2022-01-24 Paul Emsley * Release 0.9.7 2021-07-02 Paul Emsley * Release 0.9.6 2021-03-16 Paul Emsley * Release 0.9.5 2021-02-02 Paul Emsley * Release 0.9.4.1 2021-01-29 Paul Emsley * Release 0.9.4 2020-10-18 Paul Emsley * Release 0.9.3 2020-10-02 Paul Emsley * Release 0.9.2 2020-09-25 Paul Emsley * Release 0.9.1 2020-04-01 Paul Emsley * Release 0.9 2018-04-01 Paul Emsley * Release 0.8.9.2 2018-03-18 Paul Emsley * Release 0.8.9.1 2018-01-09 Paul Emsley * Release 0.8.9 2017-03-13 Paul Emsley * Release 0.8.8 2016-11-07 Paul Emsley * Release 0.8.7 2016-08-18 Paul Emsley * Release 0.8.6 2016-08-08 Paul Emsley * Release 0.8.5 2016-07-28 Paul Emsley * Release 0.8.4 2016-04-01 Paul Emsley * Release 0.8.3 2015-08-27 Paul Emsley * Release 0.8.2 2013-12-10 Paul Emsley * Release 0.8.1 2013-05-14 Paul Emsley * Release 0.8 2013-05-14 Paul Emsley * Release 0.7.1 2012-09-28 Paul Emsley * Release 0.7 2010-01-26 Paul Emsley * Release 0.6.1 2009-12-01 Paul Emsley * Release 0.6 2008-12-15 Paul Emsley * Release 0.5.2, fix silly shift labelling atoms bug. * Release 0.5.1 2008-09-24 Paul Emsley * Release 0.5 2008-01-02 Paul Emsley * Release 0.4 2007-07-12 Paul Emsley * src/graphics-info.h: add geom_p->add_planar_peptide_restraint() to graphics_info_t::init(). 2007-07-11 Paul Emsley * src/globjects.cc: changed smooth_scroll_step to 80 from 8. 2007-06-29 Paul Emsley * Release 0.3.2 2007-06-26 Paul Emsley * coot-utils/coot-shelx-ins.cc: (make_atom): set the U matrix correctly. There was a transposition of u12 and u23. Ouch. 2007-06-16 Paul Emsley * src/molecule-class-info.cc: (add try/catch mechanism round file.open_read() in read_ccp4_map()). Fixes a crash on reading a non-CCP4 map. 2007-06-21 Paul Emsley * db-main/db-main.cc (clear_results): clear the output fragment too. 2007-06-18 Paul Emsley * src/c-interface.cc: Add action view - as a direct view. But, don't we really instead want to insert such a thing into a set of views that we already have? 2007-06-17 Paul Emsley * ligand/wiggly-ligand.cc: turn off debugging for wiggly ligands. 2007-06-07 Paul Emsley * coords/Bond_lines.cc: (construct_from_atom_selection): Don't mark S, SE, CL, BR, or P as bonded. 2007-05-29 Paul Emsley * src/molecule-class-info-other.cc: change_chain_id_with_residue_range_helper_insert_or_add() the target_residue should simply be a residue that will appear in the pdb file before the inserted residue. 2007-05-18 Paul Emsley * src/c-interface.cc: (hardware_stereo_mode): kill off the SIDE_BY_SIDE_STEREO widget, if it was active. 2007-05-12 Paul Emsley * src/c-interface-build.cc (get_monomer): check that the library does not provide the restraints for the given 3-letter-code before passing to the libcheck function [Judit Debreczeni]. 2007-05-04 Paul Emsley * src/molecule-class-info.cc: (anisotropic_atoms): Add in cholesky decomposition to the matrix. 2007-05-03 Paul Emsley * src/graphics-info-modelling.cc: Added execute_simple_nucleotide_addition() function. 2007-05-01 Paul Emsley * src/molecule-class-info.cc: Kevin Cowtan provided a patch for CNS map reading. 2007-04-13 Paul Emsley * src/pick.cc: Added Segid info to picked atom output info [Christie Durnham] 2007-04-07 Paul Emsley * Release 0.3.1 * enable NCS ghosts. Add fractional matrix for LSQing. * Release 0.3 2007-03-31 Paul Emsley * src/graphics-info.cc: (destroy_edit_backbone_rama_plot): set edit_phi_psi_plot to null so that it is not left dangling when we do edit phi/psi the the N-terminal residue, where there is no Ramachandran plot made. Fixes Richard Baxter bug. (update_molecule_to): don't call molecule_class_info_t's update_molecule_to if there are no atoms in the guide point vector. This stops the creation of a molecule with no atoms in it, which causes problems because it seems to be closed. Also this means that the model is not modified without creating a new atom selection. Fixes Richard Baxter bug. 2007-03-19 Paul Emsley * src/cc-interface.hh: Add USE_GUILE protection to dictionaries_read(). 2007-03-06 Paul Emsley * src/c-interface-build.cc: (replace_fragment): function added. 2007-03-05 Paul Emsley * src/c-interface.h: (zoom_factor) function added. 2007-02-13 Paul Emsley * mapview.glade: Fix typo in "No Restraints" window [Steven Sheriff]. 2007-02-10 Paul Emsley * configure.in: Changed to version 0.2.1-pre-2 as I manually apply diffs from Paris. 2007-02-08 Paul Emsley * src/callbacks.c: Many functions: change return types from gchar* to const char * [typically from entries] to compile cleanly with GTK2. * src/c-interface-info.cc: (generic_string_vector_to_list_internal): needs USE_GUILE protection. * macros/guile-gtk.m4 (AM_PATH_GUILE_GTK): Use coot_gtk2 to set the version of libguilegtk-x.y.la for GUILE_GTK_LIBS. 2007-02-07 Paul Emsley * src/Makefile.am (INCLUDES): reordered because we want GTK flags and GUILE flags to come first because they could be in a different directory - when test building. * src/molecule-class-info-other.cc: (get_term_type) return "singleton" as a possible terminal residue type. * ligand/residue_by_phi_psi.cc: (residue_by_phi_psi) and other functions: add support for terminus type "singleton". Treat as a C-terminal addition. * src/graphics-info-modelling.cc: (execute_rotate_translate_ready): change the code path to check for atoms being in the same chain before putting up the GUI and making an intermediate molecule. * src/graphics-info-modelling.cc: (execute_rigid_body_refine): change the code path to check for atoms being in the same chain before doing rigid body refine. Does that fix Bob Nolte's bug? 2007-01-30 Paul Emsley * ligand/rigid-body.cc: (rigid_body_fit): Assign a (0,0,0) grad_vec when the occupancy of the atom is 0, otherwise it was undefined. Fixes crazy alpha helix placement? 2007-01-04 Paul Emsley * Release 0.2 2006-12-05 Paul Emsley * src/graphics-info-state.cc: (save_state_file) save the map sampling rate if it not the default. 2006-11-06 Paul Emsley * src/c-interface.cc: (dragged_refinement_steps_per_frame): return the number of steps so that we can save them. 2006-11-02 Paul Emsley * src/c-interface-build.cc: (set_show_chi_angle_bond): Add a redraw so that the new mode of chi angle drawing [typically called from callbacks.c functions] are made effective [green bond no longer left behind]. * src/c-interface-preferences.cc: (save_accept_reject_dialog_window_position): only [dereference and] save the position if the dialog is not null. 2006-11-03 Paul Emsley * src/molecule-class-info.cc: (handle_read_draw_molecule): only update the bond width if this is NOT a undo. 2006-09-17 Paul Emsley * src/graphics-info-modelling.cc: (rot_trans_adjustment_changed): add in code to check for CA bonds in master molecule and find bonds appropriately. * src/molecule-class-info.cc: remove intermediate pair of Cartesians in draw_skeleton(), suggestion from Ezra Peisach. 2006-08-31 Paul Emsley * src/globjects.cc (key_press_event): mark as handled GDK_Meta_L and GDK_Meta_R [for mac]. 2006-08-23 Paul Emsley * Release 0.1.2. 2006-08-24 Paul Emsley * src/callbacks.c (on_auto_open_mtz_activate): correctly set the sort_button [fixes random crash maybe]. * ligand/ligand.cc: ligand constructor: Change the default map_atom_mask_radius to 2.0A. 2006-08-20 Paul Emsley * src/c-interface.cc: also c-interface-preferences.cc and globjects.cc, callback.c and graphics-info-state.cc: Add code to store, save and restore the position of the ramachandran plot. 2006-08-19 Paul Emsley * src/molecule-class-info-ncs.cc: (copy_residue_range): completely re-written to fix bug noted by Panagis Filippakopoulos. 2006-08-14 Paul Emsley * src/c-interface-preferences.cc: (Add functions to save the position of major widgets). 2006-08-08 Paul Emsley * src/globjects.cc: (handle_scroll_event): abstracted from long glarea_button_press [More of the same please!]. Now scroll_events [GTK2?] are handled similarly. 2006-08-08 Paul Emsley * src/geometry-graphs.cc: (render_geometry_distortion_blocks_internal): Use sane_occupancy to convert from shelx occupancies. Stops geometry distortions going negative. * src/c-interface.cc: function to set the default bond thickness, saved/used in save_state_file(). * src/c-interface-build.cc: (on_merge_molecules_check_button_toggled): Use GPOINTER_TO_INT to type user data. LTE bug. * src/c-interface-build.cc (execute_refmac): Use GPOINTER_TO_INT to get user data from active item. LTE bug. * src/c-interface.cc (on_filename_filter_toggle_button_toggled): Use GPOINTER_TO_INT to type user data. LTE bug. * src/graphics-info-modelling.cc: (rot_trans_adjustment_changed): Use GPOINTER_TO_INT to type user_data. LTE bug. 2006-08-07 Paul Emsley * src/graphics-info.cc: (on_change_current_chi_button_clicked): use GPOINTER_TO_INT to type user data. LTE bug. (difference_map_peaks_neighbour_peak): user GPOINTER_TO_INT to type result of gtk_object_get_user_data(). LTE bug. (rotamer_dialog_neighbour_rotamer): user GPOINTER_TO_INT to type user_data. LTE bug. (bonds_colour_rotation_adjustment_changed): use GPOINTER_TO_INT. LTE bug. 2006-08-04 Paul Emsley * src/graphics-info.cc: (float_to_string): Valgrind was complaining about uninitialized memory. Not sure why. Index the arrays to 99 instead when zeroing. * coords/Bond_lines.cc: (construct_from_asc): when outputing UDD error for atom [it sholdn't happen] index the correct array. Valgrind 2006-08-03 Paul Emsley * src/molecule-class-info.cc: (label_atom): only draw the atom labels if the molecule is being displayed. * src/geometry-graphs.cc: (render_geometry_distortion_blocks_internal): Don't do things for atom index -1 [Not sure why atom index *is* -1 though]. This and below fixes bug on geometry validation of 1HJ9 [Ulrich Englich]. * ideal/simple-restraint.cc: (distortion_score_plane_internal): Don't do things for atom index -1. 2006-07-24 Paul Emsley * doc/user-manual.texi (masks): mask-map-by-molecule not mask-map-by-protein. * src/graphics-info-defines.cc: (check_if_in_pepflip_define): do a redraw of the graphics after a pepflip. 2006-07-22 Paul Emsley * macros/glut.m4 (AM_PATH_GLUT): Add i686-apple-darwin* option. 2006-07-17 Paul Emsley * coot-utils/coot-shelx-ins.cc: move the precision setting out of the format statement [ooops!] - fixes Doug Kuntz bug. 2006-07-28 Paul Emsley * build-it: Fix position of test of status of making guile. * README: Removed the joke at the start of the README. It is stale and misleading and I am not sure anyone got the joke (the URL no longer gave a useful page). 2006-06-23 Paul Emsley * ligand/find-ligand.cc (main): add wiggly [flexible] ligand option. * src/molecule-class-info-other.cc: (delete_residue_with_altconf): when we have a shelxl molecule with just 1 alt conf left, set the remaining occs to 11.0. 2006-06-16 Paul Emsley * coords/Bond_lines.cc: (construct_from_asc): Don't draw unbonded hydrogens if the we are not drawing hydrogens. Fixed bug of Donnie B. 2006-06-22 Paul Emsley * ligand/ideal-rna.cc: (make_molecule): put the antisense residues in the chain in reverse order [so that they appear in the pdb file in increasing order] by using a vector of residues. 2006-06-08 Paul Emsley * sequence-view/sequence-view.cc: (mol_to_canvas): check that strand is non-null before doing anything with it. Fixes crash with 1h5w reported by Roeland Boer [rbocri@cid.csic.es]. 2007-06-05 Paul Emsley * ideal/simple-restraint.cc: (find_link_type): Allow D-peptides as well as L-peptides. 2006-06-05 Paul Emsley * geometry/protein-geometry.cc: (init_standard): use CLIBD_MON if it is set. 2006-06-04 Paul Emsley * src/molecule-class-info-widget-work.cc: (fill_ncs_control_frame_internal): don't test for display_it_flag before setting the toggle button. [Actually, that whole frame should be desensitised according to display_it button state]. 2006-05-24 Paul Emsley * src/c-interface.h: enable documentation for superpose functions. 2006-05-22 Paul Emsley * src/c-interface.cc: read_phs_and_make_map_using_cell_symm_from_mol renamed to read_phs_and_make_map_using_cell_symm_from_mol_using_implicit_phs_filename. read_phs_and_make_map_using_cell_symm_from_previous_mol created. read_phs_and_make_map_using_cell_symm_from_mol created. So that putting phs data on the command line will use the given pdb. command line data handling needs to be call this function. (add_filename_filter_button): filter button created. (set_file_selection_pre_filtered): function created. To satisfy Phil, I think. * coot-utils/coot-shelx-ins.cc: (write_ins_file): use precision(9) when outputting coords - stops [unreadable] accidental exponential output formatting. * src/c-interface-build.cc: (set_undo_molecule): Allow the setting of the undo molecule to a molecule that might have 0 selected atoms [e.g. we have a ligand as a molecule and accidently delete it] 2006-05-21 Paul Emsley * src/c-interface-build.cc: (ideal_nucleic_acid): downcase the sequence. 2006-05-30 Paul Emsley * src/c-interface.cc: (get_text_for_aniso_limit_radius_entry): don't write over the end of the malloced memory. 2006-05-19 Paul Emsley * Release 0.1.1 2006-05-15 Paul Emsley * src/c-interface-build.cc: (save_symmetry_coords_from_fileselection): remove origin pre-shift from trans of symm atom before writing coords. 2006-05-11 Paul Emsley * coords/Bond_lines.cc: (construct_from_asc): Added in cross-bonds to hydrogens that don't have bonds. Blasted hydrogens will no longer seem to disappear. 2006-05-10 Paul Emsley * src/molecule-class-info.h: ghost_molecule_display_t, cleaned up usage of display_it_flag [valgrind was complaining [rightly]]. 2006-05-09 Paul Emsley * src/c-interface.cc: (set_show_unit_cells_all): Check maps too! [PRE]. * src/callbacks.c (on_unit_cell_no_radiobutton_toggled): unit cell radio button callbacks added. Now these radio button pair has immediate effect [PRE]. 2006-04-25 Paul Emsley * src/molecule-class-info.cc: (add_typed_pointer_atom): Set attributes correctly for user-typed pointer atom. 2006-04-24 Paul Emsley * ligand/Makefile.am: Use libcoot-ligand.la throughout. 2006-04-24 Paul Emsley * src/rama_plot.cc: (draw_2_phi_psi_sets_on_canvas): remove bad shadowing of loop variable. [FR]. * src/molecule-class-info-other.cc: proper syntax for coot::nomenclature [remove extra qualification] [FR]. * src/molecule-class-info-ncs.cc: make copy_residue_range_using_from_ncs_master_to_other_using_ghost() return a value [FR]. 2006-04-19 Paul Emsley * src/c-interface.cc: (set_graphics_window_size) add use_graphics_interface_flag protection. 2006-04-17 Paul Emsley * src/c-interface-info.cc: (place_text), (remove_text) Added fuctions. Add 3-d text [the text doesn't rotate, it stays readable]. * src/c-interface.cc: Created function get_monomer() from the internals of handle_get_libcheck_monomer_code(). get_monomer() can be used from the scripting layer. * src/c-interface.cc (safe-scheme-command). Now returns a value, SCM, which can be decoded in the calling function. A good thing. [This means that libguile.h had to be included in c-interface.h]. 2006-04-15 Paul Emsley * coot-utils/peak-search.hh (coot): remove extra qualification for find_protein_to_origin_translations() [test compile with 4.1.0]. 2006-04-14 Paul Emsley * src/molecule-class-info.h: remove molecule_class_info_t from function declaration for change_chain_id_with_residue_range [DB]. * src/rama_plot.hh: remove coot::rama_plot:: from function declaration for get_phi_psi [DB]. * coot-utils/coot-map-heavy.hh (ffear_search): remove class component of function name for filter_by_distance_to_higher_peak() [also DB]. * coords/Cartesian.h: add proper declaration of friend functions. Ancient broken code (however did it compile before?)! Compilation problem spotted Donnie Berkholz. 2006-04-12 Paul Emsley * src/molecule-class-info-mutate.cc (mutate_base_internal): Allow Ud and Tr as possible bases from which to mutate. 2006-04-13 Paul Emsley * ligand/wiggly-ligand.cc: Added #include for coot-utils.hh, it seems to be needed in the case where GSL is not defined? Anyway, no harm in explicitly including it. 2006-04-11 Paul Emsley * src/graphics-info-navigation.cc: (fill_go_to_atom_residue_list): make the 2000 residue item limit change to 20000. Now the widget behaviour is different, but you can exapand chains past the G chain [the 2000th residue] individually. This is better, I suppose. 2006-04-11 Paul Emsley * src/graphics-info.cc: (apply_undo): Update the ramachandran plot [if it exists for this molecule]. * coot-utils/coot-utils.cc: (create_directory): moved body of make_directory_maybe here and changed logic of fstat vs is_dir tests so that we don't test for a directory before file exists. 2006-04-04 Paul Emsley Release 0.1 * src/graphics-info-modelling.cc: (new_alt_conf_occ_adjustment_changed): Don't change the alt conf for fully occupied atoms. 2006-04-03 Paul Emsley * src/callbacks.c (on_rotate_translate_obj_cancel_button_clicked): COOT_ROTATE_TRANSLATE_DIALOG remembers where it was put when we press the Cancel button. 2006-04-01 Paul Emsley * src/c-interface-build.cc (delete_residue_range): check the status of the "Keep Active" dialog before trying to close the dialog. Bug reported by Bernhard Lohkamp. 2006-03-30 Paul Emsley * src/c-interface-waters.cc (renumber_waters): function added * src/molecule-class-info-other.cc (renumber_waters): function added. * src/c-interface.cc: (auto_read_make_and_draw_maps): if "FWT", "DELFWT" column labels fail, try "2FOFCWT" and "FOFCWT" also. * src/rama_plot.cc: created function phi_psi_pair_helper_t make_phi_psi_pair() which is the engine for making phi/psi pairs from 2 chains. Uses new utility function std::pair get_phi_psi(). The GUI menu item has been renamed to "Kleywegt Plot" as per conversation with George Sheldrick. 2006-02-26 Paul Emsley * ligand/Makefile.am (test_fffear_in_coot_LDADD): Add coot-compat to get the correct getopt_long() as suggested by Ezra. * src/main.cc and cmtz-cinterface.cc: Patch as Ezra suggests commenting out NLS code. 2005-12-02 Paul Emsley * coords/Bond_lines.cc: (do_colour_by_chain_bonds) and (do_colour_by_molecule_bonds): both now look at the atom element and draw_hydrogens_flag. Also removed atom selection indexing and just just atom pointers (which should be propogated to other functions in this class). 2005-12-01 Paul Emsley * src/c-interface.cc: (apply_bond_parameters): remove looking for the "carbons only" checkbuton. 2005-11-30 Paul Emsley * src/molecule-class-info.cc: (initialize_coordinate_things_on_read_molecule_internal): add setting of the [initial] bond colour map rotation step and "doit" flag. 2005-11-12 Paul Emsley * src/molecule-class-info.cc: (insert_coords_chage_altconf) and (insert_coords_atoms_into_residue_internal): Add shelx occupancy. -1 is used when this is not from a shelx file. * coot-utils/coot-shelx-ins.cc: Add add_fvar function which added a free variable and returns the index of the new free variable * coords/mmdb.cc: (get_atom_selection): added ifdefs for HAVE_MMDB_IGNORE_HASH. May need to sort this out by hand. 2005-11-11 Paul Emsley * src/molecule-class-info-widget-work.cc: (ncs_control_change_ncs_master_to_chain_update_widget): created. When we change the NCS master the toggle buttons for the displayed ghost chains need to change too. 2005-11-10 Paul Emsley * src/cmtz-interface.cc: (get_f_phi_columns): use try/catch mechanism to stop crash on trying to CCP4MTZfile::open_read a cif file. 2005-11-06 Paul Emsley * The move to CCP4 distribution of fftw, cmtz, cmap, mmdb, ssm, clipper libraries. Substantial changes not documented here. This diff is 38,000 lines. mmtz and mmtz-extras have gone. New clipper-based mtz looking routine added (cmtz-interface.cc). Crystal and dataset info now appear in the mtz column chooser and this had to be accounted for, so much splitting and recombining of strings (new functions added). macros updates to match ccp4 placing of include files. The autobuilder is updated. 2005-11-05 Paul Emsley * geometry/protein-geometry-mmdb.cc (comp_atom_pad_atom_name): I was getting the atom name wrong for "CCB" with element "C", so now a check is made to see if first letter is the element name. 2005-10-31 Paul Emsley * macros/with-guile.m4, macros/with-python.m4: applied Ezra's patch to use AM_CONDITIONAL to get to the wrapped guile interface. 2005-10-30 Paul Emsley * src/c-interface.cc: (handle_read_draw_molecule_with_recentre): add statusbar text when the molecule fails to read. 2005-10-29 Paul Emsley * src/globjects.cc (key_press_event): add call to new scheme function graphics-general-key-press-hook for as yet undefined keys [Bryan Lepore]. 2005-10-19 Paul Emsley * src/c-interface.cc: (another_level_from_map_molecule_number): only try to mess with the contor levels of molecule istat if istat is not an error [-1, e.g. from map, not mtz file]. Fixes another-level crash. 2005-10-18 Paul Emsley * coot-utils/coot-fffear.cc: file created. For fffear class, moved out of coot-map-heavy.cc * coot-utils/coot-coord-utils.cc (pad_atom_name): copied from geometry class. Should rationalize at some stage. * coot-utils/coot-shelx-ins.cc: (make_atom_name): new version which uses atom element and calls new util function pad_atom_name(). 