molenc_std.py: add -p|--preserve-stereo

[François Bérenger]

keep stereo chemistry info if present; currently I think any of it is discarded

[François Bérenger]

and really test it compared to the previous version

[François Bérenger]

    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

[François Bérenger]

included in v16.14.2