Test: linux.gcc.unit 「view this page in B3 βῆτα server」
Branch: master 「revision: №61997」
Test files: 「file-system-view」 「file-list-view」
Daemon: nobu-1     Started at: 2023-04-07 15:33:39     Run time: 0:59:08      State: failed

Failed sub-tests (click for more details):
core:PDB_w_glycans_IO:test_pdb_io

apps:LigandDockTest:test_select_best_poses basic:CitationManagerTests:test_database_load basic:CmdlineOptionsOrderTests:test_options_order_just_cmdline basic:CmdlineOptionsOrderTests:test_options_order_just_flagsfiles basic:CmdlineOptionsOrderTests:test_options_order_just_one_file basic:CmdlineOptionsOrderTests:test_options_order_mixed basic:DatabaseResourceLocatorTests:test_DatabaseResourceLocator_query_sqlite_database basic:ExecuteTest:test_shell basic:FileSystemResourceLocatorTests:test_FileSystemResourceLocator_locate_file basic:HierarchicalDataMapTests:test_failed_lookups basic:HierarchicalDataMapTests:test_hierarchical_lookups basic:HierarchicalDataMapTests:test_optional_name_lookups basic:HierarchicalDataMapTests:test_successful_lookups basic:OptionsSystemTests:test_find_key_cl_error basic:OptionsSystemTests:test_find_key_cl_good basic:OptionsSystemTests:test_initialize_local_option_collection_from_global basic:OptionsSystemTests:test_set_value basic:ResourceLoaderFactoryTests:test_register_one_creator_twice_with_ResourceLoaderFactory basic:ResourceLoaderFactoryTests:test_register_one_creator_with_ResourceLoaderFactory basic:ResourceManagerTests:test_parse_resource_definition_file basic:ResourceManagerTests:test_parse_resource_definition_file_w_circular_dependencies basic:ResourceManagerTests:test_parse_resource_definition_file_w_multiple_dependencies basic:ResourceManagerTests:test_parse_resource_definition_w_dependency basic:ResourceManagerTests:test_schema_structure basic:SVDSolverTest:test_Solv_SLE_no_unique_solution basic:SVDSolverTest:test_Solv_SLE_with_unique_solution basic:StringResourceStreamTests:test_null core:AACompositionEnergyTests_10pctaro:test_energy_eval_ten_percent_aromatic core:AACompositionEnergyTests_1W1Y:test_energy_eval_one_trp_one_tyr core:AACompositionEnergyTests_1W:test_energy_eval_exactly_one_trp core:AACompositionEnergyTests_20pctpro:test_energy_eval_twenty_percent_pro core:AACompositionEnergyTests_20pctprofract:test_energy_eval_twenty_percent_pro_fract_ranges core:AACompositionEnergyTests_2WY:test_energy_eval_exactly_two_trportyr core:AACompositionEnergyTests_2aro:test_energy_eval_two_aromatics core:AACompositionEnergyTests_3ACPC:test_energy_eval_exactly_three_transACPC core:AACompositionEnergyTests_aliphnotpro:test_energy_eval_aliphatic_not_pro core:AACompositionEnergyTests_bools:test_energy_eval_complex_boolean_logic core:AACompositionEnergyTests_consttail:test_tailfunctions_const_lin core:AACompositionEnergyTests_interpolate_linear:test_interpolation_linear_tails core:AACompositionEnergyTests_linconsttail:test_tailfunctions_lin_const core:AACompositionEnergyTests_packer:test_energy_annealing core:AACompositionEnergyTests_quadratail:test_tailfunctions_quadratic core:AACompositionEnergyTests_quadratic_interpolation:test_interpolation_quadratic_tails core:AARepeatEnergyTests:test_energy_annealing core:AARepeatEnergyTests:test_energy_cases core:AARepeatEnergyTests:test_energy_eval core:ABEGOManagerTest:test_abego core:AltCodesIOTests:test_read_alternative_3_letter_codes_from_database_file core:AmberPeriodicFuncTests:test_serialize_AmberPeriodicFunc core:AmbiguousConstraintTests:test_serialize_AmbiguousConstraint core:AmbiguousNMRConstraintTests:test_serialize_AmbiguousNMRConstraint core:AmbiguousNMRDistanceConstraintTests:test_serialize_AmbiguousNMRDistanceConstraint core:AndJumpSelectorTests:test_AndJumpSelector_fail_parse_subtag core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag_no_provided_selectors core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag_selectors_not_in_datamap core:AndJumpSelectorTests:test_AndJumpSelector_parse_subtag_v1 core:AndJumpSelectorTests:test_AndJumpSelector_parse_subtag_v2 core:AndJumpSelectorTests:test_and_jump_selector_odd_1mod5_lots_of_jumps core:AndJumpSelectorTests:test_and_jump_selector_odd_1mod5_no_jumps core:AndResidueSelectorTests:test_AndResidueSelector_fail_parse_subtag core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag_no_provided_selectors core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag_selectors_not_in_datamap core:AndResidueSelectorTests:test_AndResidueSelector_parse_subtag core:AndResidueSelectorTests:test_and_residue_selector_odd_1mod5 core:AngleConstraintTests:test_angle_constraint_clone core:AngleConstraintTests:test_angle_constraint_equality_operator core:AngleConstraintTests:test_angle_derivatives core:AngleConstraintTests:test_angle_score core:AngleConstraintTests:test_serialize_AngleConstraint core:AnnotatedSequenceTests:test_make_pose_from_saccharide_sequence core:AnnotatedSequenceTests:test_residue_types_from_saccharide_sequence 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:ArgCationPiEnergyTests:test_arg_cation_pi core:AspartimidePenaltyEnergyTests:test_D_scoring core:AspartimidePenaltyEnergyTests:test_L_scoring core:AspartimidePenaltyEnergyTests:test_cyclic_geometry_scoring core:AtomICoorTests:test_atom_icoord_build core:AtomICoorTests:test_id_nonpoly core:AtomICoorTests:test_id_poly