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Revisions №60640

branch: master 「№60640」
Commited by: Vikram K. Mulligan
GitHub commit link: 「a8cf775b9cd9a68f」 「№3829」
Difference from previous tested commit:  code diff
Commit date: 2019-03-05 18:00:14
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 mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.mpi integration.release_debug integration.tutorials integration maintenance.documentation performance profile release.PyRosetta4.Debug release.PyRosetta4.Release release.source 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

Merge pull request #3829 from RosettaCommons/vmullig/fix_shape_grid_water Tweak ShapeGrid so that it doesn't crash with ligands. Looks like it's pretty hard-coded for canonical amino acids. I started to generalize it but gave up. The main change here is an if statement to skip ligands.

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: linux.clang.performance

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

Failed sub-tests (click for more details):
core:BinarySilentMultiposeTests:test_save_multiple_poses_and_restore core:BinarySilentMultiposeTests:test_save_multiple_poses_with_resize_and_restore core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_dun core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_hbonds core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_omega core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_pro_close core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_rama core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_rama_prepro core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_talaris2014 core:CyclicGeometryTwoChain_nmethyl_Tests:test_cyclic_permutation_yhh_planarity core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_beta_nov15 core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_dun core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_lk_ball_wtd core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_omega core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_rama core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_rama_prepro core:CyclicGeometry_betanov15_Tests:test_cyclic_permutation_yhh_planarity core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_beta_nov16 core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_cart_bonded core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_atr core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_dun_dev core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_dun_rot core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_dun_semi core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_elec core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_intra_atr_xover4 core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_intra_elec core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_intra_rep_xover4 core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_intra_sol_xover4 core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_rep core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_fa_sol core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_hbonds core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_hxl_tors core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_lk_ball core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_lk_ball_bridge core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_lk_ball_bridge_uncpl core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_lk_ball_iso core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_omega core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_p_aa_pp core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_pro_close core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_rama core:CyclicGeometry_nmethyl_betanov16_Tests:test_cyclic_permutation_rama_prepro core:FullatomDisulfideEnergyTests:test_disulfE_deriv_check_w_partial_flexibility core:FullatomDisulfideEnergyTests:test_disulfE_deriv_check_w_total_flexibility core:HBondGraphTests:test_AtomInfo core:HBondGraphTests:test_hbond_graph core:MPSpanInsertionEnergyTests:test_calc_span_score core:MPSpanInsertionEnergyTests:test_compute core:MPSpanInsertionEnergyTests:test_create_updated_spans core:MPSpanInsertionEnergyTests:test_finalize_total_energy core:MPSpanInsertionEnergyTests:test_spline_by_z core:NetChargeEnergyTests_packer:test_energy_annealing core:NetChargeEnergyTests_packer_symm:test_energy_annealing_symmetric core:PolylinearInterpolationTests:test_1D core:PolylinearInterpolationTests:test_1D_wraparound core:PolylinearInterpolationTests:test_polylinear_interpolation_2D_derivs