3.33 ------------------------------------------------------------------------ r519 | pemsley | 2007-12-06 15:04:52 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc Update coot_wrap_guiles to use swig 1.3.33 ------------------------------------------------------------------------ r518 | pemsley | 2007-12-06 11:44:28 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/src/main.cc Comment out initcoot_python(). It's not defined. ------------------------------------------------------------------------ r517 | pemsley | 2007-12-06 01:20:17 +0000 (Thu, 06 Dec 2007) | 2 lines Changed paths: M /trunk/scheme/clear-backup.scm Remove debugging. ------------------------------------------------------------------------ r516 | pemsley | 2007-12-06 01:19:45 +0000 (Thu, 06 Dec 2007) | 3 lines Changed paths: M /trunk/scheme/clear-backup.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h The problem of exact division in clear-backups resolved. Add colouring to command string hilighting. ------------------------------------------------------------------------ r515 | pemsley | 2007-12-05 15:30:47 +0000 (Wed, 05 Dec 2007) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-scm.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c Make a function in c-interface-scm that tests for undefinededness. Used in run_clear_backups(). Update GUI so that it has Python and scheme scripting windows. ------------------------------------------------------------------------ r514 | pemsley | 2007-12-05 15:24:55 +0000 (Wed, 05 Dec 2007) | 3 lines Changed paths: A /trunk/update-wraps A script for updating the coot_wrap_*.ccs, because swig puts the new ones in the build directory. ------------------------------------------------------------------------ r513 | b.lohkamp | 2007-12-05 15:12:13 +0000 (Wed, 05 Dec 2007) | 1 line Changed paths: M /trunk/src/main.cc fix main.cc for use_gui_qm ------------------------------------------------------------------------ r512 | pemsley | 2007-12-05 11:11:58 +0000 (Wed, 05 Dec 2007) | 7 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-scm.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc Mutate and Autofit button in model toolbar should not focus. Add tooltips for delete, undo and redo. Add highlighting of scheme commands written to console. toggle_idle_function renamed to toggle_idle_spin_function. scheme-commands were being added wrongly to history. Now we have a DIRECT_SCM_STRING to direct behaviour. ------------------------------------------------------------------------ r511 | pemsley | 2007-12-04 01:10:26 +0000 (Tue, 04 Dec 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/atomic-numbers.cc M /trunk/dnotes A /trunk/pixmaps/add-water.svg M /trunk/src/c-interface-build.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c Add a vertical toolbar with icons. Easy. Quick. Useful? ------------------------------------------------------------------------ r510 | pemsley | 2007-12-03 19:58:00 +0000 (Mon, 03 Dec 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-inner-main.c M /trunk/src/gtk2-interface.c Update Gtk2 main window with vertical modelling toolbar. No callbacks yet. ------------------------------------------------------------------------ r509 | pemsley | 2007-12-03 19:57:03 +0000 (Mon, 03 Dec 2007) | 2 lines Changed paths: M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Updates to Rama plot for green dot. Needs testing? ------------------------------------------------------------------------ r508 | pemsley | 2007-12-03 17:53:07 +0000 (Mon, 03 Dec 2007) | 2 lines Changed paths: M /trunk/python/Makefile.am Correct directory for python_coot_docs.py ------------------------------------------------------------------------ r507 | b.lohkamp | 2007-12-03 17:52:55 +0000 (Mon, 03 Dec 2007) | 1 line Changed paths: M /trunk/python/python_coot_docs.py fit python_coot_docs.py ------------------------------------------------------------------------ r506 | b.lohkamp | 2007-12-03 17:14:48 +0000 (Mon, 03 Dec 2007) | 43 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-utils.cc M /trunk/ideal/with-map.cc M /trunk/macros/glut.m4 M /trunk/macros/with-python.m4 M /trunk/python/Makefile.am M /trunk/python/americanisms.py D /trunk/python/background-demo.py A /trunk/python/background_demo.py A /trunk/python/cns2coot.py D /trunk/python/coot-lsq.py D /trunk/python/coot-utils.py A /trunk/python/coot_gui.py M /trunk/python/coot_load_modules.py.in A /trunk/python/coot_lsq.py A /trunk/python/coot_utils.py A /trunk/python/extensions.py A /trunk/python/filter.py M /trunk/python/fitting.py M /trunk/python/gap.py A /trunk/python/generic_objects.py D /trunk/python/get-ebi.py A /trunk/python/get_ebi.py A /trunk/python/group_settings.py M /trunk/python/hello.py A /trunk/python/libcheck.py A /trunk/python/local_code.py M /trunk/python/mutate.py A /trunk/python/ncs.py M /trunk/python/povray.py A /trunk/python/python_coot_docs.py M /trunk/python/raster3d.py M /trunk/python/refmac.py M /trunk/python/shelx.py A /trunk/python/tips.py A /trunk/python/tips_gui.py M /trunk/sequence-view/sequence-view.cc M /trunk/setup/coot.csh.in M /trunk/setup/coot.sh.in coot-utils/coot-coord-utils.cc python functions for coot::util::interesting_things_list and coot::util::interesting_things_list_with_fix coot-utils/coot-utils.cc some windows fixes for USER(NAME) and slash handling coot-utils/Makefile.am include WITH_GULE/PYTHON_CFLAG, i.e. USE_GUILE/PYTHON for interesting_things python ideal/with-map.cc move GNU_SOURCE and GNU_LIBRARY up, otherwise getopt errors on some systems macros/glut.m4 changes for mingw system macros/with-python.m4 fixes for windows system check for pygtk (if we have a gtk2 system) python/coot_load_modules.py.in updated for all python 'modules' and w or w/o grpahics python/Makefile.am make a texi doc file (if we have python) include all python 'modules' (OBS: names with '-' changed to '_') python/ 'new' modules: ncs.py, coot_gui.py, group_settings.py, extensions.py, tips.py, tips_gui.py, filter.py, libcheck.py, generic_objects.py, loacl_code.py, cns2coot.py, python_coot_docs.py sequence-view/sequence-view.cc make labels bigger for MINGW setup/ set env variable COOT_PYTHON_DIR, and swap PYTHONDIR ------------------------------------------------------------------------ r505 | pemsley | 2007-12-03 13:01:00 +0000 (Mon, 03 Dec 2007) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc Reorder include files (Python after graphics-info.h) to bypass problem of Python + FF1 in ssm_superpose.h on Darwin. ------------------------------------------------------------------------ r504 | pemsley | 2007-12-03 12:38:16 +0000 (Mon, 03 Dec 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc Reorder the position of including Python.h to previent FF1 mixup in ssm_superpose.h ------------------------------------------------------------------------ r503 | pemsley | 2007-12-03 01:16:55 +0000 (Mon, 03 Dec 2007) | 7 lines Changed paths: M /trunk/build-it M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ligand/richardson-rotamers.cc M /trunk/scheme/bones-reader.scm M /trunk/scheme/fascinating-things.scm M /trunk/scheme/gap.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/coot_wrap_python.cc M /trunk/src/geometry-graphs.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Adjust python setting in build it. Remove debugging from bones-reader.scm Add cluster limit to fascinating things. Add bones to render output. Use #ifdef USE_PYMAC_INIT for initing Python on a mac (USE_PYMAC_INIT is not properly set). ------------------------------------------------------------------------ r502 | pemsley | 2007-12-02 19:00:46 +0000 (Sun, 02 Dec 2007) | 2 lines Changed paths: M /trunk/configure.in Make version -pre-2 now that we are pythonizing. ------------------------------------------------------------------------ r501 | pemsley | 2007-12-02 12:58:34 +0000 (Sun, 02 Dec 2007) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm Extra notes on dialog box of buttons. Not well used by Views. Needs a fix. ------------------------------------------------------------------------ r500 | pemsley | 2007-11-30 12:37:31 +0000 (Fri, 30 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Enable python coot. ------------------------------------------------------------------------ r499 | pemsley | 2007-11-30 12:31:00 +0000 (Fri, 30 Nov 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/dnotes M /trunk/scheme/bones-reader.scm More work on bones-reader. The xyz-list is now in order. ------------------------------------------------------------------------ r498 | pemsley | 2007-11-28 21:52:24 +0000 (Wed, 28 Nov 2007) | 10 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/Makefile.am M /trunk/src/c-inner-main.c M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc A /trunk/src/c-interface-scm.cc A /trunk/src/c-interface-scm.hh M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/rama_plot.cc Dynamically add views to the Views Panel [FvD]. Create new c-interface file for SCM functions. Rework the Go To Atom Window, put next and previous residue on the same line. Rework the clear-backup function, particularly the case where the scm file is not loaded and the function not available. Draw the green box for GLYs. Still get submarined though. Dont allow toolbar buttons to accept focus. Fix the WhatIsSet tests on writing out Shelx atoms. How did it ever work before? ------------------------------------------------------------------------ r497 | pemsley | 2007-11-28 08:12:43 +0000 (Wed, 28 Nov 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Remove "can focus" from toolbar buttons. ------------------------------------------------------------------------ r496 | pemsley | 2007-11-27 02:23:24 +0000 (Tue, 27 Nov 2007) | 2 lines Changed paths: M /trunk/scheme/clear-backup.scm Fix problem of non-exiting Coot when there are no backup files to delete. ------------------------------------------------------------------------ r495 | pemsley | 2007-11-26 13:59:47 +0000 (Mon, 26 Nov 2007) | 3 lines Changed paths: M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Flash_selection now takes inscode args. New function update_environment_distances_by_rotation_centre_maybe added. ------------------------------------------------------------------------ r494 | pemsley | 2007-11-26 12:30:49 +0000 (Mon, 26 Nov 2007) | 8 lines Changed paths: M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/mapview.glade M /trunk/scheme/clear-backup.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-ncs.cc with-auto-accept should (accept-regularizement), I think. clear-backup works nicely with unsaved changes and state file writing. Fix typo: graphics_to_occupancy_representation, this will cause some pain. Tidy up debuggings on NCS reading. Add insertion code data to refine and regularize function in graphics-info. Finalize GPOINTER_TO_INT usage for map properties. get_asc_index in simple-restraint.cc takes an insertion code now. ------------------------------------------------------------------------ r493 | pemsley | 2007-11-26 10:31:54 +0000 (Mon, 26 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Another try to fix setting of systype for MacOSX. ------------------------------------------------------------------------ r492 | pemsley | 2007-11-26 01:11:04 +0000 (Mon, 26 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Fix setting of systype for MacOSX, hopefully. ------------------------------------------------------------------------ r491 | pemsley | 2007-11-25 19:52:56 +0000 (Sun, 25 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Fix typo. ------------------------------------------------------------------------ r490 | pemsley | 2007-11-25 18:57:18 +0000 (Sun, 25 Nov 2007) | 7 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/scheme/bones-reader.scm M /trunk/scheme/clear-backup.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/greg-extensions.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc Add the ability to run just one regression test (greg-one-test). More tinkering with bones. Give up for now. Add carriage return callback on generic-chooser-and-file-selector. Add user-setable dates/times for clear-backup running. Fix up scale_cell function. Add chiral restraints. ------------------------------------------------------------------------ r489 | pemsley | 2007-11-25 14:16:41 +0000 (Sun, 25 Nov 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/scheme/bones-reader.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc Remove the probability limit for Richardson Rotamers. Improve the bones reader for guile 1.8 ------------------------------------------------------------------------ r488 | pemsley | 2007-11-24 15:04:21 +0000 (Sat, 24 Nov 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/macros/libglade.m4 Update dnotes. ------------------------------------------------------------------------ r487 | pemsley | 2007-11-24 14:44:58 +0000 (Sat, 24 Nov 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/src/c-inner-main.c M /trunk/src/c-inner-main.h M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc try_load_scheme_extras_dir() function added. Remove unnecessary dirents from several .ccs. ------------------------------------------------------------------------ r486 | pemsley | 2007-11-24 03:07:43 +0000 (Sat, 24 Nov 2007) | 4 lines Changed paths: M /trunk/build-it M /trunk/scheme/Makefile.am M /trunk/src/graphics-info-pick.cc M /trunk/src/gtk-manual.c In build-it, try different args from uname -a to grep processor. Clean up debugging in combo-box. Change test for boxes.size() from 1 to 0, fixing symm pick problems? ------------------------------------------------------------------------ r485 | pemsley | 2007-11-24 00:49:32 +0000 (Sat, 24 Nov 2007) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-defines.cc Actually install clear-backup.scm. Make the delete sidechain close the delete item dialog properly. ------------------------------------------------------------------------ r484 | pemsley | 2007-11-23 18:07:57 +0000 (Fri, 23 Nov 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Add title (molecule name) to geometry graphs (as per EJD request). ------------------------------------------------------------------------ r483 | pemsley | 2007-11-23 16:57:42 +0000 (Fri, 23 Nov 2007) | 2 lines Changed paths: M /trunk/scheme/clear-backup.scm Copyright notice for clear-backup and remove some testing code. ------------------------------------------------------------------------ r482 | pemsley | 2007-11-23 16:56:47 +0000 (Fri, 23 Nov 2007) | 2 lines Changed paths: M /trunk/mapview.glade A /trunk/scheme/clear-backup.scm M /trunk/scheme/coot.scm M /trunk/src/c-interface-gui.cc Add scheme GUI to clear out back up, called in coot_checked_exit(). ------------------------------------------------------------------------ r481 | pemsley | 2007-11-23 02:13:18 +0000 (Fri, 23 Nov 2007) | 3 lines Changed paths: M /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/gtk-manual.c M /trunk/src/molecule-class-info.cc Set map level in absolute and sigma in single map properties dialog. Remove some archaic int casting in the use of this widget. ------------------------------------------------------------------------ r480 | pemsley | 2007-11-22 23:53:52 +0000 (Thu, 22 Nov 2007) | 2 lines Changed paths: M /trunk/mapview.glade M /trunk/src/interface.c M /trunk/src/interface.h Ooops, remove baggage from mapview.glade ------------------------------------------------------------------------ r479 | pemsley | 2007-11-22 22:17:23 +0000 (Thu, 22 Nov 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/positioned-widgets.h M /trunk/src/support.c M /trunk/src/support.h Enable . and , key presses to move in the checked waters baddies dialog. ------------------------------------------------------------------------ r478 | pemsley | 2007-11-22 19:55:11 +0000 (Thu, 22 Nov 2007) | 2 lines Changed paths: A /trunk/pixmaps/appointment-new.png A /trunk/pixmaps/change-chain-id.svg A /trunk/pixmaps/coot-save-symm.png A /trunk/pixmaps/coot-save.png A /trunk/pixmaps/env-distances.png A /trunk/pixmaps/gnome-run.png A /trunk/pixmaps/renumber-residues.svg Add pixmaps and svn that Bill said were missing. ------------------------------------------------------------------------ r477 | pemsley | 2007-11-22 18:17:49 +0000 (Thu, 22 Nov 2007) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/mapview.glade M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h M /trunk/src/support.c M /trunk/src/support.h Add a greg test case for alt conf waters. Add widgets to GUI to set the contour level (not connected up). Add a destroy callback for checked_waters_baddies_dialog so that (in future) , and . can act on the button list. Add scale_cell function for EM (not tested). ------------------------------------------------------------------------ r476 | pemsley | 2007-11-22 11:02:07 +0000 (Thu, 22 Nov 2007) | 5 lines Changed paths: M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info.cc Fix up minimol, the constructor for atoms in particular to copy over alt conf info. Change rigid body refine code to properly handle alt confs. Fixes Stephen Graham bug. ------------------------------------------------------------------------ r475 | pemsley | 2007-11-21 16:47:10 +0000 (Wed, 21 Nov 2007) | 2 lines Changed paths: M /trunk/build-it set the architecture for ubuntu systems. ------------------------------------------------------------------------ r474 | pemsley | 2007-11-21 16:13:07 +0000 (Wed, 21 Nov 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/dnotes No longer make the full tar file. ------------------------------------------------------------------------ r473 | pemsley | 2007-11-20 17:44:52 +0000 (Tue, 20 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Get libungif from YSBL now. ------------------------------------------------------------------------ r472 | pemsley | 2007-11-20 13:58:09 +0000 (Tue, 20 Nov 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface.cc Make the torsion angle available to the Cis Pep gui. ------------------------------------------------------------------------ r471 | pemsley | 2007-11-19 22:03:28 +0000 (Mon, 19 Nov 2007) | 2 lines Changed paths: A /trunk/scheme/bones-reader.scm Add bones reader to repo, I won't lose it now. ------------------------------------------------------------------------ r470 | pemsley | 2007-11-19 15:46:03 +0000 (Mon, 19 Nov 2007) | 4 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.h Add in support to bring cis peptides to the scripting layer. create cis_peptides() function, and use the SCM return value to make a GUI. ------------------------------------------------------------------------ r469 | pemsley | 2007-11-19 12:08:44 +0000 (Mon, 19 Nov 2007) | 2 lines Changed paths: A /trunk/pixmaps/connect-to-ccp4.svg A /trunk/pixmaps/connect-to-oca.svg Add more svg icons. Stops complaining of Bill's Coot? ------------------------------------------------------------------------ r468 | pemsley | 2007-11-17 14:45:01 +0000 (Sat, 17 Nov 2007) | 8 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/python/coot-utils.py M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/scheme/generic-objects.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-modelling.cc Fix graphics_general_key_press_hook template for python. Add function label-all-CAs and add it to extensions. Export map added to extensions. Tidy extensions menu. generic-chooser-entry-and-file-selector and generic-chooser-and-file-selector now take a chooser filter. Improve Accept/Reject GUI when run out of cycles. ------------------------------------------------------------------------ r467 | pemsley | 2007-11-08 19:57:27 +0000 (Thu, 08 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Version 1.08-ysbl-3 of mmdb. ------------------------------------------------------------------------ r466 | pemsley | 2007-11-08 15:51:19 +0000 (Thu, 08 Nov 2007) | 2 lines Changed paths: M /trunk/scheme/libcheck.scm Fix problem of Get Monomer putting new monomers at the origin. ------------------------------------------------------------------------ r465 | pemsley | 2007-11-08 15:06:53 +0000 (Thu, 08 Nov 2007) | 5 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/mapview.glade M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Add placeholder for Chiral Volume violations in Accept/Reject dialog and use it. check_and_warn_bad_chirals_and_cis_peptides() now uses add_extra_text_to_accept_reject_dialog instead of info_dialog(). ------------------------------------------------------------------------ r464 | pemsley | 2007-11-08 01:39:03 +0000 (Thu, 08 Nov 2007) | 6 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-utils.cc M /trunk/ideal/simple-restraint.cc M /trunk/mapview.glade M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Tinker with the alignement and spacing of the extra text label in accept/reject dialog. Update chi squareds in accept/reject dialog, without blanks. Remove some debugging. Fix float_to_string_using_dec_pl(). ------------------------------------------------------------------------ r463 | pemsley | 2007-11-07 21:23:52 +0000 (Wed, 07 Nov 2007) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/mapview.glade M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/support.c Put text into the Accept/Reject window (the Chi Squareds from the refinement/regularization) Add an extra widget to accept/reject dialog. Not used yet. Add new class coot::refinement_results_t to contain results from simple_restraint. ------------------------------------------------------------------------ r462 | pemsley | 2007-11-07 21:07:58 +0000 (Wed, 07 Nov 2007) | 5 lines Changed paths: M /trunk/build-it M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/db-main/db-strands.cc M /trunk/dnotes M /trunk/macros/mmdb.m4 M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Changes to roll back to mmdb-1.0.9 Introducde definition HAVE_MMDB_WITH_CISPEP Tinkered with reference-structure dir for sec struct references. Allow sequence number offset for shelx .ins molecules. ------------------------------------------------------------------------ r461 | pemsley | 2007-11-06 14:22:32 +0000 (Tue, 06 Nov 2007) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm The additions to map masking to add a radius to the masked atom. New generic hinted entries window added. ------------------------------------------------------------------------ r460 | pemsley | 2007-11-05 13:00:43 +0000 (Mon, 05 Nov 2007) | 2 lines Changed paths: M /trunk/build-it Swap out DL Clipper for York clipper. --enable-cns. ------------------------------------------------------------------------ r459 | pemsley | 2007-11-04 23:57:19 +0000 (Sun, 04 Nov 2007) | 5 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Debugging and eventual fix to problem of Sec Strcuct Calc for shelx molecules. Was problem in setting the indexes of residues in chains (created as -1, it should have been something sensible. And that created an error in mmdb's CMMDBCoorManager::FindSeqSection()). ------------------------------------------------------------------------ r458 | pemsley | 2007-11-02 12:47:04 +0000 (Fri, 02 Nov 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h More debugging and reworking for the NCS ghosts of .res molecules. ------------------------------------------------------------------------ r457 | pemsley | 2007-11-02 09:50:44 +0000 (Fri, 02 Nov 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc Add some debugging to trace chain/atom selection problem in NCS finding from SHELX .res. ------------------------------------------------------------------------ r456 | pemsley | 2007-10-31 16:39:52 +0000 (Wed, 31 Oct 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/ligand/richardson-rotamers.cc M /trunk/src/graphics-info-graphs.cc Fix crash due to compiler bug (maybe) in geometry graphs of multiple models. ------------------------------------------------------------------------ r455 | pemsley | 2007-10-30 19:58:07 +0000 (Tue, 30 Oct 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-gui.cc Fix unsmallenable initial window problem (JED bug). ------------------------------------------------------------------------ r454 | pemsley | 2007-10-30 02:27:50 +0000 (Tue, 30 Oct 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/callbacks.c M /trunk/src/graphics-info-defines.cc Mutate stub button back? Needs testing. Reading a cif file sets the directory for fileselections now. ------------------------------------------------------------------------ r453 | pemsley | 2007-10-30 02:19:52 +0000 (Tue, 30 Oct 2007) | 2 lines Changed paths: A /trunk/macros/libglade.m4 add libglade.m4, forgotten before. ------------------------------------------------------------------------ r452 | pemsley | 2007-10-30 01:18:34 +0000 (Tue, 30 Oct 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/coot M /trunk/src/main.cc bash coot limit coredumsize comment. ------------------------------------------------------------------------ r451 | pemsley | 2007-10-29 09:24:19 +0000 (Mon, 29 Oct 2007) | 3 lines Changed paths: M /trunk/configure.in M /trunk/coot-utils/coot-utils.hh M /trunk/dnotes M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/scheme/generic-objects.scm M /trunk/src/Makefile.am M /trunk/src/main.cc M /trunk/src/support.c Properly configure LIBGLADE. move_helix_centre_point() now has a max density cut-off (Au Lys from CSHL). ------------------------------------------------------------------------ r450 | pemsley | 2007-10-21 16:07:25 +0100 (Sun, 21 Oct 2007) | 2 lines Changed paths: A /trunk/coot-gtk2-try2.glade Add try2 of the coot GTk2 glade interface. ------------------------------------------------------------------------ r449 | pemsley | 2007-10-12 13:22:34 +0100 (Fri, 12 Oct 2007) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile_pre.cc Update generated src/coot_wrap_guile_pre.cc by hand. Hmm... ------------------------------------------------------------------------ r448 | pemsley | 2007-10-12 13:19:50 +0100 (Fri, 12 Oct 2007) | 2 lines Changed paths: M /trunk/scheme/entry+do-button.