Merge pull request #648 from RosettaCommons/jkleman/mp_updates
Jkleman/mp updates
SASA:
* added functions in core/scoring/sasa/util that (1) compute the total per-residue-SASA, (2) relative per-residue-SASA, and (3) is_residue_exposed boolean function; this is all based on Jared's code
* added sasa calculator pilot app that uses those functions: pilot/jkleman/per_residue_sc_sasa.cc
* added integration test
Apps:
* add helix_from_sequence app with integration test, works both for soluble as well as membrane helices
* cleaned up interface_statistics app for membrane proteins, still more to refine
Docking:
* MPDockingSetupMover: added options to optimize membrane positions for both partners before concatenation
* MPFindInterfaceMover: cleaned up, added options, checking in the code from before Gordon conference, still needs work
* MPQuickRelaxMover: cleaned up, added options, checking in code from before Gordon conference, still needs work
RosettaMP:
* MembraneInfo: added function in_membrane that returns boolean
* SpanningTopology: fixed bug in concatenating topology objects that was not caught by unit test, included that in unit test now
* Embedding: added functions for add_span_embedding
* TransformIntoMembraneMover: added option to optimize embedding, still needs test
* TranslationRotationMover: removed unused fullatom variable and option that was never used
* VisualizeEmbeddingMover: debugged, but more debugging to do
* most membrane movers: added check at the beginning of the apply function to check the foldtree, after apply the foldtree is reset to the original one
* fixed a whole bunch of bugs, unit test oversights and integration test changes that weren't caught in the renaming of the integration tests for the membrane framework
* cleaned up some of the center/normal tags and commandline initializations that didn't yet use Rebecca's function
* protocols/membrane/util: added a whole bunch of useful functions: create_membrane_foldtree with anchor points at chain COMs, create_membrane_foldtree with anchor points at COMs of TM regions of chains, helper function for both, chain COM, chain TM COM, rsd closest to chain COM, rsd closest to chain TM COM, split topology by chain, compute embeddings by chain; added unit tests for all of those
Other:
* pose/util: added get_chains function
Unit test failures: none
Integration test changes: mostly cosmetic, helix_from_sequence and per_res_sc_sasa didn't exist, mp_mutate_relax and mp_quickrelax changed because the protocol changed