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Revisions №59514

branch: master 「№59514」
Commited by: Vikram K. Mulligan
GitHub commit link: 「769df8c0a7939a8b」 「№2075」
Difference from previous tested commit:  code diff
Commit date: 2017-06-02 22:10:22

Merge pull request #2075 from RosettaCommons/vmullig/add_trimesic_acid Add trimesic acid (crosslinker) This adds trimesic acid, a three-way crosslinker that can be used in peptide synthesis. Tasks: - [x] Add params file (note that crosslinkers are off by default in residue_types.txt). - [x] Set up virtual atoms. - [x] Set up connections. - [x] Ensure overall neutral charge. - [x] Ensure symmetry. - [x] MM atom types. - [x] Chi definitions and rotamers (using PROTON_CHI lines in params file). Note that trimesic acid prefers +/- 30 or +/-150 degrees for chi1, chi2, and chi3. - [x] Add symmetric version of params file. - [x] Add DAP, if it doesn't already exist --> It exists; params file updated. (Called DPP in PDB; renamed to DPP in database, too.) - [x] Add DAB, if it doesn't already exist. --> It exists; params file updated. - [x] Update ornithine params file. - [x] Add sidechain conjugation patch for LYS, ORN, DAB and DAP, if it doesn't already exist. - [x] Unit test for this. - ~~Deprecate LYX? (Will have to update integration tests that use it.)~~ --> maybe in the future. - [x] Add support for TMA to CrosslinkerMover: - [x] Cherry-pick in change of name from ThreefoldLinkerMover to CrosslinkerMover (from pull request #1839). - [x] Add setup logic for TMA in the asymmetric case. - [x] Add setup logic for TMA in the symmetric case. - [x] Allow LYS, ORN, DAB, or DAP side-chains to present TMA. - [x] Unit test for functional form of constraints. - [x] Integration test -- asymmetric case. - [x] Integration test -- symmetric case. - [x] Documentation. - [x] Add support to simple_cycpep_predict for TMA. - [x] Integration test. - [x] Documentation. - [x] Add weight option to GaussianFunc (needed for the construction of a suitable torsional potential for TMA). - [x] Document changes to GaussianFunc. - [x] Calculate correct values for torsion potential to ensure +/- 30 degree minima (calculus -- yay). - [x] Add potential offset to give minimum value of 0 (more calculus). - [x] Update PatchOperations to report their own names for errors / debugging. - [x] Beauty. - [x] Document change of name of ThreefoldLinkerMover --> CrosslinkerMover. @gbhardwaj

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