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc Add function clear-and-update-model-molecule-from-file. ------------------------------------------------------------------------ r447 | pemsley | 2007-10-12 09:35:43 +0100 (Fri, 12 Oct 2007) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Update comments on transform-map-using-lsq-matrix function. ------------------------------------------------------------------------ r446 | pemsley | 2007-10-12 09:34:32 +0100 (Fri, 12 Oct 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/build-it M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/c-inner-main.c M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/main.cc Keep guile (don't slim it). Add set_molecule_name() function. ------------------------------------------------------------------------ r445 | pemsley | 2007-10-12 08:11:17 +0100 (Fri, 12 Oct 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Apply an inverse() to about point. Now one passes the target position and the position from which the map is drawn is calculated (not passed). ------------------------------------------------------------------------ r444 | pemsley | 2007-10-12 08:03:34 +0100 (Fri, 12 Oct 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc Add some debugging of transform map (which transforms map using "from-pt"). ------------------------------------------------------------------------ r443 | pemsley | 2007-10-11 18:24:31 +0100 (Thu, 11 Oct 2007) | 2 lines Changed paths: M /trunk/coords/mmdb.cc Test for (legitimate) null model in fix_nucleic_acid_residue_names(). ------------------------------------------------------------------------ r442 | pemsley | 2007-10-10 13:15:51 +0100 (Wed, 10 Oct 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Fix syntax error. ------------------------------------------------------------------------ r441 | pemsley | 2007-10-10 13:07:13 +0100 (Wed, 10 Oct 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Remove glade includes and libs for now. ------------------------------------------------------------------------ r440 | pemsley | 2007-10-10 12:32:33 +0100 (Wed, 10 Oct 2007) | 3 lines Changed paths: M /trunk/build-it M /trunk/src/c-inner-main.c M /trunk/src/main.cc Change the logic to overwriting coot_wrap_guile.cc when python is used. Some debugging added to test SWIG_init() usage. ------------------------------------------------------------------------ r439 | pemsley | 2007-10-10 10:22:22 +0100 (Wed, 10 Oct 2007) | 2 lines Changed paths: M /trunk/build-it ENABLE_PYTHON_COOT=no for now. ------------------------------------------------------------------------ r438 | pemsley | 2007-10-10 09:07:34 +0100 (Wed, 10 Oct 2007) | 2 lines Changed paths: M /trunk/src/c-interface-mutate.cc Add note describing preprocessor problems. ------------------------------------------------------------------------ r437 | pemsley | 2007-10-10 09:05:20 +0100 (Wed, 10 Oct 2007) | 7 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/molecule-class-info-ncs.cc Rework brighten maps to make darken maps trivial. set_environment_distances_distance_limits() function introduced. Reorder includes in src/c-interface-mutate.cc. There maybe a precompiler bug, some strange substitutions are going on. (Fails differently on mac an PC - hopefully this will be suitable for both). ------------------------------------------------------------------------ r436 | pemsley | 2007-10-09 07:12:57 +0100 (Tue, 09 Oct 2007) | 4 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/ligand/find-ligand.cc M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-ligands.cc M /trunk/src/graphics-info-state.cc Add to stdout description of findligand usage, the script file for coot. (molecule-number-list) returns only valid molecules now. Add environment distances to state file. ------------------------------------------------------------------------ r435 | pemsley | 2007-10-08 20:43:19 +0100 (Mon, 08 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Fix extra fi, uncommented typo. ------------------------------------------------------------------------ r434 | pemsley | 2007-10-08 20:15:25 +0100 (Mon, 08 Oct 2007) | 9 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/graphics-info.h M /trunk/src/main.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-surface.cc M /trunk/src/molecule-class-info.h Add Richardsons to About dialog. Fast NCS detection on read modified. Add some test code for using libglade. Rewrite set_find_ligand_mols() in graphics-info.h Pass the correct kind of wiggly ligand info to set_find_ligand_mols() with new pair usage. Add libglade to Makefile.am. Temporary only should be. It needs its values to come from configure. ------------------------------------------------------------------------ r433 | pemsley | 2007-10-06 12:30:58 +0100 (Sat, 06 Oct 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Create stub function for representation of density as solid surface. Remove stub flag usage from autofit rotamer - it doesn't make sense there. ------------------------------------------------------------------------ r432 | pemsley | 2007-10-06 07:53:03 +0100 (Sat, 06 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Adjust python scripting for coot's configure. ------------------------------------------------------------------------ r431 | pemsley | 2007-10-05 18:27:14 +0100 (Fri, 05 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Fix slim_dir ------------------------------------------------------------------------ r430 | pemsley | 2007-10-05 16:57:26 +0100 (Fri, 05 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Fix post_install_slim call. ------------------------------------------------------------------------ r429 | pemsley | 2007-10-05 16:23:57 +0100 (Fri, 05 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Add some debugging to make_tar. It doesn't seem to work currently. ------------------------------------------------------------------------ r428 | pemsley | 2007-10-05 01:30:34 +0100 (Fri, 05 Oct 2007) | 2 lines Changed paths: M /trunk/scheme/filter.scm Fix filter so that it doesn't overflow the stack. ------------------------------------------------------------------------ r427 | pemsley | 2007-10-03 14:56:36 +0100 (Wed, 03 Oct 2007) | 9 lines Changed paths: M /trunk/build-it M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-utils.hh M /trunk/coot-utils/test-utils.cc M /trunk/density-contour/Vectors.h M /trunk/dnotes M /trunk/mapview.glade M /trunk/scheme/ncs.scm M /trunk/scheme/quat-convert.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Clean up Vectors.h as per Ezra P.s suggestion. Add NCS orientation to NCS chain skipping. Create a quaternion class - and test it in testcootutils apply_ncs_to_view_orientation() function created. ncs_ghost_chain_is_a_target_chain_p() function created. Remove path to dictionaries in state file preamble. Remove CCP4 from map dialog title. Update glade files. ------------------------------------------------------------------------ r426 | pemsley | 2007-10-02 18:05:05 +0100 (Tue, 02 Oct 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Add a flag to allow offsets in NCS check (not used yet). ------------------------------------------------------------------------ r425 | pemsley | 2007-10-02 14:38:16 +0100 (Tue, 02 Oct 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes Trivial save coordinates utility function. ------------------------------------------------------------------------ r424 | pemsley | 2007-10-02 14:11:53 +0100 (Tue, 02 Oct 2007) | 2 lines Changed paths: M /trunk/build-it Add comment line and change version to 2.10. ------------------------------------------------------------------------ r423 | pemsley | 2007-10-02 14:10:43 +0100 (Tue, 02 Oct 2007) | 3 lines Changed paths: M /trunk/build-it Post install slim the binaries. Attept to make a tar file and put it on the web site. ------------------------------------------------------------------------ r422 | pemsley | 2007-10-01 23:46:55 +0100 (Mon, 01 Oct 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/dnotes Add in post-install slimming to build-script. Needs testing? ------------------------------------------------------------------------ r421 | pemsley | 2007-10-01 23:43:02 +0100 (Mon, 01 Oct 2007) | 2 lines Changed paths: M /trunk/ideal/Makefile.am Add in compat library to with-map, now that we use get-opt there. ------------------------------------------------------------------------ r420 | pemsley | 2007-10-01 23:27:19 +0100 (Mon, 01 Oct 2007) | 2 lines Changed paths: M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h Small speed-up patch from Ezra - speeds up operator= for Cartesians. ------------------------------------------------------------------------ r419 | pemsley | 2007-10-01 19:47:07 +0100 (Mon, 01 Oct 2007) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/dnotes Fix colour by chain and colour by molecule with multiple models. (Except hydrogens are incorrectly bonded - but who cares about them?) ------------------------------------------------------------------------ r418 | pemsley | 2007-10-01 18:35:32 +0100 (Mon, 01 Oct 2007) | 9 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/process-greg-log.awk M /trunk/python/coot-utils.py M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add python function stub graphics_general_key_press_hook() Bond by model in Bond-lines.cc Needs testing with big multi-model NMR structures. Remove wrong CIS peps at write, not read. Added test for CIS pep models. Fix bug in CIS PEP removal/replacement. Stub function for monomer restraints. Add cis-trans conversion scripting function. ------------------------------------------------------------------------ r417 | pemsley | 2007-10-01 11:37:02 +0100 (Mon, 01 Oct 2007) | 8 lines Changed paths: M /trunk/dnotes M /trunk/scheme/exercise-scm-mol.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/command-line.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h In exercise scm mol, allow gtk events. Fix a crash - don't display a dialog in no-graphics mode when deleting baddie waters. Protect nothing bad dialog for no-graphics. Add a command line argument: --ccp4-project which sets the file selection string to that of the given ccp4 project. Include notes from Sept Phenix meeting. ------------------------------------------------------------------------ r416 | pemsley | 2007-10-01 09:47:41 +0100 (Mon, 01 Oct 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/globjects.cc Add graphics_general_key_press_hook() usage if compiled with python. ------------------------------------------------------------------------ r415 | pemsley | 2007-09-22 10:07:04 +0100 (Sat, 22 Sep 2007) | 3 lines Changed paths: M /trunk/macros/clipper.m4 Reorder the clipper libraries to get past a cootaneer-demo linking problem on bubbles. ------------------------------------------------------------------------ r414 | pemsley | 2007-09-21 12:33:06 +0100 (Fri, 21 Sep 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info-state.cc Save the bonding state (CA, ligands, B-factor etc) in the state file. ------------------------------------------------------------------------ r413 | pemsley | 2007-09-21 12:28:31 +0100 (Fri, 21 Sep 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Remove all CISPEPs and add back the good ones - using mmdb current interface. ------------------------------------------------------------------------ r412 | pemsley | 2007-09-21 12:25:57 +0100 (Fri, 21 Sep 2007) | 2 lines Changed paths: M /trunk/scheme/coot-utils.scm Fix typo in guess-refinement-map. ------------------------------------------------------------------------ r411 | pemsley | 2007-09-21 12:24:20 +0100 (Fri, 21 Sep 2007) | 2 lines Changed paths: M /trunk/build-it Add a function to slim the binaries directory. ------------------------------------------------------------------------ r410 | pemsley | 2007-09-20 14:34:48 +0100 (Thu, 20 Sep 2007) | 2 lines Changed paths: M /trunk/README M /trunk/dnotes M /trunk/src/graphics-info.cc Resolve conflict. Update README. ------------------------------------------------------------------------ r409 | pemsley | 2007-09-20 14:34:05 +0100 (Thu, 20 Sep 2007) | 3 lines Changed paths: M /trunk/src/gtk-manual.c Expand the string size for the molecule number in the combo boxes - now we can use more than 100 molecules. ------------------------------------------------------------------------ r408 | pemsley | 2007-09-20 14:27:27 +0100 (Thu, 20 Sep 2007) | 3 lines Changed paths: M /trunk/standard-residues.pdb Update standard residues so that they are in Richardson Rotamers number 1 conformation. ------------------------------------------------------------------------ r407 | pemsley | 2007-09-19 15:02:33 +0100 (Wed, 19 Sep 2007) | 4 lines Changed paths: M /trunk/scheme/libcheck.scm Move libcheck.lib if it exists before over-writing it. Use new-form move-molecule here and always copy libcheck.lib to monomer-xxx.cif ------------------------------------------------------------------------ r406 | pemsley | 2007-09-19 14:25:31 +0100 (Wed, 19 Sep 2007) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/libcheck.scm Use "cached" (previously calculated) libcheck results: monomer-xx.pdb and libcheck_xxx.cif if they exist for faster "Get Monomer". ------------------------------------------------------------------------ r405 | pemsley | 2007-09-19 13:21:45 +0100 (Wed, 19 Sep 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info.cc Check for valid model before deleting in delete_residue(). ------------------------------------------------------------------------ r404 | pemsley | 2007-09-17 19:37:19 +0100 (Mon, 17 Sep 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-superpose.cc M /trunk/src/graphics-info.cc Fix outstanding SetSpaceGroup() issues. ------------------------------------------------------------------------ r403 | pemsley | 2007-09-17 19:36:31 +0100 (Mon, 17 Sep 2007) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Some removal of debugging code, reorganisation, so that it is easier to delete a CISPEP when I know how to do it (mmdb interface is not the best currently, I think). ------------------------------------------------------------------------ r402 | pemsley | 2007-09-17 19:35:13 +0100 (Mon, 17 Sep 2007) | 3 lines Changed paths: M /trunk/scheme/libcheck.scm Check for existence of monomer-xxx.pdb and the cif file. If they exist, don't run libcheck to make them. ------------------------------------------------------------------------ r401 | pemsley | 2007-09-17 12:48:29 +0100 (Mon, 17 Sep 2007) | 8 lines Changed paths: M /trunk/TODO M /trunk/build-it M /trunk/coords/Bond_lines.cc M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/db-main/db-strands.cc M /trunk/dnotes M /trunk/macros/mmdb.m4 M /trunk/sequence-view/sequence-view.cc M /trunk/src/c-interface-mutate.cc M /trunk/src/molecule-class-info.cc Use new mmdb (version 110 aka 1.0.10). Many consequences: Change mmdb macro to test for this new version. Change calls to CalcSecStructure(). Add function remove_wrong_cis_peptides() on reading a pdb file. Change the header order of several files to get the past some bizarre compiler problem on reading CCisPep in coot-cood-utils.hh Add function to return cis peptide info: cis_peptides_info_from_coords(). ------------------------------------------------------------------------ r400 | pemsley | 2007-09-16 15:46:28 +0100 (Sun, 16 Sep 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Fix conversion of fractional shelx anisotropic ADPs to orthogonal using clipper's U_aniso_frac::u_aniso_orth(cell). ------------------------------------------------------------------------ r399 | pemsley | 2007-09-16 15:44:20 +0100 (Sun, 16 Sep 2007) | 1 line Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/scheme/coot-utils.scm ------------------------------------------------------------------------ r398 | pemsley | 2007-09-16 01:11:40 +0100 (Sun, 16 Sep 2007) | 2 lines Changed paths: M /trunk/ideal/Makefile.am Add $(top_srcdir)/compat to INCLUDES to pickup coot-compat.h for with-map.cc ------------------------------------------------------------------------ r397 | pemsley | 2007-09-16 01:10:43 +0100 (Sun, 16 Sep 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h NEW_COORDS_REPLACE mode is now divided into NEW_COORDS_REPLACE and NEW_COORDS_REPLACE_CHANGE_ALTCONF. ------------------------------------------------------------------------ r396 | pemsley | 2007-09-15 11:05:26 +0100 (Sat, 15 Sep 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/doc/user-manual.texi A /trunk/pixmaps/calculate-ghosts.svg M /trunk/pixmaps/connect-to-usf.svg M /trunk/pixmaps/merge-molecules.svg M /trunk/pixmaps/stereo-view.svg M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c More icons. ------------------------------------------------------------------------ r395 | pemsley | 2007-09-14 21:09:13 +0100 (Fri, 14 Sep 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/06-ssm.scm M /trunk/src/c-interface.cc M /trunk/src/graphics-info-superpose.cc Tinker with greg tests. Add valid molecule protection for graphics_to_ca_plus_ligands_representation(). Add aligned residue limit in outputing alignment table. Not sure it is the right thing. But it fixes a crash. ------------------------------------------------------------------------ r394 | pemsley | 2007-09-14 20:15:23 +0100 (Fri, 14 Sep 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/graphics-info-superpose.cc Add some debugging for Alice Dawson SSM bug. ------------------------------------------------------------------------ r393 | pemsley | 2007-09-14 18:21:38 +0100 (Fri, 14 Sep 2007) | 4 lines Changed paths: M /trunk/atom-utils/Makefile.am M /trunk/dnotes A /trunk/greg-tests/06-ssm.scm M /trunk/sequence-view/Makefile.am M /trunk/src/graphics-info-superpose.cc M /trunk/src/graphics-info.h Fix silly SSM problem when using partial chain atom selection (wrong array limit). Fixes FvD SSM problem. Add a greg test for the above. ------------------------------------------------------------------------ r392 | pemsley | 2007-09-14 13:50:29 +0100 (Fri, 14 Sep 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/src/c-interface-mutate.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Fix space group issues in c-interface-mutate.cc (cootaneering). Remove some debugging. ------------------------------------------------------------------------ r391 | pemsley | 2007-09-14 12:47:06 +0100 (Fri, 14 Sep 2007) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc Simple fix to the symm evironment distances problems - but took me 4 hours to find it. Baah. translate_atoms() was being used, which is old-style and did not take into account pre-cell-shift. Use trans_sel() instead. ------------------------------------------------------------------------ r390 | pemsley | 2007-09-14 01:05:02 +0100 (Fri, 14 Sep 2007) | 3 lines Changed paths: M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh Use COM when mode values are not present for additionally allow pseudo-rotamers in the richardson dictionary. ------------------------------------------------------------------------ r389 | pemsley | 2007-09-13 19:14:08 +0100 (Thu, 13 Sep 2007) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/dnotes M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/gtk-manual.c Change the colours for env distances (carbon clash is now yellow). Create function clase_graphics_display_control_window(). ------------------------------------------------------------------------ r388 | pemsley | 2007-09-13 16:10:11 +0100 (Thu, 13 Sep 2007) | 3 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/dnotes M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix Steven Grahams's symmetry hydrogen bug. It was 2 one-liners, but took me an hour to correctly place them :(. ------------------------------------------------------------------------ r387 | pemsley | 2007-09-12 18:46:23 +0100 (Wed, 12 Sep 2007) | 5 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h Export rotamer graph info to the scripting layer for testing. Add rotamer graph tests. Add the rotamer name to the rotamer graphs tool-tips. Add calls to expand_molecule_space_maybe() fixes many molecules crashes. ------------------------------------------------------------------------ r386 | pemsley | 2007-09-11 22:22:16 +0100 (Tue, 11 Sep 2007) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Add weight line to usage output. ------------------------------------------------------------------------ r385 | pemsley | 2007-09-11 21:04:59 +0100 (Tue, 11 Sep 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/penultimate-to-code.awk M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc A /trunk/src/c-interface-widgets.