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Revisions №60642

branch: master 「№60642」
Commited by: Brahm Yachnin
GitHub commit link: 「4ab48a76160c8882」 「№3131」
Difference from previous tested commit:  code diff
Commit date: 2019-03-07 11:30:15
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.ubsan integration performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python36.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 unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3131 from CyrusBiotechnology/smlewis/rescue_indigo/nmer_refactor_plus_commonsmerge2 This PR merges @indigogo 's re-factored NMerSVMEnergy (currently used by Cyrus) into the Rosetta master branch, and now uses the `EnergyMethodOptions` system (courtesy of @vmullig ). This paves the way for @cbaileykellogg and myself to complete and merge #3464 (`MHCEpitopeEnergy`), which integrates nmer into the packer-compatible mhc_energy scoreterm. Integration test failures are due to writing out `EnergyMethodOptions` lists to PDB files, and are purely cosmetic. @indigogo 's description of these changes: Changes to NMerSVMEnergy scoring method and associated filter. This adds normalized score rank percentage calculation to NMerSVMEnergy. Why? Here's the problem: when using NMerSVMEnergy to predict T cell epitopes from MHC binding predictions, some MHC allele types bind more or less strongly on average. However, this is not indicative of more or less average predisposition to causing T cell activation. To correctly combine predictions across a repertoire of MHC types, we need to normalize the scores reported by different SVM models. To do this, I predicted MHC binding for 100k random 15mers from the human genome for every allele svm in the rosetta database and stored those distributions back in the database. Every time NMerSVMEnergy calculates a score, it also calculates the rank fraction of that score against the precalculated distribution; this info is retrievable from the scoring method directly, or you can pass a non-default cmdline option to switch to reporting that rank fraction as the score terms 'energy' instead of using the raw score. This allows one to properly combine the predictions of multiple alleles during deimmunization design in rosetta. Also tagging @smlewis ,

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Test: linux.clang.integration.release_debug_no_symbols

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 design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA fast_relax_scripts hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm ligand_dock_ensemble mp_find_interface mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_span_ang_ref2015_memb oligourea_predict perturb_helical_bundle remodel_helical_repeat res_lipo_ref2015_memb 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_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid 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 test_energy_method_options zinc_heterodimer zinc_homodimer_design
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker glycan_tree_relax
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 continuous_sewing_hasher coupled_moves design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA discontinuous_sewing_hasher fast_relax_scripts hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm ligand_dock_ensemble mp_find_interface mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_span_ang_ref2015_memb oligourea_predict pepspec perturb_helical_bundle remodel remodel_disulfides remodel_helical_repeat res_lipo_ref2015_memb 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_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid 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 test_energy_method_options zinc_heterodimer zinc_homodimer_design
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.gcc.cxx11thread.serialization.unit

Failed sub-tests (click for more details):
protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea_s2_symm protocols:EnergyBasedClusteringTests_oligourea:test_dihedral_cluster_cyclic_oligourea protocols:MPLipidAccessibilityTest:test_mp_lipid_accessibility protocols:MPLipidAccessibilityTest:test_parse_my_tag_input protocols:MembraneUtil:test_angle_rmsd_method protocols:MembraneUtil:test_average_antiparallel_embeddings protocols:MembraneUtil:test_average_embeddings protocols:MembraneUtil:test_calc_helix_angles protocols:MembraneUtil:test_calc_helix_axis protocols:MembraneUtil:test_chain_com protocols:MembraneUtil:test_check_vector protocols:MembraneUtil:test_compute_embeddings_by_chain protocols:MembraneUtil:test_compute_structure_based_embedding1 protocols:MembraneUtil:test_compute_structure_based_embedding2 protocols:MembraneUtil:test_compute_structure_based_embedding3 protocols:MembraneUtil:test_compute_structure_based_embedding4 protocols:MembraneUtil:test_compute_structure_based_embedding5 protocols:MembraneUtil:test_compute_structure_based_embedding6 protocols:MembraneUtil:test_compute_structure_based_embedding7 protocols:MembraneUtil:test_compute_structure_based_embedding8 protocols:MembraneUtil:test_create_membrane_docking_foldtree_from_partners protocols:MembraneUtil:test_create_membrane_foldtree_anchor_com protocols:MembraneUtil:test_create_membrane_foldtree_anchor_pose_tmcom protocols:MembraneUtil:test_create_membrane_foldtree_anchor_tmcom protocols:MembraneUtil:test_create_membrane_multi_partner_foldtree_anchor_tmcom protocols:MembraneUtil:test_create_specific_membrane_foldtree protocols:MembraneUtil:test_is_fixed_on_fixed_memb protocols:MembraneUtil:test_is_fixed_on_moveable_memb protocols:MembraneUtil:test_is_independently_moveable_on_fixed_memb protocols:MembraneUtil:test_is_independently_moveable_on_independently_moveable_memb protocols:MembraneUtil:test_membrane_bb_rmsd_no_super protocols:MembraneUtil:test_membrane_bb_rmsd_no_super_allatom protocols:MembraneUtil:test_membrane_bb_rmsd_with_super protocols:MembraneUtil:test_membrane_bb_rmsd_with_super_allatom protocols:MembraneUtil:test_pose_tm_COM protocols:MembraneUtil:test_rsd_closest_chain_com protocols:MembraneUtil:test_rsd_closest_chain_tm_com protocols:MembraneUtil:test_rsd_closest_pose_tm_COM protocols:MembraneUtil:test_split_topology_by_chain_noshift protocols:MembraneUtil:test_split_topology_by_jump protocols:MembraneUtil:test_split_topology_by_jump_noshift protocols:MembraneUtil:test_tm_com protocols:NubInitioMoverTests:test_name protocols:NubInitioMoverTests:test_one_motif protocols:NubInitioMoverTests:test_two_motifs protocols:RotamerRecoveryTests:test_RotamerRecovery_main