2005-10-16 Paul Emsley * src/graphics-info.cc: (drag_refine_refine_intermediate_atoms): created. Function for Frank von Delft. * src/globjects.cc: (glarea_motion_notify): if dragged refinement intermediate refinement set then refine intermediate atoms. * src/molecule-class-info-other.cc: (add_OXT_to_residue): instead of finding total 4 atoms, check that each of them has been found. Now we can add OXT to residues with an alt conf. 2005-10-04 Paul Emsley * src/graphics-info-pick.cc (rotate_intermediate_atoms_round_screen_x): function created. Called by rotate_intermediate_atoms_maybe(). * src/globjects.cc: (glarea_motion_notify): rotate_intermediate_atoms_maybe() now has axis argument and uses y diff for rotation round the screen X axis. 2005-09-23 Paul Emsley * src/graphics-info-state.cc: (save-state_command): If contoured_by_sigma_p() I meant to push back command strings, not display strings. Fixes saving contour state issue for Bob Nolte. * src/graphics-info-graphs.cc: (rotamers_from_mol): use dunbrack constructor that adds extra PHE/TYR. 2005-09-20 Paul Emsley * coot-utils/peak-search.cc: (get_peaks): don't move the negative cluster centres to local peak. * ligand/ligand.cc: (fit_ligand_to_cluster): Try each orientation eigen. Changed [created a version with extra args of the eigen ori] of transform_ligand_atom() and fit_ligand_copy(). (calculate_cluster_centres_and_eigens): After sorting the eigen values, check the matrix determinant. If negative, swap axes 2 and 3. No longer inverts [chiral] ligands. * coot-utils/peak-search.cc: (get_peaks): Don't used move_grid_to_peak on cluster centres of negative peaks. 2005-09-19 Paul Emsley * coords/Bond_lines.cc: (handle_MET_or_MSE_case): Add alt conf testing to bonds. Also changed CYS case. * ligand/ligand-extras.cc: (fit_water_internal): major rewrite. Now uses list for clusters rather than vector. We only calculate clusters once. Sphericity test has been removed. 2005-09-16 Paul Emsley * ideal/simple-restraint.cc: (make_link_restraints): test for neighbouring residues [by residue seq number]. Fixes problem of refining next to residue with all atoms in alt confs. * src/molecule-class-info-other.cc: (do_180_degree_side_chain_flip): make the alt conf work by using a residue copy. 2005-09-15 Paul Emsley * geometry/protein-geometry.cc: (try_dynamic_add): Add in logic to try to find "XXX-b-D.cif" or "XXX-a-L.cif" * ideal/simple-restraint.cc: (find_link_type): override the return value of find_glycosidic_linkage_type() until find_glycosidic_linkage_type() returns sensible result. Fixing flying carbohydrate. 2005-09-12 Paul Emsley * src/molecule-class-info-other.cc: (make_ball_and_stick): put the glMaterialfv() call for specular inside the bond loop to colour for bond type and comment out GL_AMBIENT_AND_DIFFUSE and GL_EMISSION [no idea why they were there - not clear thinking...]. Ball and stick looks good now. I need to be able to remove the object at some stage. 2005-09-11 Paul Emsley * src/graphics-info-defines.cc: (other_modelling_tools_toggle_button_name_list): correct name of cis/trans button. * ligand/residue_by_phi_psi.cc: extract function build_C_terminal_ALA() and build_N_terminal_ALA() out of residue_by_phi_psi class [from construct_prev_res_from_rama_angles() and construct_next_res_from_rama_angles()]. * ligand/helix-placement.cc: (build_on_N_end, build_on_C_end, trim_end, build_N_terminal_ALA, build_C_terminal_ALA): created to extend or trim the placed helix. * src/graphics-info-render.cc: (povray): Move the eye back. (povray_molecule): change the scale of the rendered objects to 1.0. 2005-09-08 Paul Emsley * mini-mol/mini-mol.cc: add occupancy characteristic to a minimol atom. Update pdb reading and writing. * ligand/ligand.cc: (get_rigid_body_angle_components): The scaling of the gradients to [angle] steps was too high, leading to overstepping the minimum and therefore oscillations. 0.03 changed to 0.01. Resulting in more rapid and more robust rigid body refinement now. 2005-09-06 Paul Emsley * ligand/find-ligand.cc (main): corrected usage text. 2005-09-05 Paul Emsley * src/c-interface.cc: (parse_ccp4i_defs): line length limit was 100 chars on read. How *could* I have been so short-sighted? expanded to 1000. Fixes crash reported by Lari Lehtiƶ I hope. 2005-09-02 Paul Emsley * src/molecule-class-info-other.cc: (change_chain_id_with_residue_range): Fix crash reported by GSK's Nino: ie. crash when Change Chain ID residue range to a chain id that already exists [nresidues -> to_chain_nresidues]. 2005-09-01 Paul Emsley * src/callbacks.c (on_raster3d1_activate): and friends. Added default filename. * ccp4mg-utils/Makefile.am: Clean up Makefile.am [remove the fink hardcoding of CXXFLAGS for png]. PNG is not available then. * src/graphics-info.cc: (update_residue_by_chi_change): update chi_ang.change_by() to use pointer to Geom. * src/c-interface-ligands.cc: (execute_ligand_search): update install_simple_wiggly_ligands call to pass the pointer to Geom. * geometry/protein-geometry.cc: (get_monomer_torsions_from_geometry): now we have dynamic add, this function is not const. 2005-08-31 Paul Emsley * src/callbacks.c (on_screendump_image_ok_button_clicked): Created. Call the image creation functions according to fileselection type. * src/c-interface.cc: (make_image_raster3d) and (make_image_povray) functions created to be used by new Snapshot menu items. * coot-utils/coot-shelx-ins.cc: (make_atom): abstracted out to make the keyword conditions a bit more readable. Fixed read of isotropic B factor and keep HKL card for output. As per GMS instructions. (write_ins_file): use function remove_leading_spaces for the atom names. * coot-utils/coot-utils.cc: (remove_leading_spaces): function created [used for shelx output atom names]. * src/graphics-info-defines.cc (check_if_in_reverse_direction_define): Created for new button on other modelling tools menu. (setup_reverse_direction) created too in c-interface-build.cc 2005-08-29 Paul Emsley * geometry/protein-geometry.cc: (get_monomer_torsions_from_geometry): try_dynamic_add was not being used if the monomer_type was not found in the list. It is now. This needs to be passed read_number. * src/graphics-info.cc: (set_transient_and_position): a copy of the c-interface.cc's function - so that widgets created from inside graphics-info.cc can be transiented and positioned [e.g. chi angles and rotamers]. Needed the creation of (positioned-widgets.h) which is included by c-interface.cc, callbacks.c and graphics-info.cc. * high-res/high-res.cc: (buccafilter): removed the fragment-sort-by-length. 2005-08-25 Paul Emsley * analysis/bfkurt.cc: Tidied up with unsigning the for loop ints. Also pass extra flag to write_table that allows the output of every residue, not just the questionables. * src/molecule-class-info.cc: (mutate): 5364 uncommented and repositioned the DeleteSelection(). Or it should be. check me. 2005-08-23 Paul Emsley * doc/user-manual.texi (SHELX .ins/.res files): section created. * coot-utils/coot-shelx-ins.cc: (debug) added. * src/molecule-class-info-other.cc: (reverse_direction_of_fragment): Given a residue spec, find the fragment that that residue was in and reverse the direction of that fragment leaving only CAs. * src/c-interface-build.cc: (fill_partial_residues): function created. Uses the new missing_atoms() function. * src/molecule-class-info-other.cc (missing_atoms): created. Do a check against the atom names in the dictionary and return a class that contains a vector of CResidue *s of atoms that don't have all their atoms. * coot-utils/coot-coord-extras.hh: Added missing atom helper classes. * src/graphics-info-pick.cc: (symmetry_atom_pick): Kevin inserted some throw/catch code here on the setting of the space group name. Also, construct the space group from the symops, not the space group name. * coords/Bond_lines.cc: (handle_MSE_case) changed considerably. Also handled here now are CYS and MET. The normal construct bond length limit has been reduced to 1.7A [whcih left Sulfur bonds which this routine deals with]. * coot-utils/coot-shelx-ins.cc: (symm_card_composition_t): correct the indexing of the ele array to set the symmetry card correctly [rather than totally mis-indexed, as it had been]. * src/graphics-info-defines.cc: (check_if_in_180_degree_flip_define): created and extensive changes. Ligand fitting was moved out of the model/fit/refine dialog and the 180 degree flip moved in. A mol is created from the residue, so that we can call update_geometry_graphs [which has presumed an intermediate atom molecule], so that 180 degree flips can upate the rotamer graph. A chi_angles function rotate_chi2_180() was created. * src/c-interface.cc: (handle_read_draw_molecule_with_recentre): rather than use the shelx split in get_atom_selection(), where a normal atom_sel is returned [and the ShelxIns is lost], we call read_shelx_ins_file directly and molecule_class_info_t keeps the ShelxIns. Now shelx ins files can be output. * coords/Bond_lines.cc: (add_atom_centres): put a lower limit on the occupancy needed to have a zero occ spot, so that shelx molecule with occ -61 is correctly represented. 2005-08-21 Paul Emsley * ligand/chi-angles.cc: (add_IUPAC_extras_PHE_and_TYR_rotamers): new function created. Used in intialization of chi angles. We add extra rotamers for PHE and TYR to cope with the 180 degree flip to match IUPAC convention, but rotamer there didn't exist. 2005-08-13 Paul Emsley * high-res/high-res.cc: buccafilter() function created and also function to add cbetas and o positions. Had 2 goes at the filtering. The first was to average the position of the similarly placed atom - but it was too complex. So I then tried scoring by fragment length then just deleting the other atoms if they overlapped. * mini-mol/mini-mol-utils.cc (o_position, cbeta_position): created file and functions and added to Makefile.am These are called by post-buccaneer filtering. 2005-08-12 Paul Emsley * setup/coot.sh.in: and coot.csh.in. Don't override the PYTHONPATH if it was set already. 2005-08-08 Paul Emsley * src/callbacks.c: on_residue_info_b_factor_apply_all_checkbutton_toggled and on_residue_info_occ_apply_all_checkbutton_toggled: toggle the sensitivity of the entries so that people can't make edits until the edits are active. 2005-08-04 Paul Emsley * src/globjects.cc: scroll-wheel event handling altered - no longer can get maps that can be increased in level, but not decreased. * doc/user-manual.texi (Maps in General): Add documentation for "Expert mode". 2005-08-03 Paul Emsley * src/read-phs.c: add stdio for clean compile. * src/c-inner-main.c: Add string.h and stdio for a clean compile. * src/gtk-manual.c: include stdio.h, stdlib.h and string.h to clean the compilation on GCC 4.0 (FC4). * src/read-cif.c: include stdio.h to declare printf() * src/c-interface-superpose.cc: (superpose_with_chain_selection) add ifdef HAVE_SSMLIB to this function [Jinghua Tang reported the compilation error]. 2005-08-02 Paul Emsley * coords/Bond_lines.cc: (do_Ca_plus_ligands_bonds): ooops, remove tmp debugging line that set atom_colour_type to COLOUR_BY_RAINBOW for everything. 2005-07-28 Paul Emsley * high-res/globularize.cc: globularize_protein now takes --centre-x [etc] arguments. 2005-07-26 Paul Emsley * geometry/protein-geometry.cc: now partial charges are not needed for the dictionary to read correctly. 2005-07-25 Paul Emsley * Fixed: Alt conf split on water [ignores the value in the dialog]. * Fixed: occupancy of remaining single atoms set to 1.0 on deletion. * Fixed: set the cell and symmetry in setup of minimol. * Fixed: remove the Control Delete description [it doesn't work]. * The water distance validation check now works. * Update: Go To Atom window after renumber-residue-range. * scheme/fitting.scm: added fit-waters function. Needed atom_index_first_atom_in_residue() function. * Fixed: waters added to protein model with no waters had the waters added to the last chain [instead of a new chain]. * Created: high-res/globularize.cc 2005-06-30 Paul Emsley * Release 0.0.33 2005-06-29 Paul Emsley * src/graphics-info-state.cc: (save_state_file): use molecule_count to find the go_to_atom_molecule for the output script [not i]. * src/molecule-class-info.cc: (insert_waters_into_molecule): Create insert_waters_into_molecule() and rename old function of that name to append_to_molecule(). insert_waters_into_molecule() checks that we have a solvent chain, and if it does then add waters to that chain, not create a new chain. * analysis/bfkurt.cc: (stats) Add a new element to store the residue name [and then use it to label the b-factor validation graph blocks]. 2005-06-28 Paul Emsley * src/c-interface.cc: (new_close_molecules): it is not an error for the sequence view not to be displayed. 2005-06-28 Paul Emsley * ligand/chi-angles-autogen.cc (add_all_rotamers): generated new chi-angles-autogen.sh, but I needed to kludge in a MSE rotamer so that we didn't get 100s of the "Oops, MSE not found in typed_rotamers" messages in the console. * ligand/read-dunbrack.awk: if chi2 for TYR and PHE is > 90, take 180 from the angle to fit to IUPAC nomenclature. 2005-06-28 Paul Emsley * src/graphics-info.cc: (smooth_scroll_maybe) get an extra pair of args, a target zoom and a flag. Now reset view has animate zoom too. * src/molecule-class-info.cc: (display_bonds): Put if test round set_bond_colour_by_mol_no(), suggested by Ezra Peisach. 2005-06-27 Paul Emsley * src/molecule-class-info-other.cc: (cis_trans_convert) and (cis_trans_convertion) created for CIS <-> TRANS conversion and other graphics_info_t and c-interface infrastructure to deal with it. * "Other Modelling Tools" menu item and dialog created. * src/command-line.cc (handle_command_line_data): add --auto handler [which does auto_read_make_and_draw_maps]. (parse_command_line): add --auto command-line option. 2005-06-26 Paul Emsley * mapview.glade: move Residue/monomer to top of list. * src/callbacks.c (on_run_refmac_run_button_clicked): Add some debugging. * src/c-interface-build.cc: (wrapped_create_delete_item_dialog): If we were in water delete mode, then set the appropriate radio button. * src/graphics-info.cc: (execute_rotate_translate_ready): Swap from copying the whole of the molecule to using a residue selection and using create_mmdbmanager_from_res_selection(). Fixes memory leak hopefully and allows CA mode for intermediate atoms without crashing on accept of the moving atoms. 2005-06-25 Paul Emsley * src/graphics-info.cc: (make_moving_atoms_graphics_object): Make bonds in CA mode if the moving atoms molecule was in CA mode. * src/graphics-info-pick.cc: (move_moving_atoms_by_simple_translation): Make bonds in CA mode if the moving atoms molecule was in CA mode. * src/c-interface.cc (map_scroll_wheel_mol_selector_activate): Call activate_scroll_radio_button_in_diplay_manager() so that the display manager is consistent. 2005-06-24 Paul Emsley * src/graphics-info-graphs.cc: (rotamer_graphs): in missing atoms case, set a string_user_data to signal missing data and in geometry-graphs.cc's plot_block change the colour of the block for missing atoms case. 2005-06-23 Paul Emsley * ligand/dunbrack.cc: (probability_of_this_rotamer): Kludge the residue type to MET from MSE *after* the atom pairs have been assigned. Fixes Juergen Bosch "MSE in rotamer graph bug". * geometry/protein-geometry.cc: (init_refmac_mon_lib): use the read_number_in to determine if this file should update the chem_comp info [in the refmac libs, the chem_comp information is given twice, in the mon_lib_list.cif and a/ALA.cif - we only want the second one or we get allresidues added to the dictionary [which may not be a bad thing for the future]]. * ideal/simple-restraint.cc: (find_link_type): created. Given 2 residues and the dictionary, find the linkage type. * (find_glycosidic_linkage_type): for pyranoses and furanoses. This is just a stub function at the moment. It should be filled and return the correct linkage. We need to find the anomericity of the linking oxygen. There are issues of the linking oxygen - the convention in refmac might be different to conventional biochemistry. Needs investigation at some stage. 2005-06-22 Paul Emsley * src/graphics-info-navigation.cc: (split_resno_inscode): allow for residues with negative residue numbers. Fixes bug reported by Qingping Xu. * geometry/protein-geometry.cc: (chem_comp), (mon_lib_add_chem_comp): created. mon_lib_add_chem_comp() does the trashing of the old residue restraints so that a new file will update create a new usable library. mon_lib_add_chem_comp() adds monomer information such as the group [e.g. "L-peptide"] used in determining the linkage type. (init_refmac_mon_lib): now takes a read_number argument. Why the read number? Currently [20050620] the way the restraints are found is FIFO. we start from entry 0 and check upwards for the matching residue/monomer type. But we need to be able to "override" the current restraints by reading in a new file. How do we do that? When reading in a restraint and trying to add it, we find that a dictionary entry for that residue type exists. Do we want to override it? In init_refmac_mon_lib() we would want to check through dict_res_restraints for the existance of this restraint. If it does exist, kill it by changing its name to blank. However, we don't know the name of the restraint yet! We only know that at the add_atom(), add_bond() [etc] stage. So, at each of those stages we need to know if this we are adding to an already existing dictionary entry or this restraint is from a different file to the previous entry. We want to do different things they are different. * geometry/protein-geometry.cc: (clear_dictionary_residue): created. * src/graphics-info-pick.cc: (symmetry_atom_pick): On Kevin's advice add the string type to the constructor of the Spgr_descr. * coot-utils/coot-shelx-ins.cc: (read_file): On Kevin's advice add the string type to the constructor of the Spgr_descr. 2005-06-17 Paul Emsley * src/c-interface-build.cc: (delete_atom): now calls simply go_to_atom_molecule() rather than look at the option menu to find the active position. Fixes delete water crash [EJD, Bob Nolte]. * src/c-interface.cc: (set_pick_cursor_index) added so that users can set their own pick cursor. * ideal/Makefile.am: noinst the programs here [test-indexing, with-map, with-geometry]. 2005-06-16 Paul Emsley * src/graphics-info.cc: (make_pointer_distance_objects): only draw pointer distances to displayed molecules. 2005-06-13 Paul Emsley * ligand/find-waters.cc (main): add --chop functionality. * src/molecule-class-info-other.cc: (bad_chiral_volumes): return also a vector of residue types for which we fail to find restraints. Use this to change the label of a warning pop-up. * coords/mmdb.cc: (get_atom_selection): IgnoreHash flag added. * db-main/db-main.cc: -Wall fixes. * geometry/protein-geometry-mmdb.cc (comp_atom_pad_atom_name): Properly pad hydrogen names of length 2. HH of TYR no longer explodes. * density-contour/CIsoSurface.cpp: (add): Ezra's suggestion 1 -> i. 2% better FPS. 2005-06-11 Paul Emsley * ligand/ligand.cc: (mask_map): Make the mask_map functions consistent re: xmap_masked. * coot-utils/trim.cc (trim_molecule_by_map): Add extra flag, waters_only. * ligand/find-waters.cc (main): add support for --chop flag, i.e. call trim_molecule_by_map() [with waters only]. 2005-06-10 Paul Emsley * ligand/find-waters.cc (main): Add --chop command line option. * src/main.cc: (show_citation_request): Add Refmac dictionary reference. * src/c-interface-info.cc: (output_residue_info): Handle Master Atom entries and check buttons. * src/graphics-info-defines.cc: (check_if_in_delete_item_define): Make checks for waters for residue and water modes. Now waters can be deleted only in water mode, and residue in residue mode. * src/callbacks.c (on_delete_item_cancel_button_clicked): Add clear of pending picks on close [and also in the destroy callback], so that the graphics can rotate. * src/graphics-info.cc: (wrapped_create_edit_chi_angles_dialog): transiented dialog. 2005-06-09 Paul Emsley * src/molecule-class-info.cc: (map_fill_from_mtz_with_reso_limits): Apply the *dataset* reso limit [rather than the mtz file reso limit] from Kevin for Eleanor. 2005-06-04 Paul Emsley * src/molecule-class-info-ncs.cc: (fill_ghost_info) [and other upstream functions]: takes the argument of the [user-changable] homology level. * ideal/simple-restraint.cc: (minimize): change the meaning of the flag so that it controls the output of the *initial* chi squared. Now always on termination, we get to see the final chi squareds. * src/c-interface-info.cc: (apply_residue_info_changes): add a redraw when we finish. * src/Makefile.am move coot-shelx in the linking list. * ligand/Makefile.am add coot-shelx for findligand and findwaters. 2005-06-02 Paul Emsley * src/graphics-info-state.cc: (save_state_file): Add [sleezy] molecule number usage to save the active and displayed state of molecules. * src/c-interface.cc (set_save_molecule_number): created for use in callback from callbacks.c * src/callbacks.c (on_save_coordinates1_activate), graphics_info_t: change mechanism of passing the molecule number of coordinates to be saved, created graphics_info_t::save_imol. * src/c-interface-build.cc: (set_model_fit_refine_rotate_translate_zone_label) and (set_model_fit_refine_place_atom_at_pointer): add configurability to Model/Fit/Refine dialog. * src/molecule-class-info-other.cc: (find_water_baddies_OR): Added flags dependent on the value of the passed parameters.. maybe it would have been better to simply pass the flags too. * src/c-interface-validate.cc: (do_check_waters_by_widget): Add check buttons to Check/Delete water tests. Add a list of usage flags that depend on the state of the "Active" checkbuttons. These alter the values that are passed to molecule_class_info_t's find_water_baddies(). 