You need to look at the definition in the original reference; you won't be able to reproduce the model unless you use the same definitions.
I'm pretty sure that it doesn't involve 3d structures or partial charge calculations. Think about how you would identify hydrophobic atoms given a molecular diagram. Everything that's not carbon, would be a good starting point. Regarding the carbons, is it only sp3 they mean? Who knows. - Noel On Tue, 20 Nov 2018 at 23:53, Leif Peterson <leifepeter...@sbcglobal.net> wrote: > One of the weights for a particular LogS method requires the number of > hydrophobic carbons. So I added hydrogens, transformed to three > dimensions, energy minimized with gradient descent (don't need conformers > here), then parsed the mol2 output to fetch the partial charge on the far > right side. While this is the partial charge of each atom in its 3d > protonated form, I wonder if this is overkill? OBAtom doesn't have an > atom.IsPolar or atom.HasCovalentBond, and the atom.GetpartialCharge is zero > for every carbon. Is there an easy way to do this for LogS? > > > > > > Get Outlook for Android <https://aka.ms/ghei36> > > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >
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