Merge pull request #702 from RosettaCommons/JWLabonte/sugars/input
Carbohydrates: making Rosetta correct PDB files created by GLYCAM on input
GLYCAM is a popular MD tool for carbohydrates. Unfortunately, it has its own three-letter code and treats the HO- group or RO- group of reducing end residues as their own residues. This merge will try and have Rosetta fix this problem automatically with the -glycam_pdb_format flag.
This merge will also make it so that one no longer has to use the -override_rsd_type_limit with sugars. -include_sugars will set that option automatically.
only expected carbohydrates test changes from changed flag and input files