core:PolylinearInterpolationTests:test_polylinear_interpolation_3D_derivs core:PolylinearInterpolationTests:test_polylinear_interpolation_3D_derivs_wraparound core:PolylinearInterpolationTests:test_polylinear_interpolation_lysine_derivs core:RotamerTrials:test_rotamer_trials core:SymmGlyTests:test_symm_gly_cart_bonded core:SymmGlyTests:test_symm_gly_default_scorefxn core:SymmGlyTests:test_symm_gly_fa_atr core:SymmGlyTests:test_symm_gly_fa_dun core:SymmGlyTests:test_symm_gly_fa_elec core:SymmGlyTests:test_symm_gly_fa_intra_rep core:SymmGlyTests:test_symm_gly_fa_rep core:SymmGlyTests:test_symm_gly_fa_sol core:SymmGlyTests:test_symm_gly_hbonds core:SymmGlyTests:test_symm_gly_omega core:SymmGlyTests:test_symm_gly_p_aa_pp core:SymmGlyTests:test_symm_gly_rama core:SymmGlyTests:test_symm_gly_rama_prepro core:SymmGlyTests:test_symm_gly_talaris2014 core:SymmetricRotamerTrials:test_symmetric_rotamer_trials core:Symmetric_Binary_Protein_Silent_File_Tests:test_save_and_restore core:mmcif_IO:test_mmcif_input core:mmcif_IO:test_mmcif_output core:mmcif_IO:test_mmcif_vs_pdb_input core:mmcif_IO:test_multimodel_cif core:rtmin_setup_Tests:test_noop_test core:rtmin_setup_Tests:test_rtmin_setup 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 protocols:CoupledMovesProtocolTests:test_apply protocols:CoupledMovesProtocolTests:test_bad_init protocols:DDGBindOptEDataTests:test_get_score protocols:DdGScan:test_calculate protocols:DdGScan:test_filter_parsing protocols:DdgFilter:test_filter_parsing protocols:DdgFilter:test_use_filter protocols:DisulfideInsertionMoverTests:test_apply_function protocols:DisulfideInsertionMoverTests:test_cyclization_viability_function protocols:DisulfideInsertionMoverTests:test_rosettascripts_options protocols:DisulfidizeMoverTests:test_disulfidize protocols:DisulfidizeMoverTests:test_multiplex protocols:DockingTest:test_DockingPacking protocols:DockingTest:test_DockingProtocolFunctions protocols:DockingTest:test_DockingProtocol_clone protocols:DockingTest:test_DockingRigidBodyMinimize protocols:DockingTest:test_DockingSlideIntoContact protocols:DockingTest:test_EllipsoidalRandomizationMover protocols:DynamicAggregateFunctionTests:test_EntityFunc_AA_SET_command protocols:DynamicAggregateFunctionTests:test_EntityFunc_AA_SET_command_missing_commas protocols:DynamicAggregateFunctionTests:test_EntityFunc_AA_SET_command_missing_equals_sign protocols:DynamicAggregateFunctionTests:test_EntityFunc_AA_SET_command_missing_right_curly_brace protocols:DynamicAggregateFunctionTests:test_EntityFunc_SET_CONDITION_command_from_AA_SET protocols:DynamicAggregateFunctionTests:test_EntityFunc_SET_CONDITION_command_from_AA_SET_bad_name protocols:DynamicAggregateFunctionTests:test_EntityFunc_SET_CONDITION_command_from_aa_list protocols:DynamicAggregateFunctionTests:test_EntityFunc_SET_CONDITION_command_from_aa_list_missing_comma protocols:DynamicAggregateFunctionTests:test_EntityFunc_SET_CONDITION_command_from_aa_list_missing_lcurly protocols:DynamicAggregateFunctionTests:test_EntityFunc_SUB_EXPRESSION_command protocols:DynamicAggregateFunctionTests:test_EntityFunc_read_simple_file protocols:DynamicAggregateFunctionTests:test_daf_POSE_ENERGY_command protocols:DynamicAggregateFunctionTests:test_daf_POSE_ENERGY_into_VECTOR_VARIABLE_command protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_duplicate_varname protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_function_varname protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_illegal_varname protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_missing_listfile protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_missing_listfile2 protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_missing_varname protocols:DynamicAggregateFunctionTests:test_daf_STATE_VECTOR_command_missing_varname2 protocols:DynamicAggregateFunctionTests:test_daf_STATE_command protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_correspondence_file protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_correspondence_file2 protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_pdb_file protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_pdb_file2 protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_secondary_resfile protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_missing_secondary_resfile2 protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_varname_duplicated protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_varname_function_name protocols:DynamicAggregateFunctionTests:test_daf_STATE_command_varname_illegal_name protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_EXPRESSION_command protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_EXPRESSION_command_duplicated_local_varname protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_EXPRESSION_command_nocap_IN protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_EXPRESSION_command_two_local_variables protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_EXPRESSION_command_two_local_variables_misplaced_comma protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_VARIABLE_command protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_VARIABLE_command_bad_varname protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_VARIABLE_command_bad_vecvarname protocols:DynamicAggregateFunctionTests:test_daf_VECTOR_VARIABLE_command_func_vecvarname protocols:DynamicAggregateFunctionTests:test_daf_mean_of_vector_variable_command protocols:DynamicAggregateFunctionTests:test_daf_scalar_NPD_PROPERTY_command protocols:DynamicAggregateFunctionTests:test_daf_vector_NPD_PROPERTY_command protocols:DynamicAggregateFunctionTests:test_initialize_empty_DAF protocols:EnergyBasedClusteringTests_alpha_aa:test_cartesian_cluster_cyclic_alpha_aa protocols:EnergyBasedClusteringTests_alpha_aa:test_dihedral_cluster_cyclic_alpha_aa protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea_s2_symm protocols:EnergyBasedClusteringTests_oligourea:test_dihedral_cluster_cyclic_oligourea protocols:EnergyJobSummaryTests:test_basic_energy_job_summary protocols:ExtendChainMoverTests:test_append protocols:ExtendChainMoverTests:test_input protocols:ExtendChainMoverTests:test_prepend protocols:FAVirtMoverTests:test_fa_to_virt protocols:FAVirtMoverTests:test_virt_scoring protocols:FAVirtMoverTests:test_virt_to_fa protocols:FastRelaxTests:test_beta_custom_script protocols:FastRelaxTests:test_beta_dualspace_script protocols:FastRelaxTests:test_default_script protocols:FastRelaxTests:test_dualspace_script protocols:FastRelaxTests:test_fastrelax_B3N protocols:FastRelaxTests:test_fastrelax_B3N_mod_termini protocols:FastRelaxTests:test_local_script protocols:FastRelaxTests:test_nonexistent_local_script protocols:FeaturesReporterTests:test_identifier_generation protocols:FeaturesReporterTests:test_main protocols:FeaturesReporterTests:test_trajectory_report_to_db protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_L_alpha_backbone protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_L_alpha_backbone_lowmem protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_mixed_DL_alpha_backbone protocols:GenerateMainchainPotentialTests:test_full_run_ALA protocols:GenerateMainchainPotentialTests:test_full_run_B3N protocols:GenerateMainchainPotentialTests:test_full_run_GLY_asymm protocols:GenerateMainchainPotentialTests:test_full_run_GLY_symm protocols:GenerateMainchainPotentialTests:test_full_run_VAL protocols:GenerateMainchainPotentialTests:test_full_run_VAL_prepro protocols:GenerateMainchainPotentialTests:test_pose_generation protocols:GenerateMainchainPotentialTests:test_pose_generation_prepro protocols:GenericSimulatedAnnealerTests:test_acceptance protocols:GenericSimulatedAnnealerTests:test_boltzmann protocols:GenericSimulatedAnnealerTests:test_checkpointing protocols:GraftingTest:test_graft_classes protocols:GraftingTest:test_utility_functions protocols:HBNetMoverTests:test_hbnet_mover_setup protocols:HBondCalculatorsTest:test_hb_calculators protocols:InteractionGraphSummaryMetricTests:test_summary_from_trpcage_repack protocols:InterfaceHbondsFilterTests:test_InterfaceHbondsFilter protocols:InvrotTreeTest:test_invrot_tree protocols:LimitAromaChi2OperationTests:test_limit_aroma_chi2 protocols:LoopAnalyzerMoverTests:test_Cterm_adjacent protocols:LoopAnalyzerMoverTests:test_Nterm_adjacent protocols:LoopAnalyzerMoverTests:test_at_Nterm protocols:LoopAnalyzerMoverTests:test_internal_termini protocols:LoopAnalyzerMoverTests:test_internal_terminiCterm protocols:LoopAnalyzerMoverTests:test_simple_loop protocols:MPLipidAccessibilityTest:test_mp_lipid_accessibility protocols:MPLipidAccessibilityTest:test_parse_my_tag_input protocols:MSDMoverTest:test_consensus_sequence protocols:MSDMoverTest:test_correct_constraints protocols:MSDMoverTest:test_keeps_constraints protocols:MSDMoverTest:test_resfile_parsing protocols:MembraneUtil:test_angle_rmsd_method protocols:MembraneUtil:test_average_antiparallel_embeddings protocols:MembraneUtil:test_average_embeddings protocols:MembraneUtil:test_calc_helix_angles protocols:MembraneUtil:test_calc_helix_axis protocols:MembraneUtil:test_chain_com protocols:MembraneUtil:test_check_vector protocols:MembraneUtil:test_compute_embeddings_by_chain protocols:MembraneUtil:test_compute_structure_based_embedding1 