molenc_std.py: add -p|--preserve-stereo
UnixJunkie opened this issue · comments
keep stereo chemistry info if present; currently I think any of it is discarded
and really test it compared to the previous version
def super_parent(self, mol, skip_standardize=False):
"""Return the super parent of a given molecule.
THe super parent is fragment, charge, isotope, stereochemistry and tautomer insensitive. From the input
molecule, the largest fragment is taken. This is uncharged and then isotope and stereochemistry information is
discarded. Finally, the canonical tautomer is determined and returned.
:param mol: The input molecule.
:type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The super parent molecule.
:rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
"""
if not skip_standardize:
mol = self.standardize(mol)
# We don't need to get fragment parent, because the charge parent is the largest fragment
mol = self.charge_parent(mol, skip_standardize=True)
mol = self.isotope_parent(mol, skip_standardize=True)
mol = self.stereo_parent(mol, skip_standardize=True)
mol = self.tautomer_parent(mol, skip_standardize=True)
mol = self.standardize(mol)
return mol
included in v16.14.2