Thanks for looking into it. I'm happy to see.it wasn't just a mistake by me ;-)
I hope we can find what's wrong there. Best, Gustavo. -- Gustavo Seabra ________________________________ From: Adelene LAI <adelene....@uni.lu> Sent: Friday, October 23, 2020 11:28:55 PM To: Gustavo Seabra <gustavo.sea...@gmail.com>; RDKit Discuss <rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key Hi Gustavo, <https://gist.github.com/adelenelai/59a8794e1f030941c19bcb50aa8adf3f>https://gist.github.com/adelenelai/59a8794e1f030941c19bcb50aa8adf3f In the gist above, I tried doing some further investigating. It seems for the example you gave, the rdkit functions indeed give the same inchikey and inchi, but different aux info. Why this different aux info doesn't translate into different inchikeys/inchis, I'm not sure. Adelene Doctoral Researcher Environmental Cheminformatics UNIVERSITÉ DU LUXEMBOURG LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE 6, avenue du Swing, L-4367 Belvaux T +356 46 66 44 67 18 [github.png] adelenelai ________________________________ From: Gustavo Seabra <gustavo.sea...@gmail.com> Sent: Friday, October 23, 2020 6:43:07 PM To: RDKit Discuss Subject: [Rdkit-discuss] Nitrogen sp2 isomers get the same InChI Key Hi all, I run into an issue here, and I'd appreciate your input. I noticed that compounds that differ only on the cis-trans isomerization around an sp2 nitrogen get the same InChI Key from RDKit. For example: > inchi_cis = > Chem.inchi.MolToInchiKey(Chem.MolFromSmiles("C/N=C(/NC#N)NCCSCc1nc[nH]c1C")) > inchi_cis 'AQIXAKUUQRKLND-UHFFFAOYSA-N' > inchi_trans = > Chem.inchi.MolToInchiKey(Chem.MolFromSmiles("C/N=C(\\NC#N)NCCSCc1nc[nH]c1C")) > inchi_trans 'AQIXAKUUQRKLND-UHFFFAOYSA-N' > inchi_cis == inchi_trans True I wonder if this is a limitation of the InChI Key definition, or an implementation issue. Thanks a lot, -- Gustavo Seabra.
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