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Revisions №61297

branch: master 「№61297」
Commited by: Brandon Frenz
GitHub commit link: 「9c2ed7261a0b664c」 「№4743」
Difference from previous tested commit:  code diff
Commit date: 2020-05-29 15:08:32
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 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 #4743 from CyrusBiotechnology/bfrenz/wildtype-opt Added option to refine the wild type structure when running Cartesian DDG with new refactored code.

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Test: ubuntu.clang.code_quality.clang_tidy

Failed sub-tests (click for more details):
src/apps/public/rna/rna_denovo.cc
Test: mac.clang.unit

Failed sub-tests (click for more details):
core:AACompositionEnergyTests_packer:test_energy_annealing core:AARepeatEnergyTests:test_energy_annealing core:AARepeatEnergyTests:test_energy_cases core:AARepeatEnergyTests:test_energy_eval core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_natural_corrections1_cross_chain_test core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_packing_thr_ser_to_bb_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET_O core:ApproximateBuriedUnsatPenaltyTests:test_scoring_4SER core:ApproximateBuriedUnsatPenaltyTests:test_scoring_APA core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_natural_corrections1_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_thr_ser_to_bb_test core:AtomTreeCollectionTests:test_atom_tree_collection_from_rotamer_set_ctor core:AtomTreeCollectionTests:test_atom_tree_collection_from_rotamer_sets_ctor core:AtomTreeCollectionTests:test_construct_residue_atom_tree_collection core:AtomTreeDiffTests:test_save_and_restore core:BetaNov16WithAutoSetupMetalsTests:test_auto_setup_metals_with_ser_mn core:BinarySilentMultiposeTests:test_save_multiple_poses_and_restore core:BinarySilentMultiposeTests:test_save_multiple_poses_with_resize_and_restore core:BinarySilentTests:test_read_badly_formatted_silent_file core:BinarySilentTests:test_save_and_restore core:BinarySilentTests:test_save_and_restore_centroid core:BinarySilentTests:test_save_and_restore_inserting_residues core:BuriedUnsatPenaltyGraphSymmetricTests:test_graph_setup core:BuriedUnsatPenaltyGraphSymmetricTests:test_smallpose_graph_setup core:BuriedUnsatPenaltyGraphTests:test_graph_setup core:BuriedUnsatPenaltyGraphTests:test_smallpose_graph_setup core:BuriedUnsatPenaltySymmetricTests:test_simple_symmetric_scoring core:BuriedUnsatPenaltySymmetricTests:test_simple_symmetric_scoring2 core:BuriedUnsatPenaltySymmetricTests:test_symmetric_packing core:BuriedUnsatPenaltySymmetricTests:test_symmetric_setup_for_packing core:BuriedUnsatPenaltyTests:test_packing core:BuriedUnsatPenaltyTests:test_packing_steps core:BuriedUnsatPenaltyTests:test_setup_for_packing core:BuriedUnsatPenaltyTests:test_simple_scoring core:ClashBasedRepackShellTests:test_xml_tag core:ClashBasedShellSelectorTests:test_add_clashes_to_shell core:ClashBasedShellSelectorTests:test_bool_mask_from_resnums core:ClashBasedShellSelectorTests:test_bool_mask_from_task core:ClashBasedShellSelectorTests:test_is_sc_xx_clash core:ClashBasedShellSelectorTests:test_parse_my_tag core:ClashBasedShellSelectorTests:test_resnums_from_bool_mask core:ClashBasedShellSelectorTests:test_resnums_from_task core:ClashBasedShellSelectorTests:test_selections core:ClashBasedShellSelectorTests:test_task_from_bool_mask core:ClashBasedShellSelectorTests:test_task_from_resnums core:ConstraintIOTests:test_constraint_read_in core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_beta_nov16 core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_hxl_tors core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_lk_ball core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_omega core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_rama core:CyclicGeometry_betanov16_Tests:test_cyclic_permutation_rama_prepro core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_beta core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_hxl_tors core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_lk_ball core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_omega