Hi rdkitters,
I wrote a very small python snippet to detect all chiral centers of a
molecule, including unspecified ones:
# from rdkit import Chem
def getStereo(smiles):
m = Chem.MolFromSmiles(smiles)
Chem.AssignStereochemistry(m,
cleanIt=True,flagPossibleStereoCenters=True, force=True)
return Chem.FindMolChiralCenters(m, includeUnassigned=True)
However this seems to provoke errors in some cases (or I'm confused!),
for instance:
> smiles='C=S(c1ccccc1)S(=C)c1ccccc1'
> getStereo(smiles)
[(1, '?'), (8, '?')]
I did not expect these sulphur atoms to be considered chiral.
Another example would be:
> smiles='C[C@@H]1O[C@H](C)CC[NH+]1CC1CC(=O)Oc2cc3ccccc3cc21'
> getStereo(smiles)
[(1, 'S'), (3, 'R'), (7, '?'), (9, '?')]
This means that the [NH3+] is considered chiral, is it expected?
Any idea of what went wrong? Or am I missing something?
I read the 'Possible stereo centers incorrectly assigned?' thread and
tested John's function, but as far as I know"_CIP" properties are
present only on assigned chiral atoms, so it would not (directly) answer
my needs.
Thank you for your help!
Jose Manuel
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