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_python.cc M /trunk/src/graphics-info-modelling.cc Start separation of scripting from GUI layer. create widgets file c-interface-widgets.cc. Tinkering with rotamer/chi angle coe to include the rotamer name in the GUI. Quote handle-read-draw-molecule-with-recentre in history - FvD bug. ------------------------------------------------------------------------ r384 | pemsley | 2007-09-11 21:00:44 +0100 (Tue, 11 Sep 2007) | 2 lines Changed paths: M /trunk/ideal/with-map.cc More additions to with-map functionality. Now user-setable weight. ------------------------------------------------------------------------ r383 | pemsley | 2007-09-11 18:20:18 +0100 (Tue, 11 Sep 2007) | 2 lines Changed paths: M /trunk/ideal/with-map.cc Extend with-map so that it takes command line arguments and can work given a map. ------------------------------------------------------------------------ r382 | pemsley | 2007-09-10 23:44:06 +0100 (Mon, 10 Sep 2007) | 3 lines Changed paths: M /trunk/ligand/penultimate-to-code.awk M /trunk/ligand/richardson-rotamers.cc Correct the finding of the number of chi angles for a given residue type. Hence the mode and com values for those chis. ------------------------------------------------------------------------ r381 | pemsley | 2007-09-10 21:39:17 +0100 (Mon, 10 Sep 2007) | 2 lines Changed paths: M /trunk/ligand/penultimate-to-code.awk M /trunk/ligand/richardson-rotamers.cc Add MSE as a copy of MET. ------------------------------------------------------------------------ r380 | pemsley | 2007-09-10 21:34:36 +0100 (Mon, 10 Sep 2007) | 2 lines Changed paths: M /trunk/ligand/richardson-rotamers.cc Edit Complete_rotamer_lib.csv so that it produces code for GLN. ------------------------------------------------------------------------ r379 | pemsley | 2007-09-10 16:07:10 +0100 (Mon, 10 Sep 2007) | 4 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh Start taking out dunbrack rotamers and adding Richardson rotamers. Confusion because of poor choice of names for classes and their richardson equivalents - baah. ------------------------------------------------------------------------ r378 | pemsley | 2007-09-10 16:04:26 +0100 (Mon, 10 Sep 2007) | 2 lines Changed paths: M /trunk/doc/coot-shelx.tex M /trunk/doc/user-manual.texi Tinker a bit with the shelx manual. Nothing substantial added. ------------------------------------------------------------------------ r377 | judit.debreczeni | 2007-09-02 21:28:32 +0100 (Sun, 02 Sep 2007) | 1 line Changed paths: M /trunk/doc/coot-shelx.tex A /trunk/doc/hydrogens-fixed.eps A /trunk/doc/hydrogens-incorrect.eps A /trunk/doc/viscotoxin.eps M /trunk/scheme/shelx-extensions.scm M /trunk/scheme/shelx.scm shelx tutorial -- first draft ------------------------------------------------------------------------ r376 | pemsley | 2007-08-30 17:37:46 +0100 (Thu, 30 Aug 2007) | 2 lines Changed paths: A /trunk/pixmaps/connect-to-usf.svg A /trunk/pixmaps/connect-to-world.svg A /trunk/pixmaps/diff-map.png A /trunk/pixmaps/env-distances.svg A /trunk/pixmaps/generic-display-objects.svg A /trunk/pixmaps/merge-molecules.svg A /trunk/pixmaps/residue-info.png A /trunk/pixmaps/residue-info.svg A /trunk/pixmaps/rigid-body.png M /trunk/pixmaps/rotamers.png A /trunk/pixmaps/scroll-wheel.svg A /trunk/pixmaps/stereo-view.svg Catch up with icons, new and updated. ------------------------------------------------------------------------ r375 | pemsley | 2007-08-30 07:47:23 +0100 (Thu, 30 Aug 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc Fix syntax error from conflict (resolution). ------------------------------------------------------------------------ r374 | pemsley | 2007-08-30 00:20:08 +0100 (Thu, 30 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Fix syntax error in coot-gui.scm ------------------------------------------------------------------------ r373 | pemsley | 2007-08-29 16:52:47 +0100 (Wed, 29 Aug 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/gtk2-interface.c Tinker with the icons. ------------------------------------------------------------------------ r372 | pemsley | 2007-08-29 15:19:27 +0100 (Wed, 29 Aug 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Add generic_int_vector_to_list_internal(). Max n_molecules 200. Hmm.. flag mechanism for handling wiggly ligands made more robust. Add function to analyse ligand differences (for testing). ------------------------------------------------------------------------ r371 | pemsley | 2007-08-29 15:15:51 +0100 (Wed, 29 Aug 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc Add extra info from graph matching (i.e. include a score) not just the rtop. ------------------------------------------------------------------------ r370 | pemsley | 2007-08-29 15:14:49 +0100 (Wed, 29 Aug 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/begin.grg Add a test for multiple molecules. Test not tested. ------------------------------------------------------------------------ r369 | pemsley | 2007-08-29 15:13:30 +0100 (Wed, 29 Aug 2007) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/filter.scm M /trunk/scheme/libcheck.scm M /trunk/scheme/remote-control.scm Enhancements to libcheck interface, remove debugging in coot-gui, tinker with molecule list functions. ------------------------------------------------------------------------ r368 | pemsley | 2007-08-28 20:11:32 +0100 (Tue, 28 Aug 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/rotamer.hh M /trunk/src/coot-nomenclature.cc Trivial fixes - resolving conflicts. ------------------------------------------------------------------------ r367 | pemsley | 2007-08-28 20:08:39 +0100 (Tue, 28 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/fascinating-things.scm M /trunk/scheme/quat-convert.scm M /trunk/scheme/snarf-coot-docs.scm Fix issues with snarfing docs from .scm files. ------------------------------------------------------------------------ r366 | pemsley | 2007-08-28 19:55:32 +0100 (Tue, 28 Aug 2007) | 2 lines Changed paths: A /trunk/ligand/richardson-rotamer.cc Add missing richardon-rotamer.cc ------------------------------------------------------------------------ r365 | pemsley | 2007-08-28 13:20:54 +0100 (Tue, 28 Aug 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Add "All" buttons to turn on/off all Maps/Molecules. ------------------------------------------------------------------------ r364 | pemsley | 2007-08-25 12:15:54 +0100 (Sat, 25 Aug 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ligand/Makefile.am M /trunk/ligand/chi-angles.hh M /trunk/ligand/dunbrack.cc M /trunk/ligand/dunbrack.hh M /trunk/ligand/richardson-rotamer.hh M /trunk/ligand/rotamer.cc M /trunk/ligand/rotamer.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/molecule-class-info-other.cc Convert to Richardson Rotamers. Part-way through. ------------------------------------------------------------------------ r363 | pemsley | 2007-08-25 12:14:59 +0100 (Sat, 25 Aug 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh Add "laplacian" function. ------------------------------------------------------------------------ r362 | pemsley | 2007-08-25 12:13:39 +0100 (Sat, 25 Aug 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add function has_unsaved_changes_p(). ------------------------------------------------------------------------ r361 | pemsley | 2007-08-25 12:12:22 +0100 (Sat, 25 Aug 2007) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm Rewrite number-list as tail-recursive. Add some small macros. ------------------------------------------------------------------------ r360 | pemsley | 2007-08-25 12:11:16 +0100 (Sat, 25 Aug 2007) | 2 lines Changed paths: M /trunk/ideal/simple-restraint.cc Simple reformatting. ------------------------------------------------------------------------ r359 | pemsley | 2007-08-09 10:55:59 +0100 (Thu, 09 Aug 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc Fix output aniso U order - fix problem reported by Annette Langkilde. ------------------------------------------------------------------------ r358 | pemsley | 2007-08-09 10:28:23 +0100 (Thu, 09 Aug 2007) | 2 lines Changed paths: A /trunk/doc/coot-faq.texi A /trunk/doc/coot-shelx.tex Add coot-faq and coot-shelx to documentation. ------------------------------------------------------------------------ r357 | pemsley | 2007-08-06 20:36:18 +0100 (Mon, 06 Aug 2007) | 2 lines Changed paths: A /trunk/ligand/richardson-rotamer.hh Add richardson_rotamer.hh ------------------------------------------------------------------------ r356 | pemsley | 2007-08-06 18:40:31 +0100 (Mon, 06 Aug 2007) | 4 lines Changed paths: M /trunk/dnotes M /trunk/ligand/Makefile.am M /trunk/ligand/dunbrack.cc M /trunk/ligand/dunbrack.hh A /trunk/ligand/rotamer.cc A /trunk/ligand/rotamer.hh M /trunk/src/coot-nomenclature.cc Start making changes to rotamers, deriving dunbrack and richardson_rotamer from a common class. This revision compiles but is pprobably broken. ------------------------------------------------------------------------ r355 | pemsley | 2007-08-04 15:16:41 +0100 (Sat, 04 Aug 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/db-main/db-strands.cc M /trunk/dnotes M /trunk/ligand/helix-placement.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mutate.cc Add some debugging to db_strands::get_reference_pdb_list(). Fix a crash in Cootaneering - when the confidence was low, we got back unassigned chnnum and tried to use it. assign-pir-sequence added to history. ------------------------------------------------------------------------ r354 | pemsley | 2007-08-04 14:08:47 +0100 (Sat, 04 Aug 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-utils.cc Use the umask() to set the directory permission. Stupid umask interface, IMHO. ------------------------------------------------------------------------ r353 | pemsley | 2007-08-03 21:52:47 +0100 (Fri, 03 Aug 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/03-ligand.scm M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.h Add a function clear_ncs_ghost_matrices(). Use it in manual-ncs-ghosts. ------------------------------------------------------------------------ r352 | pemsley | 2007-08-03 21:37:53 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/ncs.scm Close the copy molecule, we don't need it now. ------------------------------------------------------------------------ r351 | pemsley | 2007-08-03 21:36:54 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/ncs.scm Fix typo in chain ids for add-ncs-matrix in manual-ncs-ghosts. ------------------------------------------------------------------------ r350 | pemsley | 2007-08-03 19:27:41 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Use the updated splash screen. ------------------------------------------------------------------------ r349 | pemsley | 2007-08-03 19:27:03 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/05-rna-ghosts.scm Tidy up tests, add some views. ------------------------------------------------------------------------ r348 | pemsley | 2007-08-03 19:25:54 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh Fiddling with Richardson Rotamer code. ------------------------------------------------------------------------ r347 | pemsley | 2007-08-03 19:25:29 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Document UNK. ------------------------------------------------------------------------ r346 | pemsley | 2007-08-03 17:28:29 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.4-pre.xpm Add a border to the splash screen. ------------------------------------------------------------------------ r345 | pemsley | 2007-08-03 17:25:03 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.4-pre.xpm Temporary 0.4-pre splashscreen. ------------------------------------------------------------------------ r344 | pemsley | 2007-08-03 12:46:51 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/ncs.scm Add a manual-ncs-ghost function. ------------------------------------------------------------------------ r343 | pemsley | 2007-08-03 12:31:20 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: M /trunk/greg-tests/05-rna-ghosts.scm Make it a proper greg test. ------------------------------------------------------------------------ r342 | pemsley | 2007-08-03 12:30:23 +0100 (Fri, 03 Aug 2007) | 2 lines Changed paths: A /trunk/greg-tests/05-rna-ghosts.scm Add a test for adding NCS ghosts for RNA. ------------------------------------------------------------------------ r341 | pemsley | 2007-08-03 12:29:34 +0100 (Fri, 03 Aug 2007) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/ideal-rna.cc M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc Fix RNA NCS problem (well, the problem of using add_ncs_matrix() function. Add a set_atom_attribute() test. Some messing with chi-angles in preparation of Richardson Rotatmers. ------------------------------------------------------------------------ r340 | pemsley | 2007-08-02 16:30:20 +0100 (Thu, 02 Aug 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/molecule-class-info.cc Fix crash on Cootaneering due to atom label list problem. ------------------------------------------------------------------------ r339 | pemsley | 2007-08-02 15:21:41 +0100 (Thu, 02 Aug 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/src/callbacks.c Fix typo in Add Terminal Residue greg test. ------------------------------------------------------------------------ r338 | pemsley | 2007-08-02 14:34:14 +0100 (Thu, 02 Aug 2007) | 3 lines Changed paths: M /trunk/src/graphics-info-modelling.cc Make Rotate/Translate Y trans positive adjustment move in screen +Y direction [Steven Sheriff]. ------------------------------------------------------------------------ r337 | pemsley | 2007-08-02 14:21:33 +0100 (Thu, 02 Aug 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/04-cootaneer.scm A /trunk/process-greg-log.awk More greg-test updates. ------------------------------------------------------------------------ r336 | pemsley | 2007-08-02 13:09:01 +0100 (Thu, 02 Aug 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/coot-utils/coot-utils.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/pixmaps/add-peptide-1.png M /trunk/pixmaps/add-peptide-1.svg M /trunk/pixmaps/crosshairs.png M /trunk/pixmaps/crosshairs.svg M /trunk/pixmaps/diff-map.svg M /trunk/pixmaps/flip-peptide.png M /trunk/pixmaps/flip-peptide.svg M /trunk/pixmaps/geom.svg M /trunk/pixmaps/plane-distances.png M /trunk/pixmaps/plane-distances.svg M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.cc More pixmap updates - still pixellated. Add Pointer atom adjusted to add an atom to a user-specified molecule. ------------------------------------------------------------------------ r335 | pemsley | 2007-08-02 13:03:25 +0100 (Thu, 02 Aug 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm M /trunk/greg-tests/02-shelx.scm A /trunk/greg-tests/04-cootaneer.scm Add a test for Cootaneering (there currently is a crash on Cootaneering). ------------------------------------------------------------------------ r334 | pemsley | 2007-08-02 00:37:32 +0100 (Thu, 02 Aug 2007) | 6 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/mmdb.cc M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/callbacks.c M /trunk/src/geometry-graphs.cc M /trunk/src/geometry-graphs.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info.h Enable live updating of peptide omega graph. Needs omega_distortions_from_mol function. on_accept_reject_refinement_dialog_destroy unsets graphics_info_t::accept_reject_dialog and clears up moving atoms. Remove messing about with copying spacegroup string on unshelx(). ------------------------------------------------------------------------ r333 | pemsley | 2007-08-01 20:35:36 +0100 (Wed, 01 Aug 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes Update notes. ------------------------------------------------------------------------ r332 | pemsley | 2007-08-01 18:54:35 +0100 (Wed, 01 Aug 2007) | 4 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-preferences.cc M /trunk/src/callbacks.c on_accept_reject_refinement_dialog_destroy() needs to unset the static for graphics_info_t::accept_reject_dialog. Fixes crash (I think) reported by Ketan Gajiwala. ------------------------------------------------------------------------ r331 | pemsley | 2007-08-01 18:15:45 +0100 (Wed, 01 Aug 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/analysis/bfactan.cc M /trunk/analysis/bfkurt.cc M /trunk/analysis/bfkurt.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/graphics-info-graphs.cc M /trunk/src/junk.cc M /trunk/src/molecule-class-info.h Change B factor analysis to take a is_shelx_mol flag and use it to tweak logic of b factor sums. Add to shelx ins reader the ability to make a synthetic b_iso from the u values - now B factor analysis work for shelx molecules (and works well, it seems). ------------------------------------------------------------------------ r330 | pemsley | 2007-08-01 18:12:04 +0100 (Wed, 01 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Put Cootaneering in a sub menu. ------------------------------------------------------------------------ r329 | pemsley | 2007-08-01 14:30:34 +0100 (Wed, 01 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Date check the .fcf.cif file before reading it (rather than the .fcf file). ------------------------------------------------------------------------ r328 | pemsley | 2007-08-01 13:32:49 +0100 (Wed, 01 Aug 2007) | 6 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add a function that adds a line to a shelx ins file for a given molecule. Don't recentre on reading a shelx .res file. If the shelx .res file is a protein, we don't want to see hydrogens, if it isn't then we do. So add a flag into shelx_read_file_info_t that describes this. ------------------------------------------------------------------------ r327 | pemsley | 2007-08-01 13:27:44 +0100 (Wed, 01 Aug 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Updates for shelx. ------------------------------------------------------------------------ r326 | pemsley | 2007-08-01 13:19:31 +0100 (Wed, 01 Aug 2007) | 2 lines Changed paths: M /trunk/pixmaps/chiral.svg M /trunk/pixmaps/edit-chi.svg New svg icons. ------------------------------------------------------------------------ r325 | pemsley | 2007-07-31 20:44:30 +0100 (Tue, 31 Jul 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix function name error spotted by Tom Terwilliger. ------------------------------------------------------------------------ r324 | kevin.cowtan | 2007-07-25 14:56:22 +0100 (Wed, 25 Jul 2007) | 2 lines Changed paths: M /trunk/build-it 3rd attempt: Ubuntu distro and version ------------------------------------------------------------------------ r323 | kevin.cowtan | 2007-07-25 14:26:09 +0100 (Wed, 25 Jul 2007) | 2 lines Changed paths: M /trunk/build-it 2nd attempt: pick up ubuntu version ------------------------------------------------------------------------ r322 | kevin.cowtan | 2007-07-25 13:55:36 +0100 (Wed, 25 Jul 2007) | 2 lines Changed paths: M /trunk/build-it Pick up Linux distro/version info from /etc/issue if not available from RPM ------------------------------------------------------------------------ r321 | pemsley | 2007-07-22 15:51:35 +0100 (Sun, 22 Jul 2007) | 2 lines Changed paths: A /trunk/scheme/shelx-extensions.scm Add shelx-extensions from the ACA Shelx demo. ------------------------------------------------------------------------ r320 | pemsley | 2007-07-19 15:23:01 +0100 (Thu, 19 Jul 2007) | 7 lines Changed paths: M /trunk/coords/mmdb.cc M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Use the hydrogen names fix on the reading of shelx files. In the hydrogen name fix convert " H0 " to " H ". Not converted back on writing yet though. Some debugging added (needs to be removed). Add a setting to not display chiral volume errors. Stop reading a PIR file on "*". ------------------------------------------------------------------------ r319 | pemsley | 2007-07-16 18:01:23 +0100 (Mon, 16 Jul 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/greg-tests/01-pdb+mtz.scm A /trunk/greg-tests/03-ligand.scm M /trunk/greg-tests/begin.grg M /trunk/happy-coot-diary.html M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Change from FASTA to PIR Move greg tests about. ------------------------------------------------------------------------ r318 | pemsley | 2007-07-16 09:38:34 +0100 (Mon, 16 Jul 2007) | 4 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/ideal/simple-restraint.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc Fix gridding density problem in blob_under_cursor(). Change the smooth_scroll function to have acceleration. Add bad chirals check, popup annoying dialog. ------------------------------------------------------------------------ r317 | pemsley | 2007-07-16 09:32:48 +0100 (Mon, 16 Jul 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc Add count_cis_peptides() function. ------------------------------------------------------------------------ r316 | pemsley | 2007-07-16 09:30:47 +0100 (Mon, 16 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Change variable name. ------------------------------------------------------------------------ r315 | pemsley | 2007-07-13 17:26:58 +0100 (Fri, 13 Jul 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm D /trunk/greg-tests/02-cif.scm A /trunk/greg-tests/02-shelx.scm (from /trunk/greg-tests/02-cif.scm:314) Rename 02-cif to 02-shelx for greg tests. ------------------------------------------------------------------------ r314 | pemsley | 2007-07-13 17:26:31 +0100 (Fri, 13 Jul 2007) | 2 lines Changed paths: M /trunk/greg-tests/02-cif.scm No sensible HOF cif file - remove the test for it. ------------------------------------------------------------------------ r313 | pemsley | 2007-07-13 17:25:07 +0100 (Fri, 13 Jul 2007) | 3 lines Changed paths: M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.h M /trunk/src/cmtz-interface.cc Make find-waters return a molecule number, similarly for new_molecule_by_atom_selection(). ------------------------------------------------------------------------ r312 | pemsley | 2007-07-13 17:01:22 +0100 (Fri, 13 Jul 2007) | 2 lines Changed paths: A /trunk/scheme/greg-extensions.scm Add GUI extension for running greg. ------------------------------------------------------------------------ r311 | pemsley | 2007-07-13 13:41:03 +0100 (Fri, 13 Jul 2007) | 5 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/pixmaps/kleywegt.svg M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-graphs.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk2-interface.c M /trunk/src/pick.cc coot-gtk2.glade for those new icons. Remove superfluous gtkgl/gtkglarea.hs. Put imol protection in turn on/off backups. Add Alias reading to CCP4i defs parsing. ------------------------------------------------------------------------ r310 | pemsley | 2007-07-12 22:09:35 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: M /trunk/coot-gtk2.glade And the glade file for the new icons. ------------------------------------------------------------------------ r309 | pemsley | 2007-07-12 19:34:34 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: M /trunk/pixmaps/auto-fit-rotamer.svg A /trunk/pixmaps/chiral.png A /trunk/pixmaps/chiral.svg A /trunk/pixmaps/density-fit.svg A /trunk/pixmaps/diff-map.svg A /trunk/pixmaps/geom.svg A /trunk/pixmaps/gln-asn-b-factors.svg A /trunk/pixmaps/gln-asn-b-factorssvg.svg A /trunk/pixmaps/kleywegt.svg A /trunk/pixmaps/peptide-omega.png A /trunk/pixmaps/peptide-omega.svg A /trunk/pixmaps/probe-clash.svg M /trunk/pixmaps/ramachandran.png A /trunk/pixmaps/temperature.png A /trunk/pixmaps/temperature.svg A /trunk/pixmaps/unknown-blob.png A /trunk/pixmaps/unknown-blob.svg A /trunk/pixmaps/water-diff-map.svg A /trunk/pixmaps/water-drop.svg Add icon svgs and pngs. ------------------------------------------------------------------------ r308 | pemsley | 2007-07-12 14:47:16 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: A /trunk/pixmaps/ramachandran.png Add rama pixmap. ------------------------------------------------------------------------ r307 | pemsley | 2007-07-12 14:45:11 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm fix sphere test typo. ------------------------------------------------------------------------ r306 | pemsley | 2007-07-12 14:44:20 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: M /trunk/greg-tests/01-pdb+mtz.scm Add sphere test - test not tested. ------------------------------------------------------------------------ r305 | pemsley | 2007-07-12 13:57:14 +0100 (Thu, 12 Jul 2007) | 2 lines Changed paths: M /trunk/setup-greg update setup-greg. ------------------------------------------------------------------------ r304 | pemsley | 2007-07-11 12:53:48 +0100 (Wed, 11 Jul 2007) | 4 lines Changed paths: M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/ideal/simple-restraint.cc M /trunk/ideal/simple-restraint.hh M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc Moved bad_chiral_volumes() to simple-restraint.cc. Move is_valid_model_molecule() and is_valid_map_molecule() into graphics_info.h. Add SHELX BIND keyword. ------------------------------------------------------------------------ r303 | pemsley | 2007-07-11 11:53:39 +0100 (Wed, 11 Jul 2007) | 2 lines Changed paths: M /trunk/dnotes Rearrange so that "Things to do list for release" is at the top. ------------------------------------------------------------------------ r302 | pemsley | 2007-07-11 11:52:52 +0100 (Wed, 11 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm resolve conflict. ------------------------------------------------------------------------ r301 | pemsley | 2007-07-11 11:39:45 +0100 (Wed, 11 Jul 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/pixmaps/atom-at-pointer.png M /trunk/pixmaps/atom-at-pointer.svg M /trunk/pixmaps/edit-chi.png M /trunk/pixmaps/edit-chi.svg M /trunk/pixmaps/ghosts.png M /trunk/pixmaps/ghosts.svg M /trunk/pixmaps/plane-distances.svg M /trunk/pixmaps/pointer-distances.png M /trunk/pixmaps/pointer-distances.svg M /trunk/pixmaps/refine-1.svg M /trunk/pixmaps/regularize-1.svg M /trunk/pixmaps/regularize.png M /trunk/pixmaps/rigid-body.svg M /trunk/pixmaps/rotamers.png M /trunk/pixmaps/rotamers.svg M /trunk/pixmaps/rtz.png M /trunk/pixmaps/rtz.svg M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-state.