「view this page in B3 βῆτα server」

Revisions №60639

branch: master 「№60639」
Commited by: Labonte
GitHub commit link: 「fd1bdffb01b7866d」 「№2468」
Difference from previous tested commit:  code diff
Commit date: 2019-03-05 15:28:05
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 linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration.ubsan integration performance profile 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

Merge pull request #2468 from RosettaCommons/JWLabonte/PDB_IO PDB IO: Title Section IO Following an idea/request from @cdbahl at RosettaCON 2017, I have added functionality for automatically adding a time stamp and Rosetta version number to all output `.pdb` files. The default output uses proper/standard/PDB-defined records, _e.g._: ``` HEADER 21-FEB-19 XXXX EXPDTA THEORETICAL MODEL REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 DATE OF DATA COLLECTION : 21-FEB-19 REMARK 220 REMARK 220 REMARK: MODEL GENERATED BY ROSETTA REMARK 220 VERSION 2019.04.post.dev+165.HEAD.646026d ``` This way, one will always know whence a `.pdb` came, and it will lead to better reproducibility of results. One could also easily adapt this system, using JD2 or JD3, to automatically include specific protocol information to the file. This merge will also allow input and output of `AUTHOR` records: ``` HEADER 21-FEB-19 XXXX EXPDTA THEORETICAL MODEL AUTHOR LABONTE ``` To include a list of authors, simply use the option flag `-set_pdb_author` with a comma-delimited list of names, according to the PDB format: ``` -set_pdb_author "I.M.A.JUNIOR JR.,I.HYPHENATE-MY-SURNAME,LABONTE" ``` If integration tests are running, the system automatically outputs the date as `xx-MMM-xx` and the version number as `INTEGRATION TEST` to ensure that integration tests do not fail every time from the changing date and version output. This merge also corrects some bugs in `HeaderInformation`. All unit tests pass. Almost every single integration test changes, as every `.pdb` file now has a default title section prepended. I have looked through about 10% of the >400 tests and did not find any unexpected changes. Likewise, 5 score tests are changed and 2 mpi integration tests.

