Hi Emanuel, the RDKit perceives double bond stereochemistry on read, and encodes on write, based on 2D coordinates in the molblock,
I put together an example gist here: https://gist.github.com/ptosco/9ffae8814e84bcf189da7663775748e5 I hope that addresses your question , if not feel free to get back to me. Cheers, p. On Wed, Jul 29, 2020 at 11:17 AM Emanuel Ehmki <emanuel.eh...@gmail.com> wrote: > Dear All, > > I am currently working with the RDKit generated SDF String that is stored > in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26. > My workflow is: > > - pull SDF (V2000) from SQL table > - generate internal molecule representation (NAOMI ChemBio tool-kit if > that means anything to you) > - generate InChI string and key from molecule > - compare with InChI string and key that are stored in the ChEMBL > database > > When comparing the InChI string for the molecule with the id CHEMBL6223, I > get two differing strings due to different stereochemistry (last characters) > > ChEMBL > InChI: > InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/ > *b12-10+* > NAOMI InChI > : > InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/ > *b12-10-* > > While researching why that happens I realized that the SDF string doesn't > make use of the chirality bit that can be set in the counts line. > When digging deeper I found the disabled block in the MolFileWriter.cpp -> > MolToMolBlock function > > https://github.com/rdkit/rdkit/blob/f14f8a60de0ecf4bf5294d73b177d19055e0096d/Code/GraphMol/FileParsers/MolFileWriter.cpp#L1395 > > Do I understand correctly that RDKit does not store any information about > chirality in V2000 and includes chiral information only in V3000 SDF format? > > Does anyone know when ChEMBL might switch to that version? > > Kind regards, > Emanuel > _______________________________________________ > Rdkit-devel mailing list > Rdkit-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-devel >
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