Hello, I'm trying to find a mapping between two molecules, specifically matching up the corresponding atoms. I've had success with SubstructMatch, if one of the molecules is a proper substructure of the other, but that doesn't generalize well.
My initial attempts at a general solution have been with the findMCS function, using the resultant SMARTS string to generate a query molecule, then using SubstructMatch to find each molecules mapping to the query molecule, and converting those results to a direct molecule-molecule mapping. Not only does it seem rather circuitous, I've run into situations where findMCS gives back a reasonable SMARTS string, but the SubstructMatch steps don't find matches to the original molecules. It's probably some subtle atom/bond property issue, as after bouncing the molecules through SMILES strings I can get matches. (Which is to say I don't have an isolatable case I could share.) Is there an easier way of mapping atoms between two molecules with RDKit? (I'm doing this on the C++ level, and am not adverse to some light patching of the RDKit source code.) Thanks, -Rocco
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