2005-05-29 Paul Emsley * src/c-interface-build.cc: (execute_refmac): Now that the coordinates use the conventional mechanism, I had to move from get_user_data on the active menu item and introduce and use a graphics_info_t static called refmac imol. 2005-05-28 Paul Emsley * coot-utils/peak-search.cc: (get_peaks): New interface created that also uses a CMMDBManager. make_sample_protein_coords(), move_point_close_to_protein() and min_dist_to_protein() created to help out. 2005-05-27 Paul Emsley * src/graphics-info-superpose.cc (superpose_with_atom_selection): Turn off symmetry on the molecule that has been superposed. * src/callbacks.c (on_save_coords_dialog_save_button_clicked): reworked the transfer of the save model info, from a pointer to a graphics_info_t static [save_imol]. Access is this static is provided at the c-interface: save_molecule_number_from_option_menu(). 2005-05-26 Paul Emsley * src/c-interface.cc: (fill_go_to_atom_window): completely gutted the option menu usage to make it conventional usage where we also pass the default molecule number. Removed other version from the c-interface which did not use the molecule number. Go To Atom and other option menus now work as they should [or seem to]. 2005-05-25 Paul Emsley * src/molecule-class-info-other.cc: (bad_chiral_volumes): added console message when the restraint was not found for that residue/monomer type. 2005-05-24 Paul Emsley * src/molecule-class-info.cc: (draw_unit_cell_internal): change to segmented lines. * src/globjects.cc (key_press_event): add hooks for dot and comma pressed. * src/graphics-info-superpose.cc (superpose_with_atom_selection): After atom transformation, no longer show the symmetry of the moved molecule. 2005-05-23 Paul Emsley * src/molecule-class-info.cc: (name_sans_extension): No longer ignore the include_path_flag. * src/c-interface.cc: (print_sequence_chain): Filled the stub. * setup/Makefile.am: moved coot.csh and coot.sh from bin_SCRIPTS to EXTRA_DIST. 2005-05-22 Paul Emsley * src/c-interface.cc: (wrapped_create_display_control_window): The display manager was changed to a pane and the size parts of it get saved in a static. Here we create the widget dependent on its bits [included the pane position]. * src/callbacks.c (on_show_symmetry_ok_button_clicked): Use set_show_symmetry_master(). 2005-05-19 Paul Emsley * mapview.glade: removed "Import all Dictionary CIFs" too slow. Not needed now that we have "dynamic" addition of dictionary. * src/callbacks.c (on_model_refine_dialog_delete_button_clicked): If not atom mode, then set the residue delete mode [it may have been in residue hydrogens mode and previously it was getting stuck there]. 2005-05-18 Paul Emsley * cootrc: Buttons put in order and recoloured. * src/graphics-info-defines.cc: (model_fit_refine_button_name_list): add refmac button to list. * coot-utils/coot-shelx-ins.cc: (read_shelx_ins_file): substantial changes. The latt card is used to generate the strings to init the clipper space group. * src/callbacks.c (on_mutate_sequence_do_autofit_checkbutton_toggled): fix the typo so that this checkbutton works correctly. 2005-05-17 Paul Emsley * src/read-phs.c: (try_read_phs_file): pha [from SHELX] is a phs file too. 2005-05-15 Paul Emsley * src/graphics-info.cc: (display_geometry_distance_symm): added distance to status bar. 2005-05-12 Paul Emsley * coot-utils/coot-shelx-ins.cc: (read_file): added more shelx keywords so that Coot knows they are not atoms. 2005-05-11 Paul Emsley * doc/user-manual.texi (set-scroll-by-wheel-mouse): add Ezra's doc fixes. * Release 0.0.32 2005-05-10 Paul Emsley * src/globjects.cc: (glarea_button_press): z_is_pressed non-clickable atoms problem fixed? 2005-05-09 Paul Emsley * coords/Cartesian.cc: (on_a_face): include Ezra's NO_FACE cleanup. * build/Makefile.am (testcabuild_LDADD): Use .la linking [Ezra]. * ligand/Makefile.am (findwaters_LDADD): better not to use the lib dir when the lib is in this directory [SMP - Ezra]. * geometry/Makefile.am: As Ezra suggests, use .la linking. * src/globjects.cc: (display_density_level_maybe): apply Ezra's suggestion of removing the depth cueing for the density level text. 2005-04-26 Paul Emsley * src/molecule-class-info.cc: (make_maybe_backup_dir): use umask to set the permission on coot-backup. (handle_map_colour_change): check for swapped difference map colours [fixes Dirk's bug]. * src/callbacks.c (on_save_state_ok_button1_clicked): save state now connected to a fileselection for the state file. This sets the static save_state_file_name. 2005-04-23 Paul Emsley * coords/Bond_lines.cc: (addSymmetry_whole_chain): delete the atoms of transsel too. 2005-04-19 Paul Emsley * src/callbacks.c (on_model_refine_dialog_delete_button_clicked): now this calls set_transient_and_position for the delete item dialog so it is recreated where it was last time. * src/c-interface.cc: (undo_last_move): created. uses old_rotation_centre_? variables. Bound to keyboard U. 2005-04-18 Paul Emsley * src/c-interface-preferences: add_status_bar_text() created. * pixmaps/coot-16-bevel.xpm make the hat top more orange [Neil Paterson]. 2005-04-18 Paul Emsley * src/graphics-info.cc: (execute_rotate_translate_ready): Use gtk_window_set_transient_for to keep rotate_translate on top. (do_accept_reject_dialog): Use gtk_window_set_transient_for to keep accept/reject window on top. 2005-04-15 Paul Emsley * src/geometry-graphs.cc: close_yourself(); set the block to null in the vector if it has been deleted. 2005-04-09 Paul Emsley * src/molecule-class-info.cc: (change_contour): allow contouring of negative peaks that are lower than the highest positive peak [Charlie Bond]. 2005-04-08 Paul Emsley * src/c-interface.cc: (auto_read_make_and_draw_maps): Make the FWT map be the one that scrolls, not the difference map [Randy Read]. 2005-04-05 Paul Emsley * src/c-interface.cc: (reset_view): Go to next molecule if we are already centred on one. 2005-04-02 Paul Emsley * src/c-interface-superpose.cc: (superpose_with_atom_selection): created - you can superpose any atom selection now given an mmdb atom selection string. * src/molecule-class-info-other.cc: (find_water_baddies_AND): use map_sigma not map_sigma_in; * src/graphics-info-defines.cc: (check_if_in_edit_backbone_torsion_define) change = to == in if statement [sharp intake of breath when that was discovered!]. 2005-04-01 Paul Emsley * src/graphics-info.cc: (load_needed_monomers): fix indexing error - how did it ever work before? 2005-03-31 Paul Emsley * Release 0.0.31 * src/callbacks.c (on_delete_item_cancel_button_clicked): set the stored delete_item_widget pointer to NULL, fixed a crash when this was referenced by do_refine(). * src/c-interface-build.cc: (wrapped_create_add_OXT_dialog): fixed option menu so internal status variable matched the displayed molecule option. * src/graphics-info-state.cc: (save_state_file): add status messages. * src/c-interface-build.cc: (wrapped_create_merge_molecules_dialog): fix option menu so internal variable matches the displayed molecule option. 2005-03-28 Paul Emsley * src/graphics-info-pick.cc: (symmetry_atom_pick): override distance to centre limit when CA mode or whole chain mode [Fixes PRE bug?]. 2005-03-25 Paul Emsley * src/graphics-info-state.cc: (save_state_file): put show-symmetry after the molecules have been read. * src/c-interface.cc: (set_show_symmetry): display no symmetry popup warning only if there were models available. 2005-03-21 Paul Emsley * skeleton/BuildCas.cc: (setup_internal): Fixed Ezra non-inited variable. * ideal/simple-restraint.cc: Ezra notes problems. Fixed. 2005-03-20 Paul Emsley * src/c-interface-build.cc (fit_loop_from_widget): created. Now we can call scheme function (fit-gap ..) from interface. * src/c-interface.cc: (refine_zone): add valid model molecule protection [fixes fit-gap crash]. (set_show_symmetry): Test for zero molecules that symmetry available [called from Cell & Symmetry OK button callback]. * src/molecule-class-info.cc: (set_bond_colour_by_mol_no): rotation size multiplier is now non-zero for imol=0, so the colour map can be [is] also rotated for the 0th molecule. (draw_map_unit_cell): turn off the cell drawing when the map is not displayed. (draw_coord_unit_cell): turn off the cell drawing when the coords are not displayed. 2005-03-16 Paul Emsley * src/gtk-manual.c: on_display_control_mol_displayed_button_toggled and friends gslist_for_scroll_in_display_manager_p() and scroll_radio_button_1 in the display manager now gives us clickable scrollable map, rather than having to use the menus. Horrah - within a minute I realise that it's a Good Thing. Will this please Charlie Bond? 2005-03-15 Paul Emsley * src/molecule-class-info.cc: (make_backup): don't test on n_selected_atoms, use mol [Joel Bard ligand deleting bug]. (save_molecule_filename): use name_for_display_manager() if unpathed_backup_file_names_flag is set. * coords/Bond_lines.cc: (add_atom_centres) Don't add H atom centres when hydrogens are not drawn [Robin Owen bug]. 2005-03-11 Paul Emsley * src/main.cc: (check_reference_structures_dir): Created. * Release 0.0.30 * doc/Makefile.am (user-manual.html): various fixes here to make things go on bubbles too. * ligand/dunbrack.cc: Add MSE special cases - now we have MSE rotamers. 2005-03-09 Paul Emsley * ccp4mg-utils/mgtree.cc: (RecurseCalculateTree): Fix suggested by Joel Bard in the case where (coordk->GetParentID()==-1&&scanned[*k]!=1) fails. 2005-03-08 Paul Emsley * db-main/db-main.hh (coot): remove class name from mainchain_fragment() declaration [Ezra Peisach]. * coords/mmdb-crystal.cc: (point_is_in_box): add coot namespace for dot_produc [Ezra Peisach]. * coot-utils/coot-fasta.hh: remove coot::fasta:: from declaration of is_fasta_aa [Ezra Peisach]. * angles/AngleInfo.h: moved definition of nint inline and into class. * src/molecule-class-info-other.cc: (bad_chiral_volumes): is_bad_chiral_atom_p is in namespace coot [Ezra Peisach]. * skeleton/BuildCas.cc: Remove unused variables [Ezra Peisach]. * configure.in: add -LANG:std to CXXFLAGS if CC on irix if not there already [Ezra Peisach]. * coords/Bond_lines.cc: (addSymmetry_whole_chain) Use PCAtom not (CAtom *) [which could be mis-understood as a casting] for transsel [Ezra Peisach]. * coords/Bond_lines_ext.cc (find_molecule_middle): Use vector of int not dynamic [g++ extention] array of ints [Ezra Peisach]. * coords/Bond_lines.h: (Bond_lines_container) removed class name in front of make_graphical_bonds() [Ezra Peisach]. * src/c-interface.cc: (handle_cns_data_file) should return a value [Ezra Peisach]. * high-res/high-res.hh (high-res): fill_globular_protein should have differently named args [Ezra Peisach]. * src/graphics-info.h: state_command string should have differently named args [Ezra Peisach]. 2005-03-03 Paul Emsley * src/c-interface.cc: add pick_cursor [how can it not have been there before!] and use it for delete item. 2005-03-02 Paul Emsley * src/Makefile.am (COOT_EXTRA_LIBS): Use .la linking * other Makefile.ams: Use .la linking as Ezra suggests. 2005-03-01 Paul Emsley * src/molecule-class-info.cc: (add_typed_pointer_atom): Changed " OW1" to standard " O " here too. * ligand/ligand-extras.cc: Changed " OW1" to standard " O ". Spotted by PRE. 2005-02-28 Paul Emsley * Release 0.0.29 2005-02-25 Paul Emsley * db-main/db-main.cc: (match_target_fragment): Add ires protection from start of fragment [bug found when fragment didn't contain any Calphas]. 2005-02-24 Paul Emsley * ligand/ligand.cc: (ligand class): changed xmap_masked to xmap_cluster and now use xmap_masked to score ligands, not xmap_pristine. * ligand/ligand.cc: (import_map_from): the version with sigma added also should set xmap_masked. 2005-02-24 Paul Emsley * src/molecule-class-info.cc: (export_coordinates): added statusbar text. * ligand/wiggly-ligand.cc: (install_simple_wiggly_ligands): don't write 1.pdb 2.pdb etc for wiggly ligands. 2005-02-23 Paul Emsley * src/molecule-class-info.cc: (add_typed_pointer_atom): use max_resno_in_chain to find the resno off added water/thing. * coot-utils/coot-coord-utils.cc: (max_resno_in_chain): created. To be used by add pointer atom function so that we don't get pointer atoms/SO4s in the same chain with the same residue number. * ligand/ligand.cc: changed map_masked to map_clustered and introduced map_masked. ligand-extras.cc now uses map_masked [not map_cluster, how did it ever work before?]. 2005-02-22 Paul Emsley * src/pick.cc: (atom_pick): moved the console pick info. * src/c-interface.cc: (new_close_molecules): update go to atom molecule if it had been set to a deleted molecule [Phil Evans bug]. * doc/coot.tex (subsection{Raster3D output}): Add F8 to doc. * src/callbacks.c (on_model_refine_dialog_dismiss_button_clicked): Use close_model_fit_dialog() to destroy the hbox and let us know if the dialog needs destroying. * src/c-interface.cc: (): created [sometimes the model/refine/dialog has been sucked in - we need to hide the frame for dialog's hbox in that case]. * src/density-score-by-residue.cc: (density_score_molecule): add scored residue class and scored atom class fix up output. Joel Bard request. 2005-02-21 Paul Emsley * src/molecule-class-info-other.cc: (merge_molecules): add the adding_chain chain_id to this molecules chain ids, so that new [other] molecules don't come up with the same chain id. Fixes Harvard bug. 2005-02-20 Paul Emsley * src/c-interface-build.cc added functions for scripting translation/refinement/rotamers: chain_n_residues(), molecule_centre_internal(), resname_from_serial_number(), seqnum_from_serial_number(), insertion_code_from_serial_number(), chain_id(), n_chains(). * src/c-interface.cc: (set_colour_by_molecule): created. fixed up gtk-manual.c and .h and Bond-lines.cc/.hh and molecule_info_class too. 2005-02-19 Paul Emsley * src/graphics-info-state.cc (save_state_file) Add vt-surface to the state file. * Makefile.am (SUBDIRS): Moved high-res after ideal. * src/graphics-info.cc: (display_geometry_torsion): Created code for Torsions too, needed do_torsion_define() and gui elements [as per angle]. Angles and distances are now displayed on the graphics. * src/graphics-info-defines.cc: (clear_pending_picks): clears the a_is_pressed flag too which is often what we want [even though it is possible that it may not be true]. 2005-02-16 Paul Emsley * src/graphics-info.cc: (refine): Removed annoying "That water molecule doesn't have restraints" message. 2005-02-15 Paul Emsley * src/molecule-class-info.cc: (save_molecule_filename): Disaster! People report crashing on Accept moving atoms. reverted to version that worked and patched up. Still not sure what the problem was. Thank goodness for svn. 2005-02-13 Paul Emsley * Release 0.0.28 2005-02-13 Paul Emsley * src/globjects.cc: (glarea_button_press): Bin [synthetic] double click events which were giving us 2 "Accept Refinement" dialogs. * src/molecule-class-info.cc: Various changes involving WINDOWS_MINGW to make Bernhard's job easier. 2005-02-12 Paul Emsley * src/xmap-utils.cc: (map_density_distribution): bins to vector. Berhard bug. 2005-02-10 Paul Emsley * src/c-interface.cc: Filled the read_shelx_ins_file() and write_shelx_ins_file() stubs. 2005-02-08 Paul Emsley * src/graphics-info-graphs.cc (density_fit_from_residues): Created. called both density_fit_graphs and density from mol [the update of the graph from intermediate atoms]. (update_geometry_graphs): created. Moved out out accept_moving_atoms. We need 2 version of this, one for moving atoms molecule and the other a residue/residue range for things like pepflip or auto-fit rotamer [i.e. things which don't create intermediate atoms]. 2005-02-07 Paul Emsley * src/c-interface.cc: residue_density_fit_scale_factor() add interface to set this [useful for CNS/mapman users?] 2005-02-04 Paul Emsley * ideal/regularize-minimol.cc (regularize_minimol_molecule): created. Called from wiggly-ligands install_wiggly_ligands(). Fixed up Makefile.am and various headers. Cool - minimized torsioned ligands. This took about an hour on the train to Oxford. * ideal/simple-restraint.cc: Change the chain_id in the restraints constructor and the init_from_mol chain_id to const char *. * ligand/wiggly-ligand.cc: (install_simple_wiggly_ligands): change RotateAboutBond() to SetDihedralAngle() now that ccp4mg tree has changed the function. * ligand/dunbrack.cc: (ordered_residue_atoms): Remove "needs reordering" debugging line. * ccp4mg-utils (mgtree): Un-apply adjustments suggested by Joel Bard [rotamers on prolines don't return - it gets stuck in a tree function]. 2005-02-03 Paul Emsley * src/graphics-info.cc: (execute_edit_chi_angles): If MSE change clicked atom to C to set the tree right [Phil Evans bug]. * ligand/chi-angles.cc: (change_by): all these functions return the angle now as well as the status [now in a pair]. * src/graphics-info.cc: (update_residue_by_chi_change): Display the chi angle [like Dirk asked for]. * src/gtk-manual.c (on_map_col_sel_cancel_button_clicked): update to pass tmd [and change create_map_colour_selection_window() to pass it]. Along with molecule_info_class and c-interface save and restore_previous_map_colour() we eventually get the colour map selection cancel button to Do The Right Thing. * src/molecule-class-info.cc: (save_previous_map_colour) (restore_previous_map_colour): created. 2005-02-03 Paul Emsley * doc/coot.tex (section{Environment Variables}): add reference structures to index. 2005-02-02 Paul Emsley * src/Makefile.am (coot_wrap_python_pre.cc): coot.i should be prefixed by top_srcdir for out of tree building. 2005-02-02 Paul Emsley * ccp4mg-utils (mgtree): apply adjustments suggested by Joel Bard. 2005-01-30 Paul Emsley * src/molecule-class-info.cc: (store_refmac_params): Fixed screen output typo. * ligand/ligand.cc: (find_clusters): Tell us the distance limits too. * src/molecule-class-info.cc: (delete_atom), (delete_atoms), (delete_residue), (delete_residue_with_altconf): update the symmetry too on object deletion. * src/graphics-info-defines.cc: (check_if_in_delete_item_define): delete by symmetry atom click now enabled. * src/c-interface-build.cc: (clear_pending_delete_item): added zeroing of delete_item_residue_hydrogens [too]. Fixes bug in notes. (delete_atom_by_atom_index): Use [also] the dialog's checkbuton to see if the dialog should be destroyed. * src/c-interface-validate.cc: (unset_geometry_graph): added null graphs protection. (free_geometry_graph): added null graphs protection. * src/globjects.cc: (graphics_info_t::display_lists_for_maps_flag): now that map colour update works, make display list for maps the default. * src/molecule-class-info.cc: (compile_density_map_display_list): created - so that we can make update_map separate from the compilation of the display list. Caled from molecule-class-info.cc's handle_map_colour_change(). 2005-01-29 Paul Emsley * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): use $with_ssmlib_prefix in MMDBSSM_CXXFLAGS [Oops]. Hopefully fixes problems spotted by Joel Bard and Joseph Toth. * src/graphics-info-pick.cc: (symmetry_atom_pick): tried to add null protection going from mmdb char * spacegroup to clipper Sprg_descr. 2005-01-28 Paul Emsley * src/globjects.cc (key_release_event): Added GDK_CONTROL_MASK checking and setting of internal params. 2005-01-27 Paul Emsley * src/molecule-class-info-ncs.cc (ncs_chains_match_p): Fix for non-consistant chain additions - should find NCS more consistantly now. * src/molecule-class-info-mutate.cc: (align_on_chain): more tinkerining with the array indexing [fixes crashes]. 2005-01-25 Paul Emsley * src/molecule-class-info-surface.cc (make_surface): put surface graphics object into a display list. * src/c-interface.cc: (set_display_lists_for_maps): created. Tinkers with graphics info variable and is [now] used in molecule-class-info.cc's update_map() and draw_density_map(). 2005-01-24 Paul Emsley * doc/coot.tex (section{Scripting}): say that parentheses are important. 2005-01-18 Paul Emsley * Release 0.0.27 * src/graphics-info.cc: (moving_atoms_graphics_object): Make Ns be blueish and oxygens redish. * src/c-interface-build.cc: (wrapped_create_align_and_mutate_dialog): deal with pathological case of closed first molecule when filling chain optionmenu. INFO:: All chain option menu dialogs should use this construction. 2005-01-14 Paul Emsley * src/graphics-info.h: Added brief_atom_labels_flag for Ian Tickle. * src/molecule-class-info.cc: (mutate) I deleleted the DeleteSelection(). Not sure this is safe - should test on PC [seems OK on Mac - yep seems OK]. * coot-utils/coot-coord-utils.cc: (get_ori_to_this_res): updated error message. * ligand/ligand.cc: (make_sample_protein_coords): Use proper minimol limits to residues vector. Fixes Marianne's water/ligand addition crash. 2005-01-13 Paul Emsley * src/molecule-class-info-other.cc: (recent_backup_file_info): Added COOT_BACKUP_DIR configurability. 2005-01-11 Paul Emsley * src/graphics-info.cc: (new_alt_conf_occ_adjustment_changed): callback from [altconf] rotamer occupancy hscale sets the occ of intermediate atoms. 