core:AtomPairConstraintTests:test_PDBno_readin core:AtomPairConstraintTests:test_atom_pair_constraint_clone core:AtomPairConstraintTests:test_atom_pair_constraint_equality_operator core:AtomPairConstraintTests:test_atom_pair_derivatives core:AtomPairConstraintTests:test_atom_pair_score core:AtomPairConstraintTests:test_atom_to_axis core:AtomPairConstraintTests:test_serialize_AtomPairConstraint core:AtomTests:test_atom_initialization core:AtomTests:test_atom_setters 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:AtomTreeTests:test_atom_tree_assignment_operator core:AtomTreeTests:test_serialize_atom_tree core:AtomTypeDatabaseIOTests:test_atom_type_set_name core:AtomTypeSetTests:test_add_atom_types_from_command_line core:AtomTypeSetTests:test_atom_type_index core:AtomTypeSetTests:test_atom_type_set_name core:AtomTypeSetTests:test_n_atomtypes core:AtomTypeSetTests:test_operator_brackets core:AtomicDepthTests:test_AtomicDepth_depth_test_14 core:AtomicDepthTests:test_AtomicDepth_depth_test_40 core:AtomicDepthTests:test_AtomicDepth_depth_test_oob core:AtomicDepthTests:test_AtomicDepth_depth_test_polyleu_40 core:AtomicDepthTests:test_AtomicDepth_depth_test_util_40 core:AutomorphismTest:test_automorphism_counts core:BBTorsionSRFDTest:test_cartesian_coordinates core:BBTorsionSRFDTest:test_cartesian_coordinates_iter core:BackboneAATests:test_backbone_aa_p_aa_pp core:BackboneAATests:test_backbone_aa_rama core:BackboneAATests:test_backbone_aa_rama_prepro core:BackboneStubConstraintTests:test_serialize_BackboneStubConstraint core:BackboneStubLinearConstraintTests:test_serialize_BackboneStubLinearConstraint core:BasicDesignTests:test_design_custom core:BasicDesignTests:test_design_custom_TF core:BasicDesignTests:test_design_rotamers core:BasicDesignTests:test_design_rotamers_TF core:BetaNov16WithAutoSetupMetalsTests:test_auto_setup_metals_with_ser_mn core:BigBinConstraintTests:test_read_def core:BigBinConstraintTests:test_serialize_BigBinConstraint core:BinSelectorTests:test_binselector_abin core:BinTransitionCalculatorTests:test_BinTransitionCalculator_p_iplus1_given_i core:BinTransitionCalculatorTests:test_BinTransitionCalculator_read core:BinTransitionCalculatorTests:test_BinTransitionData_trim_subbin_edges_and_rescale_subbin 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_read_silent_file_with_rna_remark core:BinarySilentTests:test_save_and_restore core:BinarySilentTests:test_save_and_restore_centroid core:BinarySilentTests:test_save_and_restore_inserting_residues core:BlockSelectorTests:test_blockselector core:BondLengthsTests:test_bond_lengthsl core:BondedSelectorTests:test_BondedResidueSelector_parse_my_tag core:BondedSelectorTests:test_detects_adjacent_residues core:BondedSelectorTests:test_detects_declared_chemical_bonds core:BoundConstraintTests:test_bound_func core:BoundConstraintTests:test_serialize_BoundFunc core:BoundConstraintTests:test_serialize_OffsetPeriodicBoundFunc core:BoundConstraintTests:test_serialize_PeriodicBoundFunc core:BoundConstraintTests:test_show_definition 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:CCS_IMMSEnergyTests:test_ccs_imms core:CHIEnergyFunctionTests:test_CHI_energy_derivatives core:CHIEnergyFunctionTests:test_CHI_energy_function core:CHIEnergyFunctionTests:test_CHI_sampling_data core:CachableDataTypeTests:test_get_name core:CacheableResidueTypeSetsTests:test_setting core:CalculatorMetricsTests:test_calculatormetric core:CalculatorMetricsTests:test_parsing core:CalculatorMetricsTests:test_schema core:CarbohydrateDatabaseIOTests:test_read_codes_and_roots_from_database_file core:CarbohydrateDatabaseIOTests:test_read_linkage_conformers_from_database_file core:CarbohydrateDatabaseIOTests:test_read_nomenclature_table_from_database_file core:CarbohydrateDatabaseIOTests:test_read_ring_sizes_and_morphemes_from_database_file core:CarbohydrateInfoManagerTests:test_linkage_conformer_data_access core:CarbohydrateInfoTests:test_CarbohydrateInfo_branch_point core:CarbohydrateInfoTests:test_CarbohydrateInfo_last_carbon_in_ring core:CarbohydrateInfoTests:test_Pose_chain_sequence_w_polysaccharide core:CarbohydrateInfoTests:test_Pose_chi_w_polysaccharide core:CarbohydrateInfoTests:test_Pose_phi_psi_omega_w_polysaccharide core:CarbohydratePoseIOTests:test_sugar_modifications_from_suffix core:CarbohydratePoseUtilityFunctionTests:test_TorsionID_query_functions core:CarbohydratePoseUtilityFunctionTests:test_exocyclic_detection core:CarbohydratePoseUtilityFunctionTests:test_find_seqpos_of_saccharides_relatives core:CarbohydratePoseUtilityFunctionTests:test_get_downstream_residue_that_this_torsion_moves core:CarbohydratePoseUtilityFunctionTests:test_get_glycosidic_TorsionIDs core:CarbohydratePoseUtilityFunctionTests:test_get_glycosidic_bond_residues core:CarbohydratePoseUtilityFunctionTests:test_get_linkage_position_of_saccharide_residue core:CarbohydratePoseUtilityFunctionTests:test_get_non_NU_TorsionID_from_AtomIDs core:CarbohydratePoseUtilityFunctionTests:test_get_reference_atoms core:CarbohydratePoseUtilityFunctionTests:test_glycan_branch core:CarbohydratePoseUtilityFunctionTests:test_glycan_iupac_movemap_setup core:CarbohydratePoseUtilityFunctionTests:test_glycan_leafs core:CarbohydratePoseUtilityFunctionTests:test_glycan_movemap_setup core:CarbohydratePoseUtilityFunctionTests:test_glycan_trimming