Hi Rocco, I'm glad you found that, it saves us all a lot of head scratching. :-) I think the approach you describe - do an MCS calculation and then use the resulting SMARTS to determine the atom mapping - is the best approach for finding a mapping between molecules if you aren't sure that one is a substructure of the other.
best, -greg On Sun, Oct 18, 2015 at 11:50 PM, Rocco Moretti <rmoretti...@gmail.com> wrote: > Oops. Turns out that the issue I had with the found substructure SMARTS > not matching the original molecules was a rather bone-headed bug in my code > -- I was accidentally swapping the molecules with respect to the function > signature. Sorry for the false alarm. > > I'm still curious if there is an easier way to match up atoms in two > structures, though. > > Thanks, > -Rocco > > > On Sat, Oct 17, 2015 at 5:18 PM, Rocco Moretti <rmoretti...@gmail.com> > wrote: > >> 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 > >
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
