I see, thanks. It looks like there's something else going on, as I've looked at the reaction I'm meant to be encoding here, and the intention is to have a 'wildcard' atom attached to the mapped carbon on the reactant to make it a CH2-* type environment. Clearly that's not happening, but that's on me rather than the library code, so I'll take a run at that too.
As for the other side, some sort of substructure matching to the original reactants should do it, I just need to fix the first part and see what I get before going too deep into it. On Mon, 6 Dec 2021 at 05:54, Greg Landrum <greg.land...@gmail.com> wrote: > 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 >> >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
