It's not currently possible. This is functionality that would need to be added at the C++ level and then made available to Python. This is definitely an expert-level task and may take a bit of time to get done and tested.
I will create a GitHub entry for this in the next day or so On Sunday, November 15, 2015, Janusz Petkowski <[email protected]> wrote: > Dear Greg, > > > Thank you very much for addressing my macrocycles question. > > > If this is not to much trouble for you could you give me a short guide how > should I proceed with editing RingInfo data structure so it "forgets" that > rings above a certain size exist? > > > I am sorry to burden you with this but I only started learning programming > around two months ago and my python programming skills are still quite > limited. > > > Thanks a lot for all your help! > > > Janusz Petkowski > ------------------------------ > *From:* Greg Landrum [[email protected] > <javascript:_e(%7B%7D,'cvml','[email protected]');>] > *Sent:* Saturday, November 14, 2015 11:37 PM > *To:* Janusz Petkowski > *Cc:* [email protected] > <javascript:_e(%7B%7D,'cvml','[email protected]');> > *Subject:* Re: [Rdkit-discuss] defining the size of the ring in the > ringMatchesRingOnly and completeRingsOnly methods - the macrocycles case > > Dear Janusz, > > This isn't currently possible. > The most straightforward way I could think to implement it (maybe someone > else has a better idea?) would be to allow the molecule's RingInfo data > structure to be edited so that you could, for example, tell it to "forget" > that rings above a certain size exist. > > This would be relatively straightforward to do and I could imagine that > functionality being useful in other places as well. > > -greg > > > On Sun, Nov 15, 2015 at 12:08 AM, Janusz Petkowski <[email protected] > <javascript:_e(%7B%7D,'cvml','[email protected]');>> wrote: > >> One other question about MCS, in addition to my previous one on >> hybridization: >> >> In the RDKit documentation in the Maximum Common Substructure (MCS) >> section it is mentioned that one can restrict mapping linear fragments on >> to rings using two methods: ringMatchesRingOnly and completeRingsOnly. >> >> It is an extremely useful method but is there a possibility to restrict >> execution of this method by defining the size of the rings for which ring >> bonds will match only ring bonds in a given molecule? But at the same time, >> for rings of a certain size (let's say for rings that have below 8 atoms) >> the function is still executed? I am trying to avoid the problem of not >> finding linear fragments in the macrocycles structures. I want linear >> fragments to be matched in macrocycles but not in rings of smaller >> ("regular") size, all within the same molecule of course. Is there a way to >> do that? >> >> Just as an illustration of the problem: >> >> Is it possible to find ClCC=C fragment in CC(F)C1CC\C=C(C)\C(Cl)C2C=CC( >> Br)CC2[C@H](C)[C@]2(O)OC3=C(C)C(=O)C(O)=C([C@@H]4O[C@H]1[C@H](C)[C@H >> ](O)[C@H]4C)C3=C2 >> but at the same time avoid finding CC(Br)C=C in it, by using the >> ringMatchesRingOnly and completeRingsOnly methods? >> With current implementation of ringMatchesRingOnly and completeRingsOnly >> methods they treat all the rings the same way, no matter the size. >> If not, how would one do that? >> >> Thanks a lot for your help! >> >> Have a great weekend! >> >> Best regards, >> >> Janusz Petkowski >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> <javascript:_e(%7B%7D,'cvml','[email protected]');> >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >> >
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