2005-01-10 Paul Emsley Release 0.0.26 2005-01-05 Paul Emsley * ligand/dunbrack.cc: use SetDihedralAngle not RotateAboutBond for as the Tree function [Urgh.. this needs a fix]. 2005-01-04 Paul Emsley * src/molecule-class-info.cc: (show_spacegroup): don't try to construct a string from a null char *. Fixes crash [thanks Michal Jakob]. * coot-utils/coot-coord-lsq.cc: Created for lsq interface. Called by graphics-info-lsq.cc function. 2004-12-23 Paul Emsley * Release 0.0.25 [At long last] 2004-12-20 Paul Emsley * src/c-interface-build.cc: (align_and_mutate), (do_align_mutate_sequence): and friends created. * src/molecule-class-info-mutate.cc created for "align and mutate" functions. 2004-12-20 Paul Emsley * ligand/ligand-extras.cc: removed high-res.hh dependencies. high-res now depends on ligand libs so is moved after ligand dir. * src/molecule-class-info.cc: (make_map_from_cif): Added state commands. 2004-12-14 Paul Emsley * db-main/db-main.cc: (get_fragment_ca_atoms): change to new style minimol indexing. (mainchain_ca_coords_of_db_frag): ditto. * coot-utils/coot-coord-utils.cc (get_ori_to_this_res): moved from molecule_class_info_t. Tedious. * src/molecule-class-info-ncs.cc: (ncs_averaged_maps): extend the extends by 5A. * src/molecule-class-info.cc: (mutate): tinkered with the DeleteSelection placement. * src/molecule-class-info-other.cc: (apply_atom_edits): created - new interface used by apply_residue_info_changes() changing several atoms at once. * src/graphics-info.cc: (apply_residue_info_changes): complete re-written to instead check the values of the widget at "Apply" time rather than keep a list of edits as they happen [and that was failing because the edits were not recorded if the entry widget didn't have focus - which was quite possible with a swipper like Tracey]. Make a list of edits and apply them all at one. 2004-12-13 Paul Emsley * coot-utils/coot-coord-utils.cc: (extents): function created. Return a pair of Coord_orths [top left and bottom right - not face centres]. * src/molecule-class-info-ncs.cc: Use Coord_orth extents to box a map [as per density contouring] to use in NCS averaging. * src/graphics-info-defines.cc: Added atom name labelling [as per refine check] for check_if_in_db_main_define(), rigid_body and totate/translate checks. 2004-12-07 Paul Emsley * src/c-interface-info.cc: (do_residue_info): Added check of pending residues edits before generating the widget. * src/graphics-info.cc: (refine): trap refinement of a water and use Rigid body Fit Zone instead. 2004-12-06 Paul Emsley * src/c-interface-validate.cc: do_check_waters_by_widget(), wrapped_create_check_waters_dialog(), wrapped_checked_waters_baddies_dialog() created to make a water checking interface. 2004-12-04 Paul Emsley * coords/Bond_lines.cc: (trans_sel): in the trans_selection atoms set those atoms residues to be the same as the atom from which they are copied. * src/graphics-info-pick.cc: (symmetry_atom_pick): changed min_dist to 0.4 [like regular pick]. Now we don't get suprious/unexpected symmetry atom click hits. 2004-12-03 Paul Emsley * db-main/db-main.cc: (match_target_fragment): changed max_devi from 2.0 to 2.6, less gaps now when converting to mainchain? (fit_reference_structures): change from 0.3 to 0.4 for similar_eigens() similarity test. * ligand/ligand.cc: (mask_map): introduced new version with Selection Handle that does the mask inversion [i.e. only leave map around the atom selection]. It's cool. * coords/Bond_lines.cc: (do_normal_bonds_no_water): Use SKEY_NEW for atom selection to exclude waters - not the naive way it was done before causing atom indexing problems [thanks Ward Smith]. 2004-12-01 Paul Emsley * src/molecule-class-info.cc: delete_residue, delete_residue_with_altconf, delete_residue_hydrogens, delete_atom all now have a call to delete_ghost_selections(). Are we stable now? * src/molecule-class-info-ncs.cc: (delete_ghost_selections): created. To be called whenever we do a deletion of the atom_sel. Followed by an update_ghosts() after the modification. 2004-11-30 Paul Emsley * src/graphics-info.cc: (fill_bond_parameters_internals): Set the adjustment for the new hscale - a much better interface than the text entry box. 2004-11-29 Paul Emsley * coords/Bond_lines.cc (Bond_lines_container): Changed 1.82 to 1.86. * src/graphics-info.cc: (rot_trans_adjustment_changed): change to mmdb-idiomatic CAtom * for rotation centre holder rather than its index [Fixes Stephen Graham's alt conf rot/trans bug]. * coot-utils/coot-coord-utils.cc: (get_selection_handle): from a coot::atom_spec_t. Used first in rot/trans. Hopefully useful in future. * coot-utils/coot-coord-utils.hh: (atom_spec_t): added constructor from a hierarchy CAtom *. * src/graphics-info.cc: (flash_selection): added DeleteSelection(). 2004-11-26 Paul Emsley * src/c-interface-waters.cc: (execute_find_waters_real): mask waters is no longer optional. * src/c-interface-build.cc: (execute_refmac_real): add extra params so that we can choose to swap the map colour of post refmac maps to be the same as the pre-refmac map. * src/main.cc: (show_citation_request): enable this code [at last, yey!] * src/callbacks.c (on_model_refine_dialog_refmac_button_clicked): Set the difference map check button to be on by default. 2004-11-25 Paul Emsley * src/c-interface.cc: (do_refine) and (do_regularize): kill off the delete item dialog and unset the pending delete state if state is on. * src/graphics-info-superpose.cc (superpose_with_atom_selection): Tinker with atom limits. Not sure if it's correct to be honest. Stops Miguel's crash though. * src/c-interface.cc: (fill_option_menu_with_skeleton_options): call the version of the option_menu filter that also sets the active position. [Skeletonization problems gone, I hope]. * src/graphics-info.cc: (skeleton_map_select): Set the radio buttons according to the skeletonization state of the current map. * src/molecule-class-info.cc: (close_yourself): also turn off the skeleton. * density-contour/CIsoSurface.cpp: (returnTriangles): fix typo in line checking [thanks Ezra]. 2004-11-24 Paul Emsley * src/pick.cc: (atom_pick): added a test on number of pickable molecules and display a dialog if there are none. * src/graphics-info-defines.cc: (check_if_in_delete_item_define): added check to see if a symmetry atom was picked and if so give a warning. * mini-mol/mini-mol.cc: (setup): completely re-written. * src/graphics-info-render.cc: (render_molecule): Use atom centre info also to add balls to sticks. * coords/Bond_lines.cc: (add_atom_centres): graphical bonds container now contains atom centre info. * src/molecule-class-info.cc: (set_bond_colour_by_mol_no): When we run out of colours make some up based on i - fixed may grey Ca chains problem. 2004-11-21 Paul Emsley * src/molecule-class-info.cc: (make_map_from_phs): changed the default return status [as error] to -1. 2004-11-20 Paul Emsley * coords/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS [for coot-close.cc usage]. 2004-11-19 Paul Emsley * sequence-view/Makefile.am (INCLUDES): added CLIPPER_CXXFLAGS * analysis/Makefile.am (INCLUDES): Added CLIPPER_CXXFLAGS 2004-11-16 Paul Emsley * src/molecule-class-info.cc: (add_typed_pointer_atom): check for chain that is chain only of the same type as added residue type before creating new chain. 2004-11-15 Paul Emsley * coot-utils/Makefile.am: add MMDB_CXXFLAGS to INCLUDE [thanks Joseph Toth]. * surface/CXXSphereNode.h: removed the ; again! 2004-11-14 Paul Emsley * ligand/Makefile.am (findligand_LDADD): use $(top_builddir) (findwaters_LDADD): Use $(top_builddir). * high-res/Makefile.am (testatomgraph_LDADD): corrected testatomgraph_LDADD. (tracehighres_LDADD): corrected for coot-coord-utils usage. * src/globjects.cc: (glarea_motion_notify): Tinkered with key modifier mask - should remove being stuck in "Translate Only" mode. (key_press_event): Added anomaly corrector here too. * src/molecule-class-info.cc: (add_typed_pointer_atom): Check for a chain of a type before creating a new chain. * coot-utils/coot-coord-utils.cc (chain_only_of_type): Find a chain in a molecule that is only of the given type. If not, return NULL. 2004-11-13 Paul Emsley * src/pick.cc: (atom_pick): check the molecules back to front to select atoms "on top" first. * src/molecule-class-info.cc: (set_initial_contour_level): created - map creating functions [e.g. from ccp4 map file and from mtz] should call this function - which makes more sensible decisions about how to set the starting contour leve [e.g. for E-maps]. 2004-11-10 Paul Emsley * src/graphics-info-state.cc: (save_state_file): save also the go to atom info. * src/molecule-class-info-ncs.cc: created. With functions update_ghosts(), update_bonds [for ghost_molecule_display_t], fill_ghost_info(), find_ncs_matrix(), make_dynamically_transformed_maps(), install_map(), add_ncs_ghost() for first stab at NCS functions. Also various ghost display on/off flags and accessor functions in molecule_class_info_t and c-interface-preferences [for now]. Glade NCS dialogs created and static GUI elements added to graphics-info. * src/c-interface.cc: (valid_labels): check for null return of get_f_cols(), get_phi_cols() and get_weight_cols(). * src/mtz-bits.c: (get_f_cols), (get_phi_cols), (get_weight_cols): check for success of get_f_phi_columns and return NULL on badness. * mmtz-extras/mmtz-extras.c: (get_f_phi_columns): now stat and return NULL on error. 2004-11-09 Paul Emsley * src/graphics-info-state.cc: Added set go to atom info. 2004-11-08 Paul Emsley * src/c-interface-info.cc: (set_show_pointer_distances), (toggle_pointer_distances_show_distances), (execute_pointer_distances_settings) created for pointer distances functions - good for use when running through difference map peaks [but no symmetry checking]. * src/molecule-class-info-other.cc (distances_to_point): Created for pointer distances support. * src/main.cc: tinkered with gtk pending events for splash screen. * src/callbacks.c (on_open_coordinates1_activate): make add_filename_filter_button() return the button and call gtk_signal_emit_by_name with clicked argument. Added state flag to graphics-info and accessor function to c-interface.h/cc. 2004-11-07 Paul Emsley * setup/coot.csh.in: uncommented COOT_RESOURCES_FILE. 2004-11-05 Paul Emsley * src/graphics-info.cc: (rotamer_dialog_neighbour_rotamer): created: makes a sythetic "clicked" event on next/prev rotamer radio buttons when keyboard , or . pressed. * src/gtk-manual.c: (display_control_molecule_combo_box) and (display_control_map_combo_box), no expand, no fill on the molecule number [padding 3]. 2004-11-04 Paul Emsley * coords/Cartesian.h: moved getStart and getFinish into the header for in-lining - should speed up map rotation? 2004-11-03 Paul Emsley * coords/Bond_lines.cc (Bond_lines_container): [constructor with no distance args] changed 1.9 to 1.82, does this fix MSE bonding problems? 2004-10-30 Paul Emsley * src/c-interface-superpose.cc: (superpose_with_chain_selection): created for use with [new] chain selection to SSM. Moved actual invocation of ssm to graphic-info-superpose.cc. Added chain GUI elements, with a generic chain chooser. 2004-10-29 Paul Emsley * src/graphics-info-state.cc: (state_command) fix for python commands with no args [thanks Bernhard]. * src/molecule-class-info-other.cc: (map_chains_to_new_chains): removed debugging code. 2004-10-27 Paul Emsley * Release 0.0.24 * src/molecule-class-info.cc: (close_yourself): move the setting to NULL of the atom pointers until after they have been deleted [d'oh!] * setup/coot.csh.in: Added IRIX case. * setup/coot.sh.in (systype): Added IRIX cse. * src/molecule-class-info.h: (set_draw_hydrogens_state): use make_bonds_type_checked() not simply makebonds() - and don't even do that if the state is the same as it had been. * src/molecule-class-info-other.cc: (add_OXT_to_residue): added a GUI warning. * geometry/protein-geometry.cc: comp_bond, comp_angle, comp_plane, comp_chiral: added get_padded_name() to create the atom names. Note: links not done. 2004-10-26 Paul Emsley * geometry/protein-geometry.cc: (atom_id_mmdb_expand): reference the argument [oops!] and return early if atom name is 4 chars already. * src/graphics-info-navigation.cc: (fill_go_to_atom_residue_list): don't call cb_chain_tree_itemsignal() on deselect. 2004-10-25 Paul Emsley * src/c-interface.cc: (add_on_map_colour_choices), (map_scroll_wheel_mol_selector_activate), (add_on_map_colour_choices), (add_map_colour_mol_menu_item): much tediousness adding dynamic an enumerated options to the scroll map menu and map colour chooser. Still, I've been wanting to do it for months. You can no longer choose to change the colour of a closed map. * src/graphics-info.h: removed the array initialization to null for the various canvases and validation graphs as suggested by Tim Gruene. * src/c-inner-main.c: (c_inner_main): Altered logic of scheme file loading, now COOT_SCHEME_DIR if defined, has priority. * src/c-interface.cc: (set_symmetry_size): Added symmetry updating and redisplay. (graphics_to_ca_representation) and other graphics_to_* functions: added valid molecule protection. Fixes scripting crash. * src/graphics-info-navigation.cc: (update_widget_go_to_atom_values): added inscode to residue's entry string. (split_resno_inscode): created. Used by apply_go_to_atom_from_widget() which interprets the widget's entry texts. 2004-10-24 Paul Emsley * src/molecule-class-info.cc: (save_coordinates): added error dialog. (read_ccp4_map): Added non ext,map,msk extension error dialog. 2004-10-23 Paul Emsley * src/molecule-class-info.cc: (make_atom_label_string): Added ins code to atom label. (model_view_residue_tree_labels): Add ins code to residue label. 2004-10-21 Paul Emsley * src/graphics-info.cc: (place_typed_atom_at_pointer): Added closed molecule protection. Fixes crash. * src/graphics-info: (pointer_atom_molecule): added has_model() protection. * src/c-interface-ligands.cc moved ligand stuff here and fixed the "test for ligand" bug on "reading" the widget at execute time. 2004-10-20 Paul Emsley * setup/coot.sh.in export COOT_REF_STRUCTS. Argh. Is this the end to it? 2004-10-19 Paul Emsley * Release 0.0.23 * high-res/Makefile.am linking libraries order changes. 2004-10-19 Paul Emsley * Release 0.0.22 * src/callbacks.c (on_show_symmetry_ok_button_clicked): symmetry whole chain button should call symmetry_whole_chain(), not set_symmetry_atom_labels_expanded() - cutn'paste error, I guess [Dirk K's bug]. 2004-10-17 Paul Emsley * sequence-view/sequence-view.cc: (draw_mol_chain_label): Add a space when molecule name is blank. Thanks Ezra. 2004-10-16 Paul Emsley * src/gtk-manual.c (on_display_control_mol_displayed_button_toggled): Toggle the active button when the display button is toggled. * src/c-interface.cc: (handle_read_draw_molecule_with_recentre): uses expand_molecule_space_maybe() now [a strubi-induced feature]. 2004-10-15 Paul Emsley * src/graphics-info-pick.cc: (symmetry_atom_pick): don't allow symmetry atom picking if the atoms are not pickable. * src/graphics-info.cc: (Imol_Refinement_Map): return the map number only if the map has not been closed - otherwise we search for a map as before. 2004-10-14 Paul Emsley * setup/coot.csh.in (COOT_REF_STRUCTS): added - Again. Likewise. * setup/coot.sh.in (COOT_REF_STRUCTS): added - Again! I can't believe it. * analysis/bfkurt.cc: (stats): numerical instability - with potential of sqrt of a negative number trapped. Also add occupancy weighting. 2004-10-13 Paul Emsley * src/callbacks.c (on_save_coords_dialog_save_button_clicked): Don't set the directory for this widget to be the directory of the last fileselection. Save files should by default now be saved in the directory in which coot was started - which is The Right Place. * macros/clipper.m4 (AM_PATH_CLIPPER): removed fftw/lib and mccp4 -L args, they are never used these days and the linker grumbles about them not existing. 2004-10-12 Paul Emsley * src/rama_plot.cc: converted abs to fabs [for SGI build]. * src/Makefile.am (density_score_by_residue_LDADD): Added compat libs [for SGI build]. 2004-10-08 Paul Emsley * Release 0.0.21 * src/c-interface-preferences.cc: Created. * ligand/dunbrack.cc: (GetResidue): return NULL if no rotamers available for this residue [type]. * src/graphics-info.cc: (generate_moving_atoms_from_rotamer): Added protection for d.GetResidue(irot) returning NULL; * src/molecule-class-info-other.cc: (auto_fit_best_rotamer): added protection for probabilities.size() == 0. * src/molecule-class-info.cc: (mutate): Added DeleteSelection. 2004-10-07 Paul Emsley * src/gtk-manual.c (rama_plot_mol_selector_activate): Used dynarama_is_diplayed_state to get the old widget, and if not null, raise [or map] it. We can have only one ramachandran plot per molecule now - Hope this fixes Maks's bug. * src/c-interface.cc: (dynarama_is_diplayed_state): created - so that we can check if the window exists before we create a new one. 2004-10-06 Paul Emsley * src/globjects.cc: (draw_hardware_stereo): fixed angle factor. Stereo reasonable now [but not shearing]. * src/molecule-class-info.cc: (make_map_from_cif_nfofc): added. In Virginia, Marcel wanted 2Fo-Fc and Fo-Fc reading from a cif file that had calculated structure factors [this was not possible before, strangely enough]. Also added state strings for this method. 2004-10-05 Paul Emsley * sequence-view/Makefile.am (AM_CXXFLAGS): Added GSL_CFLAGS. * ideal/Makefile.am (AM_CXXFLAGS): Moved GSL_CFLAGS to here. 2004-10-04 Paul Emsley * coords/Bond_lines.cc: (handle_MSE_case): created to handle non-bonded atoms that are in MSE. Check geometry params... 2004-09-30 Paul Emsley * src/graphics-info.cc: (check_dictionary_for_residues): change "Tr " to "Tr" [etc.] before checking. * geometry/protein-geometry.cc: (try_dynamic_add): Take account of 2 letter residue names. 2004-09-29 Paul Emsley * coords/mmdb.cc: (fix_nucleic_acid_residue_names): added to change nucleic acid residue names to match refmac monomer restraints type. 2004-09-28 Paul Emsley * macros/coot-windows.m4 (AM_MINGW_WINDOWS): created. Editted src/Makefile.am and sequence-view/Makefile.am to use this variable. 2004-09-27 Paul Emsley * src/rama_plot.cc: (setup_internal): fiddled with contour levels. 2004-09-26 Paul Emsley * src/c-interface-waters.cc: (wrapped_create_check_waters_diff_map_dialog): added warning dialog when missing maps or coordinates. * src/c-interface.cc: (fill_ligands_dialog_ligands_bits): also check for ligand molecule having less than 400 atoms. * src/graphics-info-defines.cc: (check_if_in_delete_item_define): now takes a GdkModifierType argument so that we can check if Cntrl was pressed and destroy the Delete Item accordingly. Also had to change check_if_in_range_defines() [passing the state], and c-interface_build's delete_atom* functions [passing the flag]. * src/c-interface.cc: (do_refine): Test that the imol_map has not been closed. Fixes crash. * src/graphics-info.cc: (refine): Test that the imol_map has not been closed. 2004-09-25 Paul Emsley * setup/coot.csh.in: Added SYMINFO to coot.csh.in [AGAIN! Argh!]. * setup/coot.sh.in : Likewise added SYMINFO [AGAIN!]. * ideal/simple-restraint.hh: removed [commented] time_diff() function. * ideal/simple-restraint.cc: (make_link_restraints): removed timeval variable usage. * coot-utils/coot-coord-utils.cc (intelligent_this_residue_mmdb_atom): Added [a copy of the one that is in molecule_class_info_t]. I guess that I should delete the molecule_class_info_t at some stage. * src/molecule-class-info.cc: (intelligent_next_atom): added DeleteSelection. 2004-09-22 Paul Emsley * mini-mol/mini-mol.cc: (unused_chain_id): A crash was causes when a fragment_id was "". Fixed. Maybe Ezra's problem. * Release 0.0.20 * src/callbacks.c (on_antialiasing1_activate): set the Yes radio button if anti-aliasing is on. * Removed chiral volumes from the Calculate menu. Reordered SSM Superpose. * src/graphics-info.cc: (fill_go_to_atom_residue_list): removed superfluous call to show residue_sub_tree means that [as per the default for gtk trees] the residue tree is now initiated collapsed. We shall see how they like that... :) * c-interface-validate.cc, geometry-graphs.cc, geometry-graphs.hh created. [Currently experimental] validation features [geometry, omega, B factor variance]. 2004-09-17 Paul Emsley * src/graphics-info-defines.cc (check_if_in_save_symmetry_define): created. Along with save_symmetry_coords_dialog, its button callbacks, c-interface-build.cc's setup_save_symmetry_coords(), save_symmetry_coords_from_fileselection(), save_symmetry_coords() provide saving of symmetry coordinates. 2004-09-16 Paul Emsley * ideal/simple-restraint.cc: (make_restraints): We set the restraints usage flag here [earlier than minimize()]. Now we don't randomly get [or fail to get] non-bonded contact restraints. * src/c-interface.cc: (mono_mode) and (hardware_stereo_mode): added null vbox protection. Removed spurious setting of the display mode in mono_mode() that messed up the following logic and results in the internal variable representing the GL widget to be different to the actual GL widget. * ideal/simple-restraint.cc: added alt conf tests to the middle of add_bonds, add_angles, add_planes. This helps geometry graphs speed up. * coords/Bond_lines.cc: (construct_from_atom_selection): added Model test when bonding - for NMR structures. 