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)
