Merge pull request #220 from RosettaCommons/JWLabonte/sugars/output
Carbohydrates: GWS file output
This merge introduces GlycoWorkbench structure (GWS) file output to Rosetta for carbohydrate chains.
This is the standard string format used by the glycobiology community, and the files can be opened in the GlycoWorkbench software to give a 2D "polygon" topology diagram of glycans. The files can also be linked to various glyco databases.
Future work will add GWS-reading functionality.
This merge also includes a miscellany of other sugar-related stuff from other branches that I merged into this branch because I needed them, such as:
* outputting `LINK` records to `.pdb`s
* more sugars in database
* more sugar patches in database
* more lipids in database
* sugar docking scripts/pilot apps
* code clean-up of some of my older code
* output improvements to rigid-body docking protocols
* clean-up of `pilot_apps.src.settings.all`
All unit tests pass.
`carbohydrate` integration test changes expected.
Ligand-docking and related integration test changes also expected, due to a minor improvement to RigidBodyDocking output.