2004-09-15 Paul Emsley * ideal/simple-restraint.cc: (make_flanking_atoms_restraints): enable the DeleteSelection(). * src/c-interface.cc: (handle_read_draw_molecule_with_recentre): created. handle_read_draw_molecule() is now a wrapper to this. * (add_recentre_on_read_pdb_checkbutton): created - now we can optionally not recentre on reading new coordinates. * src/graphics-info.cc: (fill_go_to_atom_residue_list): Some tinkering with tree items and subtrees. 2004-09-14 Paul Emsley * src/pick.cc: (unproject) remove casting to GLdouble * src/main.cc: (setup_symm_lib): reworked the symmetry error reporting code. * setup/coot.sh.in : Added COOT_RESOURCES_DIR and COOT_RESOURCES_FILE as per the suggestion of Christian Biertuempfel. * src/molecule-class-info-other.cc: (split_residue): removed incorrect usage of delete [] residue_atoms after GetAtomTable() [Fixed Tracy's Bug, I think]. 2004-09-08 Paul Emsley * src/molecule-class-info.cc: (unused_chain_id): take out the 'while' as per Ezra's suggestion. * surface/Makefile.am (INCLUDES): Change the order to put the local includes before the clipper cxxflags. 2004-09-04 Paul Emsley * Release 0.0.19 * sequence-view/sequence-view.cc: (setup_canvas): Did some tinkering with the canvas scroll limits. It should be better placed now for most things - but still doesn't work for ribosome particle and I don't know why. * src/c-interface.cc: (set_map_line_width) and (map_line_width_state): created to allow the changing of the width of the denity mesh lines. * src/graphics-info.cc: (on_go_to_atom_residue_tree_selection_changed): So we have a tree in fill_go_to_atom_residue_list now. Several tree functions created - which obsoletes list functions. The collapsing doesn't work properly and it doesn't fill properly using ribosome particle [grr]. Don't know why. * src/callbacks.c (on_antialias_dialog_yes_radiobutton_toggled): Added anti-aliasing GUI, now that it works. 2004-09-03 Paul Emsley * src/molecule-class-info.cc: (read_ccp4_map): add ".msk" as an acceptable CCP4 map extention. * src/graphics-info.cc: (set_do_anti_aliasing): add glBlendFunc() on the suggestion of Stuart McNicholas. Antialiasing works now for me with no performance [frames/sec] degredation. Density lines look a bit strange due to blending with background. 2004-08-31 Paul Emsley * sequence-view/sequence-view.cc: "fixed" -> fixed_font variable - which gets changed [or should do] to "monospace" if we are in MINGW windows. 2004-08-24 Paul Emsley * coot-utils/coot-map-utils.cc (map_score): fix initialization of variables [thanks Ezra]. * src/globjects.cc (key_press_event): Added view Z translation to keypad 3 and . * src/molecule-class-info.h: we don't have sensible refmac parameters if this is a closed map. * setup/coot.csh.in and coot.sh.in: Further tinkerage. Now we only need to set the COOT_PREFIX line. 2004-08-21 Paul Emsley * src/molecule-class-info.cc: (draw_unit_cell_internal): label the axes, A, B, C. 2004-08-19 Paul Emsley * ideal/pepflip.cc: (pepflip): extensive changes the atom selection and deletion and function arguments to account for alt confs. * Ramachandran Plot now moved to Validate menu. * src/c-interface-waters.cc: (wrapped_create_unmodelled_blobs_dialog): along with (execute_find_blobs_from_widget) and (execute_find_blobs) provide blob validation feature. * src/globjects.cc: In line with sigma level of input map changes, the default level is changed to 1.0 sigma - which is sensible for 2FoFc maps, but not, perhaps, for difference maps. 2004-08-18 Paul Emsley * src/c-interface.cc: (filtered_by_glob): Apply Ezra's fix for correct map globbing. * src/molecule-class-info.h: removed reset_draw_vecs() function. * src/globjects.cc: (glarea_motion_notify): removing "changin state" debuging line. * src/graphics-info-pick.cc: (move_moving_atoms_by_shear_internal): use new/delete [] not GNU extension for variable d_to_moving_at. * src/xmap-utils.cc: (map_density_distribution): move to new/delete [] usage not GNU extension for variable bin. * src/molecule-class-info.cc: (insert_coords_internal): remove shadowing of asc_chain variable [ChBa bug]. * coords/Bond_lines.cc: (do_Ca_plus_ligands_bonds): remove GNU style dynamic memory allocation for ligand_atoms_selection: replace with new and delete []. * Multiple Makefile.am patches for out-of-tree building from Ezra Peisach. 2004-08-17 Paul Emsley * src/rama_plot.cc: (setup_internal): changed ramachandran levels to something less liberal. * src/c-interface.cc: (new_close_molecules) and (wrapped_create_new_close_molecules_dialog): created. Provide a new dialog that's much better for multiple molecule closing [which is what real crystallographers tend to do]. * src/globjects.cc: add_alt_conf_show intermediate atoms now set to 0 [fixes JPT/FV usability problem]. * src/callbacks.c (on_phs_cell_choice_ok_button_clicked): added have_unit_cell protection. Fixes a crash. 2004-08-16 Paul Emsley * src/graphics-info.cc: (fill_rotamer_selection_buttons): Change to radio buttons, not normal buttons. We can see the "active" rotamer now. * src/c-interface.cc: (execute_find_blobs): created - so you don't need to find waters to get this interesting info. Another validation function. * high-res/Makefile.am (tracehighres_LDADD): applied Ezra's patch to link with coot-compat too. * src/c-interface.cc: (safe_python_command): pass a const char *, not a string. * geometry/protein-geometry.cc: when trying CLIB, don't put an extra "lib" in the string. * setup/coot.sh export COOT_STANDARD_RESIDUES too. * src/graphics-info.cc: (rot_trans_adjustment_changed): Rotate a bit more, so we can get more than 100 degree rotation. Fixes KD problem. (set_bond_thickness_intermediate_atoms): created [along with c-interface]. * src/globjects.cc: return TRUE for draw() and draw_stereo(), rather than nothing. 2004-08-11 Paul Emsley * ligand/ligand.cc: (find_clusters): change the cut-off level to be n sigma of the input map, not n sigma of the map after masking. 2004-08-10 Paul Emsley * db-main/db-main.cc: ref_struct_dir should have a coot dir after $prefix/share [DATADIR] and before "reference-structures". 2004-08-04 Paul Emsley * ideal/simple-restraint.cc: replaced several pow()s. 2004-08-01 Paul Emsley * Release 0.0.18 * src/globjects.cc: (glarea_motion_notify): Add code to rotate view for in_edit_chi_mode_flag with the Ctrl key. * src/globjects.cc: (gl_extras): If we get a widget when we are trying hardware stereo set the display_mode flag [to be used in the draw method]. 2004-07-31 Paul Emsley * src/graphics-info.cc: (renumber_residue_range_molecule_menu_item_select): together with renumber_residue_range_chain_menu_item_select(), fill_renumber_residue_range_dialog(), fill_renumber_residue_range_internal() and c-interface-build's renumber_residues_from_widget() and wrapped_create_renumber_residue_range_dialog() provide the GUI inteface to residue range renumbering. 2004-07-30 Paul Emsley * src/mtz-bits.c: (get_f_cols) and (get_phi_cols) and (get_weight_cols): the malloc brackets allocating v[i] were misplaced causing random crashes. 2004-07-29 Paul Emsley * coords/Bond_lines.cc: (Bond_lines_container constructor for environment distances): fixed typo in ch2 contact id - so that now atoms in differrent chains will be given distances reguardless of residue number [fixes occasional missing environment distance to other atom in a different chain]. 2004-07-28 Paul Emsley * src/molecule-class-info-other.cc (last_residue_in_chain): created for use with add_OXT GUI. * src/graphics-info.cc: (fill_add_OXT_dialog_internal) created. Along with add_OXT_chain_menu_item_activate, fill_chain_option_menu, add_OXT_molecule_item_select and c-interface-build's apply_add_OXT_from_widget, wrapped_create_add_OXT_dialog it provides GUI for add_OXT functionality. * doc/coot.tex: Applied Ezra Peisach's typo patches. 2004-07-27 Paul Emsley * Release 0.0.17 * Release 0.0.16 * ligand/dunbrack.cc: (GetResidue): fix it again. * Release 0.0.15 * ligand/dunbrack.cc: (GetResidue): fix the delete of ordered_residue_atoms_ppcatom. [Rotamer problem fixed] 2004-07-26 Paul Emsley * Release 0.0.14 * src/c-interface.cc: (wrapped_create_bond_parameters_dialog): created. Along with graphics_info_t::fill_bond_parameters_internals() add Bond Parameters dialog functionality. Note: when adding menu items, the active item can be set only after all the items are added - not during the process. * src/molecule-class-info.cc: (handle_read_ccp4_map): added save_state_command_string codes [the reading of ccp4 maps is now saved in the state file]. 2004-07-25 Paul Emsley * src/command-line.cc: (parse_command_line): add --help argument. * geometry/protein-geometry.cc: (init_refmac_mon_lib): Ezra Peisach noted that the result of stat() should be tested before buf's content is examined. Fixes potential crash/error on reading refmac dictionary when file not found. * src/callbacks.c (on_background_colour1_activate): Created. This function is used to fix, at long last, the problem of the background colour menu radio items [used gtk_check_menu_item_set_active]. 2004-07-21 Paul Emsley * ligand/chi-angles.cc: moved coot::operator<< for simple_rotamer here [from dunbrack.cc]. * setup/coot.csh: make COOT_REFMAC_LIB_DIR be in share/coot/lib * setup/coot.sh: make COOT_REFMAC_LIB_DIR be in share/coot/lib * src/graphics-info-pick.cc: (move_moving_atoms_by_shear_internal): use const int d_array_size to dimension d_to_moving_at array. 2004-07-20 Paul Emsley * src/graphics-info.cc: (fill_option_menu_with_undo_options): added has_model() protection. Stops undo option menu overing options of closed molecules. * src/molecule-class-info-other.cc:(renumber_residue_range): created. Also c-interface wrapper. No GUI yet. (copy_and_add_residue_to_chain): filled [from stub]. Not tested. 2004-07-19 Paul Emsley * src/command-line.cc: (parse_command_line): added --stereo argument to turn on hardware stereo. * src/globjects.cc: (draw_hardware_stereo) created. Also draw() was renamed to draw_mono and an extra argument was added. draw_hardware_stereo() calls draw_mono() twice. * src/main.cc: () Don't do most things if gl_extras returns null. * src/globjects.cc: (gl_extras): Add an extra arg: try_hardware_stereo_flag. Fiddle with the attribute list if trying stereo. Don't do most things in this function if glarea was created null. * src/command-line.h: added hardware_stereo flag to class. More stereo support. * src/c-interface.cc: mono_mode() and hardware_stereo_mode() added. Starting stereo support. * setup/coot.csh SYMINFO: added syminfo. The default place for syminfo.lib is in PKGDATADIR. However, this is not available when users do a binary install. So, we set SYMINFO in the setup file and coot will use that [instead of failing to find it where in the non-existant directory where it was originally built]. Fixes problem with non-existant symmetry library in binary install. * setup/coot.sh SYMINFO: added syminfo. See above. 2004-07-17 Paul Emsley * src/c-interface-info.cc: (output_residue_info): [call] reset to zero size the residue edits info vector. Fixes the [ignored] residue info edits problem. * coords/mmdb-extras.cc: (get_first_atom_with_atom_name): Fix the format of the function definition [from Charles Ballard]. * src/molecule-class-info.cc: (change_contour): use the max contour level to stop the changing of the contour level over the maximum of the map. * src/xmap-utils.cc: (map_density_distribution): set the min and max of the map density. 2004-07-16 Paul Emsley * src/c-interface-build.cc: (run_refmac_real): fix problem of directory/filename when no ccp4i project set. Also rewrote so that we use a vector of strings that gets converted to an executable string just before execution [Python support]. * src/gtk-manual.c: (update_map_colour_menu_manual): remove a strlen debugging line. 2004-07-10 Paul Emsley * src/graphics-info.cc: (set_moving_atoms): created. So that molecule_class_info_t function split_residue() can create a moving atom object [intermediate atoms are enabled in this case]. Fixes crash, fixes alt conf back to how it used to be [with intermediate atoms, not drop straight into rotamer]. 2004-07-09 Paul Emsley * src/callbacks.c (on_rotate_translate_obj_cancel_button_clicked): removed graphics_unsetup_rotate_translate_buttons() call and the function and its declarations. * src/c-interface.cc: (valid_labels): fixed so that the frees are commented. Otherise we get a "double free" [so says Paris]. I don't understand why. Auto-open with invalid labels no longer causes a crash. 2004-07-08 Paul Emsley * geometry/protein-geometry.cc: (init_standard): make the default place be DATADIR/coot/lib/data/monomers/list [where DATADIR is PREFIX/share] [i.e. it is moved into package_data_dir]. Use CCP4 only if there is no other alternative. 2004-07-04 Paul Emsley * src/graphics-info.cc: (add_cb_to_terminal_res): Added some error checking and fixed the looping issues. Now no crash when also adding 2nd residue in add terminal residue. (execute_rigid_body_refine): Added missing definition of chain in the case of auto_rangle_flag true. Fixes crash, I hope. * src/c-interface.cc: (average_temperature_factor) return a value. (median_temperature_factor): return a value. 2004-07-03 Paul Emsley * Release 0.0.13 * src/molecule-class-info.cc: (make_backup): use __WIN32__ defines to stop the addition of .gz and compression of backup files. And the time in the filename. * macros/glut.m4 (AM_PATH_GLUT): Added cygin support for freeglut linking. 2004-07-02 Paul Emsley * Release 0.0.12 * src/command-line.cc (handle_command_line_data): remove not running script output. 2004-07-01 Paul Emsley * setup/coot.csh: and coot.sh move reference-structures to prefix/coot/share. 2004-06-29 Paul Emsley * src/c-interface.cc: (fill_option_menu_with_coordinates_options): use dotted_chopped_name(). * src/molecule-class-info.cc: (dotted_chopped_name): created. * Release 0.0.11 2004-06-28 Paul Emsley * Mutate Sequence work [which calls a scheme [mutate.scm] function]. Now available in the gui. * src/gtk-manual.c: (update_sequence_view_menu_manual): and (update_ramachandran_plot_menu_manual): added extra argument to pass the name - so that we can have a name on these menu items too. 2004-06-27 Paul Emsley * Makefile.am (install-data-local): typo scrdir to srcdir for scheme files. * geometry/protein-geometry.cc: (try_dynamic_add): change CCP4_LIB to CLIB - needed for CCP4 v5.0. * src/c-interface-build.cc: (make_backup): externally make a backup. (set_have_unsaved_changes): externally set have unsaved changes. * src/molecule-class-info.h: Add turn_on_backup function. 2004-06-25 Paul Emsley * Makefile (install-data-local): Add a fi for scheme's outside if. * src/graphics-info.cc: Function to enable anti-aliasing. Doesn't seem to do the job on this mac... it just makes the bonds/density lines thicker. 2004-06-24 Paul Emsley * Makefile.am (install-data-local): Added scheme files to coot distribution and added code here to install the files. 2004-06-24 Paul Emsley * src/molecule-class-info-other.cc: (map_chains_to_new_chains): after far too long, I've got a version that I'm happy with. Now doesn't hang. Merge molecules made available from the gui. * Auto-read MTZ file work. 2004-06-23 Paul Emsley * setup/coot.sh.in export DYLD_LIBRARY_PATH too! (GUILE_LOAD_PATH): Add guile/site [for goosh]. At long last! 2004-06-22 Paul Emsley * coot-utils/peak-search.cc: (mask_around_coord): copy, paste and fiddle with the function from ligand class. (mask_map): add coordinate masking function to peak_search. * high-res/trace-high-res.cc (main): Added the option to use weights. (main): Use new masked peak searching of peak_search function. * src/graphics-info.cc: (show_select_map_dialog): pre-set the default [refinement] map to the top of the list. 2004-06-18 Paul Emsley * mmtz-extras/mmtz-extras.c: (get_f_phi_columns): Add in anomalous data too. * mmtz-extras/mmtz-extras.h: Added anomalous data to f_phi_columns_t. * src/callbacks.c (on_column_label_ok_button_clicked): Added anomalous label logic [somewhat contorted - due to mix of mtz f column and widget menu item index mixing]. * src/molecule-class-info.cc: (test_label_symm_atom): apply has_model test. 2004-06-16 Paul Emsley * src/c-interface.cc: (fill_ligands_dialog): add the setting of the "Mask Waters?" checkbutton[s]. 2004-06-15 Paul Emsley * src/graphics-info.cc: (imol_for_skeleton): changed to match Imol_Refinement_Map() model [i.e. is set if only one map present]. * src/callbacks.c (on_dynarama_cancel_button_clicked): and (on_dynarama_ok_button_clicked) removed the call to set_dynarama_is_displayed(0), because this is done [again otherwise] now that we have the destroy window callback. * src/rama_plot.cc: (add_phi_psi): added DeleteSelection. Quite a bit faster now for big molecules. 2004-06-14 Paul Emsley * src/molecule-class-info-other.cc: split_residue and its siblings moved from graphics-info.cc to here - where they should be. Added extra code so that by default rotamers are run immediately after Add Alt Conf. A good thing. 2004-06-12 Paul Emsley * src/c-interface.cc: (median_temperature_factor): and (average_temperature_factor) added interfaces to utility functions. * geometry/protein-geometry.cc: (have_dictionary_for_residue_type): Added try_dynamic_add - not a const function any more. * coot-utils/coot-coord-utils.cc: (median_temperature_factor): added. (average_temperature_factor): Added. 2004-06-11 Paul Emsley * src/globjects.cc: (rotate_rgb): 2004-06-10 Paul Emsley * coords/Bond_lines.cc: (do_Ca_bonds_internal): added bonds_size_colour_check() before addBond(). * src/graphics-info.cc: (show_select_map_dialog): use the option map filler which sets the default menu item too. (update_go_to_atom_window_on_changed_mol): changed if (go_to_atom_imol == imol) to if (1) (fill_option_menu_with_map_options): created - this version has also is passed an int that is the molecule for the default position. 2004-06-09 Paul Emsley * src/callbacks.c (on_show_symmetry_ok_button_clicked): Added the analysis of the new checkbuttons [symmetry colouring, symop colouring, symmetry whole molecule and symmetry expanded labels ]. 2004-06-08 Paul Emsley * src/callbacks.c (on_dynarama_window_destroy): Glade created signal. Added for people who close this widget with window manager, not buttons. * src/graphics-info.cc: (execute_rigid_body_refine): rearranged code for case of auto_rangle_flag being true. 2004-06-07 Paul Emsley * src/c-interface-info.cc: (output_residue_info): added model? protection. 2004-06-04 Paul Emsley * src/graphics-info.cc: (wrapped_check_chiral_volumes_dialog), (on_bad_chiral_volume_button_clicked): created for bad chiral atom vbox dialog. OK, we have chiral volume analysis - hooked into the Calculate menu. * geometry/protein-geometry.cc: (get_monomer_chiral_volumes): created [used in bad chiral testing]. * src/molecule-class-info-other.cc (bad_chiral_volumes): created. 2004-06-01 Paul Emsley * db-main/db-main.cc: (fill_with_fragments): moved to n_filled_residues() usage and a few other things. Makes the "oops: zero atoms for residue 1 in molecule number 27" [etc] dissappear. * GLOBAL change of minimol's fragment n_residues() to max_residue_number(). Also found many loops over residues of a fragment and set their start point to min_res_no() replacing 1. 2004-05-30 Paul Emsley * coords/Bond_lines.cc: (do_Ca_bonds_internal): Add altconf check so we don't get wrong altconf bonding. 2004-05-28 Paul Emsley * ligand/ligand.cc: (mask_map [short int]): Change the water logic. * src/callbacks.c (on_symmetry_colour_patch_button_clicked): set the colour of the symmetry [at long last!]. * src/molecule-class-info.cc: (set_symm_bond_colour_mol_rotate_colour_map): put the colour map rotation outside the colour merge - so that symmetry colours are always rotated [when graphics_info_t::symmetry_rotate_colour_map_flag is set]. 2004-05-27 Paul Emsley * geometry/protein-geometry.cc: (standard_protein_monomer_files): added MSE [selenomet]. * src/mtz-bits.c: (manage_column_selector): set the phases to -1 initially. * src/callbacks.c (on_column_label_ok_button_clicked): added test for unset [-1] phi col - print an error message do nothing in such a case. * coot-utils/trim.cc: (trim_molecule_by_map): created [namespace util]. 2004-05-25 Paul Emsley * src/molecule-class-info.cc: (draw_molecule): added has_model() protection. (draw_skeleton): added has_map() protection. (draw_map_unit_cell): added has_map() protection. (anisotropic_atoms): added has_model() protection. These protections may make close molecule go away [for good this time?]. All the molecule functions of globject.cc's draw have protection now. * coords/Bond_lines.h: (bonds_size_colour_check): expand bonds if we need to. 2004-05-24 Paul Emsley * src/graphics-info-state.cc: (save_state): save 0-coot.state.py if we are using python. 2004-05-19 Paul Emsley * src/graphics-info.h: added symmetry_atom_labels_expanded_flag so we can have "-X,Y+1/2,-Z" and the like in an atom label - this is just the flag to do that - not the implementation. * src/c-interface.cc: (set_symmetry_whole_chain): Do we want the whole chain of a symmetry related molecule, rather than just a sphere of its atoms? * src/molecule-class-info.h: move symmetry_bonds_box to vector of graphical_bonds_containers [so that we can have colour-by-symop]. * high-res/sequence-assignment.hh: created [along with sequence-assignment.cc of course]. 