Hi Ling, That's a bug in AssignAtomChiralFlags(): it doesn't recognize that chirality needs to be perceived at the S atom. I will add that to the list of things to be fixed.
Thanks for reporting the problem. -greg On Sat, Sep 5, 2015 at 1:55 AM, Ling Chan <lingtrek...@gmail.com> wrote: > Dear colleagues, > > I have a sulfoxide molecule (ligand of 1A9U from the PDB, the SDF is > attached). The geometry at the sulfur is not planar. When I tried to get a > smiles with stereo data using > > AllChem.AssignAtomChiralTagsFromStructure(mol) > Chem.MolToSmiles(mol, isomericSmiles=True) > > it does not output the chirality at the sulfur. Can I force it to output > the chirality? > > Thank you. > > Ling > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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