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Revisions №61170

branch: master 「№61170」
Commited by: Vikram K. Mulligan
GitHub commit link: 「623eb78fcf36e2cd」 「№4549」
Difference from previous tested commit:  code diff
Commit date: 2020-03-07 14:50:25
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 build.cppcheck alpine.gcc.build.debug gcc-9.gcc.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 build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.PyRosetta4.Debug release.PyRosetta4.Release release.source scientific.FlexPepDock scientific.mhc_epitope_energy.debug 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 gcc-9.gcc.unit util.apps

Merge pull request #4549 from RosettaCommons/vmullig/citation_manager_incremental_merge_1 Incremental merge #1 for the citation manager This is a first incremental merge for the citation manager. All of the functionality is there, now, and works for all JD2 apps and for RosettaScripts. Future incremental merges will make this work for JD3 and PyRosetta, and will add additional citations. This is part of the functionality implemented in pull request #3087.

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/apps/public/rosetta_scripts/rosetta_scripts.cc src/basic/citation_manager/Citation.cc src/basic/citation_manager/CitationCollection.cc src/basic/citation_manager/CitationManager.cc src/basic/citation_manager/UnpublishedModuleAuthor.cc src/basic/citation_manager/UnpublishedModuleInfo.cc src/core/chemical/carbohydrates/CarbohydrateInfoManager.cc src/core/energy_methods/AACompositionEnergy.cc src/core/energy_methods/NetChargeEnergy.cc src/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/ApproximateBuriedUnsatPenalty.cc src/core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenalty.cc src/core/pack/guidance_scoreterms/hbnet_energy/HBNetEnergy.cc src/core/pack/guidance_scoreterms/voids_penalty_energy/VoidsPenaltyEnergy.cc src/core/pack/palette/CustomBaseTypePackerPalette.cc src/core/pack/palette/DefaultPackerPalette.cc src/core/pack/palette/NCAADefaultPackerPalette.cc src/core/pack/palette/NoDesignPackerPalette.cc src/core/scoring/ScoreFunction.cc src/core/select/residue_selector/AndResidueSelector.cc src/core/select/residue_selector/LayerSelector.cc src/core/select/residue_selector/NeighborhoodResidueSelector.cc src/core/select/residue_selector/NotResidueSelector.cc src/core/select/residue_selector/OrResidueSelector.cc src/core/select/residue_selector/SliceResidueSelector.cc src/core/simple_metrics/metrics/DihedralDistanceMetric.cc src/core/simple_metrics/metrics/InteractionEnergyMetric.cc src/core/simple_metrics/metrics/RMSDMetric.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/core/simple_metrics/metrics/SasaMetric.cc src/core/simple_metrics/metrics/SecondaryStructureMetric.cc src/core/simple_metrics/metrics/SelectedResidueCountMetric.cc src/core/simple_metrics/metrics/SelectedResiduesMetric.cc src/core/simple_metrics/metrics/SelectedResiduesPyMOLMetric.cc src/core/simple_metrics/metrics/SequenceMetric.cc src/core/simple_metrics/metrics/SequenceSimilarityMetric.cc src/core/simple_metrics/metrics/TimingProfileMetric.cc src/core/simple_metrics/metrics/TotalEnergyMetric.cc src/protocols/analysis/GlycanInfoMover.cc src/protocols/analysis/simple_metrics/RunSimpleMetricsMover.cc src/protocols/antibody/AntibodyCDRGrafter.cc src/protocols/antibody/AntibodyNumberingConverterMover.cc src/protocols/antibody/constraints/CDRDihedralConstraintMover.cc src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc src/protocols/antibody/constraints/ParatopeSiteConstraintMover.cc src/protocols/antibody/design/AntibodyDesignMover.cc src/protocols/antibody/design/MutateFrameworkForCluster.cc src/protocols/calc_taskop_movers/CreateSequenceMotifMover.cc src/protocols/carbohydrates/CreateGlycanSequonMover.cc src/protocols/carbohydrates/GlycanSampler.cc src/protocols/carbohydrates/GlycanTreeMinMover.cc src/protocols/carbohydrates/GlycanTreeModeler.cc src/protocols/carbohydrates/IdealizeAnomericHydrogens.cc src/protocols/carbohydrates/LinkageConformerMover.cc src/protocols/carbohydrates/RingPlaneFlipMover.cc src/protocols/carbohydrates/SimpleGlycosylateMover.cc src/protocols/carbohydrates/TautomerizeAnomerMover.cc src/protocols/cyclic_peptide/SymmetricCycpepAlign.cc src/protocols/cyclic_peptide/TryDisulfPermutations.cc src/protocols/denovo_design/movers/FastDesign.cc src/protocols/enzymatic_movers/EnzymaticMover.cc src/protocols/enzymatic_movers/GlycosyltransferaseMover.cc src/protocols/enzymatic_movers/KinaseMover.cc src/protocols/features/ReportToDB.cc src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc src/protocols/grafting/AnchoredGraftMover.cc src/protocols/grafting/CCDEndsGraftMover.cc src/protocols/grafting/simple_movers/DeleteRegionMover.cc src/protocols/grafting/simple_movers/InsertPoseIntoPoseMover.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/grafting/simple_movers/ReplaceRegionMover.cc src/protocols/helical_bundle/BackboneGridSampler.cc src/protocols/helical_bundle/BundleGridSampler.cc src/protocols/helical_bundle/MakeBundle.cc src/protocols/helical_bundle/PerturbBundle.cc src/protocols/indexed_structure_store/filters/FragmentLookupFilter.cc src/protocols/ligand_docking/FinalMinimizer.cc src/protocols/ligand_docking/HighResDocker.cc src/protocols/ligand_docking/HighResEnsemble.cc src/protocols/ligand_docking/InterfaceScoreCalculator.cc src/protocols/ligand_docking/ProtLigEnsemble.cc src/protocols/ligand_docking/StartFrom.cc src/protocols/ligand_docking/Transform.cc src/protocols/ligand_docking/TransformEnsemble.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loop_grower/SheetSampler.cc src/protocols/monte_carlo/GenericMonteCarloMover.cc src/protocols/moves/Mover.cc src/protocols/moves/MoverContainer.cc src/protocols/protein_interface_design/movers/LoopOver.cc src/protocols/relax/FastRelax.cc src/protocols/relax/RelaxProtocolBase.cc src/protocols/rosetta_scripts/ParsedProtocol.cc src/protocols/simple_moves/BBDihedralSamplerMover.cc src/protocols/simple_moves/ConvertRealToVirtualMover.cc src/protocols/simple_moves/ConvertVirtualToRealMover.cc src/protocols/simple_moves/DeleteChainsMover.cc src/protocols/simple_moves/RingConformationMover.cc src/protocols/simple_moves/SetupMetalsMover.cc src/protocols/simple_moves/SimpleThreadingMover.cc
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
threefold_symm_peptide_design
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover InterfaceAnalyzer InterfaceDdG LoopAnalyzer LoopLengthChange ModifyVariantTypeMover RBOut SSElementSelector ThreadingInputter add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer antibody_designer_camelid antibody_designer_xml antibody_numbering_converter autosetup_metals_centroid backrub_interface_ddG binselector binselector_probins buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment 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 cst_info custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_session_resource ddG_of_mutation 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 enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax favor_native_residue features_parallel features_pdb fiber_diffraction_fad fold_and_dock fold_from_loops fuzzy ga_ligand_dock genkic_bin_perturbing genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet_use_input_rot homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization hydrate_relax 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 loop_creation make_symmdef_file match_xml metalloprotein_broker 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_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 pna_base_pairs pocket_relax 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 real_virt_mover relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens res_lipo_ref2015_memb rollmover rosetta_scripts_hbond_options rosetta_scripts_include 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 seed_ensemble_JD2_JI selected_residue_count_metric set_torsion simple_glycosylation simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics 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 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: mac.clang.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover ContactMolecularSurface DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover InterfaceAnalyzer InterfaceDdG LoopAnalyzer LoopLengthChange ModifyVariantTypeMover RBOut SSElementSelector ThreadingInputter add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data antibody_designer antibody_designer_camelid antibody_designer_xml antibody_numbering_converter autosetup_metals_centroid backrub_interface_ddG binselector binselector_probins buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm cart_min_glycans ccd_ends_graft_mover_rs central_class_modification centroid_from_fullatom cleanAlignment 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 cst_info custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_session_resource ddG_of_mutation 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 enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym evolution farnesyl fast_relax favor_native_residue features_parallel features_pdb fiber_diffraction_fad fold_and_dock fold_from_loops fuzzy ga_ligand_dock genkic_bin_perturbing genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars glycan_anomers glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax grid_scores_features hbnet_use_input_rot homodimer_fnd_ref2015_memb hotspot_graft hts_io hybridization hydrate_relax 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 loop_creation make_symmdef_file match_xml membrane_relax membrane_relax_hbond metalloprotein_broker 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_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 pna_base_pairs pocket_relax 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 real_virt_mover relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens res_lipo_ref2015_memb rollmover rosetta_scripts_hbond_options rosetta_scripts_include 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 seed_ensemble_JD2_JI selected_residue_count_metric set_torsion simple_glycosylation simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics 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 threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file