protocols:MembraneUtil:test_compute_structure_based_embedding2 protocols:MembraneUtil:test_compute_structure_based_embedding3 protocols:MembraneUtil:test_compute_structure_based_embedding4 protocols:MembraneUtil:test_compute_structure_based_embedding5 protocols:MembraneUtil:test_compute_structure_based_embedding6 protocols:MembraneUtil:test_compute_structure_based_embedding7 protocols:MembraneUtil:test_compute_structure_based_embedding8 protocols:MembraneUtil:test_create_membrane_docking_foldtree_from_partners protocols:MembraneUtil:test_create_membrane_foldtree_anchor_com protocols:MembraneUtil:test_create_membrane_foldtree_anchor_pose_tmcom protocols:MembraneUtil:test_create_membrane_foldtree_anchor_tmcom protocols:MembraneUtil:test_create_membrane_multi_partner_foldtree_anchor_tmcom protocols:MembraneUtil:test_create_specific_membrane_foldtree protocols:MembraneUtil:test_is_fixed_on_fixed_memb protocols:MembraneUtil:test_is_fixed_on_moveable_memb protocols:MembraneUtil:test_is_independently_moveable_on_fixed_memb protocols:MembraneUtil:test_is_independently_moveable_on_independently_moveable_memb protocols:MembraneUtil:test_membrane_bb_rmsd_no_super protocols:MembraneUtil:test_membrane_bb_rmsd_no_super_allatom protocols:MembraneUtil:test_membrane_bb_rmsd_with_super protocols:MembraneUtil:test_membrane_bb_rmsd_with_super_allatom protocols:MembraneUtil:test_pose_tm_COM protocols:MembraneUtil:test_rsd_closest_chain_com protocols:MembraneUtil:test_rsd_closest_chain_tm_com protocols:MembraneUtil:test_rsd_closest_pose_tm_COM protocols:MembraneUtil:test_split_topology_by_chain_noshift protocols:MembraneUtil:test_split_topology_by_jump protocols:MembraneUtil:test_split_topology_by_jump_noshift protocols:MembraneUtil:test_tm_com protocols:MonteCarloTests:test_interface_mc protocols:MonteCarloTests:test_vanilla_mc protocols:MoverJobTests:test_basic_mover_job protocols:MoverJobTests:test_seq_mover_job protocols:MultiplePoseMoverTests:test_DummyMultipleOutputMover_get_additional_output protocols:MultiplePoseMoverTests:test_additionaloutputwrapper protocols:MultiplePoseMoverTests:test_import protocols:MultiplePoseMoverTests:test_import_multilevel protocols:MultiplePoseMoverTests:test_input_limit protocols:MultiplePoseMoverTests:test_invalid_import_filter protocols:MultiplePoseMoverTests:test_invalid_import_mover protocols:MultiplePoseMoverTests:test_invalid_import_mover_recursion protocols:MultiplePoseMoverTests:test_logical_selector_and protocols:MultiplePoseMoverTests:test_logical_selector_or_and protocols:MultiplePoseMoverTests:test_mover_chaining protocols:MultiplePoseMoverTests:test_mover_chaining_distribute_twice protocols:MultiplePoseMoverTests:test_mover_chaining_two_levels protocols:MultiplePoseMoverTests:test_output_limit protocols:MultiplePoseMoverTests:test_selector protocols:MultiplePoseMoverTests:test_selector_filter protocols:MultiplePoseMoverTests:test_selector_filter_reporter protocols:MultiplePoseMoverTests:test_tag_parent protocols:NMethylationTests:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov15:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov16:test_linear_nmethyl_peptide protocols:NubInitioLoopClosureMoverTests:test_labeled_closed protocols:NubInitioLoopClosureMoverTests:test_labeled_open protocols:NubInitioLoopClosureMoverTests:test_name protocols:NubInitioLoopClosureMoverTests:test_not_labeled protocols:NubInitioMoverTests:test_name protocols:NubInitioMoverTests:test_one_motif protocols:NubInitioMoverTests:test_two_motifs protocols:OptimizeMembranePositionMoverTest:test_default_constructor protocols:OptimizeMembranePositionMoverTest:test_parse_my_tag_input protocols:OversaturatedHbondAcceptorFilterTests:test_bb_bb_extra_hbond protocols:OversaturatedHbondAcceptorFilter_betanov15_Tests:test_bb_bb_extra_hbond protocols:OversaturatedHbondAcceptorFilter_betanov16_Tests:test_bb_bb_extra_hbond protocols:PeptideDeriverFilterTests:test_assignment protocols:PeptideDeriverFilterTests:test_copy_ctor protocols:PeptideDeriverFilterTests:test_protocol protocols:PeptideDeriverFilterTests:test_report_format_parsing protocols:PeptideDeriverFilterTests:test_rosettascripts_options protocols:PointMutScanDriverTests:test_calculate_neighbor_table protocols:PointMutScanDriverTests:test_fill_mutations_list protocols:PointMutScanDriverTests:test_fill_mutations_list_double_mutant_scan protocols:PointMutScanDriverTests:test_fill_mutations_list_single_mutant_scan protocols:PointMutScanDriverTests:test_make_specific_mutant protocols:PointMutScanDriverTests:test_make_specific_mutant_insertion_code protocols:PoseManipulationTests:test_linear_rigid_body_moves