core:CarbohydratePoseUtilityFunctionTests:test_glycosylate_pose core:CarbohydrateScoringDatabaseIOTests:test_read_Gaussian_parameters_from_database_file core:CarbohydrateScoringUtilityFunctionTests:test_function_assignment_based_on_type_of_linakge core:CarbohydrateStereochemTests:test_rings_and_stereochemistries core:CarbohydrateStereochemTests:test_virtual_atom_placement core:CarbonHBondEnergyTests:test_chbonds_deriv_check_matches_trunk_r38117 core:CarbonHBondEnergyTests:test_chbonds_deriv_check_w_full_torsional_flexibility core:CartGridTest:test_grid_basics core:CartGridTest:test_grid_json_serialization core:CartesianBondedEnergyBBDepTests:test_cartbonded_deriv_check_w_total_flexibility core:CartesianBondedEnergyBBDepTests:test_cartbonded_start_score_start_func_match_w_total_flexibility core:CartesianBondedEnergyBBDepTests:test_eval_energy core:CartesianBondedEnergyTests:test_cartbonded_deriv_check_w_total_flexibility core:CartesianBondedEnergyTests:test_cartbonded_start_score_start_func_match_w_total_flexibility core:CartesianBondedEnergyTests:test_eval_energy core:CenRotModelEnergyTests:test_cen_rot_atomtree_min core:CenRotModelEnergyTests:test_cen_rot_cart_min core:CenRotModelEnergyTests:test_cen_rot_dun core:CenRotModelEnergyTests:test_cen_rot_pair_env_energy core:CenRotModelEnergyTests:test_cen_rot_repack core:CenRotModelEnergyTests:test_cen_rot_vdw core:ChainSelectorTests:test_ChainSelector_parse_my_tag core:ChainSelectorTests:test_ChainSelector_parse_my_tag_no_provided_chains core:ChainSelectorTests:test_ChainSelector_parse_my_tag_w_two_chains core:ChainSelectorTests:test_chain_selector_chain_1_select_all core:ChainSelectorTests:test_chain_selector_chain_1_select_half core:ChainSelectorTests:test_chain_selector_chain_1and2_select_all core:ChainSelectorTests:test_chain_selector_chain_A_select_all core:ChainSelectorTests:test_chain_selector_chain_A_select_half core:ChainSelectorTests:test_chain_selector_chain_AandB_select_all core:ChainbreakEnergyTests:test_chainbreak_cyclic_geometry_deriv_check core:ChainbreakEnergyTests:test_chainbreak_deriv_check core:ChainbreakEnergyTests:test_chainbreak_deriv_check_with_sugars core:ChainbreakEnergyTests:test_chainbreak_n_methylation_cyclic_geometry_deriv_check core:ChainbreakEnergyTests:test_chainbreak_peptoid_cyclic_geometry_deriv_check core:ChainbreakEnergyTests:test_chainbreak_proline_cyclic_geometry_deriv_check core:Chains62Tests:test_read_62_chain_pdb core:CharmmPeriodicFuncTests:test_serialize_CharmmPeriodicFunc core:ChemistryNamespaceUtilityFunctionTests:test_is_mainchain_torsion_also_ring_torsion core:CircularGeneral1D_FuncTests:test_serialize_CircularGeneral1D_Func core:CircularHarmonicFuncTests:test_serialize_CircularHarmonicFunc core:CircularPowerFuncTests:test_serialize_CircularPowerFunc core:CircularSigmoidalFuncTests:test_serialize_CircularSigmoidalFunc core:CircularSplineFuncTests:test_serialize_CircularSplineFunc 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:CloseContactResidueSelectorTests:test_CloseContactResidueSelector_parse_my_tag_selector core:ConfluentSelectorTests:test_confluentselector core:ConformationAtomTest:test_ConformationAtom_atomtype_constructor core:ConformationAtomTest:test_ConformationAtom_copy_constructor core:ConformationAtomTest:test_ConformationAtom_default_constructor core:ConformationAtomTest:test_ConformationAtom_type_getter core:ConformationAtomTest:test_ConformationAtom_type_setter core:ConformationAtomTest:test_ConformationAtom_xyz_getter core:ConformationAtomTest:test_ConformationAtom_xyz_setter core:ConformationTests:test_Conformation_ResidueTypeSet_clone core:ConformationTests:test_Conformation_backbone_torsion_angle_atoms_cutpoint core:ConformationTests:test_Conformation_backbone_torsion_angle_atoms_oligourea core:ConformationTests:test_Conformation_observer core:ConformationTests:test_Conformation_resolve_partial_atom_id_dslf core:ConformationTests:test_Conformation_resolve_partial_atom_id_peptide core:ConformationTests:test_inter_residue_connection_partner core:ConformationTests:test_is_bonded core:ConformationTests:test_simple_conformation core:ConformationUtilityFunctionTests:test_find_bond_torsion_with_nearest_orientation core:ConformationUtilityFunctionTests:test_position_of_atom_on_ring core:ConformationUtilityFunctionTests:test_residue_from_name core:ConsensusSequenceParserTests:test_get_3_letter_codes_from_NA_consensus_sequence core:ConsensusSequenceParserTests:test_get_3_letter_codes_from_peptide_consensus_sequence core:ConstantConstraintTests:test_serialize_ConstantConstraint core:ConstantFuncTests:test_serialize_ConstantFunc core:ConstraintIOTests:test_constraint_read_in core:ConstraintSetRemappingTests:test_constraint_set_remapping core:ConstraintSetTests:test_constraints_deep_clone core:ConstraintSetTests:test_constraints_shallow_copy_in_assignment_op core:ConstraintSetTests:test_constraints_shallow_copy_in_copy_ctor core:ConstraintSetTests:test_constraintset_assignment_operator_1 core:ConstraintSetTests:test_constraintset_assignment_operator_2 core:ConstraintSetTests:test_constraintset_assignment_operator_3 core:ConstraintSetTests:test_constraintset_assignment_operator_4 core:ConstraintSetTests:test_constraintset_assignment_operator_5 core:ConstraintSetTests:test_serialize_constraint_set