Hi James, IIRC that's a known open issue with the way spirocyclic pseudochiral centers are handled:
https://github.com/rdkit/rdkit/issues/3490 Cheers, p. On Sun, May 9, 2021 at 10:15 AM James Davidson <j.david...@vernalis.com> wrote: > Dear All, > > > > I am having some issues with tetrahedral stereochemistry perception in > RDKit (2020.09.4) for a certain class of molecule. > > Here’s an example (rendered using cdk-depict): > > > > > https://www.simolecule.com/cdkdepict/depict/bot/svg?smi=F%5BC%40H%5D1C%5BC%40%40%5D2(C1)C%5BC%40H%5D(Cl)C2&w=-1&h=-1&abbr=off&hdisp=bridgehead&showtitle=false&zoom=3.65&annotate=cip&r=0 > > > > If I try to work with this class of molecule in RDKit, it seems > impossible(?) to assign stereo information to the central, spirocyclic > stereo centre. > > Exporting back out as SMILES shows that the information is not present: > > > > m = Chem.MolFromSmiles('F[C@H]1C[C@@]2(C1)C[C@H](Cl)C2') > > print(Chem.MolToSmiles(m)) > > > > >>> F[C@H]1CC2(C1)C[C@H](Cl)C2 > > > > The spiro-atom is clearly being identified as a potential stereo-centre > (strangely, the CIP labels aren’t being generated for the other two centres > – just the parity info is returned): > > > > centers = Chem.FindMolChiralCenters(m, includeUnassigned=True, > useLegacyImplementation=False) > > print(centers) > > > > >>> [(1, 'Tet_CW'), (3, '?'), (6, 'Tet_CCW')] > > > > If I look at the atom properties for the central atom, I can see > _ChiralityPossible > == 1, but I also see _ringStereochemCand == False. > > Is this the problem? > > > > Any help/advice greatly appreciated! > > > > Kind regards > > > > James > ------------------------------ > > PLEASE READ - This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or postmas...@vernalis.com. Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > Vernalis (R&D) Limited (no. 1985479) > Granta Park, Great Abington > Cambridge, CB21 6GB, United Kingdom > Tel: +44 (0)1223 895 555 > ------------------------------ > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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