commit 7a3c5987837a8cb7105205871e663a03aea5d9ac Merge: 7455700 a398a84 Date: Wed May 20 23:17:15 2015 -0700 Merge pull request #527 from RosettaCommons/revert-517-jadolfbr/antibody_design Revert "Jadolfbr/antibody design" temporarily Since this merge seems to have caused intermittent instabilities in a number of integration tests in release_debug mode, I'm temporarily reverting it until we can track down the source of those instabilities. (This isn't meant as a condemnation or criticism of you, @jadolfbr! I know that the problems didn't show up when you tested this branch in commits.) Once we figure out what's going wrong, we can re-merge. commit 745570040868a938e3d6573eafa2b94d019a39c6 Date: Wed May 20 16:57:30 2015 -0400 fixing pointers in pilot app commit eeec95864893f84bb5db1040ba2ab67b84d101db Merge: 4f52cbb bff2024 Date: Wed May 20 15:13:19 2015 -0400 Merge pull request #516 from RosettaCommons/kimdn/zipper Merge pull request #516 from RosettaCommons/kimdn/zipper [update of SandwichFeatures for upcoming publication (charge zipper) so that readers can get same results as I do] - debugged rama & p_aa_pp writing by reviving processing_decoy - prepare pymol to easily see residues with salt_bridges - allowed wt_for_pro_in_starting_loop_ etc. and readjusted those 3 weights - further refactoring regarding namespace core using - should not change any integration tests other than (expected) features and features_database_schema commit 4f52cbbe7bc7dd98c1c5ed095847157df12d3798 Merge: 9253ee6 a266e7d Date: Wed May 20 10:05:45 2015 -0700 Merge pull request #526 from RosettaCommons/fcchou/turner Fcchou/turner commit 9253ee63e39fad9d507b144e3274634788776e8f Merge: 4ce8113 6c310da Date: Tue May 19 21:40:45 2015 -0400 Merge pull request #522 from RosettaCommons/rfalford12/fix_barth07_sfxn_bug Adjustment to mpframework_fa_2007 weights file - removing extra penalties commit 4ce811391db560d977f7d76671e6f341e602b777 Merge: 317d3ad 9dbfdaa Date: Sun May 17 17:31:20 2015 -0700 Merge pull request #518 from RosettaCommons/tlinsky/disulfidizetag DisulfidizeMover now tags added disulfides as "DISULFIDIZE" in PDBInfo commit 317d3adb1fdbf62830d21790f48ccfd9704be4d6 Merge: b8e6c77 ffe83fc Date: Sat May 16 19:19:29 2015 -0400 Merge pull request #519 from RosettaCommons/aleaverfay/beauty This is a pre-commit before beautification takes place. It adds semi-colons behind some macro invocations (there shouldn't even be macro invocations!) so that the beautifier can run smoothly. It generates a number of cosmetic integration test changes as I've replaced a tab inside a string with some spaces in score.cc. If you look at the file, you see that every other output line in the "how to run this program" section is indented with spaces and so having a tab in there just distorts the output text alignment. The commit also changes the DOS line-endings to unix format for a handful of files. commit b8e6c772900c27683fbb213e39d83d1b81aa4c9a Merge: 463e09d 7a2daa1 Date: Sat May 16 13:49:46 2015 -0700 Merge pull request #493 from RosettaCommons/hahnbeom/patchs Adding mover for liquid simulation (protocols/simple_moves/PeriodicBoxMo... commit 463e09d627db9ff4e74f9b3d9f49a67be67c2901 Merge: 1d9e768 92c06ed Date: Sat May 16 11:28:59 2015 -0400 Merge pull request #517 from RosettaCommons/jadolfbr/antibody_design Jadolfbr/antibody design Updates to Rosetta Antibody Design (RabD) program Merge a long-running branch. General ======= -Clean up AntibodyInfo header - 'using namespace' should not be in headers -Add proper copy constructor to AntibodyInfo -Add protocols/antibody/task_operations namespace and associated classes to help in antibody modeling and design -Add conservative mutation database which includes full Blosum matrices in DB format, with conservative mutations. This is used by the ConservativeDesignOperation, which is now in protocols/toolbox/task_operations. Specify the data source via -cons_design_data_source -Move ResidueProbDesignOperation to protocols/toolbox/task_operations which can