core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_rama core:CyclicGeometry_nmethyl_beta_Tests:test_cyclic_permutation_rama_prepro core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_fa_rep core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_pro_close core:CyclicGeometry_nmethyl_beta_TwoChainTests_A:test_cyclic_permutation_rama_prepro core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_beta core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_cart_bonded core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_atr core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_fa_sol core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hbonds core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_hxl_tors core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_omega core:CyclicGeometry_nmethyl_beta_TwoChainTests_B:test_cyclic_permutation_rama core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_beta_nov16 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_hxl_tors core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_omega core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_rama core:CyclicGeometry_peptoid_beta_Tests:test_cyclic_permutation_rama_prepro devel:BuildSheetTests:test_flat_sheet_grid protocols:AchiralResidueTypeTests:test_import_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_import_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_import_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AddHelixSequenceConstraintsMoverTests:test_detect_helices protocols:AddHelixSequenceConstraintsMoverTests:test_limit_ala protocols:AddHelixSequenceConstraintsMoverTests:test_limit_val protocols:AddHelixSequenceConstraintsMoverTests:test_limit_val_by_hydrophobicity protocols:AddHelixSequenceConstraintsMoverTests:test_negative_nterm protocols:AddHelixSequenceConstraintsMoverTests:test_positive_cterm protocols:AntibodyCDRGrafterTests:test_graft_classes protocols:AntibodyResidueSelectorsTest:test_selectors protocols:AntibodySeqDesign:test_graft_tf_generation1 protocols:AntibodySeqDesign:test_graft_tf_generation2 protocols:AntibodySeqDesign:test_normal_tf_generation protocols:AntibodySeqDesign:test_task_ops protocols:AntibodySeqDesign:test_utility_functions protocols:AntibodyTaskOps:test_AddCDRProfileSetsOperation protocols:AntibodyTaskOps:test_AddCDRProfilesOperation protocols:AntibodyTaskOps:test_DisableAntibodyRegionOperation protocols:AntibodyTaskOps:test_DisableCDRsOperation protocols:AntibodyTaskOps:test_RestrictToCDRsAndNeighbors protocols:AtomCoordinateCstMoverTests:test_input_bounded_default protocols:AtomCoordinateCstMoverTests:test_input_harmonic_default protocols:AtomCoordinateCstMoverTests:test_input_harmonic_sidechain protocols:AtomCoordinateCstMoverTests:test_integration_native protocols:AtomCoordinateCstMoverTests:test_native_harmonic_default protocols:AtomCoordinateCstMoverTests:test_native_harmonic_sidechain protocols:AtomPairConstraintGeneratorTests:test_all_atom protocols:AtomPairConstraintGeneratorTests:test_constraints_allresidues protocols:AtomPairConstraintGeneratorTests:test_max_dist protocols:AtomPairConstraintGeneratorTests:test_native protocols:AtomPairConstraintGeneratorTests:test_residue_selector protocols:BackrubProtocolTests:test_parse_pivots_from_residue_selector protocols:BetaAlphaDisulfideTests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov15_Tests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov16_Tests:test_mixed_disulf protocols:BuildDeNovoBackboneMoverTests:test_design protocols:BuildDeNovoBackboneMoverTests:test_symmetry protocols:CoordinateConstraintGeneratorTests:test_constraints_allresidues protocols:CoordinateConstraintGeneratorTests:test_constraints_subset protocols:CoordinateConstraintGeneratorTests:test_input_bounded_default protocols:CoordinateConstraintGeneratorTests:test_input_harmonic_default protocols:CoordinateConstraintGeneratorTests:test_input_harmonic_sidechain protocols:CoordinateConstraintGeneratorTests:test_integration_native protocols:CoordinateConstraintGeneratorTests:test_native_harmonic_default protocols:CoordinateConstraintGeneratorTests:test_native_harmonic_sidechain