Hello,
Recently, I updated some Python code using
from rdkit.Chem.MolStandardize import Standardizer # rdkit <=
'2023.09.3'
to
from rdkit.Chem.MolStandardize import rdMolStandardize # rdkit >=
'2024.03.5'
Because after an rdkit fresh install, rdkit was updated and my former
code
stopped working.
My old code was this:
---
standardizer = Standardizer()
def standardize(preserve_stereo, preserve_taut, mol):
if preserve_stereo or preserve_taut:
s_mol = standardizer.standardize(mol)
# We don't need to get fragment parent, because the charge
parent is the largest fragment
s_mol = standardizer.charge_parent(s_mol, skip_standardize=True)
s_mol = standardizer.isotope_parent(s_mol,
skip_standardize=True)
if not preserve_stereo:
s_mol = standardizer.stereo_parent(s_mol,
skip_standardize=True)
if not preserve_taut:
s_mol = standardizer.tautomer_parent(s_mol,
skip_standardize=True)
return standardizer.standardize(s_mol)
else:
# standardizer.super_parent(mol): _NOT_
standardizer.standardize(mol)
# which doesn't even unsalt the molecule...
return standardizer.super_parent(mol)
---
And the new code is:
---
def standardize(preserve_stereo, preserve_taut, mol):
if preserve_stereo or preserve_taut:
# We don't need to get fragment parent, because the charge
parent is the largest fragment
s_mol = rdMolStandardize.ChargeParent(mol,
skipStandardize=False)
s_mol = rdMolStandardize.IsotopeParent(s_mol,
skipStandardize=True)
if not preserve_stereo:
s_mol = rdMolStandardize.StereoParent(s_mol,
skipStandardize=False)
if not preserve_taut:
s_mol = rdMolStandardize.TautomerParent(s_mol,
skipStandardize=False)
return s_mol
else:
return rdMolStandardize.SuperParent(mol, skipStandardize=False)
---
Which I hope is isofunctional.
The old Standardizer module had a "standardize" method.
Is this method also present in rdMolStandardize?
Has it changed name (e.g. to rdMolStandardize.Cleanup)?
Regards,
Francois.
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