Thanks Paolo - I should have found this before posting! Cheers
James On 9 May 2021, at 15:05, Paolo Tosco <paolo.tosco.m...@gmail.com> wrote: 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<mailto: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): <image002.png> 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<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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