Okay cool, yeah you can't avoid aromaticity with SMARTS :-). Yep Daylight method is correct in this case. Still need to back port Ambit SMIRKs at some point.
John Regards, John W May john.wilkinson...@gmail.com On 10 November 2015 at 15:17, Martin Gütlein <guetl...@posteo.de> wrote: > Hi John, > > thanks for the patch. > > > I should also disclaim that I don't think the concept is in general > useful, may I ask why you need it? > > You mean the daylight aromaticity concept? > We are migrating a pathway prediction system from chemaxon to cdk + > ambit-smarts. Chemaxon had apparently a similar aromaticity concept as > daylight, and the reaction rules have been defined accordingly. Some cannot > be applied when using the standard cdk aromaticity. > > Regards, > Martin > > > > > > > Am 10.11.2015 um 16:12 schrieb John M: > > Forwarding to list. > > Regards, > John W May > john.wilkinson...@gmail.com > > On 10 November 2015 at 15:04, John M <john.wilkinson...@gmail.com> wrote: > >> Patch: https://github.com/cdk/cdk/pull/172 >> >> There is no default, you need to decide what's best. I'll admit the >> naming 'cdkAromaticSet()' makes it sound useful for aromaticity but it >> was basically just a restricted set of cycles used in the old aromaticity >> model. >> >> I tend to used *Cycles.all()* or *Cycles.or(Cycles.all(), >> Cycles.edgeShort())* since the first one will fail for ring systems >> like Fullerene C60. Some might think SSSR is sensible but then in Fullerene >> C60, you'll have one ring in fullerene C60 which isn't aromatic. Another >> common approach is to restrict the size of the cycle (ala Open Babel) but >> it's easy to quickly find examples with large aromatic rings. >> >> I should also disclaim that I don't think the concept is in general >> useful, may I ask why you need it? >> >> John >> >> Regards, >> John W May >> john.wilkinson...@gmail.com >> >> On 10 November 2015 at 14:54, Martin Gütlein < <guetl...@posteo.de> >> guetl...@posteo.de> wrote: >> >>> Hi John, >>> >>> thanks for your response, so you will commit a fix for that? That would >>> be great, I would merge that fix into our cdk 1.5.11 build... >>> >>> > Also you shouldn't use cdkAromaticSet() cycles... >>> So whats the default, .all() ? >>> >>> Kind regards, >>> Martin >>> >>> >>> Am 10.11.2015 um 15:45 schrieb John M: >>> >>> Hi Martin, >>> >>> The daylight model should... but I some point I added a valence >>> constraint ( >>> https://github.com/cdk/cdk/blob/master/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java#L277). >>> Simple fix so will allow 4 and 6 for S and Se. >>> >>> Also you shouldn't use cdkAromaticSet() cycles... that's there for >>> legacy reasons and doesn't handle porphyrin correctly (for example). >>> >>> John >>> >>> Regards, >>> John W May >>> john.wilkinson...@gmail.com >>> >>> On 10 November 2015 at 08:33, Martin Gütlein < <guetl...@posteo.de> >>> guetl...@posteo.de> wrote: >>> >>>> Hi, >>>> >>>> is there an aromaticity model in CDK that works for this structure: >>>> O=s1cncc1 ? >>>> >>>> This is what I tried: >>>> String smiles = "O=s1cncc1"; >>>> IAtomContainer mol = new >>>> SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles); >>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); >>>> CycleFinder cycles = Cycles.cdkAromaticSet(); >>>> ElectronDonation model = ElectronDonation.cdk(); //.daylight() >>>> Aromaticity aromaticity = new Aromaticity(model, cycles); >>>> System.out.println("is-aromatic: " + aromaticity.apply(mol)); >>>> >>>> Kind regards, >>>> Martin >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> Cdk-user@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>> >>> >>> >>> >> > > > ------------------------------------------------------------------------------ > > > > _______________________________________________ > Cdk-user mailing > listCdk-user@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/cdk-user > > > -- > Dr. Martin Gütlein > Phone:+49 (0)6131 39 23336 (office)+49 (0)177 623 9499 (mobile) > Email:guetl...@uni-mainz.de > >
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