2004-05-18 Paul Emsley * coords/Bond_lines.cc: (do_Ca_bonds_internal): make the bond colour use the commented [strangely] code for chain colouring rather than atom type colouring [which is how it used to be]. (addSymmetry_vector_symms): created, a wrapper round individual symmetry operators, so that we return an entity that can be coloured by symmetry operator. * src/c-interface.cc: Add CCP4_SCR to ccp4i project directories. 2004-05-17 Paul Emsley * src/c-interface.cc: (set_background_colour): redraw after setting the colour. 2004-05-14 Paul Emsley * src/molecule-class-info.cc: (handle_read_draw_molecule): added test for initially unset bonds type [and set it to normal if unset] - we do this because undo does a handle_read_draw_molecule() which otherwise reset the bond type to normal. 2004-05-13 Paul Emsley * Release 0.0.8 * mini-mol/mini-mol.cc: (setup) Don't try to store residues with negative or 0 residue numbers [which caused a crash]. Print out a warning instead. 2004-05-11 Paul Emsley * src/molecule-class-info.cc: (close_yourself): set the number of labels and symmetry labels to 0. (label_atoms): put in has_model() protection. No more labels for closed molecule. (test_label_symm_atom): put in range protection to atom index. 2004-05-08 Paul Emsley * src/graphics-info-defines.cc: (check_if_in_regularize_define): Added a call to add/remove a label when an atom is clicked [and a redraw]. Visual feedback. * src/graphics-info-defines.cc: (check_if_in_refine_define): Ditto above. 2004-05-07 Paul Emsley * src/c-interface.cc: (run_command_line_scripts): created. Using new data member of graphics_info_t [command_line_scripts]. We can now run scripts from the command line. * src/c-inner-main.c: (c_inner_main): moved run_state_file_maybe() here. Also run_command_line_scripts() here. 2004-05-06 Paul Emsley * high-res/Makefile.am (INCLUDES): Add compat [bug found when trying to compile on Mac OS X]. * setup/coot.csh: moved the place of the reference structures. Now in $prefix/share/coot/reference-structures * setup/coot.csh: Ditto. * src/molecule-class-info-other.cc: (assign_fasta_sequence): 2004-05-05 Paul Emsley * src/molecule-class-info.cc: (set_skeleton_bond_colour): moved to this class - deleted from globject.cc. Added colour rotation. * src/graphics-info.cc: (fill_option_menu_with_coordinates_options_internal): created. There is a wrapper without the set_last_active_flag [set to 0] which is how the old function worked. The update_go_to_atom_window_on_new_mol() now calls this function directly rather than going through a wrapper. The result is that when a new molecule is read and the Go To Atom Window is up, then the option menu moves to the new molecule [and the residue list too, of course]. * src/c-interface.cc: (free_memory_run_refmac): put protection round usage of gtk_object_get_user_data(active_item) - we don't want to do that if the option_menu is empty and active_item is therefore null. 2004-05-04 Paul Emsley * src/graphics-info-state.cc: (save_state_file): add sigma step info if appropriate. * src/molecule-class-info.cc: (install_model): add extra argument display_in_display_control_widget_status, so that "terminal residue" doesn't appear there. (get_map_contour_sigma_step_strings): created so that we can pass it's value to the state saver. * macros/mmdb-ssm.m4 (AM_WITH_MMDBSSM): If there is no ssm, let it say so [result: no]. * coot-utils/Makefile.am (libcoot_utils_la_SOURCES): moved peak-search here from ligand, so that high-res doen't depend on ligand lib [because ligand lib depended on high res]. * high-res/coot-atom-graph.cc (peptide_search): experimenting... 2004-05-02 Paul Emsley * src/callbacks.c (on_single_map_sigma_checkbutton_toggled): created. Now there is a property of maps that so that it can be contoured by sigma. Auxillary functions set_contour_by_sigma_step_by_mol(), set_contour_by_sigma_step() and variables in molecule_class_info_t [contour_by_sigma_flag, contour_sigma_step]. 2004-05-01 Paul Emsley * src/callbacks.c (on_libcheck_monomer_ok_button_clicked): handle_get_libcheck_monomer_code needs the entry widget, not the top-level. (on_libcheck_monomer_ok_button_clicked): No need to destroy widget, that's done in handle_get_libcheck_monomer_code(). * src/c-interface.cc: (handle_get_libcheck_monomer_code): the widget is "libcheck_monomer_dialog" not "accession_code_window" * mmtz-extras/mmtz-extras.c: (mmtz_get_column_headers): malloc one more column [ncol+1] prevents valgrind write error. Fixes KD problem? [Can't see how, to be honest]. * src/graphics-info.cc: (make_moving_atoms_graphics_object): regularize_object_bonds_box.clear_up() added - valgrind saying we are loosing 200K here. 2004-04-29 Paul Emsley * Release 0.0.6 * src/main.cc (main): uncomment setup_symm_lib() call. Grr - must have been left in from testing. New release required then. * Release 0.0.5 * db-main/Makefile.am (testdbmain_LDADD): top_scrdir not top_scrdir. [not enough testing before putting release on web-site - rushing to go to Trossachs]. 2004-04-27 Paul Emsley * Release 0.0.4 * db-main/db-main.cc: Add a default place DATADIR/reference-structures that can be over-ridden by an environment variable. Non-so-nimble footwork sorting out the directory and stating added. Also fixed up Makefile.am here to add coot-utils. 2004-04-22 Paul Emsley * src/globjects.cc (key_press_event): When in baton mode, a Cntl-Z is baton_build_delete_last_residue(). * src/molecule-class-info.cc: (delete_atom): Add altconf argument - the mind boggles how I didn't include this before now... * src/callbacks.c (on_close_molecule_close_button_clicked): Don't destroy the widget when close molecule button is hit [easier now to close lots of molecules]. * Makefile.am (install-data-local): install syminfo.lib. * src/main.cc: (setup_symm_lib): setenv SYMINFO if it is not set already and point it to pkgdatadir/syminfo.lib. * src/callbacks.c (on_libcheck_monomer_ok_button_clicked): Add handle_get_libcheck_monomer_code() call, so that this button actually works now [oops :-)]. * src/molecule-class-info.cc: (map_fill_from_mtz): removed Map_stats() usage, replaced with map_density_distribution() usage [12ms for statistics now - somewhat better]. * src/molecule-class-info.cc (Have_unsaved_changes_p): return 0 when there is no model [stops maps and closed molecules returning true [no method to save maps yet [not even sure there should be]]]. 2004-04-18 Paul Emsley * Release 0.0.3 * coords/Bond_lines.cc: (atom_colour): Use DISULFIDE_COLOUR not DISPHIDE_COLOUR [in the header also]. When DISPHIDE_COLOUR return green [Fixed non-sulfur-coloured disulphide bonds now]. * src/globjects.cc (key_press_event): Added key bindings for zoom and clipping. 2004-04-17 Paul Emsley * src/molecule-class-info.cc: (get_term_type): can now return "MC" [middle residue treat as C term] and "MN" [middle residue treat as N term] depending on where the user clicked. Fixes EJD's add terminal residue bug. * ligand/residue_by_phi_psi.cc: (best_fit_phi_psi): Here and everywhere else in the class where we test for "C", the test now included "MC". 2004-04-16 Paul Emsley * mini-mol/mini-mol.cc (set_cell_symm): moved mmdb_cell to std::vector usage so that implicit copy operator works on a minimol. * ligand/ligand-extras.cc: (flood): created. No mixing and messing with water fit now. * Release 0.0.2 * src/c-interface.cc: (close_molecule): remove void * usage. Does this help? 2004-04-15 Paul Emsley * src/graphics-info.cc: (create_mmdbmanager_from_res_selection): added extra arg so that we don't confuse mmdbmanager from altconf split with that from refinement [the whole-residues rules are different]. Closes JPT's altconf split bug [but not the feature requests]. * setup/coot.sh.in move prefix before the no-modifications line. * setup/coot.csh.in: move prefix before the no-modifications line. * src/molecule-class-info.cc: (unused_chain_id): return a status too so that we know if the chain is usable. No more crashing when trying to add 27th chain. Extended to lowercase chain usage. * src/c-interface.cc: (run_script): removed macroed code and instead choose the script-running function based on extension [everything is scheme unless it ends in ".py"]. Still python SWIGged functions not available however. [Might need some on-the-fly patching]. * src/main.cc (main): Put PYTHON macroed code before GUILE, so that python is initialized when we have --with-guile --with-python, which deals with "Fatal Python error: PyThreadState_Get: no current thread". * src/molecule-class-info.cc: (map_fill_from_mtz): Added GLUT timers round MTZ to map conversion. Now we can get some numbers for how fast is Macintosh. * src/Makefile.am (INCLUDES): Added GSL_CFLAGS GSL_LIBS properly [as set by configure] - not my made-up guess. 2004-04-14 Paul Emsley * src/globjects.cc (key_press_event): Added keyboard equivalents for rotations [for Luca]. * coords/Bond_lines.cc (construct_from_atom_selection): to this and several other routines was added atom_colour_type argument. The atom colour type in the centre of the loop now calls the member function atom_colour(). (do_colour_sec_struct_bonds): created using this system - also (do_Ca_plus_ligands_colour_sec_struct_bonds) [which looks quite cute - nice one Stuart]. * Src/c-interface.cc: (handle_read_ccp4_map): added extra arg is_diff_map_flag which takes the value from the new map filefilter checkbutton. * src/molecule-class-info.cc: (change_contour): Fixed contour level logic for difference map. 2004-04-10 Paul Emsley * high-res: created. Just playing for now. 2004-04-09 Paul Emsley * src/c-interface.cc: (close_molecule): Added extra trap for null *imol [should never happen]. Does this catch the close molecule crash bug? * src/molecule-class-info.cc: (read_ccp4_map): Return 0, not nothing - how could this bug have existed for so long? Mind boggling. No longer random apparent failure to read map. 2004-04-01 Paul Emsley * src/graphics-info.cc: (geometry_objects): brightened the line and label colour. * src/molecule-class-info.cc: (label_symm_atom): Brighten symmetry label colour. * src/molecule-class-info.cc (get_map_contour_strings): and (set_contour_level), with changes in c-interface.h and graphics-info-state.cc (save_state_file): allow the setting/saving of the map contour level. * Release 0.0 2004-03-30 Paul Emsley * Release coot-0.0.0-pre-9 * src/c-interface-superpose.cc: (execute_superpose): reordered macros. * ligand/find-ligand.cc: Added getopt portability gubbins. * ligand/find-waters.cc: Likewise. 2004-03-29 Paul Emsley * macros/glut.m4 (AM_PATH_GLUT): Added /usr/X11R6 args to GLUT prefixes for powerpc-apple-darwin*. * src/c-interface-superpose.cc: (superpose): Also (execute_superpose) (wrapped_create_superpose_dialog) created for SSM superposition interface. Nice. 2004-03-27 Paul Emsley * src/molecule-class-info.cc: (full_atom_spec_to_atom_index): Deal with the case that selection with atom name "*HO2" finds all the atoms in the residue. 2004-03-26 Paul Emsley * src/molecule-class-info.cc: (name_for_display_manager): created. Used to give a name of the molecule to the Display Manager. We can optionally truncate the pathsnames. (stripped_save_name_suggestion): created [for use with save fileselection. * src/globjects.cc: change rotamer_fit_clash_flag default to on (1). 2004-03-25 Paul Emsley * src/c-interface.cc: (fill_option_menu_with_coordinates_options): Changes to the active menu item. If the molecule is not being draw, don't allow it to be the default [active] molecule [unless all molecules are undisplayed]. Concomitant test in graphics-info_t::go_to_atom_residue(). * src/main.cc (main): If no symmetry pop-up a dialog saying so. 2004-03-24 Paul Emsley * src/graphics-info.cc: (do_rot_trans_adjustments): The widget for rotations and translations was changed to use hscales. This functions sets the adjustments and the callback [which was pretty much the same as rot_trans buttons code except we added a float array to store the previous hscale adjustments. * src/graphics-info-state.cc: (save_state_file): diff_map_iso_level_increment uses function that uses specified dec pl. 2004-03-14 Paul Emsley * src/c-interface.cc: (fill_go_to_atom_window): Added gtk_container_set_focus_vadjustment call to connect the scolled window adjustment to the residue_list adjustment. Bingo! Scrolling residue list on synthetic residue selction! Woohoo! [At last]. * coords/mmdb.cc: (get_atom_selection): Added MMDBF_IgnoreRemarks to MMDB reading flags. 2004-03-12 Paul Emsley * ligand/ligand.cc: (cluster_ligand_size_match): Changed limit for big ligand vs small density from 10.0 to 7.0 2004-03-11 Paul Emsley * ligand/ligand.cc: (find_clusters): Completely re-written. Introduced new concept: stl::queue, the use of which avoids requiring recursion [trace_along() no longer required, therefore]. 2004-03-10 Paul Emsley * Menubar updated: Measures changed so that distances and angles creates a pop-up. Pop-up toggle buttons for angles and distances. * src/c-interface.cc: (handle_filename_filter): Created - now we have filename filter - "hooray!" say the users. Called after a "Return" in the entry's on_filename_filter_key_press_event(). * src/c-interface.cc: (pre_directory_file_selection): created - used by above. 2004-03-04 Paul Emsley * geometry/protein-geometry.cc: (comp_torsion): If this has an id that contains "CONST" let's not include it in variable torsions. 2004-02-28 Paul Emsley * coords/Bond_lines.cc: (do_normal_bonds_no_water): Created. (add_ligand_bonds): which is called by (created.do_Ca_plus_ligands_bonds): [created]. Now we have no_water and ca+ligand representations. 2004-02-27 Paul Emsley * Release 0.4.84. I've made lots of changes - many undocumented to fix the issues of Tue Feb 17 16:09:16 GMT 2004. 2004-02-23 Paul Emsley * src/molecule-class-info.cc: (unalt_conf_residue_atoms): Where we delete conformation B, conformation "A", the only one remaining should be renamed with altconf "". Called from delete_residue_with_altconf(). * src/graphics-info.cc: (find_atom_index_from_goto_info): Added DeleteSelection(). Use UDD to find atom index. * (intelligent_near_atom_centring): set also the altLoc from the intelligent atom return index. * coords/Bond_lines.cc: (do_disulphide_bonds): Added altLoc test. * src/globjects.cc: (do_screen_z_rotate): created. Called from mouse motion callback (glarea_motion_notify). Z-rotation on shift-rightmouse. 2004-02-22 Paul Emsley * ligand/residue_by_phi_psi.cc: (get_connecting_residue_atoms): updated to account for the fact tht if there are 2 atoms in a residue with the selected name [which happens if there is an altconf], then GetAtom() returns NULL. So we do some rather long-winded altconf testing. We can now attach a terminal residue to a residue that has an altconf. * src/graphics-info.cc: (copy_mol_and_refine): make it return a short int rather than void so that we know if we have found restraints. Likewise copy_mol_and_regularize. (create_mmdbmanager_from_res_selection): For flanking residues, set whole_res_flag to 1 so that alt confs of previous atoms are found even if "" is not. * ideal/simple-restraint.cc: (make_restraints): only calculate NBC restraints if there were restraints already [no more blowing up minimal description ligands]. (construct_non_bonded_contact_list): filter_non_bonded_by_distance() changed to 8.0. Will [hopefully] stop crashes from atoms that move big distances in pull-refine/regularize. * coords/Bond_lines.cc: (construct_from_atom_selection): only add udd_handle for "found bond" if we actually draw the bond [was failing in Florences case of a split water - close to the alt conf of itself]. Also changed the if (1) to the commented are_different_atom_selections. Not sure why it had been commented [testing some other thing?]. 2004-02-21 Paul Emsley * ideal/simple-restraint.cc: (is_nucleotide): added. Called by functions that previously presumed that the link type was "TRANS". * sequence-view/sequence-view.cc: (setup_canvas): set the usize_y of the canvas according to the number of chains [n_chains added to function args]. 2004-02-20 Paul Emsley * src/graphics-info-state.cc: (save_state_file): Added cif dictionary reader. 2004-02-19 Paul Emsley * doc/coot.tex (section{Rotate/Translate Zone}): Updated - now with control click info and alt conf info. * src/graphics-info.cc: (execute_rotate_translate_ready): Use the atom1 alt conf in the atom selection. * src/molecule-class-info.cc: (initialize_map_things_on_read_molecule): brighten differnce map. * src/graphics-info.cc: (split_residue_internal): Set the occupancy of the new atoms. * src/molecule-class-info.cc: (delete_residue_with_altconf): created - now only atoms with the same altconf [as the selected atom] get deleted. * src/c-interface-build.cc: (delete_residue_with_altconf): created as interface to the molecule_class_info_t function. 2004-02-13 Paul Emsley * src/globjects.cc: (gl_extras): add GDK_GL_DEPTH_SIZE to the attrlist - hooray depth-testing problem solved! 2004-02-11 Paul Emsley * macros/glut.m4 (AM_PATH_GLUT): Add mips special case * Release 0.4.81 * src/molecule-class-info.cc: (is_mmcif): created: we test for .cif or .mmcif so that, in that case, we write a cif file, not a pdb file. Added a tooltip to the save coordinates fileselection to that effect. * mapview.glade: various changes to improve the MTZ/refmac parameters dialogs [help button created]. * src/graphics-info.cc: (go_to_atom_atom_list_signal_handler_event): created. Just the same as the residue version. We now have double click on atom names too, woohoo! * src/graphics-info-pick.cc: (move_single_atom_of_moving_atoms): created. So that we can move just one atom [obviously]. Called by globject.cc's mouse motion handler. 2004-02-10 Paul Emsley * Release 0.4.80 * src/graphics-info.cc: (execute_setup_backbone_torsion_edit): Added search_altconf and chain_id in atom selection parameters [d'oh]. 2004-02-09 Paul Emsley * mini-mol/mini-mol.hh: (atom constructor): added data item altLoc - and made minor changes in the program elsewhere to compensate. Autofit rotamer alt conf now works. 2004-02-08 Paul Emsley * src/graphics-info.cc: (split_residue), (get_residue_alt_confs), (make_new_alt_conf), (split_residue_internal), together with: * src/molecule-class-info.cc (insert_coords_chage_altconf). Big push to get residue splitting to work. I think it does now. That's great. 2004-02-07 Paul Emsley * src/graphics-info.cc: (split_atom_name): created - called by find_atom_index_from_goto_info, which reads a gtk entry for the atom name [and that could have a , in it to specify the alt conf]. * src/molecule-class-info.cc: (insert_coords_chage_altconf): created. Change the altconf of atoms in the already-existing-set that correspond to new atoms to altconf "A". 2004-02-06 Paul Emsley * ideal/simple-restraint.cc: (make_monomer_restraints): removed the DeleteSelection(selHnd) [causes crash. It should be in the destructor]. 2004-02-05 Paul Emsley * ligand/dunbrack.cc: (GetResidue): changed the indexing order of pscontact -> vector fixes contact indices order. Hoorah - correct rotamers! * src/graphics-info.cc: (update_go_to_atom_window_on_changed_mol): Added a signal handler (go_to_atom_residue_list_signal_handler_event) to each menu item, the handler calls apply_go_to_atom_from_widget() - which I carved out of callback.c's on_go_to_atom_apply_button_clicked [which calls this new function via the c-interface]. So you can now double click on a residue name in the go to atom list and it goes there. * Release 0.4.78 * src/globjects.cc: (glarea_button_press): Added code to check if was in range define - only if not, do we then check_if_moving_atom_pull(). * ideal/simple-restraint.cc: (construct_non_bonded_contact_list): added code to remove OXT from non-bonded contact list. 2004-02-04 Paul Emsley * src/molecule-class-info.cc: (remove_atom_labels): created. Also remove_all_atom_labels in graphics-info and c-interface.cc * coords/Bond_lines.cc: (addSymmetry_calphas): remove debugging statement. * ideal/simple-restraint.cc: (make_monomer_restraints): add DeleteSelection at the end. * src/c-interface.cc: (read_phs_and_make_map_using_cell_symm_from_mol): Add have_map() protection. Also use d2rad on converting from mmdb cell to clipper cell. * src/molecule-class-info.cc: (make_map_from_phs): Use d2rad on converting from mmdb cell to clipper cell. 2004-02-03 Paul Emsley * ligand/residue_by_phi_psi.cc: (construct_prev_res_from_rama_angles): use next_ca next_n, this_c to position this_o, not some garbage geometry that I had previously. 2004-02-01 Paul Emsley * ligand/ligand-extras.cc: (move_atom_to_peak): Change shift_len limit to 0.001 [from 0.01] and add a counter max to the while loop just in case. Also change to refining against the map passed as a parameter - not the pristine map [d'uh!]. * ligand/ligand.cc: (import_map_from): create a new form of the function that sets th e rms of the map, when then gets used in a kludgey way to set the gradient scale. * ligand/ligand.cc: (calculate_gradient_scale): use the rms [if it has been set] to set the gradient_scale. 