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Update icon svgs and pixmaps. Fix problem of sizing graphics window from script in gtk2. ------------------------------------------------------------------------ r300 | pemsley | 2007-07-11 11:25:07 +0100 (Wed, 11 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/shelx.scm Improve shelx tools. ------------------------------------------------------------------------ r299 | pemsley | 2007-07-10 18:17:15 +0100 (Tue, 10 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Improved reading of SHELX lst file. ------------------------------------------------------------------------ r298 | pemsley | 2007-07-09 18:36:28 +0100 (Mon, 09 Jul 2007) | 5 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/greg-tests/begin.grg M /trunk/happy-coot-diary.html M /trunk/scheme/coot-utils.scm M /trunk/setup-greg M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c M /trunk/src/test-chol.cc M /trunk/test-with-greg.scm More widget (interface) updates. We don't want to load gui scm if we don't have GUILE_GTK. so don't pass #t to load-all-scheme in that case. Fix to transform-map-using-lsq-matrix, as pointed to by Nick Furnham. ------------------------------------------------------------------------ r297 | pemsley | 2007-07-09 18:30:50 +0100 (Mon, 09 Jul 2007) | 2 lines Changed paths: M /trunk/pixmaps/add-alt-conf.png M /trunk/pixmaps/add-alt-conf.svg M /trunk/pixmaps/flip-peptide.png M /trunk/pixmaps/flip-peptide.svg M /trunk/pixmaps/ghosts.png M /trunk/pixmaps/ghosts.svg M /trunk/pixmaps/side-chain-180.png M /trunk/pixmaps/side-chain-180.svg M /trunk/pixmaps/spin-view.png M /trunk/pixmaps/spin-view.svg More pixmap updates. ------------------------------------------------------------------------ r296 | pemsley | 2007-07-09 18:28:56 +0100 (Mon, 09 Jul 2007) | 3 lines Changed paths: M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Remove the pointer-using atom label code and replace with vector and iterator code. ------------------------------------------------------------------------ r295 | pemsley | 2007-07-09 14:45:06 +0100 (Mon, 09 Jul 2007) | 2 lines Changed paths: M /trunk/pixmaps/panel-screenshot.png lighten the screeshot icon. ------------------------------------------------------------------------ r294 | pemsley | 2007-07-09 14:12:57 +0100 (Mon, 09 Jul 2007) | 3 lines Changed paths: A /trunk/pixmaps/aniso-atom.png A /trunk/pixmaps/aniso-atom.svg A /trunk/pixmaps/cell+symm.png A /trunk/pixmaps/cell+symm.svg A /trunk/pixmaps/crosshairs.png A /trunk/pixmaps/crosshairs.svg A /trunk/pixmaps/ghosts.png A /trunk/pixmaps/ghosts.svg A /trunk/pixmaps/gtk-font.png A /trunk/pixmaps/panel-screenshot.png A /trunk/pixmaps/phenixed.svg A /trunk/pixmaps/sequence-view.png A /trunk/pixmaps/sequence-view.svg A /trunk/pixmaps/smiles.png A /trunk/pixmaps/smiles.svg A /trunk/pixmaps/spin-view.png A /trunk/pixmaps/spin-view.svg Add more pixmaps. Include stock GNOME (I guess) panel-screenshot.png gtk-font.png. ------------------------------------------------------------------------ r293 | pemsley | 2007-07-09 10:30:54 +0100 (Mon, 09 Jul 2007) | 2 lines Changed paths: D /trunk/pixmaps/reset-view-32.png.svg D /trunk/pixmaps/rtz.png.svg Delete unwatned svgs. ------------------------------------------------------------------------ r292 | pemsley | 2007-07-09 08:05:24 +0100 (Mon, 09 Jul 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/src/graphics-info-lsq.cc M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info.cc Add icons to glade file for gtk2. Add polar angles description of rotation in apply_lsq(). ------------------------------------------------------------------------ r291 | pemsley | 2007-07-09 08:03:27 +0100 (Mon, 09 Jul 2007) | 2 lines Changed paths: A /trunk/pixmaps/add-alt-conf.png M /trunk/pixmaps/add-alt-conf.svg A /trunk/pixmaps/add-peptide-1.png A /trunk/pixmaps/atom-at-pointer.png A /trunk/pixmaps/atom-at-pointer.svg A /trunk/pixmaps/auto-fit-rotamer.png M /trunk/pixmaps/auto-fit-rotamer.svg A /trunk/pixmaps/delete.png A /trunk/pixmaps/delete.svg M /trunk/pixmaps/display-manager.png M /trunk/pixmaps/display-manager.svg A /trunk/pixmaps/edit-chi.png A /trunk/pixmaps/flip-peptide.png A /trunk/pixmaps/gtk-connect-16.png A /trunk/pixmaps/gtk-open-16.png A /trunk/pixmaps/gtk-open-24.png A /trunk/pixmaps/gtk-open.png A /trunk/pixmaps/pink-pointer.png A /trunk/pixmaps/pink-pointer.svg A /trunk/pixmaps/plane-distances.png A /trunk/pixmaps/plane-distances.svg A /trunk/pixmaps/pointer-distances.png A /trunk/pixmaps/pointer-distances.svg A /trunk/pixmaps/refine.png M /trunk/pixmaps/regularize-1.svg A /trunk/pixmaps/regularize.png A /trunk/pixmaps/reset-view-32.png A /trunk/pixmaps/reset-view-32.png.svg A /trunk/pixmaps/reset-view-32.svg A /trunk/pixmaps/reset-view.png A /trunk/pixmaps/rotamers.png A /trunk/pixmaps/rtz.png A /trunk/pixmaps/rtz.png.svg A /trunk/pixmaps/side-chain-180.png M /trunk/pixmaps/side-chain-180.svg Add some svg and pixmaps for icons. ------------------------------------------------------------------------ r290 | pemsley | 2007-07-06 11:13:46 +0100 (Fri, 06 Jul 2007) | 2 lines Changed paths: A /trunk/pixmaps/add-alt-conf.svg M /trunk/pixmaps/side-chain-180.svg Icon updates. ------------------------------------------------------------------------ r289 | pemsley | 2007-07-06 10:59:34 +0100 (Fri, 06 Jul 2007) | 2 lines Changed paths: A /trunk/pixmaps/auto-fit-rotamer.svg A /trunk/pixmaps/display-manager.png A /trunk/pixmaps/display-manager.svg A /trunk/pixmaps/edit-chi.svg A /trunk/pixmaps/flip-peptide.svg A /trunk/pixmaps/reset-view.svg A /trunk/pixmaps/rigid-body.svg A /trunk/pixmaps/rotamers.svg A /trunk/pixmaps/rtz.svg A /trunk/pixmaps/side-chain-180.svg Add some svg (and png) icons. ------------------------------------------------------------------------ r288 | pemsley | 2007-07-04 18:21:45 +0100 (Wed, 04 Jul 2007) | 2 lines Changed paths: M /trunk/src/graphics-info.h Add back the dumping of a image if we are in moving making mode. ------------------------------------------------------------------------ r287 | pemsley | 2007-07-04 18:15:28 +0100 (Wed, 04 Jul 2007) | 3 lines Changed paths: M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/gtk2-interface.c Tinker with the GTK2 toolbar. Move Reset View and Display Manager into a toolbar. ------------------------------------------------------------------------ r286 | pemsley | 2007-07-04 18:14:10 +0100 (Wed, 04 Jul 2007) | 3 lines Changed paths: M /trunk/src/globjects.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h Add Terminal residue with map needs terminal_residue_addition_direct_phi variables. ------------------------------------------------------------------------ r285 | pemsley | 2007-07-04 18:00:25 +0100 (Wed, 04 Jul 2007) | 2 lines Changed paths: M /trunk/build-it Add a bit of debugging in build-it. ------------------------------------------------------------------------ r284 | pemsley | 2007-07-04 13:03:08 +0100 (Wed, 04 Jul 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/dnotes Re-arrange feature documentation. ------------------------------------------------------------------------ r283 | pemsley | 2007-07-04 12:44:22 +0100 (Wed, 04 Jul 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/cootaneer/Makefile.am M /trunk/db-main/db-main.cc Fix spewing errors for ca->mainchain. Remove cootaneer-demo.h from cootaneer Makefile.am ------------------------------------------------------------------------ r282 | pemsley | 2007-07-04 11:19:47 +0100 (Wed, 04 Jul 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-gtk2.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/gtk2-interface.c Reorder TODO. Add new molecule by sphere selection function. ------------------------------------------------------------------------ r281 | pemsley | 2007-07-03 23:28:31 +0100 (Tue, 03 Jul 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/src/c-interface-mutate.cc Allow filename for llk cootaneer data to be found by dereferencing COOT_PREFIX. ------------------------------------------------------------------------ r280 | pemsley | 2007-07-03 22:22:02 +0100 (Tue, 03 Jul 2007) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/scheme/shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add stub input reader for richard rotamers. Fix shelx-lst reader. Needs... a function to return the chain id of a given residue number from the shelxl lst file (which does not know about the chain splitting). chain_id_for_shelxl_residue_number(). Overlap many models of ligand molecules. Discard others not the best fit. Update graph_match(). Add function delete_all_except_res(). ------------------------------------------------------------------------ r279 | pemsley | 2007-07-03 17:59:03 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: M /trunk/ligand/Makefile.am M /trunk/ligand/ligand.cc M /trunk/ligand/penultimate-to-code.awk A /trunk/ligand/richardson-rotamers.cc Add some Richardsons' Rotamers code. ------------------------------------------------------------------------ r278 | pemsley | 2007-07-03 17:26:30 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: A /trunk/ligand/penultimate-to-code.awk Add Richardson rotamer library parser. ------------------------------------------------------------------------ r277 | pemsley | 2007-07-03 16:53:20 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/shelx.scm Fix parsing/splitting problems in read-shelx-lst-file. ------------------------------------------------------------------------ r276 | pemsley | 2007-07-03 10:32:45 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: A /trunk/src/c-interface-mutate.cc Oops. Add c-interface-mutate.cc too. ------------------------------------------------------------------------ r275 | pemsley | 2007-07-03 10:31:21 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Add more extensions - associate sequence. ------------------------------------------------------------------------ r274 | pemsley | 2007-07-03 09:34:35 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: A /trunk/cootaneer/Makefile.am Add Makefile.am for cootaneer. ------------------------------------------------------------------------ r273 | pemsley | 2007-07-03 09:30:39 +0100 (Tue, 03 Jul 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-info.cc M /trunk/src/cc-interface.hh Introduce a new function: closest-atom(imol), used by cootaneer-gui. ------------------------------------------------------------------------ r272 | pemsley | 2007-07-03 01:53:59 +0100 (Tue, 03 Jul 2007) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h Add a GUI for Cootaneering. Add protection for no active residue in phosphorylate-active-residue. Add a function SCM sequence_info(int imol). ------------------------------------------------------------------------ r271 | pemsley | 2007-07-02 21:37:21 +0100 (Mon, 02 Jul 2007) | 10 lines Changed paths: M /trunk/COPYING M /trunk/Makefile.am M /trunk/TODO M /trunk/configure.in M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/cootaneer/cootaneer-demo.cpp M /trunk/macros/clipper.m4 M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h GPL version 3 configure.in to version 0.4-pre-1 New macro for new clipper (with cootaneer features). mutate functions moved down to coot-coord-utils. Cootaneer added [very cool - mostly Kevin's code]. apply_sequence() function added. insert_coords_internal() extended to add chain if needed. get_fragment_from_atom_spec() function created. utility function to output an atom spec. ------------------------------------------------------------------------ r270 | pemsley | 2007-07-02 16:44:26 +0100 (Mon, 02 Jul 2007) | 2 lines Changed paths: D /trunk/pixmaps/coot-0.3.3.xpm M /trunk/pixmaps/coot-0.3.xpm Update coot-0.3.xpm to 0.3.3 July 2007 ------------------------------------------------------------------------ r269 | pemsley | 2007-07-02 16:38:57 +0100 (Mon, 02 Jul 2007) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.3.3.xpm Add new splash screen. ------------------------------------------------------------------------ r268 | pemsley | 2007-07-01 13:31:14 +0100 (Sun, 01 Jul 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/configure.in M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc Release 0.3.3 Re-work the graphics_draw() function, and draw_mono(). ------------------------------------------------------------------------ r267 | pemsley | 2007-07-01 12:59:23 +0100 (Sun, 01 Jul 2007) | 2 lines Changed paths: A /trunk/cootaneer/cootaneer-llk-2.40.dat (from /trunk/cootaneer/llk-2.40.dat:266) D /trunk/cootaneer/llk-2.40.dat Rename llk data file. ------------------------------------------------------------------------ r266 | pemsley | 2007-07-01 12:58:01 +0100 (Sun, 01 Jul 2007) | 2 lines Changed paths: M /trunk/cootaneer/buccaneer-lib.cpp M /trunk/cootaneer/buccaneer-lib.h M /trunk/cootaneer/buccaneer-prot.cpp M /trunk/cootaneer/buccaneer-prot.h M /trunk/cootaneer/buccaneer-sequence.cpp M /trunk/cootaneer/buccaneer-sequence.h M /trunk/cootaneer/cootaneer-demo.cpp M /trunk/cootaneer/cootaneer-sequence.cpp M /trunk/cootaneer/cootaneer-sequence.h A /trunk/cootaneer/llk-2.40.dat New Cootaneer code. ------------------------------------------------------------------------ r265 | pemsley | 2007-07-01 11:52:02 +0100 (Sun, 01 Jul 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/configure.in M /trunk/src/c-interface.cc Convert to 0.3.3-pre. Fix the gtk1 filter button. ------------------------------------------------------------------------ r264 | pemsley | 2007-06-30 12:26:34 +0100 (Sat, 30 Jun 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Add gtk2 post-processing files. ------------------------------------------------------------------------ r263 | pemsley | 2007-06-29 13:50:37 +0100 (Fri, 29 Jun 2007) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/configure.in M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/coot_wrap_python_pre.cc Release 0.3.2 ------------------------------------------------------------------------ r262 | pemsley | 2007-06-29 13:38:12 +0100 (Fri, 29 Jun 2007) | 2 lines Changed paths: M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc Remove debugging lines. ------------------------------------------------------------------------ r261 | pemsley | 2007-06-29 13:02:30 +0100 (Fri, 29 Jun 2007) | 7 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/ligand/helix-placement.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Make the expand_molecule_space() more robust. Crashes less now (I mean I can't get it to crash). Fiddled with the destructor of a molecule_class_info Add Aniso close button for Gtk2 interface. Add hydrogen bond usage in several Bond_lines_container constructors. Remove some debugging. ------------------------------------------------------------------------ r260 | pemsley | 2007-06-28 20:01:57 +0100 (Thu, 28 Jun 2007) | 2 lines Changed paths: M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/CIsoSurface.h Fix up some negative number problems apprent on Mac Intel. ------------------------------------------------------------------------ r259 | pemsley | 2007-06-28 20:00:23 +0100 (Thu, 28 Jun 2007) | 2 lines Changed paths: M /trunk/src/coot-glue-gtk2.c We don't want to compile this unless with have GUILE_GTK ------------------------------------------------------------------------ r258 | pemsley | 2007-06-28 12:54:39 +0100 (Thu, 28 Jun 2007) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-gtk2.glade M /trunk/happy-coot-diary.html M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/test-helix-placement.cc M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/gtk2-interface.c Add a top hat to the density contributions when finding the tube orientation. For strand fitting, try 15 strands by default (rather than 8). Fix the "Dismiss" action of CR on a Check Waters results dialog. ------------------------------------------------------------------------ r257 | pemsley | 2007-06-26 21:12:25 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Fix up libs for test-chol on penelope (tedious). ------------------------------------------------------------------------ r256 | pemsley | 2007-06-26 21:03:58 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc fix typo ------------------------------------------------------------------------ r255 | pemsley | 2007-06-26 18:18:09 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface.cc Add some protection for updating maps. Should not be needed. ------------------------------------------------------------------------ r254 | pemsley | 2007-06-26 17:37:16 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Fix type in diary. ------------------------------------------------------------------------ r253 | pemsley | 2007-06-26 17:36:35 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/scheme/exercise-scm-mol.scm M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh Fix up mmdb_manager_from_scheme_expression for guile-1.6.x. ------------------------------------------------------------------------ r252 | pemsley | 2007-06-26 16:59:51 +0100 (Tue, 26 Jun 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade New glade (goes with previous) for check/delete water baddies dialog. Update diary. ------------------------------------------------------------------------ r251 | pemsley | 2007-06-26 16:58:28 +0100 (Tue, 26 Jun 2007) | 6 lines Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/gtk-manual.c M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/support.c Add protection for firing up a Kleywegt Plot when we already have a Ramachandran Plot (without this protection there was a crash). Clean up some old screen output. Use GINT_TO_POINTER/GPOINTER_TO_INT instead of newing a pointer to int and casting. ------------------------------------------------------------------------ r250 | pemsley | 2007-06-26 15:11:37 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary a bit. ------------------------------------------------------------------------ r249 | pemsley | 2007-06-26 15:05:00 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: M /trunk/dnotes Update dnotes. ------------------------------------------------------------------------ r248 | pemsley | 2007-06-26 15:03:52 +0100 (Tue, 26 Jun 2007) | 4 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info.cc Fix up the toggling of the display control buttons when the scripting functions, set_mol_active set_mol_displayed, set_map_displayed() are used. ------------------------------------------------------------------------ r247 | pemsley | 2007-06-26 14:41:39 +0100 (Tue, 26 Jun 2007) | 2 lines Changed paths: A /trunk/greg-tests A /trunk/greg-tests/01-pdb+mtz.scm A /trunk/greg-tests/02-cif.scm A /trunk/greg-tests/begin.grg A /trunk/setup-greg A /trunk/test-with-greg.scm Add initial files for testing with Greg. ------------------------------------------------------------------------ r246 | pemsley | 2007-06-26 14:09:20 +0100 (Tue, 26 Jun 2007) | 13 lines Changed paths: M /trunk/atom-utils/Makefile.am M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/mapview.glade M /trunk/scheme/ChangeLog M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/sequence-view/Makefile.am M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.h M /trunk/src/interface.c Pharma day fixes: Fix map-molecule-list function. Add function label-all-active-residue-atoms. Fix handlers in generic-double-entry. Grenoble Fixes: Fix up graphics_draw() function to do draw, draw, swap_buffers, swap_buffers when there is side-by-side stereo. This fixes the viewing problems for Randy Read - who has a slow graphics card. It's made a mess of the code though, sadly. Fix scripting filename filter for GTK2. Update diary. sequence view now needs GL flags - urgh. So does atom-utils. ------------------------------------------------------------------------ r245 | pemsley | 2007-06-26 13:41:13 +0100 (Tue, 26 Jun 2007) | 8 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/configure.in M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/mapview.glade M /trunk/scheme/americanisms.scm M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-ligands.cc M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/coot_wrap_python_pre.cc M /trunk/src/gl-matrix.cc M /trunk/src/gl-matrix.h M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info.cc M /trunk/src/post-glade M /trunk/src/support.c A /trunk/src/test-chol.cc Move to 0.3.2-pre-2 Fix residue type in phosphorylation script. Add Apply button in Aniso dialog. Add GSL code for Cholesky decomposition. Fix Aniso U reading for SHELXL .res file. Read PART 4 for SHELXL .res file. Add test-chol.cc to test cholesky decomposition. ------------------------------------------------------------------------ r244 | pemsley | 2007-06-21 22:06:25 +0100 (Thu, 21 Jun 2007) | 12 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/db-main/db-main.cc M /trunk/dnotes M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/test-helix-placement.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/globjects.h M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Add a density level to the helix fitting code, below which residues are chopped. Mess with the graphics_draw() function. Use a static variable to decide if we need to run swap buffers from the expose call back. This fixes Randy Read's problem of non-synchoronous refresh in side by side stereo with very slow graphics. Add some gtk2 testing code for handling the filename filter in run script file selector. Fix problem of running db_main twice in one Coot session. clear residue holder. Placeholder code for function to sharpen map. ------------------------------------------------------------------------ r243 | pemsley | 2007-06-19 12:36:23 +0100 (Tue, 19 Jun 2007) | 11 lines Changed paths: M /trunk/ChangeLog M /trunk/TODO M /trunk/dnotes M /trunk/doc/tutorial.tex M /trunk/ligand/wiggly-ligand.cc M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm M /trunk/scheme/remote-control.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Diffs from Grenoble 1: Don't add debugging output of wiggly ligands. Have another go at socket reading in remote-control.scm. This time use a gtk-timeout. Make the step in stepped-refine be an optional variable. Add a nudge screen-centre gui. Add a method to dump an image every redraw, for a movie. Move screendump_image() function from c-interface.cc to graphic-info-render.cc. Add action views. Fix the remove named view method. ------------------------------------------------------------------------ r242 | pemsley | 2007-06-14 23:48:15 +0100 (Thu, 14 Jun 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/configure.in M /trunk/doc/user-manual.texi M /trunk/pixmaps/coot-0.3.xpm M /trunk/scheme/exercise-scm-mol.scm M /trunk/src/c-interface.h Update some docs and other bits from Cambridge trip. ------------------------------------------------------------------------ r241 | pemsley | 2007-06-14 23:44:46 +0100 (Thu, 14 Jun 2007) | 3 lines Changed paths: M /trunk/atom-utils/Makefile.am M /trunk/sequence-view/Makefile.am Add GLUT includes for targets in sequence-view and atom utils. Hopefully this will help build on the mac. Why are they needed now? ------------------------------------------------------------------------ r240 | pemsley | 2007-06-14 17:15:44 +0100 (Thu, 14 Jun 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Kleywegt plot interface changed. Lots of functions add themselves to history. ------------------------------------------------------------------------ r239 | pemsley | 2007-06-11 19:09:32 +0100 (Mon, 11 Jun 2007) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile_pre.cc Update wrapper. ------------------------------------------------------------------------ r238 | pemsley | 2007-06-11 19:08:58 +0100 (Mon, 11 Jun 2007) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in Remove po - problems building on Mac. ------------------------------------------------------------------------ r237 | pemsley | 2007-06-11 19:08:02 +0100 (Mon, 11 Jun 2007) | 2 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h Make overlap_ligands() return a SCM. ------------------------------------------------------------------------ r236 | pemsley | 2007-06-11 18:36:22 +0100 (Mon, 11 Jun 2007) | 6 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/dnotes M /trunk/guile.supp M /trunk/scheme/fitting.scm M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info-mutate.cc Fix tyos in fit-residue-range. Backup a spin_search(). Don't set-molecule-bonds-colour-map-rotation for maps. Improve guile suppresssions. Fix up graph match a little. ------------------------------------------------------------------------ r235 | pemsley | 2007-06-11 11:48:32 +0100 (Mon, 11 Jun 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/scheme/coot-utils.scm If there is a map available for phosphorylate-residue, give a map selector rather than running with regularize. ------------------------------------------------------------------------ r234 | pemsley | 2007-06-09 17:25:54 +0100 (Sat, 09 Jun 2007) | 5 lines Changed paths: M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info.h Improve phosphorylation fitting by using a "spin search" to find highest density for the phosphorus. Moved rotate_round_vector() to coot-coord-utils. Added some atom spec utilities and added simple torsion class. ------------------------------------------------------------------------ r233 | pemsley | 2007-06-09 00:18:06 +0100 (Sat, 09 Jun 2007) | 4 lines Changed paths: M /trunk/TODO M /trunk/doc/user-manual.texi M /trunk/scheme/extensions.scm M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info.cc Tidy up some documentation. Add CCP4mg menu item. Adjust ccp4mg picture description function. ------------------------------------------------------------------------ r232 | pemsley | 2007-06-08 21:07:59 +0100 (Fri, 08 Jun 2007) | 10 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix syntax on toggle-display-mol functions. Add functions mutate_by_overlap and phosphorylate-active-residue Change the function that returns the active residue (atom, actually). Add a function regularize_zone(). Add a utility function copy_and_delete_hydrogens(). Add a function residue_name(). Used by phosphorylate-active-residue. Fix function that converts a scm list to a list of atoms in merge_molecules() Fix function that inserts/appends a residue into/onto a chain. ------------------------------------------------------------------------ r231 | pemsley | 2007-06-08 08:00:58 +0100 (Fri, 08 Jun 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add scripting level function change_chain_id(). ------------------------------------------------------------------------ r230 | pemsley | 2007-06-07 21:28:48 +0100 (Thu, 07 Jun 2007) | 12 lines Changed paths: M /trunk/ChangeLog M /trunk/README M /trunk/RELEASE-NOTES M /trunk/TODO M /trunk/coot-utils/coot-coord-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/command-line.