Hi Kovas, For your use-case #2 should suffice, "set STEREOCIS/STEREOTRANS tags + manually set stereo atoms". This is what the EnumerateStereoisomers code does: https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/EnumerateStereoisomers.py#L38
As to what is the 'ground truth', that is a more difficult question that I fear the answer may be 'none of them'. STEREOCIS/STEREOTRANS are rather recent additions to the RDKit API, while we strived to make sure STEREOCIS/STEREOTRANS across the RDKit, there are probably looming bugs in untested parts of the RDKit that don't handle them properly. However, I think those other APIs should be fixed to handle them properly, so please do report any problems you spot into the github issue tracker. Cheers, Brian On Mon, Dec 3, 2018 at 7:00 PM Kovas Palunas <kovas.palu...@arzeda.com> wrote: > Hi All, > > > > I’m looking for a bit more clarity regarding double bond stereochem in > RDKit. Currently, my understanding is that there are 3 ways to currently > store this information: > > > > 1. STEREOE/STEREOZ tags + stereo atoms on either side of bond set by > CIP ranks, as computed when calling MolFromSmiles to make a new molecule or > AssignStereochemistry on an existing molecule > 2. Manually set STEREOCIS/STEREOTRANS tags + manually set stereo atoms > 3. ENDUPRIGHT/etc. single bond directionality tags, which are set when > reading a molecule from smiles/inchi/mol file > > > > Is one of these methods the “ground truth” that is looked for by RDKit > functions that care about this info, like the substructure matching code or > the SMILES writing code? > > > > I am currently working on code that mutates molecules using a > predetermined list of changes to be made to the molecule. I’d like to be > able to include bond stereochemistry changing/creation/destruction here, > and was thinking of doing so using the STEREOCIS/STEREOTRANS tags (and also > providing the reference stereo atoms). Before I do this I want to make > sure that molecules with these tags will be handled correctly by other > RDKit functions downstream. Would these tags be a good choice here? Are > there any caveats I should keep in mind as I work with this information? > > > > Thanks! > > > > - Kovas > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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