commit 3a2fbbe486a4601af76711ce65d8723a5ca73195 Merge: 5cbd2ce fd73870 Date: Fri Nov 2 20:39:54 2018 -0400 Revert PR 3390 "mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm" Revert "mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm" One of the release mode unit tests is failing, so we're revert the PR until we can figure out why that is and what to do about it. commit 5cbd2ce878e9d41fc9dd16603d442401b2a6de19 Merge: afe3437 3397aa2 Date: Fri Nov 2 16:47:32 2018 -0400 Merge pull request #3390 from RosettaCommons/BYachnin/mhc-epitope-new mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm This PR introduces a new scoreterm, mhc_epitope, which can be used to identify and remove T-cell epitopes from proteins. It is packer compatible, using the "design guidance scoreterm" machinery introduced by @vmullig and @asford . Thanks to @vmullig for writing the original code that we copied, and for the thorough review! The code was developed by myself and @cbaileykellogg . The simplest mode involves turning on the scoreterm to work with the "ProPred" prediction matrices to remove epitopes (MHCEpitopePredictorMatrix). The threshold for what is considered to be an epitope (i.e. how aggressively to de-immunize) can be tuned using either raw scores or relative scores. Alternatively, the user can pre-compute epitope scores for a pre-defined set of sequences using more sophisticated prediction tools (e.g. NetMHC and IEDB). These should be stored in a SQL database to be accessed in the MHCEpitopePredictorExternal class. We will be providing some scripts in the tools repo to help users generate these SQL databases, and corresponding PSSMs to limit design space with task ops. This can also be implemented as a constraint mover, allowing specific regions to be targeted using residue selectors. These can use different predictor classes (e.g. use a general MHCEpitopePredictorMatrix in the scorefunction and a MHCEpitopePredictorExternal in specific regions with residue selectors) and other settings (thresholds, etc.). The scoreterm should behave well with symmetric proteins, ligands, non-canonical amino acids, and multi-chain systems. INTEGRATION TEST CHANGES: `mhc_epitope` fails because it is new 53 tests fail because of cosmetic addition of `EnergyMethodOptions::show: mhc_epitope_setup_files:` to output pdb files (we have added this as a new EnergyMethodOption): backbonegridsampler_multiresidue, bundlegridsampler, bundlegridsampler_copy_pitch, bundlegridsampler_design, bundlegridsampler_design_nstruct_mode, bundlegridsampler_epsilon, bundlegridsampler_z0_offset, bundlegridsampler_z1_offset, coupled_moves, ligand_dock_ensemble, mp_find_interface, mp_mutate_relax, mp_mutate_repack, oligourea_predict, pepspec, perturb_helical_bundle, remodel, remodel_disulfides, remodel_helical_repeat, scaffold_matcher, simple_cycpep_predict, simple_cycpep_predict_angle, simple_cycpep_predict_anglelength, simple_cycpep_predict_cartesian, simple_cycpep_predict_cispro, simple_cycpep_predict_cterm_isopeptide_lariat, simple_cycpep_predict_cterm_isopeptide_lariat_tailless, simple_cycpep_predict_design, simple_cycpep_predict_nterm_isopeptide_lariat, simple_cycpep_predict_nterm_isopeptide_lariat_tailless, simple_cycpep_predict_octahedral_metal, simple_cycpep_predict_settings, simple_cycpep_predict_sidechain_isopeptide, simple_cycpep_predict_sidechain_isopeptide_reverse, simple_cycpep_predict_square_planar_metal, simple_cycpep_predict_square_pyramidal_metal, simple_cycpep_predict_symm_gly, simple_cycpep_predict_symmetric_sampling, simple_cycpep_predict_tbmb, simple_cycpep_predict_terminal_disulfide, simple_cycpep_predict_terminal_disulfide_internal_permutations, simple_cycpep_predict_terminal_disulfide_tails, simple_cycpep_predict_tetrahedral_metal, simple_cycpep_predict_tetrahedral_metal_asp, simple_cycpep_predict_tma, simple_cycpep_predict_trigonal_planar_metal, simple_cycpep_predict_trigonal_pyramidal_metal, simple_grafting_movers, supercharge, sweep_respair_energies, test_energy_method_options, zinc_heterodimer, zinc_homodimer_design 