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix (I think) crash due to bad scroll group in Display Control maps. Fix in c-interface-gui.cc that sets the scroll group for maps to null when all maps are deleted. Add function to change the atom label font colour. Add a function to write a ccp4mg picture description file. Almost works. Add a function to turn a scm list of strings to a vector of strings. Add a function that does merge molecules using a scm list and returns a list of chain ids (needs to be tested). Add a static string to save the directory for save coordinates dialog. Save the bond thickness to the state file for a given molecule if it not the default thickness. ------------------------------------------------------------------------ r229 | pemsley | 2007-06-07 16:51:11 +0100 (Thu, 07 Jun 2007) | 2 lines Changed paths: M /trunk/scheme/americanisms.scm M /trunk/scheme/fitting.scm Optionally animate water fitting. ------------------------------------------------------------------------ r228 | pemsley | 2007-06-07 12:38:39 +0100 (Thu, 07 Jun 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fitting.scm Add a check button to generic-double-entry. ------------------------------------------------------------------------ r227 | pemsley | 2007-06-07 09:20:56 +0100 (Thu, 07 Jun 2007) | 4 lines Changed paths: M /trunk/coords/Bond_lines.cc Tinking with the bonding again. Don't mark S, SE, CL, BR, or P as bonded. Fixes MSO bonding, but does it help or harm other things...? Some testing, looks OK. ------------------------------------------------------------------------ r226 | pemsley | 2007-06-06 17:01:38 +0100 (Wed, 06 Jun 2007) | 2 lines Changed paths: M /trunk/src/c-interface-mmdb.cc fix typo in #define ------------------------------------------------------------------------ r225 | pemsley | 2007-06-06 11:35:01 +0100 (Wed, 06 Jun 2007) | 2 lines Changed paths: M /trunk/src/coot_wrap_guile_pre.cc M /trunk/src/coot_wrap_python_pre.cc Update the wrapping functions. ------------------------------------------------------------------------ r224 | pemsley | 2007-06-06 11:24:04 +0100 (Wed, 06 Jun 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/db-main/db-strands.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface.cc M /trunk/src/coot-glue-gtk2.c M /trunk/src/post-glade M /trunk/src/support.c Add several trivial changes for MSC_VER building. Let the coot version return something about the embedded scripting. ------------------------------------------------------------------------ r223 | pemsley | 2007-06-04 18:02:49 +0100 (Mon, 04 Jun 2007) | 5 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h add function delte-atom-by-active residue, which doesn't work because active-atom does not return waters. Add an inscode the the args of delete_atom(). Add history to several functions. ------------------------------------------------------------------------ r222 | pemsley | 2007-06-01 14:10:24 +0100 (Fri, 01 Jun 2007) | 2 lines Changed paths: M /trunk/TODO update to do list. ------------------------------------------------------------------------ r221 | pemsley | 2007-06-01 14:05:54 +0100 (Fri, 01 Jun 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/history-templates Add more history to scripting functions. Very boring. ------------------------------------------------------------------------ r220 | pemsley | 2007-05-31 11:10:49 +0100 (Thu, 31 May 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/compat/coot-getopt.h M /trunk/coords/Bond_lines.cc M /trunk/coot-utils/coot-utils.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/command-line.cc M /trunk/src/density-score-by-residue.cc M /trunk/src/fix-nomenclature.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/gtk-manual.c M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/post-glade M /trunk/src/post-gtk2-glade.sh Add fixes for Windows build from Francois. ------------------------------------------------------------------------ r219 | pemsley | 2007-05-30 18:55:06 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Add ifdefs for using guile 1.6 for reading the scm view. ------------------------------------------------------------------------ r218 | pemsley | 2007-05-30 18:17:07 +0100 (Wed, 30 May 2007) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add a function go-to-view that takes a scm view and interpolates to it from the current position/orientation. ------------------------------------------------------------------------ r217 | pemsley | 2007-05-30 16:42:56 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/src/graphics-info-state.cc Add stereo mode to state file, with fixes. ------------------------------------------------------------------------ r216 | pemsley | 2007-05-30 16:29:17 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/src/graphics-info-state.cc Add stereo modes to state file. ------------------------------------------------------------------------ r215 | pemsley | 2007-05-30 16:11:21 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Use pass by reference of vectors of phi/psis when drawing. ------------------------------------------------------------------------ r214 | pemsley | 2007-05-30 14:54:23 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/src/coot-render.hh M /trunk/src/graphics-info-render.cc More fixes for Raster3D bonds and atoms parameters. ------------------------------------------------------------------------ r213 | pemsley | 2007-05-30 14:29:05 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot-render.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info-render.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c Some changes to add configurability to Raster3D atom output. ------------------------------------------------------------------------ r212 | pemsley | 2007-05-30 13:37:13 +0100 (Wed, 30 May 2007) | 2 lines Changed paths: A /trunk/src/post-gtk2-glade.sh Add post-gtk2-glade.sh, which adds to gtk2-interface.c file a GTK2 wrapper. ------------------------------------------------------------------------ r211 | pemsley | 2007-05-29 23:51:07 +0100 (Tue, 29 May 2007) | 10 lines Changed paths: M /trunk/ChangeLog M /trunk/coot-gtk2.glade M /trunk/dnotes M /trunk/scheme/ChangeLog M /trunk/scheme/coot-gui.scm M /trunk/scheme/coot-utils.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info-lsq.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Fix problem of inserted residues (change chain ids) being appended rather than inserted. transform-map-using-lsq-matrix function added. generic function: rtop_to_scm added. apply_lsq returns a scmed rtop. generic-double-entry needed a cancel button. remove ncs debugging code. Allow dialog size to change depending on whether or not there is a stats frame in rama plots. ------------------------------------------------------------------------ r210 | pemsley | 2007-05-29 00:02:58 +0100 (Tue, 29 May 2007) | 6 lines Changed paths: M /trunk/dnotes M /trunk/mapview.glade M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh M /trunk/src/support.h Add a statistics box to the ramachandran plot. Make the plotting of each point return what type of point it is. Then add them up. Interface files updated - perhaps not correctly. Add a function to turn off and on the environment distances. ------------------------------------------------------------------------ r209 | pemsley | 2007-05-28 11:43:50 +0100 (Mon, 28 May 2007) | 2 lines Changed paths: A /trunk/coot-gtk2.glade Add the Gtk2 glade file. ------------------------------------------------------------------------ r208 | pemsley | 2007-05-25 18:11:00 +0100 (Fri, 25 May 2007) | 3 lines Changed paths: M /trunk/src/c-interface-validate.cc M /trunk/src/graphics-info.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Try to allow for Kleywegt plots that don't use chain ids. Better than it was. Still not good though. ------------------------------------------------------------------------ r207 | pemsley | 2007-05-25 15:12:42 +0100 (Fri, 25 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/pick.cc Fix the problem of mutating to a stub ALA causing a crash. ------------------------------------------------------------------------ r206 | pemsley | 2007-05-25 12:50:06 +0100 (Fri, 25 May 2007) | 2 lines Changed paths: A /trunk/src/history-templates Add simple reminder of the way to add things to the history. ------------------------------------------------------------------------ r205 | pemsley | 2007-05-25 10:54:42 +0100 (Fri, 25 May 2007) | 6 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/ligand/ligand-extras.cc M /trunk/src/graphics-info-mutate.cc M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-mutate.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/pick.cc Use erase() not remove() in cluster list (ligand extras). Fixes a valgrind error. Move mutate functions to molecule-class-info-mutate.cc Add some picking debugging. Add some kleywegt plot chain id debugging. ------------------------------------------------------------------------ r204 | pemsley | 2007-05-24 16:27:30 +0100 (Thu, 24 May 2007) | 2 lines Changed paths: M /trunk/TODO M /trunk/doc/user-manual.texi Update TODO list. ------------------------------------------------------------------------ r203 | pemsley | 2007-05-24 15:19:03 +0100 (Thu, 24 May 2007) | 3 lines Changed paths: M /trunk/po/Makefile.in.in Stop Makefile depending on stamp-it. Stops things going into an endless loop on bragg3 at least [Lothar Esser]. ------------------------------------------------------------------------ r202 | pemsley | 2007-05-24 11:58:05 +0100 (Thu, 24 May 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/scheme/extensions.scm M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Allow user setting of the contour levels in Ramachandran plot and also the blocksize. ------------------------------------------------------------------------ r201 | pemsley | 2007-05-23 18:23:49 +0100 (Wed, 23 May 2007) | 2 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc More tinkering with the play views speed. ------------------------------------------------------------------------ r200 | pemsley | 2007-05-23 17:20:57 +0100 (Wed, 23 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Fix the view spin speed setting. ------------------------------------------------------------------------ r199 | pemsley | 2007-05-23 15:50:15 +0100 (Wed, 23 May 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Oppps. Fix typo in GetNumberOfModels() usage. ------------------------------------------------------------------------ r198 | pemsley | 2007-05-23 14:25:35 +0100 (Wed, 23 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc More debugging and fixing of NCS master problems. ------------------------------------------------------------------------ r197 | pemsley | 2007-05-22 20:50:40 +0100 (Tue, 22 May 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Return spacegroup in reverse_direction_of_fragment() function. ------------------------------------------------------------------------ r196 | pemsley | 2007-05-22 20:46:47 +0100 (Tue, 22 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Fix malloc bug in returning spacegroup string. ------------------------------------------------------------------------ r195 | pemsley | 2007-05-22 14:39:00 +0100 (Tue, 22 May 2007) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r194 | pemsley | 2007-05-22 14:36:57 +0100 (Tue, 22 May 2007) | 3 lines Changed paths: M /trunk/TODO M /trunk/coot-utils/coot-map-utils.cc M /trunk/dnotes M /trunk/doc/user-manual.texi M /trunk/src/c-interface.cc M /trunk/src/graphics-info-state.cc M /trunk/src/molecule-class-info.cc Fix the transform-map function. Make the documentation consistent with the new behaviour. ------------------------------------------------------------------------ r193 | pemsley | 2007-05-22 09:00:39 +0100 (Tue, 22 May 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/src/c-interface-gui.cc M /trunk/src/graphics-info-navigation-gtk1.cc Fix the startup molecule chooser to be consitent with residue list for gtk1. ------------------------------------------------------------------------ r192 | pemsley | 2007-05-21 18:25:08 +0100 (Mon, 21 May 2007) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/src/graphics-info-modelling.cc Add refinement to terminal residue nucleotide addtion. Also, match the nucleotides better using nucleotide_to_nucleotide function. ------------------------------------------------------------------------ r191 | pemsley | 2007-05-21 15:01:29 +0100 (Mon, 21 May 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-state.cc M /trunk/src/gtk-manual.c M /trunk/src/gtk-manual.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info.h Remove toggling of display and active states. Moved actual toggle functions to scheme level, they use the set functions. ------------------------------------------------------------------------ r190 | pemsley | 2007-05-21 12:57:38 +0100 (Mon, 21 May 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/src/c-interface-validate.cc M /trunk/src/rama_plot.cc M /trunk/src/rama_plot.hh Make a Ramachandran plot remember where it was put. ------------------------------------------------------------------------ r189 | pemsley | 2007-05-21 11:47:15 +0100 (Mon, 21 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/gtk2-interface.c M /trunk/src/post-glade Tinker with side by side stereo handling logic. ------------------------------------------------------------------------ r188 | pemsley | 2007-05-18 20:57:14 +0100 (Fri, 18 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-ncs.cc M /trunk/src/callbacks.c M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc Add ncs debugging lines. ------------------------------------------------------------------------ r187 | pemsley | 2007-05-18 18:10:11 +0100 (Fri, 18 May 2007) | 3 lines Changed paths: M /trunk/ChangeLog M /trunk/dnotes M /trunk/src/c-interface.cc Try to fix the problem of switching to hardware stereo mode from side by side mode. Untested. ------------------------------------------------------------------------ r186 | pemsley | 2007-05-18 13:40:37 +0100 (Fri, 18 May 2007) | 2 lines Changed paths: M /trunk/scheme/fascinating-things.scm Fix syntax error. ------------------------------------------------------------------------ r185 | pemsley | 2007-05-18 13:03:52 +0100 (Fri, 18 May 2007) | 2 lines Changed paths: M /trunk/macros/gtkgl.m4 Try to use 64 bit libs for gtkglarea. ------------------------------------------------------------------------ r184 | pemsley | 2007-05-17 13:09:02 +0100 (Thu, 17 May 2007) | 4 lines Changed paths: M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-navigation-gtk1.cc Ooops. I need to pass residue_tree to fill_go_to_atom_residue_list_gtk1, not residue_gtklist. Fixes crash. Move gui stuff from c-interface.cc to c-interface-gui.cc ------------------------------------------------------------------------ r183 | pemsley | 2007-05-17 12:11:26 +0100 (Thu, 17 May 2007) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/RELEASE-NOTES M /trunk/dnotes M /trunk/src/support.h Bill Scott compiles coot and finds problems in missing intltools and double processed support.h. Fixed. ------------------------------------------------------------------------ r182 | pemsley | 2007-05-16 20:23:02 +0100 (Wed, 16 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Oops. Fix syntax error of test in previous commit. ------------------------------------------------------------------------ r181 | pemsley | 2007-05-16 19:14:57 +0100 (Wed, 16 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/callbacks.c M /trunk/src/graphics-info.h Tinker with stereo mode code. ------------------------------------------------------------------------ r180 | pemsley | 2007-05-16 13:04:45 +0100 (Wed, 16 May 2007) | 2 lines Changed paths: M /trunk/dnotes update dnotes. ------------------------------------------------------------------------ r179 | pemsley | 2007-05-16 13:04:21 +0100 (Wed, 16 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc Fix handling of text in new (Gtk2) GtkTextViews. ------------------------------------------------------------------------ r178 | pemsley | 2007-05-16 01:48:09 +0100 (Wed, 16 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/graphics-info.cc Use gtk_container_children() for gtk1. ------------------------------------------------------------------------ r177 | pemsley | 2007-05-16 00:54:23 +0100 (Wed, 16 May 2007) | 4 lines Changed paths: M /trunk/dnotes M /trunk/happy-coot-diary.html M /trunk/src/c-interface.cc M /trunk/src/graphics-info.cc M /trunk/src/junk.cc clear up a casting in views playing. Recode the extraction of the Residue Edits now that we have a table. (it wasn't too hard, since the atom info was attached to the entry). ------------------------------------------------------------------------ r176 | pemsley | 2007-05-15 18:46:48 +0100 (Tue, 15 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface.h Add c-interface.h declarations for new view functions. ------------------------------------------------------------------------ r175 | pemsley | 2007-05-15 18:45:01 +0100 (Tue, 15 May 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Add save views function. Add it into the gui. Add set views play speed function. Add it to the gui. ------------------------------------------------------------------------ r174 | pemsley | 2007-05-15 15:58:31 +0100 (Tue, 15 May 2007) | 2 lines Changed paths: M /trunk/configure.in AC_SUBST(ALL_LINGUAS) ------------------------------------------------------------------------ r173 | pemsley | 2007-05-15 11:41:54 +0100 (Tue, 15 May 2007) | 13 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/cootrc M /trunk/dnotes M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-mmdb.cc M /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/coot-glue-gtk2.c M /trunk/src/graphics-info-state.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk-manual.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add colour by occupancy and colour by B-factor. Add set_b_factor_bonds_scale_factor() function which added a UDR_HIERARCHY float to the CMMDBManager. Add scripting interface to set b-factor scale for a given molecule number. Add gtk-manual menu items for these options. Add USE_GUILE protection to coot-glue-gtk2.c and c-interface-build.cc Add dictionary info to extracted molecule info from state file. Add some debugging to the destroying of go to atom window. Something is going wrong there. Add post-processing code to conditional MAKE_COOT_WRAP_GUILE in src/Makefile.am Change the default fg prelight in cootrc. Does this help with white on grey problems? ------------------------------------------------------------------------ r172 | pemsley | 2007-05-15 11:35:17 +0100 (Tue, 15 May 2007) | 4 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/scheme/fascinating-things.scm Add a B-factor bonds colour scale gui to extensions. In fascinating things, don't create a feature frame if there are no features. Add view annotation text with the right background colour. ------------------------------------------------------------------------ r171 | pemsley | 2007-05-15 11:32:00 +0100 (Tue, 15 May 2007) | 2 lines Changed paths: M /trunk/scheme/refmac.scm fix copyright. ------------------------------------------------------------------------ r170 | pemsley | 2007-05-15 09:30:52 +0100 (Tue, 15 May 2007) | 2 lines Changed paths: M /trunk/scheme/refmac.scm Tell us which LIBIN refmac will be using. ------------------------------------------------------------------------ r169 | pemsley | 2007-05-14 13:46:47 +0100 (Mon, 14 May 2007) | 5 lines Changed paths: M /trunk/ideal/simple-restraint.hh M /trunk/src/graphics-info-modelling.cc Remove the old and mostly dupicated function copy_mol_and_regularize() and simply call copy_mol_and_refine() with the map molecule set to -1. Use the same constructor for restraints for both now, but in the case of refine use add_map(). ------------------------------------------------------------------------ r168 | pemsley | 2007-05-13 11:32:35 +0100 (Sun, 13 May 2007) | 3 lines Changed paths: M /trunk/scheme/fitting.scm (inexact->exact (/ 1 2) now returns 1/2. In guile 1.6.x it returned 1. Allow for this. ------------------------------------------------------------------------ r167 | pemsley | 2007-05-12 14:13:52 +0100 (Sat, 12 May 2007) | 4 lines Changed paths: M /trunk/ChangeLog M /trunk/dnotes M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Check the given cif dictionary for restraints for the given 3-letter code before passing it to libcheck scheme function. Add some history functions. ------------------------------------------------------------------------ r166 | pemsley | 2007-05-12 14:12:10 +0100 (Sat, 12 May 2007) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm Render a text widget with text if there was one given in the box of buttons function. ------------------------------------------------------------------------ r165 | pemsley | 2007-05-10 14:07:25 +0100 (Thu, 10 May 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Remove some debugging. ------------------------------------------------------------------------ r164 | pemsley | 2007-05-10 13:22:24 +0100 (Thu, 10 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-mmdb.cc D /trunk/src/example-scm-mol-representation.scm scm mol improvements. ------------------------------------------------------------------------ r163 | pemsley | 2007-05-10 13:21:34 +0100 (Thu, 10 May 2007) | 3 lines Changed paths: A /trunk/scheme/example-scm-mol-representation.scm (from /trunk/src/example-scm-mol-representation.scm:162) A /trunk/scheme/exercise-scm-mol.scm Excerise the scm mol represenation. Move the example of scm mol here. ------------------------------------------------------------------------ r162 | pemsley | 2007-05-10 13:20:35 +0100 (Thu, 10 May 2007) | 2 lines Changed paths: M /trunk/src/example-scm-mol-representation.scm Tinker with scm mol represenation. ------------------------------------------------------------------------ r161 | pemsley | 2007-05-09 19:19:14 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: M /trunk/src/example-scm-mol-representation.scm Trim off the bits we don't need... ------------------------------------------------------------------------ r160 | pemsley | 2007-05-09 19:12:39 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: M /trunk/src/coot-glue-gtk2.c M /trunk/src/coot_wrap_guile.cc D /trunk/src/example-scm-mole-representation.scm bits and bobs. ------------------------------------------------------------------------ r159 | pemsley | 2007-05-09 19:11:57 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: M /trunk/src/gtk2-interface.c Add gtk version protection. ------------------------------------------------------------------------ r158 | pemsley | 2007-05-09 19:08:09 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: M /trunk/src/graphics-info.cc Add guile version protection to safe scheme debugging code. ------------------------------------------------------------------------ r157 | pemsley | 2007-05-09 18:00:05 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: A /trunk/intltool-extract.in A /trunk/intltool-merge.in A /trunk/intltool-update.in Add intltools. ------------------------------------------------------------------------ r156 | pemsley | 2007-05-09 17:47:50 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: A /trunk/po/Makefile.in.in A /trunk/po/coot.pot A /trunk/po/es_ES.po add some po files. ------------------------------------------------------------------------ r155 | pemsley | 2007-05-09 15:06:00 +0100 (Wed, 09 May 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/coot-gui.scm M /trunk/scheme/create-server.scsh M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/graphics-info.cc Tinkering with other multi-threaded paths. Still not good (a bad scm expression causes the process to abort). ------------------------------------------------------------------------ r154 | pemsley | 2007-05-09 11:52:02 +0100 (Wed, 09 May 2007) | 8 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc A /trunk/src/c-interface-mmdb.cc A /trunk/src/c-interface-mmdb.hh M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/cc-interface.hh M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/interface.h M /trunk/src/main.cc M /trunk/src/support.h Create a new file that has SCM to mmdb interface. Use new threading execution and lock system. Add raw interface function to set a view from scripting level. Add view descriptions. Remove NLS from main.cc, it happens on the command line now (from the Makefile). Update diary. ------------------------------------------------------------------------ r153 | pemsley | 2007-05-09 11:45:03 +0100 (Wed, 09 May 2007) | 2 lines Changed paths: M /trunk/scheme/refmac-problems.scm Tidy up refmac-problems a bit. ------------------------------------------------------------------------ r152 | pemsley | 2007-05-09 11:44:33 +0100 (Wed, 09 May 2007) | 4 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/fascinating-things.scm M /trunk/scheme/refmac-problems.scm Small adjustments to scheme functions: add a scripting interface to add views. Check that the refinement map is set in refmac-problems. ------------------------------------------------------------------------ r151 | pemsley | 2007-05-08 17:48:26 +0100 (Tue, 08 May 2007) | 2 lines Changed paths: A /trunk/scheme/fascinating-things.scm Add fascinating things from molprobity. ------------------------------------------------------------------------ r150 | pemsley | 2007-05-08 09:56:00 +0100 (Tue, 08 May 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/refmac-problems.scm Updates to refmac problems reading code. ------------------------------------------------------------------------ r149 | pemsley | 2007-05-04 15:25:50 +0100 (Fri, 04 May 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/refmac-problems.scm More updates to read refmac problems. ------------------------------------------------------------------------ r148 | pemsley | 2007-05-04 15:16:28 +0100 (Fri, 04 May 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm A /trunk/scheme/refmac-problems.scm Add start of refmac problems handling code, with an example. ------------------------------------------------------------------------ r147 | pemsley | 2007-05-04 12:11:51 +0100 (Fri, 04 May 2007) | 3 lines Changed paths: M /trunk/ChangeLog M /trunk/src/molecule-class-info.cc Add cholesky decomposition to the matrix for anisotropic atoms. Makes shelx .ins files look better. ------------------------------------------------------------------------ r146 | pemsley | 2007-05-04 10:46:56 +0100 (Fri, 04 May 2007) | 4 lines Changed paths: M /trunk/Makefile.am M /trunk/configure.in M /trunk/po/es.po M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/coot.py M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/main.cc Messing with internationization. Still doesn't work. Add code to generate new names for views in save view. fix fill_go_to_atom_residue_and_atom_lists_gtk1() problem. ------------------------------------------------------------------------ r145 | pemsley | 2007-05-04 10:40:15 +0100 (Fri, 04 May 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r144 | pemsley | 2007-05-03 18:48:08 +0100 (Thu, 03 May 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html update diary. ------------------------------------------------------------------------ r143 | pemsley | 2007-05-03 18:42:23 +0100 (Thu, 03 May 2007) | 2 lines Changed paths: A /trunk/src/example-scm-mol-representation.scm (from /trunk/src/example-scm-mole-representation.scm:142) Rename file. ------------------------------------------------------------------------ r142 | pemsley | 2007-05-03 12:56:48 +0100 (Thu, 03 May 2007) | 9 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/configure.in M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/dnotes M /trunk/ligand/ideal-rna.hh M /trunk/mapview.glade M /trunk/mkinstalldirs A /trunk/po A /trunk/po/ChangeLog A /trunk/po/POTFILES.in A /trunk/po/es.po M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc A /trunk/src/c-interface-gui.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info-defines.cc M /trunk/src/graphics-info-modelling.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/gtk2-interface.c M /trunk/src/interface.c M /trunk/src/junk.cc M /trunk/src/main.cc Start messing with internationization. No damage yet, I think. Add a views panel and views functions to support. Split c-interface.cc into additional c-interface-gui.cc Add utility function nucleotide_is_DNA(). Add execute_simple_nucleotide_addition() for simple addition of nucleotides. Rework the fill_output_residue_info_widget_atom so that it now uses a table. Add po directory and Miguel's es.po. Add transform_mol() utility function. ------------------------------------------------------------------------ r141 | pemsley | 2007-05-02 12:37:37 +0100 (Wed, 02 May 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/example-scm-mole-representation.scm M /trunk/src/graphics-info.cc trivial changes, remove some debugging in SCM molecule reader. ------------------------------------------------------------------------ r140 | pemsley | 2007-05-02 12:15:43 +0100 (Wed, 02 May 2007) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc A /trunk/src/example-scm-mole-representation.scm More additions to the SCM->mmdb interface, with more debugging. Add an example scm representation. ------------------------------------------------------------------------ r139 | pemsley | 2007-05-02 11:23:16 +0100 (Wed, 02 May 2007) | 2 lines Changed paths: M /trunk/dnotes M /trunk/src/c-interface-build.cc More diagnostics for a SCM molecule. ------------------------------------------------------------------------ r138 | pemsley | 2007-05-02 11:22:38 +0100 (Wed, 02 May 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Update shelxl features. ------------------------------------------------------------------------ r137 | pemsley | 2007-05-02 02:43:20 +0100 (Wed, 02 May 2007) | 3 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/cc-interface.hh M /trunk/src/molecule-class-info-other.cc Fill in clear_and_update_molecule() function, it is the SCM->mmdb interface. It seems to work. Cool. ------------------------------------------------------------------------ r136 | pemsley | 2007-05-01 19:26:53 +0100 (Tue, 01 May 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am and the Makefile to go with new post-processing of wrapper code. ------------------------------------------------------------------------ r135 | pemsley | 2007-05-01 19:24:11 +0100 (Tue, 01 May 2007) | 2 lines Changed paths: M /trunk/src/post-process-coot-wrap-guile.sh Do the SCM_STRING_CHARS substitution depending on the version of guile. ------------------------------------------------------------------------ r134 | pemsley | 2007-05-01 18:43:15 +0100 (Tue, 01 May 2007) | 9 lines Changed paths: M /trunk/ChangeLog M /trunk/RELEASE-NOTES M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/dnotes M /trunk/scheme/entry+do-button.scm M /trunk/scheme/extensions.scm M /trunk/scheme/junk.scm M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot_wrap_guile.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h A /trunk/src/post-process-coot-wrap-guile.sh More changes to support colour by occ and b-factor. Apply patch from Kevin for cns data reading. SHELXL refinement has nice new file selector now. .cns added to acceptable map extensions. Added molecule function replace_molecule() for use with updating/replacing molecules from scripting. apply_lsq_matches should return an rtop (it doesn't yet). Add post-processing of coot_wrap_guile_pre.cc so to remove SCM_STRING_CHARS. ------------------------------------------------------------------------ r133 | pemsley | 2007-05-01 18:37:12 +0100 (Tue, 01 May 2007) | 2 lines Changed paths: M /trunk/build-it Fix the $coot_version when there is no pre-release. ------------------------------------------------------------------------ r132 | pemsley | 2007-04-30 15:33:37 +0100 (Mon, 30 Apr 2007) | 2 lines Changed paths: M /trunk/dnotes More dnotes. ------------------------------------------------------------------------ r131 | pemsley | 2007-04-30 14:22:21 +0100 (Mon, 30 Apr 2007) | 5 lines Changed paths: M /trunk/doc/user-manual.texi M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h More doc updates - trivial More fiddling with socket string setting, debugging. apply_lsq_matches should return a SCM of the matching matrix. not finished yet. ------------------------------------------------------------------------ r130 | pemsley | 2007-04-30 12:11:29 +0100 (Mon, 30 Apr 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Fix documenation error for transform-map [Chris Meier]. ------------------------------------------------------------------------ r129 | pemsley | 2007-04-30 10:29:38 +0100 (Mon, 30 Apr 2007) | 3 lines Changed paths: M /trunk/dnotes M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info.h Add spins to views. Some no graphics protection added to set_socket_string_waiting(). ------------------------------------------------------------------------ r128 | pemsley | 2007-04-27 20:30:33 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/extensions.scm M /trunk/src/c-interface.h Add a gui for Spin View ------------------------------------------------------------------------ r127 | pemsley | 2007-04-27 20:21:01 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES tinker with release notes. ------------------------------------------------------------------------ r126 | pemsley | 2007-04-27 20:20:01 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES update release notes. ------------------------------------------------------------------------ r125 | pemsley | 2007-04-27 18:33:35 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: A /trunk/dnotes Start dnotes. ------------------------------------------------------------------------ r124 | pemsley | 2007-04-27 17:11:38 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: M /trunk/src/c-interface-build.cc Add GSL protection around pseudo-bond usage for secondary strture restraints. ------------------------------------------------------------------------ r123 | pemsley | 2007-04-27 14:51:25 +0100 (Fri, 27 Apr 2007) | 3 lines Changed paths: M /trunk/mapview.glade M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Remove the empty frame on the RHS of the main window (make it invisible). Add the function fill_partial_residue() for a single given atom spec. ------------------------------------------------------------------------ r122 | pemsley | 2007-04-27 13:58:05 +0100 (Fri, 27 Apr 2007) | 7 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/doc/user-manual.texi M /trunk/scheme/coot-utils.scm M /trunk/scheme/shelx.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/molecule-class-info-other.cc Fix documentation for translate-molecule-by. SHELXL refinement can now deduce its hkl filename and make the correct links. Added function to remove time extension. Reduce the colour map rotation for maps. Add a function transform_molecule_by to the scripting layer. Fix up handling of a shelx file when the file was not found (fixes a crash). ------------------------------------------------------------------------ r121 | pemsley | 2007-04-27 11:06:49 +0100 (Fri, 27 Apr 2007) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc Fix up USE_GUILE wrappings on dictionaries_read() - Martin Singleton. ------------------------------------------------------------------------ r120 | pemsley | 2007-04-26 15:59:35 +0100 (Thu, 26 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Add slerping to the quaternion interpolation, add a gui to add view. ------------------------------------------------------------------------ r119 | pemsley | 2007-04-26 15:14:08 +0100 (Thu, 26 Apr 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/graphics-info-navigation-gtk2.cc Tiny interface changes, no more rule hints. ------------------------------------------------------------------------ r118 | pemsley | 2007-04-26 14:40:29 +0100 (Thu, 26 Apr 2007) | 2 lines Changed paths: A /trunk/pixmaps/README Add readme file for pixmap directory. ------------------------------------------------------------------------ r117 | pemsley | 2007-04-26 13:20:26 +0100 (Thu, 26 Apr 2007) | 2 lines Changed paths: M /trunk/src/c-interface.cc Trivial namespace changes str_mtime for gtk1 interface. ------------------------------------------------------------------------ r116 | pemsley | 2007-04-26 10:21:32 +0100 (Thu, 26 Apr 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info-ncs.cc Fix (I think) NCS copy bug found by Michael Url at York Refinement Workshop. ------------------------------------------------------------------------ r115 | pemsley | 2007-04-25 14:33:54 +0100 (Wed, 25 Apr 2007) | 3 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/scheme/create-server.scsh M /trunk/scheme/remote-control.scm M /trunk/src/c-interface.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Much playing with mutex locks and threading. I believe that it is now in a good state. Mabye naively :) ------------------------------------------------------------------------ r114 | pemsley | 2007-04-25 00:08:56 +0100 (Wed, 25 Apr 2007) | 2 lines Changed paths: M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh Fix up the file sort button in Gtk2 interface (now we stat the full file name). ------------------------------------------------------------------------ r113 | pemsley | 2007-04-24 13:55:43 +0100 (Tue, 24 Apr 2007) | 4 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/globjects.cc Investigate the failure of the sort button in the fileselector Gtk2. It's because the whole filename is not passed to stat. ------------------------------------------------------------------------ r112 | pemsley | 2007-04-24 13:53:25 +0100 (Tue, 24 Apr 2007) | 3 lines Changed paths: M /trunk/scheme/create-server.scsh M /trunk/scheme/remote-control.scm Much testing and tinkering with remote control code. Not in a good state yet. ------------------------------------------------------------------------ r111 | pemsley | 2007-04-24 00:30:20 +0100 (Tue, 24 Apr 2007) | 2 lines Changed paths: M /trunk/build-it Fix jpeg lib dependencies round the wrong way for libtiff. ------------------------------------------------------------------------ r110 | pemsley | 2007-04-23 14:06:44 +0100 (Mon, 23 Apr 2007) | 10 lines Changed paths: M /trunk/scheme/junk.scm M /trunk/scheme/remote-control.scm M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h Change the remote control code so that we use a termination string, not completely fixed up. Add set_socket_string_waiting function. Use a mechanism to send the graphics window a configure event so that it finds waiting text. Text is in a static graphics_info_t variable, not sure if that is the best way forward. Move safe_scheme_command to graphics_info_t because we need it there to handle the configure event callback in the event of code being there to run. ------------------------------------------------------------------------ r109 | pemsley | 2007-04-22 17:55:30 +0100 (Sun, 22 Apr 2007) | 4 lines Changed paths: M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh Add functions requested by GMS to un-shelx and re-shelx a molecule, which means that the .ins molecule gets split into chains on reading and remerged on writing .ins files. ------------------------------------------------------------------------ r108 | pemsley | 2007-04-21 22:47:07 +0100 (Sat, 21 Apr 2007) | 4 lines Changed paths: M /trunk/src/cmtz-interface.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc Fixes for GT2 Go To Atom widget. Works now, I think. No longer try to read a CNS data file from File -> Open Dataset, because we would need to pass a imol argument to the cns data reader. ------------------------------------------------------------------------ r107 | pemsley | 2007-04-21 19:08:11 +0100 (Sat, 21 Apr 2007) | 9 lines Changed paths: M /trunk/ChangeLog M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/pick.cc M /trunk/src/read-cif.c M /trunk/src/read-cif.h Add segid info to picked atom output. Don't call graphics-general-key-press-hook for NCS skip or go to curent atom key presses. Move some c-interface.cc code to c-interface-build.cc Add Views interface. Needs slerping. Add more gtk2 Go To Atom code. Add CNS data reading code. Needs testing. Add blob-under-cursor-to-screen-centre function. ------------------------------------------------------------------------ r106 | pemsley | 2007-04-21 13:21:16 +0100 (Sat, 21 Apr 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/coot-utils/test-shelx-reader.cc M /trunk/coot-utils/test-utils.cc Fix the reading of shelx .res files with ^Ms, in the same way I think that SHELX does it. ------------------------------------------------------------------------ r105 | pemsley | 2007-04-21 13:19:37 +0100 (Sat, 21 Apr 2007) | 2 lines Changed paths: M /trunk/mapview.glade Add a place for the GtkHTML widget. ------------------------------------------------------------------------ r104 | pemsley | 2007-04-21 13:18:06 +0100 (Sat, 21 Apr 2007) | 3 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/tips.scm Change the mailing list info in the coot tips. Add generic-buttons-dialog function. ------------------------------------------------------------------------ r103 | pemsley | 2007-04-21 13:13:04 +0100 (Sat, 21 Apr 2007) | 2 lines Changed paths: M /trunk/macros/clipper.m4 Add the clipper-cns to used libraries. ------------------------------------------------------------------------ r102 | pemsley | 2007-04-21 13:11:18 +0100 (Sat, 21 Apr 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for reading a phs file. ------------------------------------------------------------------------ r101 | pemsley | 2007-04-20 17:29:22 +0100 (Fri, 20 Apr 2007) | 3 lines Changed paths: M /trunk/python/gap.py M /trunk/skeleton/BuildCas.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc More code for colour by occupancy and b-factor. Copyright stragglers added. ------------------------------------------------------------------------ r100 | pemsley | 2007-04-20 17:18:53 +0100 (Fri, 20 Apr 2007) | 2 lines Changed paths: M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/mmdb-extras.h Add some infrastructure for colour by occ and b factor. ------------------------------------------------------------------------ r99 | pemsley | 2007-04-20 16:01:38 +0100 (Fri, 20 Apr 2007) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Fix up extension test for reading maps. Now we can actually read user-approved filename extensions for maps - rather than just ignoring them [Pete Meyer]. ------------------------------------------------------------------------ r98 | pemsley | 2007-04-20 15:07:55 +0100 (Fri, 20 Apr 2007) | 2 lines Changed paths: M /trunk/ligand/Makefile.am M /trunk/ligand/Makefile.simple M /trunk/ligand/chi-angles.cc M /trunk/ligand/chi-angles.hh M /trunk/ligand/dunbrack.cc M /trunk/ligand/dunbrack.hh M /trunk/ligand/find-ligand.cc M /trunk/ligand/find-waters.cc M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/ideal-rna.cc M /trunk/ligand/ligand-extras.cc M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/monomer-utils.cc M /trunk/ligand/monomer-utils.hh M /trunk/ligand/residue_by_phi_psi.cc M /trunk/ligand/residue_by_phi_psi.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/rigid-body.hh M /trunk/ligand/test-fffear-in-coot.cc M /trunk/ligand/test-helix-placement.cc M /trunk/ligand/test-random.cc M /trunk/ligand/testdunbrack.cc M /trunk/ligand/wiggly-ligand.cc M /trunk/ligand/wligand.hh M /trunk/macros/Makefile.am M /trunk/macros/clipper.m4 M /trunk/macros/coot-database.m4 M /trunk/macros/coot-windows.m4 M /trunk/macros/glut.m4 M /trunk/macros/guile-gtk.m4 M /trunk/macros/mmdb-ssm.m4 M /trunk/macros/mmdb.m4 M /trunk/macros/with-guile.m4 M /trunk/macros/with-python.m4 M /trunk/mini-mol/Makefile.am M /trunk/mini-mol/mini-mol-utils.cc M /trunk/mini-mol/mini-mol-utils.hh M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/mini-mol/testminimol.cc M /trunk/python/Makefile.am M /trunk/python/americanisms.py M /trunk/python/background-demo.py M /trunk/python/coot-lsq.py M /trunk/python/coot-utils.py M /trunk/python/coot_load_modules.py.in M /trunk/python/fitting.py M /trunk/python/gap.py M /trunk/python/get-ebi.py M /trunk/python/hello.py M /trunk/python/mutate.py M /trunk/python/povray.py M /trunk/python/raster3d.py M /trunk/python/refmac.py M /trunk/python/shelx.py M /trunk/sequence-view/Makefile.am M /trunk/sequence-view/sequence-view.cc M /trunk/sequence-view/sequence-view.hh M /trunk/setup/coot.csh.in M /trunk/setup/coot.sh.in M /trunk/skeleton/Makefile.am M /trunk/src/graphics-info-lsq.cc M /trunk/surface/CXXChargeTable.cpp M /trunk/surface/CXXChargeTable.h M /trunk/surface/CXXCircle.cpp M /trunk/surface/CXXCircle.h M /trunk/surface/CXXCircleNode.cpp M /trunk/surface/CXXCircleNode.h M /trunk/surface/CXXCoord.cpp M /trunk/surface/CXXCoord.h M /trunk/surface/CXXCreator.cpp M /trunk/surface/CXXCreator.h M /trunk/surface/CXXException.cpp M /trunk/surface/CXXException.h M /trunk/surface/CXXFFTSolventMap.cpp M /trunk/surface/CXXFFTSolventMap.h M /trunk/surface/CXXFortranFile.cpp M /trunk/surface/CXXFortranFile.h M /trunk/surface/CXXMatrix4x4.h M /trunk/surface/CXXNewHood.cpp M /trunk/surface/CXXNewHood.h M /trunk/surface/CXXNode.cpp M /trunk/surface/CXXNode.h M /trunk/surface/CXXPointyBit.h M /trunk/surface/CXXQADSurface.cpp M /trunk/surface/CXXQADSurface.h M /trunk/surface/CXXQADSurfaceStaticData.cpp M /trunk/surface/CXXSpace.cpp M /trunk/surface/CXXSpace.h M /trunk/surface/CXXSphereElement.cpp M /trunk/surface/CXXSphereElement.h M /trunk/surface/CXXSphereFlatTriangle.h M /trunk/surface/CXXSphereNode.cpp M /trunk/surface/CXXSphereNode.h M /trunk/surface/CXXSphereTriangle.cpp M /trunk/surface/CXXSphereTriangle.h M /trunk/surface/CXXSphereTriangleEdge.cpp M /trunk/surface/CXXSphereTriangleEdge.h M /trunk/surface/CXXSurface.cpp M /trunk/surface/CXXSurface.h M /trunk/surface/CXXSurfaceVertex.cpp M /trunk/surface/CXXSurfaceVertex.h M /trunk/surface/CXXTorusElement.cpp M /trunk/surface/CXXTorusElement.h M /trunk/surface/CXXTorusNode.cpp M /trunk/surface/CXXTorusNode.h M /trunk/surface/CXXTorusTriangle.cpp M /trunk/surface/CXXTorusTriangle.h M /trunk/surface/CXXTorusTriangle.h.h M /trunk/surface/CXXTriangle.cpp M /trunk/surface/CXXTriangle.h M /trunk/surface/CXXUtils.cpp M /trunk/surface/CXXUtils.h M /trunk/surface/ElectroSurface.cpp M /trunk/surface/TokenIterator.h M /trunk/surface/surface.cpp M /trunk/surface/surface.h M /trunk/tw/Makefile.am M /trunk/tw/cootsound.c M /trunk/tw/tw.cc More copyright notice changes. ------------------------------------------------------------------------ r97 | pemsley | 2007-04-20 11:55:55 +0100 (Fri, 20 Apr 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Enable the setting of the unit cell colour for Dirk. ------------------------------------------------------------------------ r96 | pemsley | 2007-04-16 23:36:01 +0100 (Mon, 16 Apr 2007) | 2 lines Changed paths: M /trunk/coot-utils/Makefile.am M /trunk/coot-utils/atomic-numbers.cc M /trunk/coot-utils/coot-coord-extras.cc M /trunk/coot-utils/coot-coord-extras.hh M /trunk/coot-utils/coot-coord-lsq.cc M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/coot-utils/coot-fasta.cc M /trunk/coot-utils/coot-fasta.hh M /trunk/coot-utils/coot-fffear.cc M /trunk/coot-utils/coot-map-heavy.cc M /trunk/coot-utils/coot-map-heavy.hh M /trunk/coot-utils/coot-map-utils.cc M /trunk/coot-utils/coot-map-utils.hh M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/coot-utils/coot-shelx.hh M /trunk/coot-utils/coot-trim.hh M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/coot-utils/peak-search.cc M /trunk/coot-utils/peak-search.hh M /trunk/coot-utils/test-shelx-reader.cc M /trunk/coot-utils/test-utils.cc M /trunk/coot-utils/trim.cc M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/db-main/testdbmain.cc M /trunk/density-contour/CIsoSurface.cpp M /trunk/density-contour/CIsoSurface.h M /trunk/density-contour/Makefile.am M /trunk/density-contour/Vectors.cpp M /trunk/density-contour/Vectors.h M /trunk/geometry/Makefile.am M /trunk/geometry/Makefile.simple M /trunk/geometry/protein-geometry-mmdb.cc M /trunk/geometry/protein-geometry.cc M /trunk/geometry/protein-geometry.hh M /trunk/geometry/test-geometry.cc M /trunk/high-res/Makefile.am M /trunk/high-res/coot-atom-graph.cc M /trunk/high-res/coot-atom-graph.hh M /trunk/high-res/coot-node-info.hh M /trunk/high-res/globularize.cc M /trunk/high-res/high-res.cc M /trunk/high-res/residue-distortions.cc M /trunk/high-res/sequence-assignment.cc M /trunk/high-res/sequence-assignment.hh M /trunk/high-res/test-atom-graph.cc M /trunk/high-res/testseqalign.cc M /trunk/high-res/testseqassignment.cc M /trunk/high-res/trace-high-res.cc M /trunk/ideal/Makefile.am M /trunk/ideal/Makefile.simple M /trunk/ideal/molmantest.cc M /trunk/ideal/pepflip.cc M /trunk/ideal/pepflip.hh M /trunk/ideal/regularize-minimol.cc M /trunk/ideal/regularize-minimol.hh M /trunk/ideal/simple-restraint.cc M /trunk/ideal/test-indexing.cc M /trunk/ideal/test-indexing.hh M /trunk/ideal/with-geometry.cc M /trunk/ideal/with-map.cc More copyright corrections. ------------------------------------------------------------------------ r95 | pemsley | 2007-04-16 16:37:53 +0100 (Mon, 16 Apr 2007) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/build/CalphaBuild.cc M /trunk/build/CalphaBuild.hh M /trunk/build/Makefile.am M /trunk/build/testcabuild.cc M /trunk/ccp4mg-utils/Makefile.am M /trunk/ccp4mg-utils/cartesian.cc M /trunk/ccp4mg-utils/cartesian.h M /trunk/ccp4mg-utils/geomutil.cc M /trunk/ccp4mg-utils/geomutil.h M /trunk/ccp4mg-utils/matrix.cc M /trunk/ccp4mg-utils/matrix.h M /trunk/ccp4mg-utils/mgtree.cc M /trunk/ccp4mg-utils/mgtree.h M /trunk/ccp4mg-utils/ppmutil.cc M /trunk/ccp4mg-utils/ppmutil.h M /trunk/ccp4mg-utils/quat.cc M /trunk/ccp4mg-utils/quat.h M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/coords/Bond_lines.h M /trunk/coords/Bond_lines_ext.cc M /trunk/coords/Cartesian.cc M /trunk/coords/Cartesian.h M /trunk/coords/Makefile.am M /trunk/coords/coot-close.cc M /trunk/coords/coot-close.hh M /trunk/coords/cos-sin.cc M /trunk/coords/cos-sin.h M /trunk/coords/mmdb-crystal.cc M /trunk/coords/mmdb-crystal.h M /trunk/coords/mmdb-extras.cc M /trunk/coords/mmdb-extras.h M /trunk/coords/mmdb.cc M /trunk/coords/mmdb.h M /trunk/coords/utils.cc M /trunk/coords/utils.h M /trunk/coot-surface/Makefile.am M /trunk/coot-surface/coot-surface.cc M /trunk/coot-surface/coot-surface.hh M /trunk/coot-surface/rgbreps.cc M /trunk/coot-surface/rgbreps.h M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Another traunche of Copyright notice corrections. ------------------------------------------------------------------------ r94 | pemsley | 2007-04-14 12:35:24 +0100 (Sat, 14 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/extensions.scm Remove duplicate entry for shelxl refine. ------------------------------------------------------------------------ r93 | pemsley | 2007-04-13 17:08:17 +0100 (Fri, 13 Apr 2007) | 2 lines Changed paths: A /trunk/cootaneer A /trunk/cootaneer/Makefile-coot A /trunk/cootaneer/buccaneer-lib.cpp A /trunk/cootaneer/buccaneer-lib.h A /trunk/cootaneer/buccaneer-prot.cpp A /trunk/cootaneer/buccaneer-prot.h A /trunk/cootaneer/buccaneer-sequence.cpp A /trunk/cootaneer/buccaneer-sequence.h A /trunk/cootaneer/cootaneer-demo.cpp A /trunk/cootaneer/cootaneer-sequence.cpp A /trunk/cootaneer/cootaneer-sequence.h Inital cootaneer import. ------------------------------------------------------------------------ r92 | pemsley | 2007-04-13 13:17:35 +0100 (Fri, 13 Apr 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Output the map sampling rate when constructing a gridding, why not? ------------------------------------------------------------------------ r91 | pemsley | 2007-04-13 11:59:32 +0100 (Fri, 13 Apr 2007) | 2 lines Changed paths: M /trunk/COPYING M /trunk/src/Makefile.am M /trunk/src/align.cc M /trunk/src/c-inner-main.c M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface-info.cc M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface-ncs.cc M /trunk/src/c-interface-preferences.cc M /trunk/src/c-interface-superpose.