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 > > >
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