3 tests fail because of cosmetic addition of `INSERT INTO "score_types" VALUES(1,376,'mhc_epitope');` (and re-ordering of other score_types) in output dump files (we have added this as a new score_type): database_jd2_compact_io, database_jd2_io, features hotspot_hashing is broken in master commit afe34375a39b9ea49bea353dc73e29fde8c7b35c Merge: 4afd228 7b45112 Date: Fri Nov 2 10:18:16 2018 -0700 Merge pull request #3604 from RosettaCommons/fordas/mismatch_prob_race Fix race in psipred calls from multiple processes. commit 4afd228b2f3ababd014610c5acecad8c27ddba63 Merge: 452ce7e 6cdafdd Date: Fri Nov 2 10:00:20 2018 -0400 Merge pull request #3606 from RosettaCommons/vmullig/relax_script_manager Add a RelaxScriptManager to ensure that relax scripts are read from disk only once. This addresses issue #3605. (Note: the loading is threadsafe, lazy, and occurs once _per relax script_. Multiple relax scripts can be held in memory if multiple instances of FastRelax request different scripts.) commit 452ce7e1ac0f02f3d1157078b125e4b0b8010c21 Merge: 82beea7 cd14158 Date: Thu Nov 1 14:36:24 2018 -0400 Merge pull request #3603 from RosettaCommons/vmullig/fix_gcc_8point2_compilation Fix compilation on gcc 8.2.0. Fixing catch-by-value compilation error. This addresses issue #3596. commit 82beea70c79228d312ad139cd2c2356a1ad87f54 Merge: 87a725f 6a785df Date: Thu Nov 1 12:45:04 2018 -0500 Merge pull request #3599 from RosettaCommons/roccomoretti/spilt_init Split up protocols/init/ registrators. On my machine protocols/init/init.cc now is taking an inordinate amount of time to compile. To help with the compilation time, break the registration up into multiple cc files. commit 87a725f2543f945043e7da87b8054dfceb7c5903 Merge: 87ef733 45b61c1 Date: Thu Nov 1 08:51:24 2018 -0700 Merge pull request #3601 from RosettaCommons/fordas/numpy_version_check Add numpy version check for dtype declarations. commit 87ef73394fb6982f2db4e9f968372d436514ddb3 Merge: 20101e9 75ab10a Date: Wed Oct 31 17:06:49 2018 -0500 Merge pull request #3562 from RosettaCommons/jadolfbr/sep18 SugarBB Energy fix, Glycan Relax rename Changes: 1. Add `VIRTUAL_RESIDUE` property to a few patches that were missing them 2. Fix `SugarBBEnergy` to skip virtual residues. This addresses #3250 3. Add serialization methods to `NativeAntibodySeq`, simplify its behavior. 4. Rename `GlycanRelaxMover` -> `GlycanTreeSampler` 5. Rename `GlycanTreeRelax` -> `GlycanTreeModeler` The renaming has been planned for a while. Glycan Relax was a place holder for this code. As we are getting closer to publication, these are the final names. This will break all scripts that use these names in the wild. Since this is currently unpublished and only the lab and collaborators are using this code, I believe this name change is OK. commit 20101e9e3f6a104638df44d6420e1182da2fa2b6 Merge: 9fb056c 58fbc79 Date: Tue Oct 30 16:49:16 2018 -0700 Merge pull request #3595 from RosettaCommons/fordas/osx_conda_build_check Disable osx-64 buildkite builds. commit 