2004-01-31 Paul Emsley * src/molecule-class-info.cc: (draw_coord_unit_cell): Don't do this if there n_selected_atoms == 0; * src/globjects.cc: (glarea_motion_notify): If we are not in refine mode [last_restraints_size > 0] then simple translate moving coords. * ligand/ligand.cc: (make_pseudo_atoms): Use the mmdb write function not the clipper::MMDB for aniso-ligand-centres.pdb so that the clipper fatal error is not called. 2004-01-30 Paul Emsley * Release 0.4.77 * src/molecule-class-info.cc: (zero_occupancy_spots): display zero occupancy spots. * coords/Bond_lines.cc: (add_zero_occ_spots): created for both graphical_bonds_container and Bond_lines_container as a container for zero occupancy spots. * Release 0.4.76 * src/graphics-info-defines.cc: (check_if_in_geometry_range_defines): add symmetry atom pick so we can have distances to symmetry atoms [obviously]. Created display_geometry_distance_symm() as support. 2004-01-29 Paul Emsley * Release 0.4.75 * ligand/ligand-extras.cc: (water_fit): Created a copy of xmap post mask [xmap_pre_cluster]. Use that to refine against - not the pristine map. * src/c-interface.cc: Change set_map_atom_mask_radius value to 1.9 from 1.2 * ligand/ligand.cc: ligand::ligand Change map_atom_mask_radius to 1.2 (from 0.8). * src/c-interface-build.cc: (clear_pending_delete_item): created - used in callback of delete_item cancel button - deletes the atom/residue-to-be-delete flags. * src/callbacks.c (on_rotate_translate_obj_ok_button_clicked): use clear_up_moving_atoms() not just clear_moving_atoms_object(). (on_rotate_translate_obj_cancel_button_clicked): use clear_up_moving_atoms() not just clear_moving_atoms_object(). 2004-01-28 Paul Emsley * ligand/ligand.cc: Change the masking radius to 1.9. 1.2 [previous value] made the maps look skruffy - much better now. 2004-01-26 Paul Emsley * src/molecule-class-info.cc: (add_typed_pointer_atom): correct the positioning of the atom names for BR, CA, CL, MG, OW1. * src/c-interface.cc: (execute_find_waters_real) update the goto atom widget's molecule and residue list if appropriate. * src/molecule-class-info.cc: (install_model): add have_unsaved_changes_flag. 2004-01-25 Paul Emsley * ligand/ligand-extras.cc: (water_fit): write out the coordinates of the cluster centre that are too big to fit waters. * src/graphics-info.cc: (import_all_refmac_cifs) only close a subdir if it opened successfully and silently skip over files that are not directories. * src/c-interface.cc: (make_and_draw_map): If weights were not useds, weights_col was not defined, but was used to make a string to pass to map_fill_from_mtz - now defaults to "" when there are no_weights. 2004-01-23 Paul Emsley * coords/mmdb-extras.h: clear_contact_info(): created to give back the PSContact memory after we have finished with a contact_info. * Release 0.4.71 * macros/glut.m4 (AM_PATH_GLUT): Fixes for fedora. 2004-01-22 Paul Emsley * src/molecule-class-info.cc: (get_standard_residue_instance) Return null on failure. Add protection against standard residues not being read by using read_success. 2004-01-21 Paul Emsley * src/command-line.cc: (parse_command_line) chars are not ints! - change ch to an int - solves SGI unaccounted optarg condition. * src/c-inner-main.c: (c_inner_main) change error message to match searched-for scm file [coot.scm]. 2004-01-19 Paul Emsley * Release 0.4.68 2004-01-15 Paul Emsley * atom-utils/Makefile.am (INCLUDES): added ideal directory too. 2004-01-14 Paul Emsley * Release 0.4.67 * src/graphics-info-pick.cc: (do_post_drag_refinement_maybe) Added idle function to do minimization. * src/graphics-info-pick.cc: (check_if_moving_atom_pull): created: This is called by globject's button_press callback, and sets up moving atom drag. This is called by mouse motion callback. * src/graphics-info-pick.cc: (move_moving_atoms_by_shear_internal) created - so that the other "moving" atoms move when we move the picked moving atom. 2004-01-10 Paul Emsley * ligand/chi-angles.cc: (setup_chi_atom_pairs) change CG to CG1 for ILE - Ooops. 2004-01-07 Paul Emsley * src/pick.cc: (moving_atoms_atom_pick) created so that we can pick the atoms of the moving atoms molecule. This will allow click and drag of moving atoms - hopefully with some refinement thrown in... * src/pick.h: Add function moving_atoms_atom_pick(); 2003-12-31 Paul Emsley * macros/gtkgl.m4: changed GL_LIBS to be GL_LDOPTS - which includes the -L for the directory if needed. * macros/glut.m4: added powerpc special case because it can't find libXmu. * Release 0.4.66 * macros/guile.m4 (GUILE_PROGS): AC_MSG_ERROR for guile-config and guile removed - so that we don't fail to configure when guile is not present. * src/c-interface.cc: Added various HAVE_CANVAS preprocessor tests that I found to have problems when building on new Mac OS X laptop. 2003-12-26 Paul Emsley * src/c-interface.cc: (make_and_draw_map) return int, not void so that we can use the molecule number in a script. 2003-12-24 Paul Emsley * Release 0.4.65 * src/graphics-info.cc: (show_select_map_dialog) created. I split out the map selection from the old refine parameters dialog - and changed functions that called show_refine_params_dialog() to call this function instead. No there is no confusion about refinement parameters [torsions control] when user should be simply selecting a map. This was easier than I thought it was going to be [I've known that I've needed to make this fix for months]. * src/c-interface.cc: (show_select_map_dialog) created for model/fit/refine dialog button callback - passthough to graphics-info function. * Release 0.4.64 * macros/glut.m4 (AM_PATH_GLUT): Added -lXmu to GLUT_LDOPTS for Vanilla unix. 2003-12-23 Paul Emsley * Release 0.4.63 * sequence-view/sequence-view.hh: vector -> std::vector * sequence-view/Makefile.am (include_HEADERS): Added seq-view-interface.h [Packaging error] 2003-12-22 Paul Emsley * Release 0.4.62 * ligand/residue_by_phi_psi.cc: (fit_terminal_residue_generic) Added terminus_type "M" which creats a fragment of 1 residue instead of 2. * mini-mol/mini-mol.cc: (constructor from atom_list): use the passed chain_id, not "W", to construct a fragment. * src/c-interface.h: Changed many of the setup_* functions called from model/fit/refine togglebutton callback to take a state argument which usets the flag in graphics-info.h and returns to a normal cursor [for toggle button toggled off]. * src/c-inner-main.c: Changed mapview.scm to coot.scm 2003-12-19 Paul Emsley * src/graphics-info.cc: (geometry_objects) Created. Also (clear_simple_distances) created. These [together with the odd static vector pointer] create on-screen distances - and the removal thereof. 2003-12-17 Paul Emsley * configure.in, Makefile.am, src/Makefile.am, ligand/Makefile.am: changed to reflect new directory ccp4mg-utils, which is where ccp4mg stuff will go, rather than in the ligand directory * Release 0.4.60 * sequence-view/sequence-view.cc: Created [along with sequence-view.hh] 2003-12-10 Paul Emsley * Release 0.4.59 * src/molecule-class-info.cc: (insert_coords) Add AddResidue when serial_number returned -1. * Release 0.4.58 * surface/Makefile.am (libcoot_isosurface_la_SOURCES): make library name have coot- prefix. 2003-12-09 Paul Emsley * Release 0.4.57 * ideal/simple-restraint.cc: (init_from_mol) re-include the istart_minus_flag and iend_plus_flag that I had foolishly removed before. Now flanking atom restraints work. * src/c-interface.h: Added save_state_file() 2003-12-08 Paul Emsley * ideal/simple-restraint.hh: Added enumeration of BONDS_ANGLES_TORSIONS_PLANES_AND_NON_BONDED. * Makefile.am (subpkgdata_DATA): Add standard-residues.pdb * Release 0.4.56 * src/graphics-info.cc: (execute_rotate_translate_ready): move over to make_asc usage. (execute_rigid_body_refine) moved over to make_asc usage. 2003-12-07 Paul Emsley * src/graphics-info.cc: (copy_mol_and_refine) Massive re-write yet again. We didn't want the flanking residues to appear in the moving atoms. * ligand/dunbrack.hh: dunbrack constructor: don't run add_all_rotamers and setup_chi_atom_pairs, because we already do that in the base class. Rotamers fixed. 2003-12-06 Paul Emsley * new libtool. * src/c-interface.cc: (read_phs_and_make_map_using_cell_symm) created to re-generate a phs map from phs data. * src/molecule-class-info.cc: (make_map_from_phs) Added save_state_command_strings_ push backs. * src/globjects.cc: (glarea_button_press) added freeglut conditional compilation for the contouring timer. * src/graphics-info.cc: (SetShowFPS): added freeglut conditional compilation for the FPS timer. 2003-12-05 Paul Emsley * Release 0.4.55 * src/globjects.cc: (display_density_level_maybe) Sorted out the matrix mode change with pops - now you can click on the coordinates immediately after density has changed. Documentation amended. * src/molecule-class-info.cc: (close_yourself) Removed delete [] atom_sel.atom_selection usage - using DeleteSelection(SelectionHandle) instead. 2003-12-04 Paul Emsley * Release 0.4.54 * Makefile.am (install-data-local): changed the destination of pixmaps so that it is in PKGDATADIR which is a passed variable in the compilation. * Release 0.4.53 * src/c-interface.cc: (set_refine_max_residues) Created - so that not too many residues are refined by accident [default fencepost 20]. * src/graphics-info.cc: (copy_mol_and_refine) and (copy_mol_and_regularize) removed copy molecule and generate a moving_atoms_asc "by hand". Seems faster. 2003-12-03 Paul Emsley * coords/mmdb-extras.cc (add_atom_index_udd_as_old): Created - so that we can have a fast lookup of atoms (full_atom_spec_to_atom_index) when we accept regularization and refinement. * Release 0.4.52 * macros/glut.m4 (AM_PATH_GLUT): Move GL_LIBS into default GLUT_LDOPTS. 2003-12-02 Paul Emsley * Release 0.4.51 * src/graphics-info.cc: (change_peptide_carbonyl_by): created. (change_peptide_peptide_by): created. Along with new dialog and button on model/fit/refine dialog - provides backbone torsion angle manipulation. * src/graphics-info-state.cc: (save_state_file) added a test for non-Closed molecule before saved parameters are written. * src/c-interface.cc: (run_state_file_maybe) created. Along with a state file dialog and a set_run_state_file_status() c-interface.cc function. * src/graphics-info.cc: (set_last_map_colour) Created. 2003-11-29 Paul Emsley * Release 0.4.51-pre-3 [trying cvs] * ligand/ligand.cc: (mask_around_coord) Added distance check to atom. Needs testing. 2003-11-25 Paul Emsley * src/c-interface.cc: (set_graphics_window_size): added gtk_window_set_default_size call and argument setting in reshape in glarea.cc so that the window shape is saved in the state file. 2003-11-23 Paul Emsley * src/molecule-class-info.cc: make_map_from_cif [just the filename version]. Added warning about no calculated structure factors [rather than silently failing]. 2003-11-18 Paul Emsley * Release 0.4.49 * Makefile.am added suppressions [for valgrind]. * Release 0.4.48 * src/molecule-class-info-other.cc: (residue_edit_phi_psi) created. (edit_phi_psi_pull_residue) created. (get_phi_psi) created. All for edit phi/psi support. 2003-11-17 Paul Emsley * src/graphics-info-defines.cc (check_if_in_edit_phi_psi_define): Created. * src/callbacks.c (on_dynarama_ok_button_clicked): Added support for edit phi/psi window closure. * macros/mmdb.m4 (AM_PATH_MMDB): Added check for old mmdb by using SetAtomName(const char *). Exit if this fails. 2003-11-15 Paul Emsley * Release 0.4.46. Some pretty substantial changes here [display control widget, posting from state, symm atom picking and non-bonded contacts in refinement]. * coords/mmdb-crystal.cc: (translate_atom) has an invalid read - fixed by not deleting the atom before we construct the returned Cartesian [duh!]. Also removed the cryst_p usage. * src/globjects.cc (key_press_event): Added postings of the most useful windows from F5, F6, F7. * src/c-interface.cc: (wrapped_create_goto_atom_window) Created. (fill_go_to_atom_window) created [functionality pulled out of callbacks.c] - because it was needed by post_display_control_window() too. * src/graphics-info-state.cc: (save_state_file) added to to post model/fit/refine window if it was up. * src/graphics-info-pick.cc: (symmetry_atom_pick) Make clipper spacegroup and construction depend on there being at least one box. * ideal/simple-restraint.cc: (distortion_score_non_bonded_contact) Added. Also my_df_non_bonded and various functions and constructors of simple_restraint. Now we have working [I hope] non-bonded contacts too. * src/molecule-class-info.cc: (read_ccp4_map) Put in directory or missing file protection [at the suggestion of Charlie Bond]. 2003-11-14 Paul Emsley * ideal/simple-restraint.cc: (make_non_bonded_contact_restraints) now we have non-bonded contacts from the active residues. 2003-11-12 Paul Emsley * Release 0.4.46-pre-3 * src/graphics-info-pick.cc (fill_hybrid_atoms): Changed to use mmdb to get the matrix because mmdb and clipper symops are not in the same order. The matrix generates a mat33 and a coord_oth, which are then used to create an rtop which transforms the atom position. 2003-11-07 Paul Emsley * coords/mmdb-crystal.cc: sym_trans_t::str(): initialize t with \0s. Changed the delete to delete [] at the end. [Both from valgrind]. 2003-11-07 Paul Emsley * Release 0.4.46-pre-2 * src/main.cc: Add stuff for splash_screen. * ideal/simple-restraint.cc: (make_non_bonded_contact_restraints): started added in non-bonded contacts. 2003-11-06 Paul Emsley * coords/mmdb-crystal.cc: (which_box): Converted to to suggestion of Kevin - apply symm to centre, apply trans shift to point, finding closest *then* the +/- 1 along a, b, c. Fixes the Adrian 158A problem. 2003-11-05 Paul Emsley * macros/gtkgl.m4 (AM_PATH_GTKGL): Put -lgtkgl before the $GTK_LIBS [MacOS X sensitive to this]. 2003-11-02 Paul Emsley * Release 0.4.44 * src/gtk-manual.c: (display_control_molecule_combo_box) Removed extra toggle-button callbacks [active and displayed], which caused event recurring hell. 2003-11-01 Paul Emsley * Makefile.am (EXTRA_DIST): Added cootrc. * ligand/ligand-extras.cc: Fixed several errors. First use the right map, second use doubles for the statistics, third step from 1 not 0. Change the stop to 0.3, so that the outer shell is now 0.9 * src/globjects.cc: Changed ligand_water_variance_limit to 0.7 2003-10-30 Paul Emsley * Release 0.4.42 * src/pick.cc: (symmetry_atom_pick) the p_i.success test was coming too early. Now we finish all the boxes before testing. Long-standing symmetry picking bug gone!? * doc/Makefile.am (EXTRA_DIST): Added reference.tex 2003-10-29 Paul Emsley * src/Makefile.am (coot_SOURCES): Use macros to expand the coot_wrap source files. (libcoot_wrap_python_la_SOURCES): (libcoot_wrap_guile_la_SOURCES): Create libraries for the wrapper code so that coot_SOURCES does not depend on a macro - which I could not get to expand so that the objects for coot were correctly generated. Now the executable depends on the libraries, which gets expanded OK. Also changes in macros/with-guile.m4 and macros/with-python.m4 were needed. * Release 0.4.41 * src/gtk-manual.c: (display_control_molecule_combo_box) Add Bond Colour by Atom button. * Release 0.4.40 * src/Makefile.am (coot_SOURCES): Ooops - packaging error - now includes select-atom-info.hh 2003-10-27 Paul Emsley * src/c-interface-build.cc: (setup_mutate_auto_fit) added, with callback and graphics-info-defines:check_if_in_mutate_auto_fit() * src/globjects.cc: (draw_crosshairs_maybe) Fixed for non-square aspect ratios. 2003-10-24 Paul Emsley * Release 0.4.37 * src/graphics-info.cc: (fill_output_residue_info_widget_atom) (on_residue_info_occ_entry_key_release_event) (on_residue_info_b_factor_entry_key_release_event) (residue_info_edit_b_factor_apply_to_other_entries_maybe) (residue_info_edit_occ_apply_to_other_entries_maybe) (residue_info_add_b_factor_edit) (residue_info_add_occ_edit) (apply_residue_info_changes) (residue_info_release_memory) Phew. A long day's work. These functions created (fill_output_residue_info_widget_atom was extended) to implement residue info [occupancy and temp factor] editting. By checking the dialog's checkbutton the changes are applied to the whole residue. residue_info_release_memory causes a memory error when the deletes are uncommented. 2003-10-23 Paul Emsley * src/c-interface.cc: (set_ligand_water_to_protein_distance_limits) set min and max, not max twice [d'oh!]. * ligand/ligand-extras.cc: (move_atom_to_peak) Get values from the pristine map, not the masked one. * src/c-interface.cc: (wrapped_create_model_fit_refine_dialog) created, so that there is only one Model/Fit/Refine window. 2003-10-22 Paul Emsley * ligand/ligand-extras.cc: Use 4 character atom names in write_waters and make_pseudo_atoms(). 2003-10-18 Paul Emsley * src/c-interface.cc: (execute_find_waters_real) Added raw waters writing (set_write_raw_waters). 2003-10-16 Paul Emsley * src/graphics-info.cc: (add_cb_to_terminal_res) return an atom_selection_container_t because the number of atoms in the molecule has changed. Fixes terminal residue bug [I hope]. * geometry/protein-geometry.cc: (init_refmac_mon_lib) It seems that ReadMMCIFFile goes into an infinite loop when asked to read a directory. So put directory protection round it [using stat]]. 2003-10-14 Paul Emsley * src/molecule-class-info.cc: (insert_coords). Added make_backup(); * src/mtz-bits.c: (f_button_select) Added "DEL" and "FOFC" logic to switch to difference map. 2003-10-09 Paul Emsley * src/molecule-class-info.cc (add_multiple_dummies - both scored_skel_coord and Cartesian interface) added FinishStructEdit(). Error below goes away. * src/molecule-class-info.cc: (model_view_atom_button_labels) Added null protection for chains. This should not be necessary. It seem to be a result of mmdb corruption elsewhere - possibly DeleteChain in update_molecule_to(). * src/molecule-class-info.cc: (model_view_residue_button_labels) Added null protection for chains. 2003-10-06 Paul Emsley * Release 0.4.33 * src/molecule-class-info.cc: (previous_baton_atom) Use direction to generate the vector of [previous] coordinates. * src/graphics-info.cc (baton_next_directions) use baton_build_direction_flag. * src/graphics-info.cc: (set_baton_build_params) Created. We need to be able to build backwards - even with negative residue numbers. So we need an external function that sets the starting residue number and the direction. 2003-10-02 Paul Emsley * Release 0.4.32 * src/c-interface.cc: (set_max_skeleton_search_depth) and code in graphics-info.cc to set the static so that the skeleton search depth is publically available. * build/CalphaBuild.hh: (CalphaBuild) new constructor so that max_skeleton_search_depth is publically available. * src/graphics-info.cc: (shorten_baton), Don't change direction when in b-mode. * src/graphics-info.cc: (lengthen_baton), Don't change direction when in b-mode. * src/callbacks.c (on_virtual_trackball_menu_pops): use gtk_check_menu_item_set_active to set the virtual trackball status on popup of Virtual Trackball menu. 2003-10-01 Paul Emsley * src/graphics-info-state.cc: (save_state): save also the diff_map_iso_level_increment and the iso_level_increment. * src/graphics-info.cc: (unskeletonize_map) and src/c-interfac.cc's (skeletonize_map_by_optionmenu) are new skeletonization code so that you can skeletonize any map, not just the first one. * ideal/with-geometry.cc (main): added without GSL protection * ideal/with-map.cc: (main) added without GSL protection. 2003-09-30 Paul Emsley * src/c-interface.cc: (skeletonize_map_by_optionmenu) and associated code in c-interface.cc, graphics-info.cc, callbacks.c. Support for skeletonization of any map. * compat/getopt1.c: include coot-getopt.h [that's what we supply] not getopt.h. * mini-mol/mini-mol.cc: (pcmmdbmanager) remove the casting to char for SetAtomName argument. 2003-09-25 Paul Emsley * src/graphics-info.h: (init) Move the initialization of dynarama_is_diplayed here rather than in the static setup. 2003-09-24 Paul Emsley * src/graphics-info.cc: (set_residue_range_refine_atoms) created for calling of rigid_body fit by scripting. * src/rama_plot.cc: (init_internal) use gtk_object_set_data_full on the window so that we can look up the canvas. * src/c-interface.cc: (get_mol_from_dynarama) Use the canvas to lookup the molecule number, not the [top-level] window. 2003-09-23 Paul Emsley * Release 0.4.28 * src/c-interface.cc: (handle_read_draw_molecule) fill the option menu of the Go To Atom window, if it exists. * src/molecule-class-info.cc: (restore_from_backup) save the state commands and the imol_no from before calling handle_read_draw_molecule(). * src/graphics-info-defines.cc: (clear_pending_picks). Created. 2003-09-22 Paul Emsley * src/callbacks.c (on_delete_item_cancel_button_clicked): Filled in this function. * src/molecule-class-info-other.cc (residue_serial_number): added null residue protection code. * src/c-interface-build.cc: (delete_item_mode_is_atom_p) created to support (on_model_refine_dialog_delete_button_clicked). * src/callbacks.c (on_model_refine_dialog_delete_button_clicked): If we were in delete_atom_mode, then the atom checkbutton should be hilighted. * src/graphics-info.cc: (execute_rigid_body_refine) moved to here from c-interface.cc. Now sets imol_moving_atoms [oops]. * src/graphics-info.cc: (apply_undo), (Undo_molecule), created for "Undo" support. * src/molecule-class-info.cc: (add_pointer_multiatom) Use 4 letters in the atom names. 