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Revisions №57208

branch: master 「№57208」
Commited by: Labonte
GitHub commit link: 「87c1998e332f3d3d」
Difference from previous tested commit:  code diff
Commit date: 2014-08-18 18:51:54

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). ---------------------------------------- Unit test status: Pass Integration test status: Not Run (Only sugar code makes use of the additions.) carbohydrates: test expanded

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