Patch System: added 3 new PatchOperations
NEWS: This push introduces three new PatchOperations to the patch system:
- ADD_ATOM_ALIAS -- allows one to specify alternative atom names that Rosetta
will understand when reading in a PDB file
- ADD_BOND_TYPE -- an alternative to ADD_BOND that allows specification of
bond type
- SET_FORMAL_CHARGE -- sets the formal charge of a specified atom
All of the above new operations rely on code written by R. Moretti and co.; I
simply added the functionality to the patch system as well. (Previously, atom
aliases, bond types, and formal charges could only be added/set from .params
files.)
The above operations were added to carbohydrate patch files were applicable.
The carbohydrates integration test was expanded to specifically test that the
atom aliases work: a pdb with non-Rosetta atom names correctly loads in.
In addition, centroid-mode sugars were updated, (which at this point are
simply copies of the fa_standard ones).
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Unit test status: Pass
Integration test status: Not Run (Only sugar code makes use of the additions.)
carbohydrates: test expanded