core:ConstraintUtilTests:test_add_constraints_from_cmdline core:ConstraintUtilTests:test_add_constraints_from_cmdline_to_pose core:ConstraintUtilTests:test_add_constraints_from_cmdline_to_scorefxn core:ConstraintUtilTests:test_add_fa_constraints_from_cmdline core:ConstraintUtilTests:test_add_fa_constraints_from_cmdline_to_pose core:ConstraintUtilTests:test_add_fa_constraints_from_cmdline_to_scorefxn core:ConstraintUtilTests:test_exponential_functions core:ConstraintUtilTests:test_gaussian_functions core:ConstraintUtilTests:test_get_cst_fa_file_option core:ConstraintUtilTests:test_get_cst_file_option core:ConstraintUtilTests:test_merge_constraints_from_cmdline core:ConstraintUtilTests:test_merge_constraints_from_cmdline_to_pose core:ConstraintUtilTests:test_merge_constraints_from_cmdline_to_scorefxn core:ConstraintUtilTests:test_merge_fa_constraints_from_cmdline core:ConstraintUtilTests:test_merge_fa_constraints_from_cmdline_to_pose core:ConstraintUtilTests:test_merge_fa_constraints_from_cmdline_to_scorefxn core:ConstraintsEnergyTests:test_atom_tree_minimize_with_dist_cst core:ConstraintsEnergyTests:test_atom_tree_minimize_with_dist_cst_in_fixed_domain core:ConstraintsEnergyTests:test_atom_tree_minimize_with_interresidue_angle_cst core:ConstraintsEnergyTests:test_atom_tree_minimize_with_intraresidue_dist_cst core:ConstraintsEnergyTests:test_atom_tree_minimize_with_threebody_angle_cst core:ContactOrderEnergy_Tests:test_eval_energy core:CoordinateConstraintTests:test_serialize_CoordinateConstraint core:CopyDofsTest:test_copy_dofs_into_extended core:CoreKinematicsUtilTests:test_get_foldtree_which_partitions core:CoreKinematicsUtilTests:test_jump_which_partitions core:CountViolFuncTests:test_serialize_CountViolFunc core:CtermAmidationTests:test_cterm_amidation_on_each_aa core:CtermAmidationTests:test_cterm_amidation_on_each_aa_notermini core:CustomRealValueMetricTests:test_custom_real_value_metric core:CyclicGeometryTests:test_cyclic_permutation_cart_bonded core:CyclicGeometryTests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometryTests:test_cyclic_permutation_dslf_fa13 core:CyclicGeometryTests:test_cyclic_permutation_fa_atr core:CyclicGeometryTests:test_cyclic_permutation_fa_dun core:CyclicGeometryTests:test_cyclic_permutation_fa_elec core:CyclicGeometryTests:test_cyclic_permutation_fa_intra_rep core:CyclicGeometryTests:test_cyclic_permutation_fa_rep core:CyclicGeometryTests:test_cyclic_permutation_fa_sol core:CyclicGeometryTests:test_cyclic_permutation_hbonds core:CyclicGeometryTests:test_cyclic_permutation_omega core:CyclicGeometryTests:test_cyclic_permutation_p_aa_pp core:CyclicGeometryTests:test_cyclic_permutation_pro_close core:CyclicGeometryTests:test_cyclic_permutation_rama core:CyclicGeometryTests:test_cyclic_permutation_rama_prepro core:CyclicGeometryTests:test_cyclic_permutation_talaris2014 core:CyclicGeometryTests:test_cyclic_permutation_yhh_planarity core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_cart_bonded core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_dslf_fa13 core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_atr core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_dun core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_elec core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_intra_rep core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_rep core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_fa_sol core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_hbonds core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_omega core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_p_aa_pp core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_pro_close core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_rama core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_rama_prepro core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_talaris2014 core:CyclicGeometryTests_nmethyl:test_cyclic_permutation_yhh_planarity core:CyclicGeometryTwoChainTests:test_cyclic_permutation_cart_bonded core:CyclicGeometryTwoChainTests:test_cyclic_permutation_current_default_scorefxn core:CyclicGeometryTwoChainTests:test_cyclic_permutation_dslf_fa13 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core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_parse_my_tag_selector core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_parse_my_tag_str core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_uninitialized_pose core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_use_last_provided_source_of_focus core:NetChargeEnergyTests_packer:test_energy_annealing core:NetChargeEnergyTests_packer_symm:test_energy_annealing_symmetric core:NetChargeEnergyTests_tailfxns:test_constant_tailfxns core:NetChargeEnergyTests_tailfxns:test_linear_tailfxns core:NetChargeEnergyTests_tailfxns:test_quadratic_tailfxns core:NomenclatureManagerTestsWCL:test_default_mainchain_connectivity_from_pdb_code core:NomenclatureManagerTestsWCL:test_nomenclature_manager_test_w_command_line_alt_codes core:NomenclatureManagerTestsWCL:test_nomenclature_manager_three_name_conflicts core:NomenclatureManagerTestsWCL:test_pdb_code_from_rosetta_name core:NomenclatureManagerTestsWOCL:test_rosetta_names_from_pdb_code core:NonResidueTypeConstraintTests:test_serialize_NonResidueTypeConstraint