...
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign DARC_electrostatics DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail InterfaceAnalyzer KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_symm LayerSelector LoopLengthChange ModifyVariantTypeMover MutateResidue_selector PeptideCyclizeMover PeptideStubMover_prependRepeat RBOut ReadResfile_with_selector SSElementSelector SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup antibody_H3 antibody_H3_camelid antibody_designer antibody_graft antibody_numbering_converter autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation carbohydrates cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment cluster cluster_alns cluster_filter composition_energy_layers constel copy_rotamer_mover coupled_moves create_sequence_motif crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io ddG_ensemble density_denovo density_refine density_refine_symm design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_low_res docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal energy_based_clustering_alpha_aa entropy_correction enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution explicit_membrane extract_atomtree_diffs extract_pdbs farnesyl fast_relax_scripts favor_native_residue features fiber_diffraction fit_helixparams fit_helixparams_a3b fit_helixparams_rms fixbb flexpepdock flexpepdock_abinitio fold_from_loops fuzzy ga_ligand_dock genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench glycosylation hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbonds hbonds_sp2 hbondstoresidue_selector hbs_design helical_bundle helical_bundle_nonideal helix_from_sequence homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hybridization hydrate hydrate_relax identify_cdr_clusters interaction_graph_summary_metric jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_modeling make_and_perturb_bundle_multirepeat make_symmdef_file match_1n9l metal_setup metalloprotein_abrelax metropolis_hastings mg_modeler mg_modeler_lores mhc_epitope min_pack_min minimize_with_elec_dens mirror_symm motif_dna_packer_design motif_extraction mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_find_interface mp_interface_statistics mp_loadtime mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_range_relax mp_relax mp_span_ang_ref2015_memb mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mr_protocols msd_mover multistage_rosetta_scripts multistage_rosetta_scripts_clustering mutate ncaa_fixbb netcharge_design netcharge_design_symm next_generation_KIC nonideal_rtmin nucleobase_sample_around oligourea_predict oop_create oop_design oop_dock_design orbitals pepspec_anchor_dock peptiderive pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate place_simultaneously pna pna_base_pairs pocket_relax polyaramid_test_trivial posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pymol_cif ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces read_polymeric_components real_virt_mover recces_turner referencepose_mutateresidue relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rings rna_denovo rna_denovo_fragment_homology_exclusion rna_denovo_legacy rna_denovo_new_libs rna_design rna_helix rna_minimize rna_screen_phosphates rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sample_tilt_angles score12_docking score_jd2 sdf_reader secondary_structure_output seed_ensemble_JD2_JI select_best_unique_ligand_poses selected_residue_count_metric sequence_profile_constraints sequence_tolerance set_torsion 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_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metrics simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter startfrom_file stored_residue_subset super_aln supercharge surface_docking sweep_respair_energies swm_protein_preminimize symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetric_docking symmetrical_residue_selector symmetry_data_resource task_selector tcrmodel test1_benchmark test_idealize thermal_sampler threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling unfolded_state_energy_calc vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
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):
AddConstraintsToCurrentConformationMover AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign DARC_electrostatics DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail InterfaceAnalyzer KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_symm LayerSelector LoopLengthChange ModifyVariantTypeMover MutateResidue_selector PeptideCyclizeMover PeptideStubMover_prependRepeat RBOut ReadResfile_with_selector SSElementSelector SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup antibody_H3 antibody_H3_camelid antibody_designer antibody_graft antibody_numbering_converter autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins bridge_chains broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation carbohydrates cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment cluster cluster_alns cluster_filter composition_energy_layers constel continuous_sewing_hasher copy_rotamer_mover coupled_moves create_sequence_motif crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io ddG_ensemble density_denovo density_refine density_refine_symm design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA discontinuous_sewing_hasher disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_low_res docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal energy_based_clustering_alpha_aa entropy_correction enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution explicit_membrane extract_atomtree_diffs extract_pdbs farnesyl fast_relax_scripts favor_native_residue features fiber_diffraction fit_helixparams fit_helixparams_a3b fit_helixparams_rms fixbb flexpepdock flexpepdock_abinitio fold_from_loops fuzzy ga_ligand_dock genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench glycosylation hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbonds hbonds_sp2 hbondstoresidue_selector hbs_design helical_bundle helical_bundle_nonideal helix_from_sequence homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hybridization hydrate hydrate_relax identify_cdr_clusters interaction_graph_summary_metric inverse_rotamer_remodel jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_modeling make_and_perturb_bundle_multirepeat make_symmdef_file match_1n9l metal_setup metalloprotein_abrelax metropolis_hastings mg_modeler mg_modeler_lores mhc_epitope min_pack_min minimize_with_elec_dens mirror_symm motif_dna_packer_design motif_extraction mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_find_interface mp_interface_statistics mp_loadtime mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_range_relax mp_relax mp_relax_w_ligand mp_span_ang_ref2015_memb mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mr_protocols msd_mover multistage_rosetta_scripts multistage_rosetta_scripts_clustering mutate ncaa_fixbb netcharge_design netcharge_design_symm next_generation_KIC nonideal_rtmin nucleobase_sample_around oligourea_predict oop_create oop_design oop_dock_design orbitals pepspec pepspec_anchor_dock peptiderive pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate place_simultaneously pna pna_base_pairs pocket_relax polyaramid_test_trivial posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pymol_cif ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces read_polymeric_components real_virt_mover recces_turner referencepose_mutateresidue relax_w_allatom_cst remodel remodel_disulfides remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax res_lipo_ref2015_memb resource_database_locator rings rna_denovo rna_denovo_fragment_homology_exclusion rna_denovo_legacy rna_denovo_new_libs rna_design rna_helix rna_minimize rna_screen_phosphates rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sample_tilt_angles score12_docking score_jd2 sdf_reader secondary_structure_output seed_ensemble_JD2_JI select_best_unique_ligand_poses selected_residue_count_metric sequence_profile_constraints sequence_tolerance set_torsion 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_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metrics simple_metrics_per_residue small_molecule_lattice_dock smallmover_resselector splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter startfrom_file stored_residue_subset super_aln supercharge surface_docking sweep_respair_energies swm_protein_preminimize symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetric_docking symmetrical_residue_selector symmetry_data_resource task_selector tcrmodel test1_benchmark test_idealize thermal_sampler threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling unfolded_state_energy_calc vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
Test: linux.clang.performance

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