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?
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