Merge pull request #864 from RosettaCommons/JWLabonte/sugars/input
Carbohydrates: improving creation of glycans from sequences
This set of changes introduces the following:
* Glycans with modified sugars can be created from IUPAC sequences.
* Branched glycans can be created from IUPAC sequences.
* Protein poses can be "glycosylated" at requested positions.
* ResidueType::show() now gives information about branch point atoms.
All unit tests pass.
carbohydrates test changes expected
CCD_loop_closure test changes expected (output modifications from assigning a name to PDB_Info for sugars made from sequences)
ThreadingInputter test changes in output from change in namespace of a FoldTree function
All other integration test changes are from the usual (15) suspects, which are all (still) unstable.