core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag_no_provided_selectors core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag_selectors_not_in_datamap core:NotJumpSelectorTests:test_not_jump_selector_odd_lots_of_jumps core:NotJumpSelectorTests:test_not_jump_selector_odd_no_jumps core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag_no_provided_selectors core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag_selectors_not_in_datamap core:NotResidueSelectorTests:test_not_residue_selector_odd core:NumNeighborsSelectorTests:test_num_neighbors_selector_1 core:NumNeighborsSelectorTests:test_num_neighbors_selector_parse_my_tag core:NumNeighborsSelectorTests:test_num_neighbors_selector_parse_my_tag_w_defaults core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_deriv_check_w_partial_flexibility core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_deriv_check_w_total_flexibility core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_start_score_start_func_match_w_partial_flexibility core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_start_score_start_func_match_w_total_flexibility core:OmegaPreferencesFunctionTests:test_omega_preferences_derivatives core:OmegaPreferencesFunctionTests:test_omega_preferences_function core:OmegaTetherTests:test_alpha_aa_omega core:OmegaTetherTests:test_beta_aa_omega_min core:OmegaTetherTests:test_oligourea_omega core:OmegaTetherTests:test_oligourea_omega_min core:OperateOnResidueSubsetTests:test_disable_odd_residues_init_by_ctor core:OperateOnResidueSubsetTests:test_disable_odd_residues_init_w_functions core:OperateOnResidueSubsetTests:test_oors_parse_tag_1 core:OperateOnResidueSubsetTests:test_oors_parse_tag_2 core:OrJumpSelectorTests:test_OrJumpSelector_fail_parse_subtag core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag_no_provided_selectors core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag_selectors_not_in_datamap core:OrJumpSelectorTests:test_OrJumpSelector_parse_subtag_v1 core:OrJumpSelectorTests:test_OrJumpSelector_parse_subtag_v2 core:OrJumpSelectorTests:test_and_jump_selector_odd_1mod5_lots_of_jumps core:OrJumpSelectorTests:test_and_jump_selector_odd_1mod5_no_jumps core:OrResidueSelectorTests:test_AndResidueSelector_parse_my_tag_selectors_not_in_datamap core:OrResidueSelectorTests:test_OrResidueSelector_fail_parse_subtag core:OrResidueSelectorTests:test_OrResidueSelector_parse_my_tag core:OrResidueSelectorTests:test_OrResidueSelector_parse_my_tag_no_provided_selectors core:OrResidueSelectorTests:test_OrResidueSelector_parse_subtag 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core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_nls_manual_symmetry_handling core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_svd_automatic_symmetry_deduction core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_svd_manual_symmetry_handling core:PCSSingleSetTests:test_PCSSingleSet_instantiation_and_getters core:PCSSingleSetTests:test_PCSSingleSet_instantiation_and_scaling core:PCSSingleSetTests:test_calc_tensor_and_score_nls core:PCSSingleSetTests:test_calc_tensor_and_score_nls_fixed_XaxXrh core:PCSSingleSetTests:test_calc_tensor_and_score_nls_svd_different_weightings core:PCSSingleSetTests:test_calc_tensor_and_score_svd core:PCSSingleSetTests:test_calc_tensor_and_score_svd_on_scaled_data core:PDBInfoTests:test_PDBInfo_append_residue core:PDBInfoTests:test_PDBInfo_chain_sequences core:PDBInfoTests:test_PDBInfo_delete_residue core:PDBInfoTests:test_PDBInfo_detach_on_destroy core:PDBInfoTests:test_PDBInfo_en_masse_residue_mutators 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core:PDBReaderTests:test_store_formula_record_in_sfr core:PDBReaderTests:test_store_heterogen_name_record_in_sfr_and_store_base_residue_type_name_in_sfr core:PDBReaderTests:test_store_heterogen_synonym_record_in_sfr core:PDBReaderTests:test_store_link_record_in_sfr core:PDBReaderTests:test_store_mod_res_record_in_sfr core:PDBReaderTests:test_store_ssbond_record_in_sfr core:PDBReaderTests:test_store_unknown_records_in_sfr core:PDBSilentStruct_Tests:test_pdb_silent_disulfide core:PDBSilentStruct_Tests:test_save_and_restore core:PDB_IO:test_pdb_io core:PDB_IO:test_pdb_io_seqres core:PDB_IO:test_pdb_read_d_aa core:PDB_IO:test_pdb_read_partial_residues core:PDB_w_glycans_IO:test_glycan_fragment core:PDB_w_glycans_IO:test_pdb_io core:PREDataTests:test_PREData_creation_by_NMRFactory core:PREDataTests:test_PREData_instantiation core:PREDataTests:test_pre_score_calculation_with_explicit_spinlabel_coordinates core:PREDataTests:test_pre_score_calculation_with_implicit_spinlabel_ensemble 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core:PackerTaskTests:test_packer_task_and_extrachi_cutoff core:PackerTaskTests:test_packer_task_default_behavior_design_all_positions core:PackerTaskTests:test_packer_task_fix_his_tautomer core:PackerTaskTests:test_packer_task_name3_decision_making core:PackerTaskTests:test_packer_task_or_ex1_commutativity core:PackerTaskTests:test_packer_task_or_ex1aro_commutativity core:PackerTaskTests:test_packer_task_or_ex2_commutativity core:PackerTaskTests:test_packer_task_or_ex2aro_commutativity core:PackerTaskTests:test_packer_task_or_ex3_commutativity core:PackerTaskTests:test_packer_task_or_ex4_commutativity