Hello Per,

Apparently the default for FindMolChiralCenters is that only explicitly
specified chiral centers are output. Try the following.

Chem.FindMolChiralCenters(mh, includeUnassigned=True)

As for AssignAtomChiralTagsFromStructure , I think it detects chirality
from 3D structures. You need atomic coordinates for it to work.

Ling


On Sat, Aug 5, 2017 at 11:35 AM, Per Jr. Greisen <pgrei...@gmail.com> wrote:

> Hi all,
>
> I have an issue to correctly assign chirality through RDkit so I have the
> following isomers around a phosphorus atom:
>
> smiles = 'CCOP(C)(=O)SCC[NH+](C(C)C)C(C)C'
> m = Chem.MolFromSmiles(vx_smiles)
> mh = Chem.AddHs(m)
>
> m_s = Chem.MolToSmiles(Chem.MolFromSmiles(smiles),isomericSmiles=True)
>
> Chem.FindMolChiralCenters(mh)
>
> # returns none
> None
>
> #
> Chem.AssignAtomChiralTagsFromStructure(vxm_h)
> None
>
>
> How to resolve this - I am just starting to use RDkit and it is seems very
> promissing
>
> Thanks
>
>
> --
> With kind regards
>
> Per
>
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