2003-09-21 Paul Emsley * coords/Bond_lines.cc: (construct_from_asc) Use the non_Hydrogen_atoms array not the SelAtom.atom_selection for the calculation of non-hydrogen bonds. Hydrogens are really not displayed now when we use (draw-hydrogens 0 0). 2003-09-19 Paul Emsley * Release 0.4.27 * src/molecule-class-info-other.cc (add_OXT_to_residue): and supporting code in c-interface-build.cc * Release 0.4.26 * refmac.scm (run-refmac-by-filename): Added extra-cif-lib-filename argument. Also made changes in calling code execute_refmac_real(); * src/molecule-class-info.cc: (full_atom_spec_to_atom_index) Now us User Defined Data atom index. Needs more testing perhaps. * src/graphics-info.cc: (baton_build_delete_last_residue). Baton building now has an "Undo" button - hoorah! 2003-09-17 Paul Emsley * src/molecule-class-info-other.cc: (auto_fit_best_rotamer) Created. * mini-mol/mini-mol.cc: residue::residue(const CResidue* residue_p): created. * src/graphics-info.cc: moved the guts of set_dynarama_is_displayed() to here from c-interface.cc. Did a spelling correction of dynarama_is_diplayed and made sure references of it were array usages [there is more than one ramachandran plot now]. 2003-09-16 Paul Emsley * src/globjects.cc: Changed the default graphics_info_t::environment_min_distance to 0.0. * src/graphics-info.h: Added dynamic_map_zoom_offset and the c-interface function set_dynamic_map_zoom_offset, which addresses Kevin's wish [to have the screen full of density always] somewhat [i.e. not completely satisfactarily]. 2003-09-11 Paul Emsley * ligand/ligand.cc: Don't apply angles to ligands of size 1 (e.g. waters). No more crashing when trying to Rigid Body Refine water atoms. 2003-09-09 Paul Emsley * Release 0.4.24 * ideal/simple-restraint.cc: (make_flanking_atoms_restraints) now uses the new class variables istart_minus_flag and iend_plus_flag which are now set in (init_from_mol) which are set if we the flanking next and previous residues are in the molecule. * ligand/residue_by_phi_psi.cc: (make_2_res_joining_frag) Created. Now we create a fragment of 2 residues, because when building forward, the O of the next atom depends on the next next residue. 2003-09-08 Paul Emsley * src/molecule-class-info.cc: (make_atom_label_string) Add alt conf code to the atom label if it has one. * db-main/db-main.hh (weighted_residue::weighted_residue()): Initialize weight_sum and weight_sum_cb [fool]. [Uninitialized variable found by valgrind]. Ca -> mainchain bug fixed. 2003-09-07 Paul Emsley * Release 0.4.23 * src/c-interface.cc: (save_coordinates). Put NULL protection in the gtk_object_get_user_data - not a clean solution [still gets a Gtk-WARNING invalid cast from NULL pointer], but it doesn't crash now. * src/molecule-class-info.cc: (append_to_molecule) execute_find_waters_real now calls append_to_molecule when we want to add the waters to the masking molecule. * src/graphics-info.cc: (go_to_atom_residue) Garib's Bug: the way to do this is to set the residue number to -1 in the static (goto_to_atom_residue_number_) in globjects.cc and test for -1 when we render the goto_atom_window. If it is -1, then we use the details of the first atom of the first molecule that has atoms. I did indeed do exactly that: graphics_info_t::go_to_atom_residue() now uses intelligent_this_residue_atom(). Garib's Bug Fixed. Hoorah! * src/gtk-manual.c: (display_control_molecule_combo_box) moved gtk_option_menu_set_menu to the end of the routine and use render_optionmenu_1_menu directly in the bond_type test just above it. This allows gtk_menu_set_active to work - Hooray! C-alpha bond representation in Display Control now fixed. 2003-09-06 Paul Emsley * src/c-interface-build.cc: created new widget run_refmac dialog [which needed widget setup and analysis code], execute_refmac and execute_refmac_real and wrote refmac.scm and coot-utils.scm [which uses goosh [so I need to add that to my dependences]]. So refmac "works". This is rather pleasing. It does not currently read in the new coordinates and map, I will do that shortly. 2003-09-05 Paul Emsley * src/c-interface.cc: (set_show_aniso(int state)) redraw glarea so that callback actually changes the graphics. 2003-08-27 Paul Emsley * src/molecule-class-info.cc: (add_pointer_multiatom) Added multiatom [e.g. SO4] pointer atom code. 2003-08-26 Paul Emsley * src/c-interface-build.cc: (mutate) return a status so that the calling script knows that something went wrong [potentially]. * src/molecule-class-info.cc: Made get_ori_to_this_res and move_std_residue return error status for signalling unfilled rtop, used now in mutate_auto. 2003-08-19 Paul Emsley * src/molecule-class-info.cc: (make_backup). Activated backup code for mutations. * src/c-interface.cc: (fill_option_menu_with_coordinates_options) added an extra arg, which is the signal function callback for the item selection - [needed so that we don't do a goto atom residue list update when we save a molecule]. * src/callbacks.c (on_coordinates_recentring1_activate): Added code so that recentre_on_read_pdb is now gui-able. 2003-08-13 Paul Emsley * src/molecule-class-info.cc: (add_coords) Check for null residue [sigh]. 2003-08-12 Paul Emsley * src/rama_plot.cc: (big_square) When the model view was used to recentre view and a water was selected, we crashed in big_square, which had assued that everything was a protein. Fixed that by testing for the size of phi_spi. 2003-08-11 Paul Emsley * surface/CIsoSurface.cpp: Comment out clipper/mtz/mtz_io.h: not needed. 2003-08-08 Paul Emsley * Today I build a version for the sgi and ran it on perky. It ran! It displayed a map! It did regularization and refinement! Interestingly the graphics were pretty fast [almost as good as bubbles] but the calculation stuff [refinement, map contouring/recentering] was very very slow. 2003-08-07 Paul Emsley * src/globjects.cc: (glarea_button_press) [and key_release_event]. When map level is changed, it first checks to see if there is only one map being displayed and if there is, then that map gets moved, not the one to which the scroll-wheel is attached. * Release 0.4.22-pre-6 * src/c-interface.cc: (go_to_atom_mol_button_select) Added code to do the gtklist widgets for the residue and atom lists in the go to atom window. Note gtklists are out of deprecated and that I had to use gtk_set_data_full by hand to add the name to the widget so that it could be looked up. [I had to create it by hand for some viewport scrolling issue not supported in glade]. 2003-08-05 Paul Emsley * coords/Bond_lines.cc: (Bond_lines_container) added delete trans atom code, after using valgrind. Also in pick.cc. Valgrind stil not happy - but we are in a better position. * src/callbacks.c (on_go_to_atom1_activate): Adding list of residues and atoms to go_to_atom_window. 2003-08-04 Paul Emsley * src/callbacks.c (on_show_symmetry1_activate and others): Added Ca for symmetry option. 2003-07-26 Paul Emsley * src/molecule-class-info.cc: (set_bond_colour_by_mol_no) Limit the rotation_size to +1.0. 2003-07-25 Paul Emsley * src/c-interface.cc: (fill_close_option_menu_with_all_molecule_options) fixed the non-setting of the first molecule in the optionmenu. * src/c-interface.cc: fill_option_menu_with_coordinates_options() fixed the non-setting of active molecule menu item in optionmenu. 2003-07-18 Paul Emsley * Release 0.4.21-pre-7: I am pleased with this release. * Added "unsaved changes" flag to molecule_class_info_t along with code that ativates in when the molecule is changed and deactivated on save coordinates. Added gui code to interact with above. * Added state-saving code. 2003-07-15 Paul Emsley * src/pick.cc: symmetry_atom_pick() removed the deletion of translated and created a function clear_symm_atom_info that should be called after setRotationCentre(symm_atom_info_t) that clears it instead. * coords/Bond_lines.cc: (Bond_lines_container::construct_from_asc) added code to look for " D" as well as " H". 2003-07-14 Paul Emsley * src/graphics-info.cc: graphics_info_t::execute_rotate_translate_ready() Added the assignment to imol_moving_atoms that I had forgetten. 2003-07-09 Paul Emsley * ligand/ligand.cc: added to the class do_size_match_test. We don't want to do the test for rigid body refinement [which calls find_centre_by_ligand], but we do for a full ligand search. 2003-07-07 Paul Emsley * src/c-interface-build.cc: Added function to set lowest rotamer probability. 2003-07-07 Paul Emsley * Releases: 0.4.19, 0.4.20, fixing mutate bugs. 2003-07-04 Paul Emsley * Release 0.4.18 * close molecule functionality added [see close_yourself() in molecule_class_info_t]. 2003-07-03 Paul Emsley * Release 0.4.17-pre-1 * tree/dunbrack.cc: Added dunbrack and assocciated classes [uses mgtree Tree]. testdunbrack seems to work. Let's make a release of that. 2003-07-01 Paul Emsley * coords/Bond_lines.cc: added optional int do_disulfide_bonds_flag to constuctor so that disulfide bonds dont flash when we are doing regularization/refinement. Made necessary changes therefore to graphics_info_t::copy_mol_and_refine, copy_mol_and_regularize and makebonds() in molecule-class-info. 2003-06-24 Paul Emsley * src/pick.cc: removed atom label construction to molecule-class-info.cc 2003-06-23 Paul Emsley * src/mtz-bits.c: manage_column_selector: Added code to set FWT, PHWT as default if they exist: gtk_menu_set_active(GTK_MENU(optionmenu1_menu), i) Code works! * src/c-interface.cc: set_show_unit_cell: Added code and changed interface to be setting all molecule show_unit_cell_flag flags, not just imol=0. 2003-06-20 Paul Emsley * Release mapview-0.4.15-pre-4 * ideal/simple-restraint.cc, configure.in: Make HAVE_GSL be a source configuration option, and --with-gsl-prefix for configure. 2003-06-19 Paul Emsley * ligand/ligand.cc: Option out the best-overall-*.pdb writing by introducing a new class variable write_orientation_solutions. 2003-06-15 Paul Emsley * src/graphics-info.cc: Made many changes so that regularized_asc becomes moving_atoms_asc since it is used by many atom manipulation functions, not just regularization. 2003-06-14 Paul Emsley * src/molecule-class-info.cc: (molecule_class_info_t::pepflip), if atom is an " N ", then move to the previous atom. * coords/Bond_lines.cc: Bond_lines_container constructor: added different bonds [colour] or bond to a Carbon atom. * src/pick.cc: (make_atom_label_string) re-written as a c++ function. * src/c-interface.cc: (scale_zoom_internal): Added fabs to wrap f. 2003-06-13 Paul Emsley * ligand/residue_by_phi_psi.cc: Added then completely re-written, sill does not work properly. * src/command-line.cc: Added coot-getopt.h not getopt.h, ie we now have a copy of getopt in coot [in compat]. 2003-06-07 Paul Emsley * src/globjects.cc: Set graphics_info_t::rotate_colour_map_for_map = 31.0; degrees 2003-06-03 Paul Emsley * ligand/ligand.cc: (coot::ligand::fit_ligand_to_clusters) Added protection for setting at the end final_ligand[iclust] beyond it's size. 2003-05-30 Paul Emsley * src/molecule-class-info.cc: (initialize_map_things_on_read_molecule) now has colour map rotation for the map. * src/rama_plot.cc: (draw_phi_psi_point_internal) Fixed assignment of big_box_item. I think the ramachandran plot bug has gone away now. Phew. 2003-05-29 Paul Emsley * geometry/protein-geometry.hh: Fixed dist_esd for link planes. 2003-05-28 Paul Emsley * src/graphics-info.cc: Attempt to make some safety for regularized_asc deletion. To no avail - deletion of the molecule is commented. 2003-05-25 Paul Emsley * src/c-interface.cc: execute_rigid_body_refine(): Function added - uses ligand class. * ligand/ligand.cc (get_solution): Function added. Used for graphics. find_centre_by_ligand(): Function added: for use in rigid body refinement. * src/c-interface.h: Added these functions: void set_map_sampling_rate_text(gchar *text); void set_map_sampling_rate(float r); char* get_text_for_map_sampling_rate_text(); float get_map_sampling_rate(); * src/callbacks.c (on_density_size1_activate): Added code to get and set map_sampling_rate using widget map_sampling_rate_entry. 2003-05-18 Paul Emsley * src/gtk-manual.c: Added code to provide C-alpha pseudo bond representation menu_item. * Release 0.4.12 * ideal/simple-restraint.cc: Added map terms and now the seem to work correctly - with a substantial (1000?) weight in the constructor. 2003-05-08 Paul Emsley * ideal/simple-restraint.cc: (make_monomer_restraints) changed to istart_res and iend_res usage for the residue selection. * src/globjects.cc: changed default skeleton box radius to 40A. * angles/AngleInfo.cc: (assign_angle_torsion). We get a crash when running build Ca now. The problem is in assign_angle_torsion creating bad values for theta_bin and torsion_bin for the angle_torsion_table. Fixed by adding setup_angle_torsion_table(10,5) to the AngleInfo constructor. 2003-05-07 Paul Emsley * src/graphics-info.cc: (smooth_scroll_maybe) Had another bash at making the zoom/scroll/zoom look better. * src/Makefile.am (EXTRA_DIST): Added post-glade. * Synced upto 24 April 2003 clipper. * src/molecule-class-info.cc: Added #include "clipper/mmdbold/clipper_mmdb.h" for clipper::DBAtom_selection atoms() in make_map_from_cif_generic(). * ligand/ligand.hh: Added #include "clipper/mmdbold/clipper_mmdb.h" so that clipper::MMDB and clipper::DBAtom_selection work. * angles/AngleInfo-angle-torsions-autogen.cc (from_batched_angle_torsions_bits_540): Split into compiler-sized chunks :-). Compiles much faster now. Added the new declarations to AngleInfo.h too. * macros/with-python.m4 (AM_WITH_PYTHON): Added UTIL_LIB for PYTHON_LIBS depending on `uname` 2003-04-10 Paul Emsley * src/globjects.cc: Added colour map rotation using rgb to hsv conversion, where we add a few degrees (graphics_info_t::rotate_colour_map_on_read_pdb) to the hue. However, molecule 1 appears over the top of molecule 2, thus causing confusion, potientially. So draw the molecules in draw back to front [i.e. starting at the higest molecule number]. Add c-interface.cc support for these variables. 2003-04-08 Paul Emsley * skeleton/Makefile.am: Added ligand dir to mapview. Synced up configure.in and main Makefile.am to match. * macros/with-python.m4 (MAPVIEW_WRAP_PYTHON_CONVERT): added variable to copy blank.cc to mapview_wrap_python.cc if python was not included. * macros/with-guile.m4 likewise for guile. Also sync src/Makefile.am to reflect these changes. 2003-03-13 Paul Emsley * src/Makefile.am (INCLUDES): Changed GLUT_CLAGS to GLUT_CFLAGS. 2003-03-12 Paul Emsley * src/c-interface.h: Added mapview_exit so that Py_Finalize() gets called. Used in callbacks.c by on_exit1_activate(); 2003-03-04 Paul Emsley * src/callbacks.c (on_smooth_scrolling_window_ok_button_clicked): changed to set_smooth_scroll_limit_str because we changed the interface so that we can pass a float. 2003-02-26 Paul Emsley * macros/gtkgl.m4 (AM_PATH_GTKGL): Added -lpthread. We should check for thread first then, I guess. * skeleton/Makefile.am (test_various_LDADD): Changes references to AngleInfo to mapview-AngleInfo. * macros/Makefile.am (MACROS): Recreated [because I left it on the laptop] gtk-canvas.m4 and included it in Makefile.am 2003-11-26 Paul Emsley * Release 0.4.7-3 * */Makefile.am : Now using libtool 2003-11-25 Paul Emsley * src/molecule-class-info.cc: (make_map_from_cif) Added 2fo-fc map generation code. Yeah! How cool! [Critical code cribbed from Kevin, of course - he said alliteratively]. * macros/Makefile.am (MACROS): Added guile.m4 * src/molecule-class-info.cc: (unlabel_atom) Fixed indexing limit in for loop so that we can no delete the last atom in the list. 2003-11-20 Paul Emsley * macros/gtkgl.m4 (AM_PATH_GTKGL): Added -lpthread. Not sure about the placing. 2003-02-18 Paul Emsley * Release 0.4.6-pre-7 2003-02-17 Paul Emsley * src/Makefile.am (MAPVIEW_EXTRA_LIBS): Removed ../db-main for now. (mapview_LDADD): Removed @MAPVIEW_WRAP_LIBS@ * src/molecule-class-info.cc: Commented clipper-cif.h * src/c-interface.cc: Commented out db-main.h from includes. Commented out test_fragment(). * src/Makefile.am (EXTRA_DIST): added EXTRA_DIST for mapview.i * All sorts of gcc 3.2 fixes, using std:: a lot, removing default arguments from function definitions, etc. * configure.in: delete db-main (and from Makefile.am) for now. 2003-02-03 Paul Emsley * src/callbacks.h: removed clipping_adjustment_changed and moved it to c-interface.cc, since it is only called by do_clipping1_activate(). * src/callbacks.c (on_exit1_activate): Call gtk_exit, not gtk_main_quit() because gtk_main_quit does nothing [I don't know why] now that we have a scripting window. * (on_clipping1_activate): moved code to do_clipping1_activate() in c-interface.cc. Likewise clipping_adjustment_changed(). 2002-11-14 Paul Emsley * macros/clipper.m4 (AM_PATH_CLIPPER): take out cctbx and sgtbx from the necessary libraries. * skeleton/BuildCas.cc (all_skel_pts_in_asu): Removed the commment on the map level. 2002-10-30 Paul Emsley * Added a ton of code, phs reading, cell selection, map and molecule control, more autobuilding code. * Release 0.4.5 2002-10-30 Paul Emsley * Linking with python, following Stuart's recipe works [except that gtk takes over the console]. Attempting to link with guile make guile crash :-(. 2002-10-10 Paul Emsley * skeleton/BuildCas.cc: added "tidy up trans_selection:" code. Now *much* faster at generating symmetry expanded branch points. 2002-08-21 Paul Emsley * Release 0.4.1 [due to post-glade mix-up]. 2002-08-20 Paul Emsley * Release 0.4.0 [at long last!] * src/c-interface.cc: (goto_near_atom_maybe and friends). Added functions to do next/previous residue (go_to_atom_* functions) 2002-08-19 Paul Emsley * src/pick.cc: (atom_pick) Added an update for SelAtom so that we are looking at the molecule that had the nearest contact [fixes James Murray bug, I believe]. * src/pick.cc (symmetry_atom_pick). Similar to above [using translated]. * synced with laptop [IUCr 2002 enhancements]. 2002-07-28 Paul Emsley * src/globjects.cc: (glarea_motion_notify), (init), (draw) add in quaternion/trackball support. Hoorah! the mouse now moves the molecule as I like it. We use trackball.c from sgi. * src/c-interface.cc: (skel_foadi_on) Call initialize_coordinate_things_on_read_molecule() for the bones and the constructed atoms. Goodbye "symmetry labelling" bug. * src/globjects.cc: (glarea_button_press) Only try to pick symmetry atoms if they are being displayed. The same goes for labelling. 2002-07-09 Paul Emsley * src/globjects.cc: (anisotropic something) Tinkered with this function so that it returns "nice" values. * src/c-interface.h: Reshuffled aniso c-interface functions and dropped their molecule arguments. The Anisotropic Atoms widget has no ability to select molecules. This then is not a property of a molecule, but is a property of the graphics. float get_limit_aniso(); // not a function of the molecule short int get_show_limit_aniso(); // not a function of the molecule short int get_show_aniso(); // not a function of the molecule void set_limit_aniso(short int state); void set_aniso_limit_size_from_widget(char *text); void set_show_aniso(int state); char *get_text_for_aniso_limit_radius_entry(); void set_aniso_probability(float f); float get_aniso_probability(); 2002-06-25 Paul Emsley * skeleton/fc_skeleton.cc: (converge): change the gridding limits from -1..1 to -2..2 [like Kevin suggested]. 2002-06-17 Paul Emsley * skeleton/fc_skeleton.h (class fc_skeleton): Deleted denlist and friends and removed their usage from fc_skeleton() and ~fc_skeleton(). * skeleton/fc_skeleton.cc (initprevden): Completely rewritten according to Kevin's notes. (getprevden): Likewise. 2002-05-24 Paul Emsley * Release 0.3.93 2002-05-01 Paul Emsley * Massive rebuilding - the static maps and coordinates are gone and now are part of molecules. Much rebuilding of the interface to take account of this change. Much removal of static objects - which have been moved to dynamically allocated molecules (molecule_class_info_t). 2002-02-28 Paul Emsley * font/Makefile.am (CXXFLAGS): I mean CXXFLAGS, not CXX_FLAGS. 2002-02-23 Paul Emsley * src/pick.cc: (make_atom_label_string) fixed atom labelling. 2002-02-22 Paul Emsley * macros/clipper.m4 (AM_PATH_CLIPPER): Added -lm 2002-02-17 Paul Emsley * src/globjects.cc: (draw) Addeded and extra gtk_widget_draw() call. * src/Makefile.am (mapview_SOURCES): changed map.cc to xmap-interface.cc and similarly with the includes. 2002-02-14 Paul Emsley * surface/CIsoSurface.cpp: (done_line_list_t::done_line_list_t) set the start size to a typical number of vectors, 40000 (not 10). 2002-02-07 Paul Emsley * src/c-interface.cc: (make_and_draw_map) Added gtk_widget_draw for glarea. * coords/Bond_lines.cc: Moved out the old contructor from an atom_selection_container_t to tmp.cc 2002-02-06 Paul Emsley * coords/Bond_lines.cc: (Bond_lines_container) Added the delete contacts. * src/pick.cc: Chopped unproject into 2 so that unproject_xyz can be used by screen_x_to_real_space_vector(); * src/graphics-info.h: Added control_is_pressed as a public static. * src/gl-extras.cc (gl_extras): Added the focus grabbing so that we can get key [keyboard] presses.