def _mols2imageString(mols, size, legend, format, recalc=False, highlightMatch=None): """Take an input stream for the molecule image and return as a string""" if not mols: return '' # if recalc: # _apply(mols, _computeCoords) imageData = StringIO.StringIO() for mol in mols: try: SanitizeMol(mol, sanitizeOps=SanitizeFlags.SANITIZE_ALL ^ SanitizeFlags.SANITIZE_CLEANUPCHIRALITY ^ Chem.SanitizeFlags.SANITIZE_SETCONJUGATION ^ Chem.SanitizeFlags.SANITIZE_SETAROMATICITY) except ValueError: return imageData.getvalue() AllChem.AssignAtomChiralTagsFromStructure(mol, replaceExistingTags=False) _mols2imageStream(mols, imageData, format, size, legend, highlightMatch=highlightMatch) return imageData.getvalue()
def update_stereochemistry(self, conformer=-1): """ Updates stereochemistry tags in :attr:`Molecule.mol`. Parameters ---------- conformer : :class:`int`, optional The conformer to use. Returns ------- None : :class:`NoneType` """ for atom in self.mol.GetAtoms(): atom.UpdatePropertyCache() rdkit.AssignAtomChiralTagsFromStructure(self.mol, conformer) rdkit.AssignStereochemistry(self.mol, True, True, True)
def update_stereochemistry(mol): for atom in mol.GetAtoms(): atom.UpdatePropertyCache() rdkit.AssignAtomChiralTagsFromStructure(mol) rdkit.AssignStereochemistry(mol, True, True, True)