Merge pull request #724 from RosettaCommons/vmullig/gaurav_dcys
Adding support for D-cysteine disulfides to the Disulfidize mover. In the process, I caught a major bug in the DisulfideMatchingPotential that was greatly limiting its usefulness for finding new disulfides (e.g. in Remodel or in Disulfidize). I recommend that users who use these protocols to place disulfides update to the latest master after this merge.
Tasks:
- Add interface items to mover.
- Alter mover's process_pose() function.
- Alter find_possible_disulfides() function.
- Alter construct_poly_ala_pose().
- Alter check_disulfide_score and build_and_score_disulfide().
- Alter core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide().
- Track down and fix weird DCS "atom doesn't exist" bug.
- Integration test.
- Update documentation.
- Tweak unit test appropriately, since it now finds far more disulfides and could actually run out of time/RAM.
Changes to integration tests expected:
- dcys_disulfidize (Just added; expected to fail.)
- rs_loophash (Failing to run on test server.)
- remodel_disulfides (Previously found no disulfides; with the fix to DisulfideMatchPotential, it now finds a decent-looking one, so that's good.)
- hotspot_graft (Was failing to run on test server.)
- minimize_with_electron_density (As far as I can tell, this is related to the preservation of Residue information since cysteines are not being rebuilt unnecessarily any more. Very subtle numeric differences.)
- place_simultaneously (Was failing to run on the test server.)
- make_symdef_file (Identical PDB output, but the CYS residues, which had 0 in their temperature column before, now have values. All other residues had temperature factors that were nonzero before and after this merge. This is an unanticipated but now-expected benefit of the changes to change_cys_state(), which no longer replaces CYS residues with new Residue objects (lacking the attached data) unless it's actually switching CYS to CYD or CYD to CYS.)
- database_jd2_io (Like make_symdef_file -- identical output, but values in the temperature column for CYS.)
- repack_with_electron_density (Same thing again -- temperature factors for CYS.)
- resource_database_locator (Same thing again -- temperature factors for CYS.)
- symmetry_data_resource (Same thing again -- temperature factors for CYS.)
- resource_database_tables (Same thing again -- temperature factors for CYS.)