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Revisions №58075

branch: master 「№58075」
Commited by: Vikram K. Mulligan
GitHub commit link: 「dccc86acb441c47b」 「№724」
Difference from previous tested commit:  code diff
Commit date: 2015-08-21 00:08:39

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.)

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