core:PackerTaskTests:test_packer_task_restrict_to_repacking core:PackerTaskTests:test_packer_task_update_commutative_restrict_to_repacking1 core:PackerTaskTests:test_packer_task_update_commutative_restrict_to_repacking2 core:PairEnergyTests:test_pairE_deriv_check_w_partial_flexibility core:PairEnergyTests:test_pairE_deriv_check_w_total_flexibility 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core:PeriodicFuncTests:test_serialize_PeriodicFunc core:PhiSelectorTests:test_phiselector_negativephi core:PhiSelectorTests:test_phiselector_negativephi_no_ignore_unconnected_upper core:PhiSelectorTests:test_phiselector_positivephi core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_meta_ala core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_ortho_ala core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_para_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_meta_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_ortho_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_para_ala 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:PoseFromPDBLoaderTests:test_PoseFromPDBLoader core:PoseFromSFRBuilderTests:test_1rgr core:PoseFromSFRBuilderTests:test_build_trpcage_pdb core:PoseFromSFRBuilderTests:test_read_cyclic_peptide_with_link_record core:PoseFromSFRBuilderTests:test_read_in_acylated_nterm_residue core:PoseFromSFRBuilderTests:test_read_in_res_both_acetylated_and_cterm core:PoseFromSFRBuilderTests:test_read_pose_without_terminal_variant_types core:PoseFromSFRBuilderTests:test_splitting_of_residues core:PoseIteratorTests:test_enumerate1 core:PoseIteratorTests:test_iterators core:PoseIteratorTests:test_iterators_with_selectors core:PoseRNAUtilTests:test_remove_nonnaturals core:PoseResidueTypeSetTests:test_addition core:PoseResidueTypeSetTests:test_get_all_types_with_variants_aa core:PoseResidueTypeSetTests:test_local_vs_default core:PoseTests:test_Pose_mainchain_torsions core:PoseTests:test_Pose_observer core:PoseTests:test_append_pose_by_jump core:PoseTests:test_cutpoint_bond_rotation core:PoseTests:test_serialize_pose core:PoseTests:test_update_cutpoint_virtual_atoms_if_connected core:PoseTests:test_update_cutpoint_virtual_atoms_when_bond_declared core:PoseTests:test_update_cutpoint_virtual_atoms_when_cutpoint_variant_added core:PoseTests:test_update_residue_neighbors core:PoseToStructFileRepConverterTests:test_assignment_of_new_chainIDs_for_ligands core:PoseToStructFileRepConverterTests:test_conect_records core:PoseToStructFileRepConverterTests:test_foldtree_records core:PoseToStructFileRepConverterTests:test_membrane_hetatm core:PoseToStructFileRepConverterTests:test_title_section_records core:PoseToStructFileRepConverterTests:test_torsion_records core:PoseUtilTests:test_chain_designations core:PoseUtilTests:test_chainid_functions core:PoseUtilTests:test_chainletter_functions core:PoseUtilTests:test_compare_atom_coordinates core:PoseUtilTests:test_conformation_sha1 core:PoseUtilTests:test_fix_pdbinfo_damaged_by_insertion core:PoseUtilTests:test_jump_functions core:PoseUtilTests:test_pose_float_map core:PoseUtilTests:test_pose_string_map core:PoseUtilTests:test_reasonable_foldtree core:PoseUtilTests:test_renumber_pdbinfo_based_on_conf_chains core:PoseUtilTests:test_unique_chains core:PoseUtilTests:test_xyzVector_HashOperations core:ProClosureEnergyTests:test_eval_energy core:ProClosureEnergyTests:test_eval_energy_noring core:ProClosureEnergyTests:test_proclose_D_oligourea core:ProClosureEnergyTests:test_proclose_L_oligourea core:ProClosureEnergyTests:test_proclose_deriv_check_w_total_flexibility core:ProClosureEnergyTests:test_proclose_start_score_start_func_match_w_total_flexibility core:ProClosureEnergyTests_noringclose:test_proclose_deriv_check_w_total_flexibility_noring core:ProteinSilentTests:test_arbitrary_energies core:ProteinSilentTests:test_redundant_tags core:ProteinSilentTests:test_reverse_score_cut core:ProteinSilentTests:test_save_and_restore core:ProteinSilentTests:test_save_and_restore_centroid core:ProteinSilentTests:test_score_cut core:ProteinSilentTests:test_strict_column_mode core:ProteinSilentTests:test_string_from_pose core:ProteinSilentTests:test_string_into_pose core:RDCDataSymmetryTests:test_RDCData_score_calculation_all_media_automatic_symmetry_deduction core:RDCDataSymmetryTests:test_RDCData_score_calculation_all_media_manual_symmetry_handling core:RDCDataTests:test_RDCData_creation_by_NMRDataFactory core:RDCDataTests:test_RDCData_instantiation core:RDCDataTests:test_RDCData_score_calculation_all_media core:RDCMultiSetSymmetryTests:test_score_calculation_by_nls_automatic_symmetry_deduction core:RDCMultiSetSymmetryTests:test_score_calculation_by_nls_manual_symmetry_handling core:RDCMultiSetSymmetryTests:test_score_calculation_by_svd_automatic_symmetry_deduction core:RDCMultiSetSymmetryTests:test_score_calculation_by_svd_manual_symmetry_handling core:RDCMultiSetTests:test_RDCMultiSet_instantiation core:RDCMultiSetTests:test_score_calculation_by_nls core:RDCMultiSetTests:test_score_calculation_by_nls_da core:RDCMultiSetTests:test_score_calculation_by_nls_r core:RDCMultiSetTests:test_score_calculation_by_svd core:RDCMultiSetTests:test_score_calculation_with_normalized_data core:RDMolToRestypeTests:test_convert core:RG_Energy_Tests:test_eval_energy