9fb056c6b488ec9237169419f46a4b8e8f5e050b Merge: ce6db09 cce91c2 Date: Fri Oct 26 18:26:30 2018 -0700 Merge pull request #3592 from RosettaCommons/fordas/structure_store_fixes Fix structure_store test and build failures. commit ce6db09c81748fa9514626b6e41484d850eebf1c Merge: 32f492c e9e2357 Date: Fri Oct 26 15:40:56 2018 -0700 Merge pull request #3587 from RosettaCommons/fordas/conda_build_updates Conda build updates, add anaconda.org uploads. commit 32f492c6681bac722028a2a0b54fa05fabeab7e4 Merge: 043f2bf f1f4b66 Date: Fri Oct 26 15:40:10 2018 -0700 Merge pull request #3591 from RosettaCommons/fordas/distributed_test_update Fixup distributed test runner. commit 043f2bf480b691228ef5254a2337ad431d362525 Merge: 68fe8a8 b93c415 Date: Fri Oct 26 13:24:22 2018 -0600 Merge pull request #3588 from RosettaCommons/sergey/ui refactoring `Task` files storage from `map` to `set` and minor relevant refactories commit 68fe8a8101aa89ec2dc0d049aff7d9721ab57ad1 Merge: dba555b 6520688 Date: Thu Oct 25 17:55:29 2018 -0700 Merge pull request #3556 from RosettaCommons/longxing/interfacehbonds Interface hydrogen bonds and salt bridges filter commit dba555b813111cf5bff87e378486318a0f362977 Merge: f1a0bb9 d7734a7 Date: Thu Oct 25 11:18:34 2018 -0700 Merge pull request #2765 from RosettaCommons/fordas/structure_store Integrate indexed_structure_store updates for in-memory structure db. commit f1a0bb9f2d1a03b6db71e332e72146c5a6263c58 Merge: 755f810 653f39c Date: Thu Oct 25 11:15:06 2018 -0700 Merge pull request #3586 from RosettaCommons/fordas/fix_distributed_import Fix pyrosetta.distributed import. commit 755f81069d43c8a68a0dd5bf8d0790ad1996120c Merge: 1ff6ae1 3cdb20c Date: Thu Oct 25 07:00:08 2018 -0700 Merge pull request #3584 from RosettaCommons/everyday847/erraser2_to_public Make erraser2 a public app commit 1ff6ae1f617a6be635293ba432a48a421854fcf8 Merge: cd24852 4b7f361 Date: Wed Oct 24 17:29:53 2018 -0400 Merge pull request #3581 from RosettaCommons/JackMaguire/MoveMRSToPublic Moving Multistage Rosetta Scripts From Pilot To Public Thanks to Steven for the review! commit cd24852e7f3cd10e0a8c8f7ba5f2e23c2b1d8308 Merge: a549a4c 3f1d2c1 Date: Wed Oct 24 13:42:41 2018 -0700 Merge pull request #3582 from RosettaCommons/fordas/ensure_final_score Ensure that ParsedProtocol calls `final_score` for additional output. commit a549a4ca83c812b66507bdebae3ee65b98623321 Merge: 424047e 294cd0f Date: Wed Oct 24 13:19:54 2018 -0600 Merge pull request #3567 from RosettaCommons/sergey/ui Updating Workbench app so it compatible with new server API commit 424047e31250a3a67ac963cdf69501c05f6c1cc5 Merge: fb2ec32 a7f7038 Date: Tue Oct 23 13:12:02 2018 -0400 Merge pull request #3571 from CyrusBiotechnology/davela/add_H3_to_outlier_list_commons From @d8vela : This is a follow-up to the previous PR (#3551) which provides additions of orientation lines to the outlier_list file. Now, we are also adding H3 lines to the outlier list, which are all set to false for neutrality. These are necessary for proper function of the antibody.cc app. (The test failures are the usual junk) commit fb2ec32b2280d92574fe8ce91f871c23f0bd640e Merge: 0e48220 752f396 Date: Tue Oct 23 10:53:09 2018 -0400 Merge pull request #3573 from RosettaCommons/jkleman/sci_bench_template Jkleman/sci bench template: * updating relax scientific tests (fast_relax, fast_relax 5 iterations, cart_relax) to include cutoffs * added a readme to each of these directories * added a template directory as a starting point for adding scientific tests, these should be reasonably well commented - [x] DONE: I have documentation for it, but: - [x] TODO: it needs to be added to the wiki in some place. There are old pages about scientific tests, need to ask Rocco where to put or move pages latest run: http://benchmark.graylab.jhu.edu/revision?branch=&id=11038 documentation: https://www.rosettacommons.org/docs/wiki/development_documentation/test/Scientific-Benchmarks find the template in: `/Rosetta/main/tests/scientific/tests/_template_` commit 0e4822031ef77d5f77360e674a24f0d2099bbbbb Merge: bcccc8c 4549ef8 Date: Mon Oct 22 20:06:33 2018 -0700 Merge pull request #3577 from RosettaCommons/fordas/no_import_star Remove dot-star imports from pyrosetta demos and tests. commit bcccc8c32606f5976431abeaf24dddcd42db54a1 Merge: 3e2321a 2571246 Date: Mon Oct 22 10:53:45 2018 -0700 Merge pull request #3576 from RosettaCommons/fordas/pyrosetta_selftest_py3 Run pyrosetta self test with python3.x commit 3e2321af2ce1f095063b192a32f88346d47ad156 Merge: 10bc285 86eae51 Date: Mon Oct 22 10:22:01 2018 -0400 Pass new scorefxn along to lowres and highres movers when set (PR #3565) Previously, if you called set_lowres_scorefxn or set_highres_scorefxn, DockingProtocol would store your new scorefxn in a pointer, but wouldn't alter the docking loweres mover or the docking highres mover. Your changes were effectively ignored! This also affected rosetta_scripts, as parse_my_tag invoked these functions. Now, when you invoke any of these functions (there are four, as the set_highres_scorefxn function is overloaded), the change is passed along to the mover that's going to actually perform the docking. commit 10bc285786c913bb9039939e40e2889f09069360 Merge: 9fe880b ad4cfdb Date: Sun Oct 21 07:03:00 2018 -0700 Merge pull request #3459 from RosettaCommons/everyday847/two_scientific_tests Scientific tests for SWM and FARFAR commit 9fe880bab6acc84f6ffcd17064a21a8cf5b40ccc Merge: 5069929 3160550 Date: Sun Oct 21 02:00:27 2018 -0700 Merge pull request #3574 from RosettaCommons/fordas/forksafe_pose_pickle Fix blosc config for fork/thread safe pickle. commit 50699295817f2f8e8ee006763b185d01936b4c70 Merge: 6b4d5a6 8a8b373 Date: Fri Oct 19 12:40:28 2018 -0400 Merge pull request #3551 from CyrusBiotechnology/davela/add_orientation_to_outlier_list On @d8vela 's behalf: Add required PDB entries for the current outlier_list to reinforce the abililty to black-list templates during modeling of antibody Fv heavy to light chain orientations. This fixes antibody.cc (provides the correct input to what it expects to see) so that it will run correctly with recent addition of the filtering feature for orientation. Note that the outlier status for all existing PDB entries in the outlier list are set to "false" meaning they will not be black-listed by default. So, these additions to the outlier_list are neutral changes and will not alter the default behavior of antibody.cc. commit 6b4d5a6d8e8d05be4ac788def0adfbd72a00979e Merge: 43c8c1c 31a443f Date: Fri Oct 19 09:08:06 2018 -0500 Merge pull request #3566 from RosettaCommons/roccomoretti/fix_metal_gasteiger Add fixes for Gasteiger typing of coordinated metals. This PR does two things. First, it provides better support for "pseudobonds" in input params files, such that it works appropriately with the Gasteiger typing machinery. (Such that we can avoid treating coordinating bonds to metals as regular single bonds when Gasteiger typing.) Secondly, it adds a few ad hoc Gasteiger types for metals which aren't present. (More may need to be added, depending on the full suite of metal ions being used.)