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Revisions №60502

branch: master 「№60502」
Commited by: Brahm Yachnin
GitHub commit link: 「febbd46e06885642」 「№3612」
Difference from previous tested commit:  code diff
Commit date: 2018-11-12 17:33:15
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release unit.valgrind

Merge pull request #3612 from RosettaCommons/BYachnin/mhc-epitope-new mhc_epitope scoreterm, a flexible, packer-compatible deimmunization scoreterm This is the second attempt, after addressing a release mode unit test failure in PR #3390 . 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

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
KIC_with_fragments backbonegridsampler_multiresidue bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset coupled_moves database_jd2_compact_io database_jd2_io enzdes features helix_from_sequence ligand_dock_ensemble mhc_epitope mp_find_interface mp_mutate_relax mp_mutate_repack mp_relax_w_ligand oligourea_predict pepspec perturb_helical_bundle ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG remodel remodel_disulfides remodel_disulfides_rosettascripts remodel_helical_repeat rnp_ddg_finalize scaffold_matcher sdf_reader 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_setting 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 swm_protein_move_inside_helix_by_bond test_energy_method_options vancomycin zinc_heterodimer zinc_homodimer_design
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: mac.clang.integration

Failed sub-tests (click for more details):
backbonegridsampler_multiresidue bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset coupled_moves database_jd2_compact_io database_jd2_io features hotspot_hashing ligand_dock_ensemble mhc_epitope 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_setting 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
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol