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Revisions №61423

branch: master 「№61423」
Commited by: Frank DiMaio
GitHub commit link: 「62fb38d7e6158d52」 「№4871」
Difference from previous tested commit:  code diff
Commit date: 2020-09-15 19:00:17
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-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 code_quality.cppcheck serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.ligand_docking.debug scientific.mp_symdock scientific.peptide_pnear_vs_ic50 scientific.simple_cycpep_predict scientific.stepwise_rna_favorites 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 #4871 from RosettaCommons/dimaio/dna_phil_modes A few general fixes for DNA. - Enabling (plus fix a few deriv discontinuities) in Phil's dna_dihedral_* terms. - Fix cart_bonded for DNA - Change default of -excluded_dna_dna to true. - Adding some utility functions (from Phil) for minimizing DNA with a zig-zag atom tree Integration test changes are due to: a) changes to cart_bonded database (and consequent changes in summation order of cart_bonded terms); b) integration tests that print EnergyMethodOptions or HbondOptions (which have had defaults changed).

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Test: mac.clang.python27.build.xcode

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Test: linux.gcc.code_quality.beautification

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/core/energy_methods/DNA_DihedralEnergy.cc src/core/fragment/FragmentSetLoader.cc src/core/io/StructFileRepOptions.cc src/core/pack/task/operation/TaskOperations.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/protocols/abinitio/abscript/FragmentJumpCM.cc src/protocols/calc_taskop_filters/MultipleSigmoidsFilter.cc src/protocols/calc_taskop_filters/OperatorFilter.cc src/protocols/calc_taskop_filters/SigmoidFilter.cc src/protocols/canonical_sampling/SimulatedTempering.cc src/protocols/chemically_conjugated_docking/UBQ_GTPaseMover.cc src/protocols/cutoutdomain/CutOutDomain.cc src/protocols/cyclic_peptide/DeclareBond.cc src/protocols/cyclic_peptide/PeptideStubMover.cc src/protocols/denovo_design/components/StructureData.cc src/protocols/dna/util.cc src/protocols/dna_dock/PropagateClashCheckFilter.cc src/protocols/enzdes/EnzFilters.cc src/protocols/enzdes/PackRotamersMoverPartGreedy.cc src/protocols/evolution/NucleotideMutation.cc src/protocols/features/HBondFeatures.cc src/protocols/filters/BasicFilters.cc src/protocols/filters/ReplicateFilter.cc src/protocols/fldsgn/CircularPermutation.cc src/protocols/fldsgn/filters/InterlockingAromaFilter.cc src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.cc src/protocols/fldsgn/filters/SecondaryStructureCountFilter.cc src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/hbnet/HBNet.cc src/protocols/hbnet/HBNetStapleInterface.cc src/protocols/helical_bundle/BackboneGridSampler.cc src/protocols/helical_bundle/FitSimpleHelix.cc src/protocols/helical_bundle/MakeBundle.cc src/protocols/helical_bundle/PerturbBundle.cc src/protocols/hotspot_hashing/movers/PlaceProbeMover.cc src/protocols/hybridization/BackboneTorsionPerturbation.cc src/protocols/hybridization/BackboneTorsionSampler.cc src/protocols/hybridization/HybridizeProtocol.cc src/protocols/indexed_structure_store/movers/DirectSegmentLookupMover.cc src/protocols/ligand_docking/ProtLigEnsemble.cc src/protocols/loop_modeling/utilities/rosetta_scripts.cc src/protocols/loophash/LoopHashDiversifier.cc src/protocols/loophash/LoopHashMoverWrapper.cc src/protocols/loops/loops_definers/LoopsExplicitDefiner.cc src/protocols/matdes/ClashCheckFilter.cc src/protocols/matdes/GetRBDOFValues.cc src/protocols/matdes/OligomericAverageDegreeFilter.cc src/protocols/membrane/FlipMover.cc src/protocols/membrane/SpinAroundPartnerMover.cc src/protocols/minimization_packing/DisulfideOptimizationMover.cc src/protocols/multistage_rosetta_scripts/MRSJobQueen.cc src/protocols/ncbb/ResidueReplacementRebuildMover.cc src/protocols/parser/FragmentReader.cc src/protocols/pose_creation/RepeatPropagationMover.cc src/protocols/pose_length_moves/InsertResMover.cc src/protocols/protein_interface_design/filters/AverageDegreeFilter.cc src/protocols/protein_interface_design/filters/BoltzmannFilter.cc src/protocols/protein_interface_design/filters/DesignableResiduesFilter.cc src/protocols/protein_interface_design/filters/RmsdFilter.cc src/protocols/protein_interface_design/filters/StubScoreLoopsFilter.cc src/protocols/protein_interface_design/filters/TorsionFilter.cc src/protocols/protein_interface_design/movers/DockWithHotspotMover.cc src/protocols/protein_interface_design/movers/MapHotspot.cc src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsLoopsMover.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMover.cc src/protocols/protein_interface_design/movers/TryRotamers.cc src/protocols/relax/AtomCoordinateCstMover.cc src/protocols/relax/membrane/MPRangeRelaxMover.cc src/protocols/rna/denovo/movers/RNA_DeNovoProtocolMover.cc src/protocols/score_filters/ScoreCutoffFilter.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/seeded_abinitio/GrowPeptides.cc src/protocols/seeded_abinitio/SeedFoldTree.cc src/protocols/seeded_abinitio/SwapSegment.cc src/protocols/sewing/movers/AssemblyMover.cc src/protocols/sewing/requirements/ClashRequirement.cc src/protocols/sewing/requirements/DsspSpecificLengthRequirement.cc src/protocols/sewing/requirements/LengthInResiduesRequirement.cc src/protocols/sewing/requirements/LigandClashRequirement.cc src/protocols/sewing/requirements/SizeInSegmentsRequirement.cc src/protocols/simple_ddg/SSElementBisectddGFilter.cc src/protocols/simple_filters/DisulfideEntropyFilter.cc src/protocols/simple_filters/HelixHelixAngleFilter.cc src/protocols/simple_filters/MPSpanAngleFilter.cc src/protocols/simple_filters/NetChargeFilter.cc src/protocols/simple_filters/NonSequentialNeighborsFilter.cc src/protocols/simple_filters/PackStatFilter.cc src/protocols/simple_filters/ResidueSetChainEnergyFilter.cc src/protocols/simple_filters/SSElementMotifContactFilter.cc src/protocols/simple_filters/ShapeComplementarityFilter.cc src/protocols/simple_filters/SimpleMetricFilter.cc src/protocols/simple_filters/TaskAwareSASAFilter.cc src/protocols/simple_filters/TaskAwareScoreTypeFilter.cc src/protocols/simple_moves/AddChainMover.cc src/protocols/simple_moves/AlignChainMover.cc src/protocols/simple_moves/FavorSequenceProfile.cc src/protocols/simple_moves/SetTorsion.cc src/protocols/simple_moves/SuperimposeMover.cc src/protocols/simple_moves/asym_fold_and_dock/AsymFoldandDockMoveRbJumpMover.cc src/protocols/simple_moves/bin_transitions/InitializeByBins.cc src/protocols/simple_moves/bin_transitions/PerturbByBins.cc src/protocols/simple_task_operations/RestrictToInterface.cc src/protocols/splice/AlignEndsMover.cc src/protocols/splice/FindEndpointsOperation.cc src/protocols/splice/Splice.cc src/protocols/splice/SpliceIn.cc src/protocols/splice/SpliceInAntibody.cc src/protocols/splice/SpliceInTail.cc src/protocols/splice/SpliceOut.cc src/protocols/switches/GraftSwitchMover.cc src/protocols/task_operations/JointSequenceOperation.cc src/protocols/task_operations/ProteinInterfaceDesignOperation.cc src/protocols/task_operations/SelectBySASAOperation.cc src/protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.cc
Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
database_md5
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
antibody_designer antibody_designer_camelid antibody_designer_xml backbonegridsampler_multiresidue backrub_interface_ddG bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset cart_min_glycans cartesianddg coupled_moves database_md5 density_tools dna_interface_design erraser_minimize evolution features features_database_schema ga_ligand_dock glycan_anomers glycan_refinment hbnet_use_input_rot hybridization ligand_dock_ensemble minimize_with_elec_dens motif_dna_packer_design mp_find_interface mp_mutate_relax mp_mutate_repack mr_protocols nonideal_rtmin oligourea_predict pertmin perturb_helical_bundle pna_base_pairs readin_dna_rna_protein remodel_helical_repeat repack_with_elec_dens repeat_relax rna_denovo rna_denovo_fragment_homology_exclusion rna_denovo_new_libs rosetta_scripts_hbond_options sdf_reader sequence_profile_constraints simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_bondangle_bondlength 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_grafting_movers simple_metrics_per_residue small_molecule_lattice_dock supercharge swm_dna_bridge test1_benchmark test_energy_method_options tna_base_pairs zinc_heterodimer zinc_homodimer_design
Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
database_md5
Test: mac.clang.integration

