Merge pull request #735 from RosettaCommons/roccomoretti/gasteiger_SO4
Gasteiger atom typing updates
We weren't appropriately handling some of the "stranger" ways of specifying certain functional groups. Add fixes and unit tests, and add an "allow_unknown" option for Gasteiger atom typing, so it doesn't crash on difficult typing.
Integration test changes in "carbohydrates" expected, as we're now special-casing the N-terminus of amino acids to get the correct typing.