Branching: Various updates to branching/chemical conjugation: Part A
This is a merging in of Part A of Pull Request #459
NEWS: This merge...
* Adds a new TorsionType for branch connection torsions, which are located at
CHEMICAL EDGEs of the FoldTree.
* Adds a new BRANCH TorsionType to MoveMap.
* Adds the ability to get or set a torsion angle in the AtomTree by TorsionID
containing a BRANCH TorsionType.
* Allows the minimizer functionality to minimize TorsionIDs containing BRANCH
TorsionTypes if permitted by MoveMap.
* Has Rosetta automatically set up a FoldTree in the reverse direction for
ubiquitin on load-in from a PDB file without resorting to Movers by using
LINK records (as wanted by @hajosep).
* Has Rosetta ignore LINK records defining sugar main chains that Rosetta could
figure out on its own anyway (as wanted by @fdimaio for easier loading of
glycoproteins for crystal refinement).
* Automatically sets angle and bond constraints for chemical conjugation based
on LINK records.
@everyday847 also contributed to this branch.
I am keeping the pull request open, as not all desired/related tasks are
completed.
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Unit test status: Pass
Integration test status: 20 changed tests
carbohydrates: expected
c_term_conjugation: new
18 other tests: output modifications regarding branches or the MoveMap