addHydrogens ( atomList, *args )
Add hydrogens to maximize h-bonding and minimize steric clashes.
First, add hydrogens that are fixed and always present. Then,
find H-bonds only to possibly-hydrogen-needing donors. For
aromatic nitogens protonate at least one on a six-membered ring.
For remaining rotamers with H-bonds, place hydrogens
to maximize H-bond interactions. Then, for remaining rotamers,
minimize steric clashes via torsion-driving.
May not work well for atoms that are already partially
hydrogenated.
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Exceptions
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AssertionError, "bad geometry for atom" " (%s) with one bond partner" % atom.oslIdent()
AssertionError, "bad geometry for atom" " (%s) with three bond partners" % atom.oslIdent()
AssertionError, "bad geometry for atom" " (%s) with two bond partners" % atom.oslIdent()
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