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> 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> 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 >>> >> >> >> >
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