protocols:PoseManipulationTests:test_repack_functions protocols:PoseManipulationTests:test_rotation_rigid_body_moves protocols:ProteinProteinInterfaceUpweighterTests:test_packing_4SER protocols:ProteinSCSamplerTests:test_sc_sampler_ctor protocols:ProteinSCSamplerTests:test_sc_sampler_desymmeterize protocols:ProteinSilentReportTests:test_main protocols:PruneBuriedUnsatsOperationTests:test_burial_sanity_check protocols:PruneBuriedUnsatsOperationTests:test_pruning_arg_and_two_ser protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_bb protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_satisfied_bb protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_satisfied_ser protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_ser protocols:PseudocontactShiftTests:test_eval_abinitio_pcs_only protocols:PseudocontactShiftTests:test_eval_pcs_energy_on_abinitio_output protocols:PseudocontactShiftTests:test_eval_pcs_energy_on_native protocols:RRReporterSQLiteTests:test_RRReporterSQLite_features protocols:RRReporterSQLiteTests:test_RRReporterSQLite_full protocols:ResfileAutoRemapTest:test_resfile_auto_remap protocols:RigidBodyMoverTests:test_RigidBodyPerturbMover_int protocols:RigidBodyMoverTests:test_RigidBodyPerturbMover_no_int protocols:RigidBodyMoverTests:test_RigidBodyPerturbNoCenterMover protocols:RigidBodyMoverTests:test_RigidBodyRandomizeMover protocols:RigidBodyMoverTests:test_RigidBodySpinMover protocols:RigidBodyMoverTests:test_RigidBodyTransMover protocols:RigidBodyMoverTests:test_RigidBodyTransMover_parse protocols:RigidLigandBuilderTests:test_downstream_placement_from_sinisas_param_file protocols:RigidLigandBuilderTests:test_lig_downstream_geom protocols:RigidLigandBuilderTests:test_rigid_ligand_ds_builder_recover_input_coords protocols:RosettaScriptsParserTests:test_all_attributes_in_xsd_have_descriptions protocols:RosettaScriptsParserTests:test_allowed_multiple_dependencies protocols:RosettaScriptsParserTests:test_multiple_includes protocols:RosettaScriptsParserTests:test_prohibit_circular_dependencies protocols:RosettaScriptsParserTests:test_report_at_end protocols:RotamerBoltzmannWeight2Tests:test_calculator_ids protocols:RotamerBoltzmannWeight2Tests:test_rbw2_vs_rbw protocols:RotamerRecoveryTests:test_RotamerRecovery_main protocols:SandwichFeaturesTests:test_main protocols:SimpleCycpepPredictApplicationTests:test_designfile_read protocols:SimpleCycpepPredictApplicationTests:test_mergesort protocols:SimpleCycpepPredictApplicationTests:test_mergesort_edgecases protocols:SimpleCycpepPredictApplicationTests:test_mergesort_rmsd protocols:SimpleCycpepPredictApplicationTests:test_quicksort protocols:SimpleCycpepPredictApplicationTests:test_quicksort_cis_peptide_bonds protocols:SimpleCycpepPredictApplicationTests:test_quicksort_rmsd protocols:SimpleCycpepPredictApplicationTests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_betanov15_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_Tests:test_simple_cycpep_predict_withfile protocols:SimpleCycpepPredictApplication_design_betanov15_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_betanov15_Tests:test_simple_cycpep_predict_withfile protocols:SimpleMetricProtocolsTests:test_composite_real_metric protocols:SimpleMetricProtocolsTests:test_composite_string_metric protocols:SimpleMetricProtocolsTests:test_composite_total_energy_metric protocols:SimpleMetricProtocolsTests:test_dihedral_metric protocols:SimpleMetricProtocolsTests:test_protocol_settings_metric protocols:SimpleMetricProtocolsTests:test_real_metric protocols:SimpleMetricProtocolsTests:test_rmsd_metric protocols:SimpleMetricProtocolsTests:test_string_metric protocols:SimpleMetricProtocolsTests:test_total_energy_metric protocols:SimpleThreadingMoverTests:test_basic_class protocols:StandardPoseJobSummaryTests:test_basic_pose_job_summary protocols:SwitchChainOrderMoverTests:test_pdbinfo_labels protocols:TCRmodelGraftingTests:test_tcr_grafting protocols:TaskAwareMinMoverTests:test_TaskAwareMinMover protocols:ThreadingMover_Tests:test_basic_threading protocols:TransformIntoMembraneMoverTest:test_constructor_from_embedding protocols:TransformIntoMembraneMoverTest:test_constructor_from_embedding_and_membrane protocols:TransformIntoMembraneMoverTest:test_helix_to_normal_angle protocols:TransformIntoMembraneMoverTest:test_transform_into_default_membrane protocols:TransformIntoMembraneMoverTest:test_transform_into_userdefined_membrane protocols:cout_io:test_cout_io protocols:ddG:test_chains_to_move_invert protocols:ddG:test_filter_parsing_dimer protocols:ddG:test_filter_parsing_monomer protocols:ddG:test_use_filter_dimer protocols:ddG:test_use_filter_monomer