be used for profile-based design independant of the energy function. -Add MutationSetDesignOperation to protocols/toolbox/task_operations with can be used to sample sets of residue types during design, optionally adding weights to each set. -Add ability to select grafts based on species and germline -Add outlier control of grafts and cluster-based design data (which now includes a set of constraint files for each cluster for each outlier definition as well) -Add algorithm control specified with flag (generalized_monte_carlo and deterministic_graft) -Add ability to design camelid antibodies -Refactor the way antibody cluster-based sequence design is done, now by a primary and secondary strategy for each design. -Add CDRDihedralConstraintMover for adding cluster-based dihedral constraints or general dihedral constraints. -pilot app identify_cdr_clusters can be used with any antibody numbering scheme. Rosetta Scripts Integration =========================== All Antibody Constraint movers (ParatopeSiteConstraintMover, ParatopeEpitopeSiteConstraintMover, and CDRDihedralConstraintMover) are all now available via RS. All RabD classes can be called by RS, with the full protocol also available. All Antibody TaskOperations can be called by RS: -RestrictToCDRsAndNeighbors -DisableCDRsOperation -DisableAntibodyRegionOperation -AddCDRProfilesOperation -AddCDRProfileSetsOperation Other ===== Fixed a bug in sc_value calculation that would hit a segfault on calling the SCCalculatorException on trimming dots. The rest of the calls to that exception class will be changed to use the Rosetta exception message base in a separate pull request. Refactored backrub to enable the full protocol to be called outside of the app. Added movemap support. Added code-level options to enable dualspace relax through code and PyRosetta. Unit Tests ========== Unit tests have been added for: - all TaskOps moved to protocols/toolbox. - all antibody TaskOps Unit tests updated for antibody design Integration test changes in backrub, and the antibody tests are cosmetic. Test changes in antibody_designer are expected. commit 1d9e7684d954bc7a32fbae997726e12af8aace6d Merge: fb3dbb3 975b722 Date: Fri May 15 14:46:19 2015 -0700 Merge pull request #515 from RosettaCommons/vmullig/gamma_aas Vmullig/gamma_aas This should get the BackboneGridSampler working with repeating units of more than one residue. This also adds a number of gamma-amino acids to the database. Tasks: -- Add several gamma-amino acids to the database. -- Tweak NtermProteinFull patch for gamma-amino acids. -- Adds a TRIAZOLEMER class of residues (a new type of unnatural backbone). -- Adds support to the BackboneGridSampler for repeating units of more than one residue (to allow sampling of secondary structures that are possible with, for example, D-L-D-L or L-L-D-L-L-D patterns, or with alpha-beta-alpha-beta or whatnot). -- Add RosettaScripts parsing for setting the number of residues per repeating unit. -- Update the residue type list in the BackboneGridSampler. -- Update the fixed torsions list in the BackboneGridSampler, and add RosettaScripts parsing. -- Update the varying torsions list in the BackboneGridSampler, and add RosettaScripts parsing. -- Update text output. -- Update the BackboneGridSamplerHelper, and make sure that it samples all residues properly. -- Add integration tests. -- Ensure backward compatibility. -- Check existing integration tests for changes (cosmetic changes only are expected, since the default behaviour is still one residue per repeating unit). -- Add documentation for new features to the Gollum wiki. All unit tests pass. Integration tests pass with expected cosmetic changes to the backbonegridsampler test's output log (though full backward compatibility is maintained). Small stochastic changes to the backbonegridsamper_nstruct_mode test since this uses a nonmonotone minimizer, but no major or unexpected changes. The backbonegridsampler_multiresidue test produces appropriate output, but fails because it's new.