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
