Prelude to this: In general (but not always) I have tried to ensure that
the RDKit recognizes the centers that are considered potentially
stereogenic by InChI (Table 8 in the InChI technical manual). They put a
lot of thought into this and it makes sense to benefit from it.
On Tue, Sep 22, 2015 at 12:31 PM, Jose Manuel Gally <
jose-manuel.ga...@univ-orleans.fr> wrote:
> 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.
>
As John pointed out in the later message, x-S(=x)-x is considered
potentially stereogenic in InChI.
> 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?
>
That's not an [NH3+]. It's a four-coordinate, sp3 hybridized, N. That is a
potential stereocenter.
Best,
-greg
>
> 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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>
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