> > The GasteigerPEPEPartialCharges is based on resonance structures. If > > the method doesn't find any (line 237) and this is the case > > for c1ccccc1CN what I can see, the method goes out no setting any > > charge. > > But the ring itself will have resonance structures (?) So shouldn't > they be taken into account?
It is true. I put two test StructureResonanceGeneratorTest.testBenzylamine and StructureResonanceGeneratorTest.testBenzylamine_Aromatic. And there you can see that with detection aromaticity the detection of resonance fails. I added also the test as a bug. > > One of the problems setting charge into an atom is that > > atom.setCharge > > method does not distinguish between what charge it means: either > > sigma, > > pi or total charge. > > I'm confused as to the semantics of the PEPE class. You note that if > I use it, I don't need to use the PEOE class, since it will calculate > both. But for my example, it doesn't calculate either of the charges. > Well not exactly. I wanted to say that if you used the PEPE method you calculate the pi-charge and if you used the PEOE method you calculate the sigma-charge. The PEPE method internally used the PEOE method to calculate the sigma partial charge of the resonance structures if are found one but not the own compound. > > My suggestion could > > be to calculate the total charge, have a look to > > PartialTChargePEOEDescriptor please. > > Aah, thanks. Wouldn't it make sense to have this class as part of the > charge package and the descriptor would be a wrapper around it? For me it is perfect. ------------------------------------------------------------------------- Sponsored by: SourceForge.net Community Choice Awards: VOTE NOW! Studies have shown that voting for your favorite open source project, along with a healthy diet, reduces your potential for chronic lameness and boredom. Vote Now at http://www.sourceforge.net/community/cca08 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