Failed sub-tests (click for more details):
antibody_designer antibody_designer_camelid antibody_designer_xml app_exception_handling backbonegridsampler_multiresidue backrub_interface_ddG bundlegridsampler bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_z0_offset bundlegridsampler_z1_offset cart_min_glycans cartesianddg coupled_moves database_md5 density_tools disulfidize_beta_cys dna_interface_design erraser_minimize evolution features features_database_schema ga_ligand_dock glycan_anomers glycan_refinment hbnet_use_input_rot hybridization ligand_dock_ensemble minimize_with_elec_dens motif_dna_packer_design mp_find_interface mp_mutate_relax mp_mutate_repack mr_protocols nonideal_rtmin oligourea_predict pepspec pertmin perturb_helical_bundle pna_base_pairs readin_dna_rna_protein remodel remodel_disulfides remodel_helical_repeat repack_with_elec_dens repeat_relax rna_denovo rna_denovo_fragment_homology_exclusion rna_denovo_new_libs rosetta_scripts_hbond_options sdf_reader sequence_profile_constraints simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_bondangle_bondlength 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_grafting_movers simple_metrics_per_residue small_molecule_lattice_dock supercharge swa_rna_gagu_09_sample_virtual_ribose swm_dna_bridge test1_benchmark test_energy_method_options tna_base_pairs zinc_heterodimer zinc_homodimer_design
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.scientific.mp_symdock

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Test: linux.gcc.cxx11thread.mpi.serialization.scientific.peptide_pnear_vs_ic50

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