ccp4=$HOME/ccp4/ccp4-src-2015-02-05/ccp4-6.5
prfx=$HOME/autobuild/build-coot+rdkit-pre-release-gtk2-python
prfx=$HOME/autobuild/build-refinement-pre-release-gtk2-python

install_prefix=$prfx

# export PATH=$prfx/bin:$PATH
# export PATH=$prfx/bin:$ccp4/bin:$PATH
# export DYLD_FALLBACK_LIBRARY_PATH=$ccp4/lib:$prfx/lib
# export DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib:$ccp4/lib

echo  we add X11 here to get pthread-stubs

export PKG_CONFIG_PATH=$prfx/lib/pkgconfig:$ccp4/lib/pkgconfig:/opt/X11/lib/pkgconfig
export PATH=$prfx/bin:$PATH
# export DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib
export DYLD_FALLBACK_LIBRARY_PATH=$prfx/lib:$ccp4/lib

RDKIT_CXXFLAGS=-I$prfx/include/rdkit 

pkg-config --modversion cairo
pkg-config --cflags cairo
pkg-config --libs cairo

RDKIT_LIBS="-L$prfx/lib -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral"

# for some reason we need to name libMolDraw2D.dylib explicitly - I get linking errors if not.
RDKIT_LIBS="-L/Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib  /Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/libMolDraw2D.dylib /Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib/libForceFieldHelpers.dylib -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral"

RDKIT_LIBS="-L$prfx/lib $prfx/lib/libMolDraw2D.dylib $prfx/lib/libForceFieldHelpers.dylib $prfx/lib/libDescriptors.dylib $prfx/lib/libForceField.dylib $prfx/lib/libSubstructMatch.dylib $prfx/lib/libOptimizer.dylib $prfx/lib/libDistGeomHelpers.dylib $prfx/lib/libDistGeometry.dylib $prfx/lib/libAlignment.dylib $prfx/lib/libEigenSolvers.dylib $prfx/lib/libDepictor.dylib $prfx/lib/libMolChemicalFeatures.dylib $prfx/lib/libFileParsers.dylib  $prfx/lib/libRDGeometryLib.dylib $prfx/lib/libGraphMol.dylib $prfx/lib/libSmilesParse.dylib $prfx/lib/libDataStructs.dylib $prfx/lib/libRDGeneral.dylib -lRDGeneral"

RDKIT_LIBS="-L$prfx/lib -lRDKitMolDraw2D -lRDKitForceFieldHelpers -lRDKitDescriptors -lRDKitForceField -lRDKitSubstructMatch -lRDKitOptimizer -lRDKitDistGeomHelpers -lRDKitDistGeometry -lRDKitAlignment -lRDKitEigenSolvers -lRDKitDepictor -lRDKitMolChemicalFeatures -lRDKitFileParsers  -lRDKitRDGeometryLib -lRDKitGraphMol -lRDKitSmilesParse -lRDKitDataStructs -lRDKitRDGeneral -lboost_python -lpython2.7"

# this form is needed for "correct" libtool linking so that _coot.so gives the right libraries, viewed with otool -L
# RDKIT_LIBS="-L/Users/pemsley/autobuild/build-coot+rdkit-pre-release-gtk2-python/lib -lMolDraw2D -lForceFieldHelpers -lDescriptors -lForceField -lSubstructMatch -lOptimizer -lDistGeomHelpers -lDistGeometry -lAlignment -lEigenSolvers -lDepictor -lMolChemicalFeatures -lFileParsers  -lRDGeometryLib -lGraphMol -lSmilesParse -lDataStructs -lRDGeneral"

MOLTRIANGLES_LIBS="-L$prfx/lib -lMoleculesToTrianglesCXXSurface -lMoleculesToTrianglesCXXClasses"
MOLTRIANGLES_CPPFLAGS="-DUSE_MOLECULES_TO_TRIANGLES -I$prfx/include/MoleculesToTriangles"

compiler_flags="-g -O3 -fno-omit-frame-pointer -Wno-null-dereference -Wno-parentheses-equality -Wno-tautological-compare -Wno-deprecated-declarations -Wsign-compare -Wno-deprecated-register"


# startup problems were due to __init__.py being in the install python directory

# python needs (some of?) these to link properly (now that we use SSL).
# -lssl -lcrypto -lldap -lz
PYTHON_EXTRAS="-lssl -lcrypto -lldap -lz"

bash ../coot/configure \
   --prefix=$install_prefix \
   --with-fftw-prefix=$prfx \
   --with-goocanvas-prefix=$prfx \
   --with-boost=$prfx \
   --with-guile \
   --with-guile-gtk=$prfx \
   --with-python \
   --with-pygtk \
   --with-sqlite3 \
   --with-modern-language-tools \
   --with-enhanced-ligand-tools \
   --disable-static \
   --with-glut-prefix=/opt/X11 \
   CPPFLAGS=-I/opt/X11/include \
   LDFLAGS="-L$prfx/lib -L$ccp4/lib" \
   CXXFLAGS="$compiler_flags" \
   RDKIT_CXXFLAGS=$RDKIT_CXXFLAGS \
   RDKIT_CXXFLAGS=$RDKIT_CXXFLAGS \
   MOLTRIANGLES_CPPFLAGS="$MOLTRIANGLES_CPPFLAGS" \
   RDKIT_LIBS="$RDKIT_LIBS $PYTHON_EXTRAS" MOLTRIANGLES_LIBS="$MOLTRIANGLES_LIBS"



   # CXXFLAGS="-g -fsanitize=address -fno-omit-frame-pointer -Wno-null-dereference -Wno-parentheses-equality -Wno-tautological-compare -Wno-deprecated-declarations -Wsign-compare" 
# -Wno-null-dereference: noisy compile of guile headers
# -Wno-deprecated-declarations: noisy compile when using GLUT