std::string MolFragmentToSmilesHelper(const ROMol &mol,
python::object atomsToUse,
python::object bondsToUse,
python::object atomSymbols,
python::object bondSymbols,
bool doIsomericSmiles,
bool doKekule,
int rootedAtAtom,
bool canonical,
bool allBondsExplicit
){
std::vector<int> *avect=pythonObjectToVect(atomsToUse,static_cast<int>(mol.getNumAtoms()));
if(!avect || !(avect->size())){
throw_value_error("atomsToUse must not be empty");
}
std::vector<int> *bvect=pythonObjectToVect(bondsToUse,static_cast<int>(mol.getNumBonds()));
std::vector<std::string> *asymbols=pythonObjectToVect<std::string>(atomSymbols);
std::vector<std::string> *bsymbols=pythonObjectToVect<std::string>(bondSymbols);
if(asymbols && asymbols->size()!=mol.getNumAtoms()){
throw_value_error("length of atom symbol list != number of atoms");
}
if(bsymbols && bsymbols->size()!=mol.getNumBonds()){
throw_value_error("length of bond symbol list != number of bonds");
}
std::string res=MolFragmentToSmiles(mol,*avect,bvect,asymbols,bsymbols,
doIsomericSmiles,doKekule,rootedAtAtom,
canonical,allBondsExplicit);
if(avect) delete avect;
if(bvect) delete bvect;
if(asymbols) delete asymbols;
if(bsymbols) delete bsymbols;
return res;
}
void drawMoleculeHelper2(MolDraw2D &self, const ROMol &mol,
python::object highlight_atoms,
python::object highlight_bonds,
python::object highlight_atom_map,
python::object highlight_bond_map,
python::object highlight_atom_radii, int confId = -1) {
rdk_auto_ptr<std::vector<int> > highlightAtoms =
pythonObjectToVect(highlight_atoms, static_cast<int>(mol.getNumAtoms()));
rdk_auto_ptr<std::vector<int> > highlightBonds =
pythonObjectToVect(highlight_bonds, static_cast<int>(mol.getNumBonds()));
// FIX: support these
std::map<int, DrawColour> *ham = pyDictToColourMap(highlight_atom_map);
std::map<int, DrawColour> *hbm = pyDictToColourMap(highlight_bond_map);
std::map<int, double> *har = pyDictToDoubleMap(highlight_atom_radii);
self.drawMolecule(mol, highlightAtoms.get(), highlightBonds.get(), ham, hbm,
har, confId);
delete ham;
delete hbm;
delete har;
}
void drawMoleculeHelper1(MolDraw2D &self, const ROMol &mol,
python::object highlight_atoms,
python::object highlight_atom_map,
python::object highlight_atom_radii, int confId = -1) {
std::vector<int> *highlightAtoms =
pythonObjectToVect(highlight_atoms, static_cast<int>(mol.getNumAtoms()));
std::map<int, DrawColour> *ham = pyDictToColourMap(highlight_atom_map);
std::map<int, double> *har = pyDictToDoubleMap(highlight_atom_radii);
self.drawMolecule(mol, highlightAtoms, ham, har, confId);
delete highlightAtoms;
delete ham;
delete har;
}