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface-waters.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/main.cc Start updating copyright notices for GNU coding standards compliance. ------------------------------------------------------------------------ r90 | pemsley | 2007-04-10 14:51:19 +0100 (Tue, 10 Apr 2007) | 5 lines Changed paths: M /trunk/mapview.glade M /trunk/src/c-interface.cc M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/interface.c M /trunk/src/post-glade Tweak the Go To Atom window, slim it down a bit. More fiddling with Go To Atom residue tree callbacks. Residue tree seems to work now. Next... the atom list. ------------------------------------------------------------------------ r89 | pemsley | 2007-04-10 13:44:45 +0100 (Tue, 10 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm M /trunk/scheme/coot-utils.scm rdelim modules is needed for read-line in guile-1.8 ------------------------------------------------------------------------ r88 | pemsley | 2007-04-10 00:42:42 +0100 (Tue, 10 Apr 2007) | 4 lines Changed paths: M /trunk/scheme/coot-crash-catcher.scm M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info.h Don't try to catch a core dump if it didn't find one. Further additions to the residue tree callbacks. Now something happens on a selection change... not much though. ------------------------------------------------------------------------ r87 | pemsley | 2007-04-09 23:22:34 +0100 (Mon, 09 Apr 2007) | 8 lines Changed paths: M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation-gtk1.cc M /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h Work to get GTk2 TreeView working for the Go To Atom window. It currently displays things in the residue tree, but nothing much happens when you click on those residues. Lots of additions of GTK_MAJOR_VERSION tests. Move tree manipulation into graphics-info for the residue and atom trees remove exposure of these functions to the scripting level. Removal of very old residue list code. ------------------------------------------------------------------------ r86 | pemsley | 2007-04-09 14:34:08 +0100 (Mon, 09 Apr 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/globjects.cc M /trunk/src/graphics-info-navigation-gtk1.cc A /trunk/src/graphics-info-navigation-gtk2.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h Making changes to activate GK2 code path (GTkTreeView) for residue tree. ------------------------------------------------------------------------ r85 | pemsley | 2007-04-09 02:16:02 +0100 (Mon, 09 Apr 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r84 | pemsley | 2007-04-09 02:07:57 +0100 (Mon, 09 Apr 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Update diary. ------------------------------------------------------------------------ r83 | pemsley | 2007-04-09 00:32:40 +0100 (Mon, 09 Apr 2007) | 10 lines Changed paths: M /trunk/configure.in M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/ligand.cc M /trunk/ligand/ligand.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/test-helix-placement.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/scheme/coot-gui.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h Add zone_info() function to minimol, returning the chainid and residue range, if possible Fix crash in rigid-body fitting z-weighted fragment with atoms with zero occupancy. Improve strand fitting, by pruning solutions before rigid body refinement. Speeds things up quite a lot. Introduces find_strand_candidates_by_shift_sampling() to provde vector of unfitted solutions. Add refinement (with strand restraints) of the solution after placement. ------------------------------------------------------------------------ r82 | pemsley | 2007-04-08 11:02:12 +0100 (Sun, 08 Apr 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info.cc Delete the deleting mapcontours debugging line. ------------------------------------------------------------------------ r81 | pemsley | 2007-04-07 14:49:54 +0100 (Sat, 07 Apr 2007) | 3 lines Changed paths: M /trunk/src/molecule-class-info.cc Fix problem of updating the map contours display list when this is a coordinates molecule. ------------------------------------------------------------------------ r80 | pemsley | 2007-04-07 14:28:16 +0100 (Sat, 07 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/fitting.scm Fix extra bracket problem in fitting.scm... how did I not see this before? ------------------------------------------------------------------------ r79 | pemsley | 2007-04-07 13:41:15 +0100 (Sat, 07 Apr 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES Update Release notes for 0.3.1. ------------------------------------------------------------------------ r78 | pemsley | 2007-04-07 13:37:57 +0100 (Sat, 07 Apr 2007) | 4 lines Changed paths: M /trunk/ChangeLog M /trunk/configure.in M /trunk/coords/Bond_lines.cc M /trunk/src/molecule-class-info-ncs.cc M /trunk/src/molecule-class-info.cc Fix jump on uninitiated variable on NCS drawing. Add output of fractional matrix to coordinates transformation. Release 0.3.1 ------------------------------------------------------------------------ r77 | pemsley | 2007-04-07 13:31:16 +0100 (Sat, 07 Apr 2007) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.3.xpm Update the splashscreen to 0.3.1. ------------------------------------------------------------------------ r76 | pemsley | 2007-04-07 11:27:16 +0100 (Sat, 07 Apr 2007) | 2 lines Changed paths: M /trunk/ChangeLog M /trunk/configure.in Release 0.3 ------------------------------------------------------------------------ r75 | pemsley | 2007-04-07 10:38:03 +0100 (Sat, 07 Apr 2007) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.3.xpm Tweek the splash screen some more. ------------------------------------------------------------------------ r74 | pemsley | 2007-04-06 21:58:25 +0100 (Fri, 06 Apr 2007) | 4 lines Changed paths: M /trunk/mapview.glade M /trunk/src/gtk2-interface.c M /trunk/src/interface.c Update mapview.glade and gtk2 equivalent to 0.3 splash screen. In the process the translation strings seemed to have disappeared from gtk2-interface.c... Hmmmm. ------------------------------------------------------------------------ r73 | pemsley | 2007-04-06 18:13:40 +0100 (Fri, 06 Apr 2007) | 2 lines Changed paths: M /trunk/pixmaps/coot-0.3.xpm Tweek the splashscreen image. ------------------------------------------------------------------------ r72 | pemsley | 2007-04-06 17:55:06 +0100 (Fri, 06 Apr 2007) | 2 lines Changed paths: A /trunk/pixmaps/coot-0.3.xpm Add splashscree for 0.3. ------------------------------------------------------------------------ r71 | pemsley | 2007-04-06 14:03:20 +0100 (Fri, 06 Apr 2007) | 2 lines Changed paths: M /trunk/src/molecule-class-info-other.cc Just tidy up some hydrogen delete code. ------------------------------------------------------------------------ r70 | pemsley | 2007-04-06 13:46:43 +0100 (Fri, 06 Apr 2007) | 3 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-utils.cc M /trunk/coot-utils/coot-utils.hh M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add function file_name_non_directory to utilities. Now the File filter works on Gtk2. ------------------------------------------------------------------------ r69 | pemsley | 2007-04-06 10:26:01 +0100 (Fri, 06 Apr 2007) | 2 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/src/c-interface-gtk2.cc Add the sorted list of files back into the list store - it works! ------------------------------------------------------------------------ r68 | pemsley | 2007-04-06 09:38:16 +0100 (Fri, 06 Apr 2007) | 3 lines Changed paths: M /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc More tinkering with the new GTK2 file selection sort button callback. Now we have a list of files, sorted by date. ------------------------------------------------------------------------ r67 | pemsley | 2007-04-05 21:14:59 +0100 (Thu, 05 Apr 2007) | 5 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/scheme/coot-gui.scm M /trunk/scheme/fitting.scm M /trunk/src/c-interface-build.cc M /trunk/src/graphics-info.cc Don't turn of backups in autofit-rotamer-active residue and refine-active-residue. Add a time limit for distribution - which gives a gui. upcase the string tested for in is_fasta_aa(). ------------------------------------------------------------------------ r66 | pemsley | 2007-04-05 17:21:52 +0100 (Thu, 05 Apr 2007) | 6 lines Changed paths: M /trunk/configure.in M /trunk/happy-coot-diary.html M /trunk/src/Makefile.am D /trunk/src/c-interface-gtk.cc A /trunk/src/c-interface-gtk2.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c Add SWIG_FLAGS to define which GTK regime we are in. For use with swig and normal compilation. fileselection_sort button press callback now depends on the GTK version. Add some test/play code for file selection callback under GTK2. Update diary. ------------------------------------------------------------------------ r65 | pemsley | 2007-04-05 00:04:42 +0100 (Thu, 05 Apr 2007) | 5 lines Changed paths: M /trunk/scheme/coot-gui.scm Make the lambda functions attached to key-press-event in the extension widgets return #f (not-handled), so that the text is written to the entry. Kevin Ryde and Neil Jerram on the guile-gtk mailing list worked out how to fix that. Thanks guys. ------------------------------------------------------------------------ r64 | pemsley | 2007-04-04 18:05:31 +0100 (Wed, 04 Apr 2007) | 2 lines Changed paths: A /trunk/src/c-interface-gtk.cc oops wrong file. to be deleted. ------------------------------------------------------------------------ r63 | pemsley | 2007-04-04 15:22:36 +0100 (Wed, 04 Apr 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Reorder the libraries so the guile and guile-gtk come first. ------------------------------------------------------------------------ r62 | pemsley | 2007-04-04 15:21:43 +0100 (Wed, 04 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/extensions.scm Tidy up the generic-single-entry dialog and add a cancel button. ------------------------------------------------------------------------ r61 | pemsley | 2007-04-04 15:12:11 +0100 (Wed, 04 Apr 2007) | 2 lines Changed paths: M /trunk/macros/guile-gtk.m4 Tidy up macro. ------------------------------------------------------------------------ r60 | pemsley | 2007-04-04 12:02:28 +0100 (Wed, 04 Apr 2007) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/doc/user-manual.texi M /trunk/happy-coot-diary.html M /trunk/ideal/simple-restraint.cc M /trunk/scheme/extensions.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface-validate.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info-pick.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.h Distortions scaled down for peptide omega distortion graph. Update geometry graphs on scripting function auto-fit-best-rotamer. Keybinding uses update_go_to_atom_from_current_position() not scripting function Documentation added for rotate/translate zone rotation centre and added to Extensions. Also, factor out function to find centre of moving atoms. RELEASE-NOTES updated. Diary updated. ------------------------------------------------------------------------ r59 | pemsley | 2007-04-03 22:17:04 +0100 (Tue, 03 Apr 2007) | 4 lines Changed paths: M /trunk/src/Makefile.am M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/coot-glue-gtk2.c M /trunk/src/coot-glue.c M /trunk/src/coot_wrap_guile.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.h Fixes to move towards building with GTk2 on penelope, which has guile and guile-gtk in a different directory to the rest of the dependencies. Compiled without GSL, and fixed for that also. ------------------------------------------------------------------------ r58 | pemsley | 2007-04-03 15:01:24 +0100 (Tue, 03 Apr 2007) | 4 lines Changed paths: M /trunk/src/c-interface-info.cc M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc Move update_go_to_atom_from_current_position() into c/c++-land, not scheme code. Make it easy for Bernhard. Some debugging removed. ------------------------------------------------------------------------ r57 | pemsley | 2007-04-03 14:38:00 +0100 (Tue, 03 Apr 2007) | 5 lines Changed paths: M /trunk/happy-coot-diary.html M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/junk.cc M /trunk/src/molecule-class-info.h Add function fill_option_menu_with_coordinates_options_internal_with_active_mol and update_go_to_atom_window_on_other_molecule_chosen() so that the Go To Atom molecule chooser option menu (menu) changes it's active item properly. Update diary. ------------------------------------------------------------------------ r56 | pemsley | 2007-04-02 13:53:14 +0100 (Mon, 02 Apr 2007) | 4 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/src/c-interface-ligands.cc M /trunk/src/c-interface.h M /trunk/src/coot_wrap_guile.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add in the graph_match() function in coot-coord-utils and make simple calling wrapper finding residues and a molecule_class_info_t function that applies the matrix to the moving residue. ------------------------------------------------------------------------ r55 | pemsley | 2007-04-01 23:53:54 +0100 (Sun, 01 Apr 2007) | 9 lines Changed paths: M /trunk/RELEASE-NOTES M /trunk/coot-utils/coot-coord-utils.cc M /trunk/coot-utils/coot-coord-utils.hh M /trunk/ligand/ligand.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/scheme/Makefile.am A /trunk/scheme/coot-crash-catcher.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.cc M /trunk/src/cc-interface.hh M /trunk/src/coot M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h Add minimol atom memeber function is_hydrogen_p(). Also coot-utils function similar. Use is_hydrogen_p() in the scoring of fitting ligands. Add coot-crash-catcher, with a core dump analysis and a message to send it to me. Add coot-crash-catcher.scm to Makefile. closest_atom should try to go to a CA first. Add active_atom_spec() function to help out Bernie porting to Python. ------------------------------------------------------------------------ r54 | pemsley | 2007-04-01 21:30:28 +0100 (Sun, 01 Apr 2007) | 3 lines Changed paths: M /trunk/scheme/fitting.scm D /trunk/scheme/refine-active-residue.scm Functions in refine-active-residue moved to fitting.scm. OK, Frank, this was what you wanted (I think). ------------------------------------------------------------------------ r53 | pemsley | 2007-04-01 21:29:40 +0100 (Sun, 01 Apr 2007) | 2 lines Changed paths: M /trunk/scheme/refine-active-residue.scm Update, ready for delete. ------------------------------------------------------------------------ r52 | pemsley | 2007-04-01 12:48:55 +0100 (Sun, 01 Apr 2007) | 3 lines Changed paths: M /trunk/src/c-interface.h M /trunk/src/globjects.cc The second GL context for side-by-side stereo should share its display lists with the first one. Stuart McN told me about this fix. ------------------------------------------------------------------------ r51 | pemsley | 2007-04-01 01:10:29 +0100 (Sun, 01 Apr 2007) | 2 lines Changed paths: A /trunk/scheme/refine-active-residue.scm Add trivial "Active Residue" functions ------------------------------------------------------------------------ r50 | pemsley | 2007-04-01 00:56:35 +0100 (Sun, 01 Apr 2007) | 2 lines Changed paths: M /trunk/src/c-interface-info.cc active-residue should only apply to molecules that are being displayed. ------------------------------------------------------------------------ r49 | pemsley | 2007-03-31 17:35:55 +0100 (Sat, 31 Mar 2007) | 10 lines Changed paths: M /trunk/ChangeLog M /trunk/coot-utils/coot-shelx-ins.cc M /trunk/mapview.glade M /trunk/scheme/coot-utils.scm M /trunk/src/c-interface-info.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/callbacks.h M /trunk/src/cc-interface.hh M /trunk/src/coot_wrap_guile.cc M /trunk/src/coot_wrap_python.cc M /trunk/src/globjects.cc M /trunk/src/graphics-info.cc M /trunk/src/graphics-info.h M /trunk/src/interface.c M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.cc M /trunk/src/molecule-class-info.h M /trunk/src/rama_plot.cc Add concept of "active residue (or atom atom spec, really). Use it in (update-go-to-atom-from-current-atom) function. This is used to update the go to atom specs from the active residue. Add a button to the go to atom window that runs this function. Includes the function closest_atom(). fill_ghost_info() function commented. Add key bindings for NCS-residue-skip and update Go To Atom function above. Fixes in graphics info to fix Richard Baxter bugs. Clean up a bit the SHELX .res file reading screen output. ------------------------------------------------------------------------ r48 | pemsley | 2007-03-31 14:29:56 +0100 (Sat, 31 Mar 2007) | 2 lines Changed paths: D /trunk/aclocal.m4 D /trunk/configure Delete configure anc aclocal.m4 from repo. Too much noise in svn logs. ------------------------------------------------------------------------ r47 | pemsley | 2007-03-26 23:23:50 +0100 (Mon, 26 Mar 2007) | 6 lines Changed paths: M /trunk/happy-coot-diary.html A /trunk/scheme/quat-convert.scm M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/callbacks.c M /trunk/src/graphics-info.cc M /trunk/src/molecule-class-info-other.cc M /trunk/src/molecule-class-info.h Add quat-convert.scm. No interpolation of quat, yet. Add attribute modifier (heavyweight, though). Try to track down edit backbone angle bug/crash. We can see it in valgrind. Update diary. ------------------------------------------------------------------------ r46 | pemsley | 2007-03-26 17:20:27 +0100 (Mon, 26 Mar 2007) | 2 lines Changed paths: M /trunk/Makefile.am M /trunk/aclocal.m4 D /trunk/aux A /trunk/auxil (from /trunk/aux:45) M /trunk/configure M /trunk/configure.in aux is a reserved name under W32. So lets call the directory auxil. ------------------------------------------------------------------------ r45 | pemsley | 2007-03-23 15:14:08 +0000 (Fri, 23 Mar 2007) | 3 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/extensions.scm M /trunk/src/c-interface.cc M /trunk/src/c-interface.h Add a function to return the current idle function rotation angle. Add it into the the set rotation speed gui. ------------------------------------------------------------------------ r44 | pemsley | 2007-03-22 22:30:29 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add beta strand reference structure dir to docs. ------------------------------------------------------------------------ r43 | pemsley | 2007-03-22 22:19:08 +0000 (Thu, 22 Mar 2007) | 3 lines Changed paths: M /trunk/scheme/Makefile.am M /trunk/scheme/coot-gui.scm A /trunk/scheme/coot-scheme.texi M /trunk/scheme/coot-utils.scm A /trunk/scheme/snarf-coot-docs.scm Add code that snarfs the coot scheme files for documentation and format coot-utils and coot-gui for snarfing. ------------------------------------------------------------------------ r42 | pemsley | 2007-03-22 20:29:52 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: M /trunk/happy-coot-diary.html Spell correct happy-coot-diary (yikes! what a lot of errors). ------------------------------------------------------------------------ r41 | pemsley | 2007-03-22 12:02:09 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: D /trunk/pixmaps/arashiyama-park-3.xcf We probably don't need the xcf file either. ------------------------------------------------------------------------ r40 | pemsley | 2007-03-22 11:16:11 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: D /trunk/pixmaps/arashiyama-park-2.png D /trunk/pixmaps/coot-0.2.png D /trunk/pixmaps/coot-16-bevel.jpg D /trunk/pixmaps/coot-16-bevel.xpm.orig Remove more unecessary images. ------------------------------------------------------------------------ r39 | pemsley | 2007-03-22 11:14:35 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: D /trunk/pixmaps/arashiyama-park-2.xcf D /trunk/pixmaps/arashiyama-park.jpg D /trunk/pixmaps/coot-0.2-trees.xpm Remove large images from pixmap dir ------------------------------------------------------------------------ r38 | pemsley | 2007-03-22 10:50:36 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: M /trunk/configure M /trunk/configure.in M /trunk/db-main/db-strands.hh Update to 0.2.1-pre-6 ------------------------------------------------------------------------ r37 | pemsley | 2007-03-22 10:49:36 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am A /trunk/src/coot-dox.cfg Add doxygen config file. Forgotten in transfer to google. ------------------------------------------------------------------------ r36 | pemsley | 2007-03-22 10:43:56 +0000 (Thu, 22 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Tiny formatting change. ------------------------------------------------------------------------ r35 | pemsley | 2007-03-21 18:27:11 +0000 (Wed, 21 Mar 2007) | 2 lines Changed paths: M /trunk/src/Makefile.am Add db-main lib dependency for fix-nomenclature-errors. ------------------------------------------------------------------------ r34 | pemsley | 2007-03-21 15:24:49 +0000 (Wed, 21 Mar 2007) | 2 lines Changed paths: A /trunk/happy-coot-diary.html Add happy-coot-diary.html. ------------------------------------------------------------------------ r33 | pemsley | 2007-03-21 15:18:15 +0000 (Wed, 21 Mar 2007) | 2 lines Changed paths: M /trunk/high-res/Makefile.am M /trunk/ligand/Makefile.am Update Makefile.am to add