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Revisions №59885

branch: master 「№59885」
Commited by: Vikram K. Mulligan
GitHub commit link: 「07805efeb00dab5f」 「№2740」
Difference from previous tested commit:  code diff
Commit date: 2017-11-28 04:33:59

Merge pull request #2740 from RosettaCommons/vmullig/netcharge Adding a score term that penalizes deviation from a desired net charge in a pose or region This is to complement @dougrenfrew's refactoring of the Supercharge application (pull request #2721 and #2737). The term, called `netcharge` will be analogous to `aa_composition`, but instead of letting a user control amino acid composition, it will let him or her control regional or global net charge in any context that calls the packer. (Used in conjunction with `aa_composition`, it can also control total number of charged residues. It will also be usable with the `hbnet` score term to create hydrogen bond networks with a desired net charge.) Tasks: - [x] Copy `aa_composition` files to create the score term. - [x] Add `netcharge` score term to score terms list. - [x] Modify to penalize deviation from a desired net charge rather than a desired amino acid composition. - [x] Set up suitable interface for controlling the score term. - [x] Flags for control from commandline. - [x] Document this. - [x] Options for control from RosettaScripts/PyRosetta/C++ code. (Modify `ScoreFunctionLoader` for this.) - [x] Document this. - [x] Add `NetChargeConstraint` (a type of `SequenceConstraint`) to control desired net charge on either a pose level or a region level. - [x] Mover to add constraints to pose or region selected by a ResidueSelector. - ~~Options in mover so that I don't have to pass in a file if I don't want to.~~ --> for a future pull request. - [x] Test this. - [x] Document this. - [x] Unit tests. - [x] For symmetric case, too. - [x] Add more unit tests for out-of-bounds functions. I'm not 100% sure that my logic is correct. - [x] Good thing I checked. Correct the tailfunction behaviour. - [x] Integration tests. - [x] For symmetric case, too. - [x] Beauty. - [x] Documentation. Possibly in a future pull request: - Modify the `AddHelixSequenceConstraintsMover` to add net charge constraints to helix termini instead of amino acid constraints.