Unless you can make your reactant definitions a lot more specific, I think you're going to have to do the post-processing. The RDKit just uses all possible substructure matches of the reactant templates you provide... it makes no attempt to determine which is "best".
-greg On Sun, Dec 5, 2021 at 8:24 PM James Wallace <jeawall...@gmail.com> wrote: > Here's the specific example that I was referring to: > > I used a reaction with this SMILES, making a ChemicalReaction out of it > using the add reactant templates: > > [image: image.png] > N[CH3:1].O=C(O)C(c1ccccc1)C1CCCC1>>O=C(N[CH3:1])C(c1ccccc1)C1CCCC1 > > Taking two reagents to fit it: > [image: image.png] > OC(=O)C(C1CCCC1)c1ccccc1 > > [image: image.png] > NC(=O)Nc1ccc(C(=O)O)cc1 > > Gives us products > > [image: image.png] > O=C(NC(=O)C(c1ccccc1)C1CCCC1)Nc1ccc(C(=O)O)cc1 > > [image: image.png] > NC(=O)NC(=O)C(c1ccccc1)C1CCCC1 > > [image: image.png] > O=C(O)c1ccc(NC(=O)C(c2ccccc2)C2CCCC2)cc1 > > In my case, I want to just see the result that uses the most of the > reagent in each case, and not the ones where the reagent is fragmented. > > Is that possible directly, or do I need to filter my results post hoc? > > On Thu, 2 Dec 2021 at 20:04, Paolo Tosco <paolo.tosco.m...@gmail.com> > wrote: > >> Hi James, >> >> I am not quite sure I understand what you have done and what you'd like >> to achieve. >> Ideally, could you please post: >> >> * the reaction you are using >> * some example reactants >> * the desired product(s) >> * the undesired product(s) >> >> Thanks, cheers >> p. >> >> On Thu, Dec 2, 2021 at 6:03 PM James Wallace <jeawall...@gmail.com> >> wrote: >> >>> Hi, >>> I've been working with the EnumerateLibraryFromReaction function to >>> generate some quick access molecule libraries, using standard lists of >>> reagents. >>> >>> However, when I get the output back, I notice that I get results that >>> chop up the reactants I use wherever they match the reaction rule, so for a >>> rule looking for NH I would effectively get the yellow ringed area here >>> used as a structure as well as the desired red one. >>> [image: image.png] >>> As well, since this contains acid character, it would also match there, >>> but I accept that I can't necessarily remove that. >>> >>> Is there any way I can filter out the partial usages, or am I stuck with >>> using the substructures as well? >>> >>> Thanks, >>> >>> James >>> _______________________________________________ >>> 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 >
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