libcoot-db-main dependencies for libcoot-ligand. ------------------------------------------------------------------------ r32 | pemsley | 2007-03-21 15:16:34 +0000 (Wed, 21 Mar 2007) | 2 lines Changed paths: A /trunk/aux/catcheck/Makefile.am A /trunk/aux/rama/Makefile.am A /trunk/aux/sec-str/Makefile.am A /trunk/aux/strand-analysis/Makefile.am A /trunk/aux/vectors/Makefile.am Restorre aux Makefile.ams to version control. ------------------------------------------------------------------------ r31 | pemsley | 2007-03-21 15:14:42 +0000 (Wed, 21 Mar 2007) | 2 lines Changed paths: D /trunk/aux/catcheck/Makefile.am D /trunk/aux/catcheck/Makefile.in D /trunk/aux/rama/Makefile.am D /trunk/aux/rama/Makefile.in D /trunk/aux/sec-str/Makefile.am D /trunk/aux/sec-str/Makefile.in D /trunk/aux/strand-analysis/Makefile.am D /trunk/aux/strand-analysis/Makefile.in D /trunk/aux/vectors/Makefile.am D /trunk/aux/vectors/Makefile.in Mess around with aux Makefiles. ------------------------------------------------------------------------ r30 | pemsley | 2007-03-20 17:20:49 +0000 (Tue, 20 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm Add a gui for strand placement. ------------------------------------------------------------------------ r29 | pemsley | 2007-03-19 21:17:21 +0000 (Mon, 19 Mar 2007) | 10 lines Changed paths: M /trunk/ChangeLog M /trunk/build-it M /trunk/db-main/db-main.cc M /trunk/db-main/db-main.hh M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh M /trunk/ligand/rigid-body.cc M /trunk/ligand/test-helix-placement.cc M /trunk/mini-mol/mini-mol.cc M /trunk/mini-mol/mini-mol.hh M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/cc-interface.hh M /trunk/src/coot M /trunk/src/molecule-class-info.cc Add a transform method to a minimol. Add option to fit a strand to test-helix-placement. Z-weight the rigid body refinement Score (helix) fragment according to occupancy Fit strand method (currently no rigid body refinement) db_strands class filled with functions. build-it spelling corrections. add (place-strand-here nres) function to interface. try to run guile -s crash-catcher when coot-real crashes. ------------------------------------------------------------------------ r28 | pemsley | 2007-03-19 13:40:18 +0000 (Mon, 19 Mar 2007) | 4 lines Changed paths: M /trunk/aclocal.m4 M /trunk/db-main/Makefile.am M /trunk/db-main/db-strands.cc M /trunk/db-main/db-strands.hh M /trunk/ligand/Makefile.am M /trunk/ligand/helix-placement.cc M /trunk/ligand/helix-placement.hh Cut out the tube-fitting part from fit helices, to be used in strand fitting. Fix up Makefile.am typos so that we can compile now. ------------------------------------------------------------------------ r27 | pemsley | 2007-03-19 13:27:46 +0000 (Mon, 19 Mar 2007) | 2 lines Changed paths: M /trunk/db-main/Makefile.am D /trunk/db-main/db-strand.cc D /trunk/db-main/db-strand.hh A /trunk/db-main/db-strands.cc (from /trunk/db-main/db-strand.cc:26) A /trunk/db-main/db-strands.hh (from /trunk/db-main/db-strand.hh:26) Apply the filename change. ------------------------------------------------------------------------ r26 | pemsley | 2007-03-19 13:26:07 +0000 (Mon, 19 Mar 2007) | 2 lines Changed paths: M /trunk/db-main/Makefile.am A /trunk/db-main/db-strand.cc A /trunk/db-main/db-strand.hh Add db-strand templates. ------------------------------------------------------------------------ r25 | pemsley | 2007-03-19 09:22:48 +0000 (Mon, 19 Mar 2007) | 2 lines Changed paths: M /trunk/build-it Remove == comparisons. ------------------------------------------------------------------------ r24 | pemsley | 2007-03-19 09:20:30 +0000 (Mon, 19 Mar 2007) | 2 lines Changed paths: A /trunk/build-it Add build-it script. ------------------------------------------------------------------------ r23 | pemsley | 2007-03-18 22:31:36 +0000 (Sun, 18 Mar 2007) | 3 lines Changed paths: M /trunk/aux/strand-analysis/strand-analysis.cc M /trunk/aux/strand-analysis/strand-analysis.hh More additions to strand-analysis. Now output format seems OK for input to fitch. ------------------------------------------------------------------------ r22 | pemsley | 2007-03-15 19:36:49 +0000 (Thu, 15 Mar 2007) | 3 lines Changed paths: M /trunk/aux/strand-analysis/strand-analysis.cc Output data in fitch format (FWIW). Outliers are making a mess of the tree. Why are they there? ------------------------------------------------------------------------ r21 | pemsley | 2007-03-15 17:43:18 +0000 (Thu, 15 Mar 2007) | 3 lines Changed paths: M /trunk/aux/strand-analysis/strand-analysis.cc M /trunk/aux/strand-analysis/strand-analysis.hh More strand analysis development. Now we get a table of values at the end. Some of them look waky. ------------------------------------------------------------------------ r20 | pemsley | 2007-03-15 15:56:14 +0000 (Thu, 15 Mar 2007) | 2 lines Changed paths: D /trunk/Makefile.in M /trunk/aclocal.m4 D /trunk/analysis/Makefile.in D /trunk/angles/Makefile.in D /trunk/atom-utils/Makefile.in D /trunk/aux/Makefile.in D /trunk/build/Makefile.in D /trunk/ccp4mg-utils/Makefile.in D /trunk/compat/Makefile.in D /trunk/coords/Makefile.in D /trunk/coot-surface/Makefile.in D /trunk/coot-utils/Makefile.in D /trunk/db-main/Makefile.in D /trunk/density-contour/Makefile.in D /trunk/doc/Makefile.in D /trunk/geometry/Makefile.in D /trunk/high-res/Makefile.in D /trunk/ideal/Makefile.in D /trunk/ligand/Makefile.in D /trunk/macros/Makefile.in D /trunk/mini-mol/Makefile.in D /trunk/python/Makefile.in D /trunk/scheme/Makefile.in D /trunk/sequence-view/Makefile.in D /trunk/skeleton/Makefile.in D /trunk/src/Makefile.in D /trunk/surface/Makefile.in D /trunk/tw/Makefile.in Delete the Makefile.ins from the repository. ------------------------------------------------------------------------ r19 | pemsley | 2007-03-15 13:07:06 +0000 (Thu, 15 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/extensions.scm minor tidying. ------------------------------------------------------------------------ r18 | pemsley | 2007-03-15 13:06:39 +0000 (Thu, 15 Mar 2007) | 2 lines Changed paths: M /trunk/doc/user-manual.texi Add documentation for binding a key to a function. ------------------------------------------------------------------------ r17 | pemsley | 2007-03-15 13:04:46 +0000 (Thu, 15 Mar 2007) | 3 lines Changed paths: M /trunk/aux/strand-analysis/strand-analysis.cc M /trunk/aux/strand-analysis/strand-analysis.hh More work on strand analysis. Setting up to calculate the distances between fragments. ------------------------------------------------------------------------ r16 | pemsley | 2007-03-14 16:55:37 +0000 (Wed, 14 Mar 2007) | 3 lines Changed paths: M /trunk/coot-utils/coot-utils.cc M /trunk/mini-mol/mini-mol.cc M /trunk/src/c-interface-build.cc M /trunk/src/c-interface.cc M /trunk/src/graphics-info-navigation-gtk1.cc Fix functions not returning values as they should and other small fixes from Francois for the WindowXX build. ------------------------------------------------------------------------ r15 | pemsley | 2007-03-14 15:57:51 +0000 (Wed, 14 Mar 2007) | 3 lines Changed paths: M /trunk/aux/strand-analysis/Makefile.am M /trunk/aux/strand-analysis/Makefile.in M /trunk/aux/strand-analysis/strand-analysis.cc M /trunk/aux/strand-analysis/strand-analysis.hh Fix up Makefile.am so that strand-analysis compiles. Start turning it into a class. ------------------------------------------------------------------------ r14 | pemsley | 2007-03-14 15:16:15 +0000 (Wed, 14 Mar 2007) | 2 lines Changed paths: A /trunk/aux/strand-analysis/strand-analysis.hh Add missing strand-analysis.hh to repository. ------------------------------------------------------------------------ r13 | pemsley | 2007-03-14 11:58:41 +0000 (Wed, 14 Mar 2007) | 3 lines Changed paths: M /trunk/Makefile.am M /trunk/Makefile.in A /trunk/aux A /trunk/aux/Makefile.am A /trunk/aux/Makefile.in A /trunk/aux/catcheck A /trunk/aux/catcheck/Makefile.am A /trunk/aux/catcheck/Makefile.in A /trunk/aux/catcheck/Makefile.simple A /trunk/aux/catcheck/catcheck.cc A /trunk/aux/catcheck/catcheck.hh A /trunk/aux/rama A /trunk/aux/rama/Makefile.am A /trunk/aux/rama/Makefile.in A /trunk/aux/rama/Makefile.simple A /trunk/aux/rama/fit-rama.scm A /trunk/aux/rama/rama-data.cc A /trunk/aux/rama/rama-doughnut.cc A /trunk/aux/rama/run.scm A /trunk/aux/rama/stats.awk A /trunk/aux/rama/test-arr A /trunk/aux/rama/test-arr.scm A /trunk/aux/sec-str A /trunk/aux/sec-str/Makefile.am A /trunk/aux/sec-str/Makefile.in A /trunk/aux/sec-str/Makefile.simple A /trunk/aux/sec-str/sec-str-dist-check.cc A /trunk/aux/sec-str/sec-str-dist-check.hh A /trunk/aux/strand-analysis A /trunk/aux/strand-analysis/Makefile.am A /trunk/aux/strand-analysis/Makefile.in A /trunk/aux/strand-analysis/Makefile.simple A /trunk/aux/strand-analysis/strand-analysis.cc A /trunk/aux/vectors A /trunk/aux/vectors/Makefile.am A /trunk/aux/vectors/Makefile.in A /trunk/aux/vectors/Makefile.simple A /trunk/aux/vectors/diff-vec.cc A /trunk/aux/vectors/filter-vecs.scm M /trunk/configure M /trunk/configure.in aux directory added with check_PROGRAM directives, so that usually they will not be compiled. ------------------------------------------------------------------------ r12 | pemsley | 2007-03-14 11:42:57 +0000 (Wed, 14 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/coot-gui.scm M /trunk/scheme/entry+do-button.scm remove the (testing) gtk-main usage from entry+do-button. ------------------------------------------------------------------------ r11 | pemsley | 2007-03-14 07:14:04 +0000 (Wed, 14 Mar 2007) | 3 lines Changed paths: M /trunk/scheme/coot-utils.scm M /trunk/scheme/filter.scm "Fix" problem of glob->regexp not working like I expected. I that think a * should be translated to ".*" not "[^.]*". ------------------------------------------------------------------------ r10 | pemsley | 2007-03-14 06:21:21 +0000 (Wed, 14 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/ChangeLog M /trunk/scheme/Makefile.in M /trunk/scheme/ncs.scm M /trunk/src/c-interface.cc Clean up debugging for NCS chain skipping. ------------------------------------------------------------------------ r9 | pemsley | 2007-03-13 17:47:27 +0000 (Tue, 13 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/coot.scm Add ncs.scm to loaded scheme files. ------------------------------------------------------------------------ r8 | pemsley | 2007-03-13 17:47:05 +0000 (Tue, 13 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/Makefile.am A /trunk/scheme/ncs.scm (from /trunk/scheme/skip-to-next-ncs-chain.scm:7) D /trunk/scheme/skip-to-next-ncs-chain.scm Rename to ncs.scm and add it to the Makefile.am ------------------------------------------------------------------------ r7 | pemsley | 2007-03-13 17:45:30 +0000 (Tue, 13 Mar 2007) | 2 lines Changed paths: M /trunk/scheme/skip-to-next-ncs-chain.scm skip to next NCS chain now seems to work. ------------------------------------------------------------------------ r6 | pemsley | 2007-03-13 15:48:49 +0000 (Tue, 13 Mar 2007) | 3 lines Changed paths: A /trunk/scheme/entry+do-button.scm A /trunk/scheme/skip-to-next-ncs-chain.scm Add extra functions and widgets written on the flight home. Still needs work. ------------------------------------------------------------------------ r5 | pemsley | 2007-03-13 15:30:08 +0000 (Tue, 13 Mar 2007) | 3 lines Changed paths: M /trunk/Makefile.in M /trunk/aclocal.m4 M /trunk/analysis/Makefile.in M /trunk/angles/Makefile.in M /trunk/atom-utils/Makefile.in M /trunk/build/Makefile.in M /trunk/ccp4mg-utils/Makefile.in M /trunk/compat/Makefile.in M /trunk/configure M /trunk/coords/Makefile.in M /trunk/coot-surface/Makefile.in M /trunk/coot-utils/Makefile.in M /trunk/db-main/Makefile.in M /trunk/density-contour/Makefile.in M /trunk/doc/Makefile.in M /trunk/geometry/Makefile.in M /trunk/high-res/Makefile.in M /trunk/ideal/Makefile.in M /trunk/ligand/Makefile.in M /trunk/macros/Makefile.in M /trunk/mini-mol/Makefile.in M /trunk/python/Makefile.in M /trunk/scheme/Makefile.in M /trunk/sequence-view/Makefile.in M /trunk/skeleton/Makefile.in M /trunk/src/Makefile.am M /trunk/src/Makefile.in M /trunk/src/coot.py M /trunk/src/coot_wrap_python_pre.cc M /trunk/surface/Makefile.in M /trunk/tw/Makefile.in Fix up the problems with the generated wrapped code dependencies? Conflated with upgrade to autoconf/make (hence new .in files etc). ------------------------------------------------------------------------ r4 | pemsley | 2007-03-13 14:46:37 +0000 (Tue, 13 Mar 2007) | 3 lines Changed paths: M /trunk/src/c-interface.cc M /trunk/src/c-interface.h M /trunk/src/graphics-info-navigation.cc M /trunk/src/graphics-info.h M /trunk/src/molecule-class-info.cc Updates for C++ code from the ORD->LHR flight, adding scripting interface to the go to atom values. ------------------------------------------------------------------------ r3 | pemsley | 2007-03-12 11:18:18 +0000 (Mon, 12 Mar 2007) | 3 lines Changed paths: A /trunk/ABOUT-NLS A /trunk/AUTHORS A /trunk/BUGS A /trunk/COPYING A /trunk/ChangeLog A /trunk/INSTALL A /trunk/Makefile.am A /trunk/Makefile.in A /trunk/NEWS A /trunk/README A /trunk/RELEASE-NOTES A /trunk/TODO A /trunk/acconfig.h A /trunk/aclocal.m4 A /trunk/analysis A /trunk/analysis/Makefile.am A /trunk/analysis/Makefile.in A /trunk/analysis/Makefile.simple A /trunk/analysis/bfactan.cc A /trunk/analysis/bfkurt.cc A /trunk/analysis/bfkurt.hh A /trunk/angles A /trunk/angles/AngleInfo-angle-torsions-autogen.cc A /trunk/angles/AngleInfo-theta_2-autogen.cc A /trunk/angles/AngleInfo.cc A /trunk/angles/AngleInfo.h A /trunk/angles/Makefile.am A /trunk/angles/Makefile.in A /trunk/angles/angle-torsion-autogen.awk A /trunk/angles/ncube.h A /trunk/angles/wrapped-ncube.h A /trunk/atom-utils A /trunk/atom-utils/Makefile.am A /trunk/atom-utils/Makefile.in A /trunk/atom-utils/atom-utils.cc A /trunk/atom-utils/atom-utils.h A /trunk/autogen.sh A /trunk/build A /trunk/build/CalphaBuild.cc A /trunk/build/CalphaBuild.hh A /trunk/build/Makefile.am A /trunk/build/Makefile.in A /trunk/build/build.txt A /trunk/build/testcabuild.cc A /trunk/ccp4mg-utils A /trunk/ccp4mg-utils/Makefile.am A /trunk/ccp4mg-utils/Makefile.in A /trunk/ccp4mg-utils/cartesian.cc A /trunk/ccp4mg-utils/cartesian.h A /trunk/ccp4mg-utils/convert.sh A /trunk/ccp4mg-utils/geomutil.cc A /trunk/ccp4mg-utils/geomutil.h A /trunk/ccp4mg-utils/get-new-utils.sh A /trunk/ccp4mg-utils/matrix.cc A /trunk/ccp4mg-utils/matrix.h A /trunk/ccp4mg-utils/mgtree.cc A /trunk/ccp4mg-utils/mgtree.h A /trunk/ccp4mg-utils/ppmutil.cc A /trunk/ccp4mg-utils/ppmutil.h A /trunk/ccp4mg-utils/quat.cc A /trunk/ccp4mg-utils/quat.h A /trunk/colours.def A /trunk/compat A /trunk/compat/Makefile.am A /trunk/compat/Makefile.in A /trunk/compat/coot-getopt.h A /trunk/compat/getopt.c A /trunk/compat/getopt1.c A /trunk/config.guess A /trunk/config.sub A /trunk/configure A /trunk/configure.in A /trunk/coords A /trunk/coords/Bond_lines.cc A /trunk/coords/Bond_lines.h A /trunk/coords/Bond_lines_ext.cc A /trunk/coords/Bond_lines_ext.h A /trunk/coords/Cartesian.cc A /trunk/coords/Cartesian.h A /trunk/coords/Makefile.am A /trunk/coords/Makefile.in A /trunk/coords/coot-close.cc A /trunk/coords/coot-close.hh A /trunk/coords/cos-sin.cc A /trunk/coords/cos-sin.h A /trunk/coords/mmdb-crystal.cc A /trunk/coords/mmdb-crystal.h A /trunk/coords/mmdb-extras.cc A /trunk/coords/mmdb-extras.h A /trunk/coords/mmdb.cc A /trunk/coords/mmdb.h A /trunk/coords/utils.cc A /trunk/coords/utils.h A /trunk/coot-surface A /trunk/coot-surface/Makefile.am A /trunk/coot-surface/Makefile.in A /trunk/coot-surface/coot-surface.cc A /trunk/coot-surface/coot-surface.hh A /trunk/coot-surface/rgbreps.cc A /trunk/coot-surface/rgbreps.h A /trunk/coot-utils A /trunk/coot-utils/Makefile.am A /trunk/coot-utils/Makefile.in A /trunk/coot-utils/atomic-numbers.cc A /trunk/coot-utils/coot-coord-extras.cc A /trunk/coot-utils/coot-coord-extras.hh A /trunk/coot-utils/coot-coord-lsq.cc A /trunk/coot-utils/coot-coord-utils.cc A /trunk/coot-utils/coot-coord-utils.hh A /trunk/coot-utils/coot-fasta.cc A /trunk/coot-utils/coot-fasta.hh A /trunk/coot-utils/coot-fffear.cc A /trunk/coot-utils/coot-lsq-types.h A /trunk/coot-utils/coot-map-heavy.cc A /trunk/coot-utils/coot-map-heavy.hh A 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/trunk/doc/Makefile.in A /trunk/doc/coot-plain-2.ps A /trunk/doc/coot-reference-manual.texi A /trunk/doc/coot.tex A /trunk/doc/crib-sheet.tex A /trunk/doc/derivatives-part.tex A /trunk/doc/derivatives.tex A /trunk/doc/function-filter.scsh A /trunk/doc/functions.tex A /trunk/doc/reference.tex A /trunk/doc/tutorial.tex A /trunk/doc/user-manual.texi A /trunk/function-notes A /trunk/geometry A /trunk/geometry/Makefile.am A /trunk/geometry/Makefile.in A /trunk/geometry/Makefile.simple A /trunk/geometry/notes A /trunk/geometry/protein-geometry-mmdb.cc A /trunk/geometry/protein-geometry.cc A /trunk/geometry/protein-geometry.hh A /trunk/geometry/read-sbase.cc A /trunk/geometry/read-sbase.hh A /trunk/geometry/test-geometry.cc A /trunk/guile.supp A /trunk/high-res A /trunk/high-res/Makefile.am A /trunk/high-res/Makefile.in A /trunk/high-res/coot-atom-graph.cc A /trunk/high-res/coot-atom-graph.hh A /trunk/high-res/coot-node-info.hh A /trunk/high-res/globularize.cc A /trunk/high-res/high-res.cc A /trunk/high-res/high-res.hh A /trunk/high-res/residue-distortions.cc A /trunk/high-res/sequence-assignment.cc A /trunk/high-res/sequence-assignment.hh A /trunk/high-res/test-atom-graph.cc A /trunk/high-res/testseqalign.cc A /trunk/high-res/testseqassignment.cc A /trunk/high-res/trace-high-res.cc A /trunk/install-sh A /trunk/libtool A /trunk/ligand A /trunk/ligand/Makefile.am A /trunk/ligand/Makefile.in A /trunk/ligand/Makefile.simple A /trunk/ligand/chi-angles-autogen.cc A /trunk/ligand/chi-angles.cc A /trunk/ligand/chi-angles.hh A /trunk/ligand/dunbrack.cc A /trunk/ligand/dunbrack.hh A /trunk/ligand/find-ligand.cc A /trunk/ligand/find-waters.cc A /trunk/ligand/findligand A /trunk/ligand/findwaters A /trunk/ligand/helix-placement.cc A /trunk/ligand/helix-placement.hh A /trunk/ligand/ideal-rna.cc A /trunk/ligand/ideal-rna.hh A /trunk/ligand/ligand-extras.cc A /trunk/ligand/ligand.cc A /trunk/ligand/ligand.hh A /trunk/ligand/monomer-utils.cc A /trunk/ligand/monomer-utils.hh A /trunk/ligand/read-dunbrack.awk A /trunk/ligand/residue_by_phi_psi.cc A /trunk/ligand/residue_by_phi_psi.hh A /trunk/ligand/rigid-body.cc A /trunk/ligand/rigid-body.hh A /trunk/ligand/test-fffear-in-coot.cc A /trunk/ligand/test-helix-placement.cc A /trunk/ligand/test-random.cc A /trunk/ligand/testdunbrack.cc A /trunk/ligand/wiggly-ligand.cc A /trunk/ligand/wligand.hh A /trunk/ltmain.sh A /trunk/macros A /trunk/macros/Makefile.am A /trunk/macros/Makefile.in A /trunk/macros/aclocal-include.m4 A /trunk/macros/clipper.m4 A /trunk/macros/clipper.m4.old A /trunk/macros/compiler-flags.m4 A /trunk/macros/coot-database.m4 A /trunk/macros/coot-windows.m4 A /trunk/macros/glut.m4 A /trunk/macros/gtk-canvas.m4 A /trunk/macros/gtkgl.m4 A /trunk/macros/guile-gtk.m4 A /trunk/macros/guile.m4 A /trunk/macros/mmdb-ssm.m4 A /trunk/macros/mmdb.m4 A /trunk/macros/with-guile.m4 A /trunk/macros/with-python.m4 A /trunk/make-patches A /trunk/make-scheme-tar A /trunk/mapview.glade A /trunk/mini-mol A 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/trunk/src/callbacks.h A /trunk/src/cc-interface.hh A /trunk/src/cmtz-interface.cc A /trunk/src/cmtz-interface.hh A /trunk/src/command-line.cc A /trunk/src/command-line.h A /trunk/src/coot A /trunk/src/coot-align.cc A /trunk/src/coot-align.hh A /trunk/src/coot-database.hh A /trunk/src/coot-glue-gtk2.c A /trunk/src/coot-glue.c A /trunk/src/coot-nomenclature.cc A /trunk/src/coot-nomenclature.hh A /trunk/src/coot-render.hh A /trunk/src/coot.defs A /trunk/src/coot.i A /trunk/src/coot.py A /trunk/src/coot_wrap_guile.cc A /trunk/src/coot_wrap_guile_pre.cc A /trunk/src/coot_wrap_python.cc A /trunk/src/coot_wrap_python_pre.cc A /trunk/src/density-score-by-residue.cc A /trunk/src/fix-gettext.sh A /trunk/src/fix-nomenclature.cc A /trunk/src/geometry-graphs.cc A /trunk/src/geometry-graphs.hh A /trunk/src/gl-matrix.cc A /trunk/src/gl-matrix.h A /trunk/src/globjects.cc A /trunk/src/globjects.h A /trunk/src/graphics-info-defines.cc A /trunk/src/graphics-info-graphs.cc A /trunk/src/graphics-info-lsq.cc A /trunk/src/graphics-info-modelling.cc A /trunk/src/graphics-info-mutate.cc A /trunk/src/graphics-info-navigation-gtk1.cc A /trunk/src/graphics-info-navigation.cc A /trunk/src/graphics-info-pick.cc A /trunk/src/graphics-info-render.cc A /trunk/src/graphics-info-state.cc A /trunk/src/graphics-info-superpose.cc A /trunk/src/graphics-info.cc A /trunk/src/graphics-info.h A /trunk/src/gtk-manual.c A /trunk/src/gtk-manual.h A /trunk/src/gtk2-interface.c A /trunk/src/history_list.hh A /trunk/src/interface.c A /trunk/src/interface.h A /trunk/src/junk.cc A /trunk/src/main.cc A /trunk/src/mol-hierachy.cc A /trunk/src/molecule-class-info-mutate.cc A /trunk/src/molecule-class-info-ncs.cc A /trunk/src/molecule-class-info-other.cc A /trunk/src/molecule-class-info-surface.cc A /trunk/src/molecule-class-info-widget-work.cc A /trunk/src/molecule-class-info.cc A /trunk/src/molecule-class-info.h A /trunk/src/pick.cc A /trunk/src/pick.h A /trunk/src/positioned-widgets.h A /trunk/src/post-glade A /trunk/src/rama_mousey.cc A /trunk/src/rama_mousey.hh A /trunk/src/rama_plot.cc A /trunk/src/rama_plot.hh A /trunk/src/read-cif.c A /trunk/src/read-cif.h A /trunk/src/read-phs.c A /trunk/src/read-phs.h A /trunk/src/select-atom-info.hh A /trunk/src/support.c A /trunk/src/support.h A /trunk/src/trackball.c A /trunk/src/trackball.h A /trunk/src/triangle-extras.h A /trunk/src/xmap-utils.cc A /trunk/src/xmap-utils.h A /trunk/standard-residues.pdb A /trunk/surface A /trunk/surface/CXXChargeTable.cpp A /trunk/surface/CXXChargeTable.h A /trunk/surface/CXXCircle.cpp A /trunk/surface/CXXCircle.h A /trunk/surface/CXXCircleNode.cpp A /trunk/surface/CXXCircleNode.h A /trunk/surface/CXXCoord.cpp A /trunk/surface/CXXCoord.h A /trunk/surface/CXXCreator.cpp A /trunk/surface/CXXCreator.h A /trunk/surface/CXXException.cpp A /trunk/surface/CXXException.h A /trunk/surface/CXXFFTSolventMap.cpp A /trunk/surface/CXXFFTSolventMap.h A /trunk/surface/CXXFortranFile.cpp A /trunk/surface/CXXFortranFile.h A /trunk/surface/CXXMatrix4x4.h A /trunk/surface/CXXNewHood.cpp A /trunk/surface/CXXNewHood.h A /trunk/surface/CXXNode.cpp A /trunk/surface/CXXNode.h A /trunk/surface/CXXPointyBit.h A /trunk/surface/CXXQADSurface.cpp A /trunk/surface/CXXQADSurface.h A /trunk/surface/CXXQADSurfaceStaticData.cpp A /trunk/surface/CXXSpace.cpp A /trunk/surface/CXXSpace.h A /trunk/surface/CXXSphereElement.cpp A /trunk/surface/CXXSphereElement.h A /trunk/surface/CXXSphereFlatTriangle.h A /trunk/surface/CXXSphereNode.cpp A /trunk/surface/CXXSphereNode.h A /trunk/surface/CXXSphereTriangle.cpp A /trunk/surface/CXXSphereTriangle.h A /trunk/surface/CXXSphereTriangleEdge.cpp A /trunk/surface/CXXSphereTriangleEdge.h A /trunk/surface/CXXSurface.cpp A /trunk/surface/CXXSurface.h A /trunk/surface/CXXSurfaceVertex.cpp A /trunk/surface/CXXSurfaceVertex.h A /trunk/surface/CXXTorusElement.cpp A /trunk/surface/CXXTorusElement.h A /trunk/surface/CXXTorusNode.cpp A /trunk/surface/CXXTorusNode.h A /trunk/surface/CXXTorusTriangle.cpp A /trunk/surface/CXXTorusTriangle.h A /trunk/surface/CXXTorusTriangle.h.h A /trunk/surface/CXXTriangle.cpp A /trunk/surface/CXXTriangle.h A /trunk/surface/CXXUtils.cpp A /trunk/surface/CXXUtils.h A /trunk/surface/ElectroSurface.cpp A /trunk/surface/Makefile.am A /trunk/surface/Makefile.in A /trunk/surface/TokenIterator.h A /trunk/surface/surface.cpp A /trunk/surface/surface.h A /trunk/syminfo.lib A /trunk/theor-helix-70.pdb A /trunk/tw A /trunk/tw/Makefile.am A /trunk/tw/Makefile.in A /trunk/tw/coot-tw.hh A /trunk/tw/cootsound.c A /trunk/tw/tiddly.cc A /trunk/tw/tw.cc Initial import to Google Code. Importing coot-0.2.1-pre-5 (which does not contain aux). ------------------------------------------------------------------------ r2 | pemsley | 2007-03-12 10:49:28 +0000 (Mon, 12 Mar 2007) | 2 lines Changed paths: A /trunk/ideal A /trunk/ideal/Makefile.am A /trunk/ideal/Makefile.in A /trunk/ideal/Makefile.simple A /trunk/ideal/molmantest.cc A /trunk/ideal/notes A /trunk/ideal/pepflip.cc A /trunk/ideal/pepflip.hh A /trunk/ideal/regularize-minimol.cc A /trunk/ideal/regularize-minimol.hh A /trunk/ideal/simple-restraint.cc A /trunk/ideal/simple-restraint.hh A /trunk/ideal/test-indexing.cc A /trunk/ideal/test-indexing.hh A /trunk/ideal/with-geometry.cc A /trunk/ideal/with-map.cc Add ideal directory. ------------------------------------------------------------------------ r1 | (no author) | 2007-03-12 10:36:07 +0000 (Mon, 12 Mar 2007) | 1 line Changed paths: A /branches A /tags A /trunk Initial directory structure. ------------------------------------------------------------------------