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Revisions №61757

branch: master 「№61757」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「1cdf90890c543030」 「№5184」
Difference from previous tested commit:  code diff
Commit date: 2021-09-20 16:36:21
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-10.gcc.build.debug gcc-11.gcc.python39.build.debug gcc-9.gcc.build.debug linux.clang.hdf5.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels build.ninja_debug graphics static mac.clang.static.build.release beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.addsan integration.mpi integration.release_debug integration.tensorflow integration.thread integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python37.release.PyRosetta4.Debug linux.clang.python38.release.PyRosetta4.Debug linux.clang.python39.release.PyRosetta4.Debug mac.clang.python39.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python37.release.PyRosetta4.MinSizeRel linux.clang.python38.release.PyRosetta4.MinSizeRel linux.clang.python39.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python37.release.PyRosetta4.MinSizeRel ubuntu.clang.python38.release.PyRosetta4.MinSizeRel ubuntu.clang.python39.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release linux.clang.python37.release.PyRosetta4.Release linux.clang.python38.release.PyRosetta4.Release linux.clang.python39.release.PyRosetta4.Release mac.clang.python39.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release ubuntu.clang.python37.release.PyRosetta4.Release ubuntu.clang.python38.release.PyRosetta4.Release ubuntu.clang.python39.release.PyRosetta4.Release release.PyRosetta4.conda.Release release.source scientific.antibody_h3_modeling scientific.design_fast scientific.loop_modeling_kic_12res scientific.protein_data_bank_diagnostic.cif scientific.protein_data_bank_diagnostic.full scientific.sb_talaris13_docking 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 mac.clang.unit.release unit.ubsan gcc-10.gcc.unit gcc-11.gcc.python39.unit gcc-9.gcc.unit util.apps windows.build.debug windows.build.release

Merge pull request #5184 from RosettaCommons/aleaverfay/rs_schema_validator_singleton2 This commit adds a new singleton to construct the schema for RosettaScripts and to then hold the (expensive to construct) XMLSchemaValidator. This validator can then be requested repeatedly without requiring the costly construction of the schema or the costly construction of the validator. This should make repeated calls to the XMLObjects' methods much faster. Thanks @weitzner for hashing out this idea with me. Thanks @bkuhlman for bringing the problem to our attention. This is the alternative fix to the issue that PR #5179 was meant to address

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover InterfaceAnalyzer InterfaceDdG LoopAnalyzer LoopLengthChange ModifyVariantTypeMover RBOut SSElementSelector add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backrub backrub_interface_ddG binselector binselector_probins buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring constraints_metric create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm 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 cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_session_resource ddG_scan design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet_use_input_rot homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric kinemage_grid_output ligand_database_io 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 make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_span_ang_ref2015_memb mp_symmetry_load netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin phiselector place_simultaneously pna_base_pairs 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 rdkit_metrics real_virt_mover recon_design remodel_helical_repeat repack_with_elec_dens res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric set_torsion simple_glycosylation simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock 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 swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetry_data_resource target_clash threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
Protein-Protein-Docking
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover InterfaceAnalyzer InterfaceDdG LoopAnalyzer LoopLengthChange ModifyVariantTypeMover RBOut SSElementSelector add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer_xml autosetup_metals_centroid backrub backrub_interface_ddG binselector binselector_probins buried_area_filter buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs centroid_from_fullatom cleanAlignment coarse_rna_scoring constraints_metric create_sequence_motif crosslinkermover_1_4_bbmb_asymm crosslinkermover_1_4_bbmb_c2_symmetry crosslinkermover_1_4_bbmb_s2_symm 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 cst_info custom_basetype_packer_palette cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_session_resource ddG_scan design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA disulfidize_beta_cys dock_with_hotspot_place_simultaneously enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl favor_coupling_tensor favor_native_residue features features_parallel features_pdb fold_from_loops fuzzy ga_ligand_dock ga_ligand_dock_amino_acid genkic_bin_perturbing genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet_use_input_rot homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization interaction_graph_summary_metric inverse_rotamer_remodel kinemage_grid_output ligand_database_io 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 make_symmdef_file match_xml metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mhc_epitope mhc_epitope_nmer_preload minimize_with_elec_dens mirror_symm motif_score_filter mp_ligand_interface mp_quick_relax_ref2015_memb mp_relax mp_relax_w_ligand mp_span_ang_ref2015_memb mp_symmetry_load netcharge_design netcharge_design_symm nonideal_rtmin oligourea_design pertmin phiselector place_simultaneously pna_base_pairs 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 rdkit_metrics real_virt_mover recon_design remodel_helical_repeat repack_with_elec_dens res_lipo_ref2015_memb resource_database_locator rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_only_silence sdf_reader secondary_structure_output selected_residue_count_metric set_torsion simple_glycosylation simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_in_protocols simple_metrics_per_residue small_molecule_lattice_dock 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 swm_add_rosettascripts symm_disulfidize symm_rotamer_boltzmann symmetry_data_resource target_clash threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file
Test: linux.clang.scientific.antibody_h3_modeling

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Test: linux.clang.scientific.protein_data_bank_diagnostic.cif

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Test: linux.clang.scientific.protein_data_bank_diagnostic.full

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