core:RNA_FA_ElecEnergyTests:test_rnaelec_deriv_check_w_full_torsional_flexibility_smoothed_wo_ddd core:RNA_FA_ElecEnergyTests:test_rnaelec_nblist_autoupdate_no_smoothing core:RNA_FA_ElecEnergyTests:test_score_rna_pdb core:RNA_ScoreFunctionTest:test_no_full_model_info_scoring core:RTConstraintTests:test_rt_constraint_clone core:RTConstraintTests:test_rt_constraint_equality_operator core:RTConstraintTests:test_rt_constraint_score core:RTConstraintTests:test_rt_constraint_serialize core:RTConstraintTests:test_rt_constraint_zero_score core:RamaPreProEnergyTests:test_atoms_w_dof_deriv core:RamaPreProEnergyTests:test_rama_cart_deriv_check_partial_flexibility core:RamaPreProEnergyTests:test_rama_deriv_check_full_flexibility core:RamaPreProEnergyTests:test_rama_deriv_check_partial_flexibility core:RamaPreProEnergyTests:test_setup_for_minimizing_with_rama_and_full_bb_flex core:RamaPreProEnergyTests:test_setup_for_minimizing_with_rama_and_partial_bbflex core:RamaPreProEnergyTests:test_symm_rama_cart_deriv_check_partial_flexibility core:RamaPreProTests:test_correct_score_stored core:RamaPreProTests:test_get_atoms_w_dof_derivatives core:RamaPreProTests:test_get_mainchain_torsions_covered_bb_aa core:RamaPreProTests:test_random_phipsi_canonical core:RamaPreProTests:test_random_phipsi_canonical_d_aa core:RamaPreProTests:test_random_phipsi_canonical_d_aa_prepro core:RamaPreProTests:test_random_phipsi_canonical_prepro core:RamaPreProTests:test_random_phipsi_noncanonical core:RamaPreProTests:test_random_phipsi_noncanonical_d_aa core:RamaPreProTests:test_random_phipsi_noncanonical_d_aa_prepro core:RamaPreProTests:test_random_phipsi_noncanonical_prepro core:RamaPreProTests_oligourea:test_random_tors_canonical core:RamaPreProTests_oligourea:test_random_tors_canonical_d_aa core:RamaPreProTests_oligourea:test_random_tors_canonical_d_aa_prepro core:RamaPreProTests_oligourea:test_random_tors_canonical_prepro core:RamaPreProTests_symmgly:test_random_phipsi_gly core:RamaPreProTests_symmgly:test_random_phipsi_gly_invert core:RamaPreProTests_symmgly:test_random_phipsi_gly_prepro core:RamaPreProTests_symmgly:test_random_phipsi_gly_prepro_invert core:Ramachandran2BTests:test_rama2b_left_cdf_creation core:Ramachandran2BTests:test_rama2b_left_cdf_creation_for_ppo_torbin_A core:Ramachandran2BTests:test_rama2b_right_cdf_creation core:Ramachandran2BTests:test_rama2b_right_cdf_creation_for_ppo_torbin_A core:Ramachandran2BTests:test_random_phipsi_from_rama_by_torsion_bin_left core:Ramachandran2BTests:test_random_phipsi_from_rama_by_torsion_bin_right core:RamachandranEnergyTests:test_rama_deriv_check core:RamachandranEnergyTests:test_setup_for_minimizing_with_rama_and_full_bb_flex core:RamachandranEnergyTests:test_setup_for_minimizing_with_rama_and_partial_bbflex core:RamachandranEnergy_SymGlyTests:test_eval_symm_energy core:RamachandranPowerTest:test_eval_rama_score_residue core:RamachandranTest:test_eval_rama_score_residue core:RamachandranTest:test_phipsi_in_allowed_rama core:RamachandranTest:test_rama_cdf_creation core:RamachandranTest:test_rama_cdf_creation_for_ppo_torbin_A core:RamachandranTest:test_random_phipsi_from_rama core:RamachandranTest:test_random_phipsi_from_rama_by_torsion_bin core:RamachandranTest:test_uniform_phipsi_from_allowed_rama core:RandomResidueSelectorTests:test_RandomResidueSelector_parse_my_tag core:RecordDefIOTests:test_read_record_definitions_from_file core:ReferencePoseTests:test_ReferencePoseSet_deleting core:ReferencePoseTests:test_ReferencePoseSet_setup core:ReferencePoseTests:test_ReferencePose_string_parsing core:ResFilterFactoryTests:test_all_res_filters_define_valid_xsds core:ResFilterFactoryTests:test_res_filter_factory_w_bad_xsd core:ResFilterFactoryTests:test_res_filter_factory_xsd_creation core:ResLvlTaskOperationFactoryTests:test_all_res_lvl_task_ops_define_valid_xsds core:ResLvlTaskOperationFactoryTests:test_res_lvl_task_op_factory_w_bad_xsd core:ResLvlTaskOperationFactoryTests:test_res_lvl_task_op_factory_xsd_creation core:ResfileReaderTests:test_resfile_EX_commands core:ResfileReaderTests:test_resfile_primary_modes core:ResfileReaderTests:test_resid_parsing core:Resfile_Silent:test_silent_resfile_io core:ResidueGraphTypesTests:test_acceptor_atom_filter core:ResidueGraphTypesTests:test_apolar_hydrogen_atom_filter core:ResidueGraphTypesTests:test_aromatic_hydrogen_filter core:ResidueGraphTypesTests:test_heavy_atom_filter core:ResidueGraphTypesTests:test_heavy_atom_with_hydrogens_filter core:ResidueGraphTypesTests:test_heavy_atom_with_polar_hydrogen_filter core:ResidueGraphTypesTests:test_hydrogen_atom_filter core:ResidueGraphTypesTests:test_polar_hydrogen_atom_filter core:ResidueInSequenceMotifSelectorTest:test_residue_selectors core:ResidueIndexSelectorTests:test_NeighbohoodResidueSelector_fail_no_resnums core:ResidueIndexSelectorTests:test_ResidueIndexSelector_fail_index_out_of_range core:ResidueIndexSelectorTests:test_ResidueIndexSelector_parse_my_tag core:ResidueIndexSelectorTests:test_ResidueIndexSelector_parse_my_tag_mixed_str core:ResidueIndexSelectorTests:test_ResidueIndexSelector_pdb_numbered_ranges core:ResidueNameSelectorTests:test_NeighbohoodResidueSelector_fail_no_resnums core:ResidueNameSelectorTests:test_ResidueNameSelector_fail_bad_name core:ResidueNameSelectorTests:test_ResidueNameSelector_fail_bad_variant core:ResidueNameSelectorTests:test_ResidueNameSelector_name3 core:ResidueNameSelectorTests:test_ResidueNameSelector_name_and_name3 core:ResidueNameSelectorTests:test_ResidueNameSelector_parse_my_tag core:ResiduePDBInfoHasLabelSelectorTests:test_NeighbohoodResidueSelector_fail_no_label core:ResiduePDBInfoHasLabelSelectorTests:test_ResiduePDBInfoHasLabelSelector_parse_my_tag core:ResiduePropertiesTests:test_properties core:ResiduePropertiesTests:test_property_enums core:ResiduePropertiesTests:test_variant_types core:ResiduePropertySelectorTests:test_selector core:ResiduePropertySelectorTests:test_xml_interface core:ResidueRangesTests:test_ResidueRanges_parse_my_tag core:ResidueSelectorFactoryTests:test_ResidueSelectorFactory_all_ResidueSelector_all_attributes_have_descriptions core:ResidueSelectorFactoryTests:test_ResidueSelectorFactory_all_ResidueSelector_complexTypes_have_descriptions core:ResidueSelectorFactoryTests:test_all_residue_selectors_define_valid_xsds core:ResidueSelectorFactoryTests:test_output_residue_selector_xsds core:ResidueSelectorFactoryTests:test_register_one_creator_twice_with_ResidueSelectorFactory core:ResidueSelectorFactoryTests:test_register_one_creator_with_ResidueSelectorFactory core:ResidueSelectorFactoryTests:test_throw_on_unregistered_selector_name_ResidueSelectorFactory core:ResidueTest:test_Residue_resolve_partial_atom_id_dslf core:ResidueTest:test_Residue_resolve_partial_atom_id_peptide core:ResidueTest:test_fill_missing_atoms core:ResidueTest:test_fill_missing_atoms_polymer core:ResidueTest:test_insert_partial_atom_ids_for_mainchain_torsion core:ResidueTest:test_isDNA core:ResidueTest:test_isLigand core:ResidueTest:test_recursive_identification_of_connection_dependencies core:ResidueTest:test_recursive_identification_of_connection_dependencies_peptoid core:ResidueTest:test_residue_serialization core:ResidueTypeBloatTests:test_number_of_residue_types core:ResidueTypeConstraintTests:test_serialize_ResidueTypeConstraint core:ResidueTypeFinderTests:test_base_overlapping_name3 core:ResidueTypeFinderTests:test_base_overlapping_name3_no_CCD core:ResidueTypeFinderTests:test_get_best_atom_names core:ResidueTypeFinderTests:test_get_best_atom_names_no_CCD core:ResidueTypeFinderTests:test_get_by_aa core:ResidueTypeFinderTests:test_get_by_all_possible core:ResidueTypeFinderTests:test_get_by_all_possible_no_CCD core:ResidueTypeFinderTests:test_get_by_odd_name3 core:ResidueTypeFinderTests:test_get_by_std_name3 core:ResidueTypeLinkingConstraintTests:test_constraints core:ResidueTypeLinkingConstraintTests:test_linked_identity_constraints core:ResidueTypeLinkingConstraintTests:test_map_constraints core:ResidueTypeLinkingConstraintTests:test_residue_type_linking_constraints_mod_bonus_map core:ResidueTypeLinkingConstraintTests:test_residue_type_linking_constraints_setters core:ResidueTypeLinkingConstraintTests:test_serialize_ResidueTypeLinkingConstraint core:ResidueTypeSetCacheConcurrencyTests:test_cys_to_scy_query_after_read_lock_released_two_threads core:ResidueTypeSetCacheConcurrencyTests:test_five_treads_read_from_RTS_restypefinder core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_after_read_lock_released_five_threads_restypefinder core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_after_read_lock_released_two_threads_name_mapOP core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_after_read_lock_released_two_threads_restypefinder core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_after_write_lock_released_two_threads_name_mapOP core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_after_write_lock_released_two_threads_restypefinder core:ResidueTypeSetCacheConcurrencyTests:test_load_new_restype_single_thread core:ResidueTypeSetCacheConcurrencyTests:test_restype_finder_loading_new_restypes_in_single_thread core:ResidueTypeSetCacheConcurrencyTests:test_ser_to_sep_query_after_read_lock_released_two_threads core:ResidueTypeSetCacheConcurrencyTests:test_two_treads_read_from_RTS_gen_patch_cys_to_scy core:ResidueTypeSetCacheConcurrencyTests:test_two_treads_read_from_RTS_gen_patch_ser_to_sep core:ResidueTypeSetCacheConcurrencyTests:test_two_treads_read_from_RTS_name_mapOP core:ResidueTypeSetCacheConcurrencyTests:test_two_treads_read_from_RTS_restypefinder core:ResidueTypeSetTests:test_get_mirror_type core:ResidueTypeSetTests:test_residue_type_sets core:ResidueTypeTests:test_atom_add core:ResidueTypeTests:test_chi_assignment core:ResidueTypeTests:test_icoor_reassignment core:ResidueTypeTests:test_odd_proline_ring_detection core:ResidueTypeTests:test_residue_type_initialization core:ResidueTypeTests:test_round_trip core:ResidueTypeTests:test_round_trip_cen core:ResidueTypeTests:test_variant_matching core:ResidueTypeTests:test_vd_has core:RestypeToRDMolTests:test_charge_states core:RestypeToRDMolTests:test_charged_reprotonation core:RestypeToRDMolTests:test_convert core:RingClosureEnergyTests:test_eval_energy_cisACHC core:RingClosureEnergyTests:test_eval_energy_cisACPC core:RingClosureEnergyTests:test_eval_energy_proline core:RingClosureEnergyTests:test_ringclose_deriv_check_w_total_flexibility core:RingConformerIOTests:test_conformers_from_database_file_for_ring_size core:RingConformerSetTests:test_get_all_nondegenerate_conformers core:RingConformerSetTests:test_get_conformer_methods core:RingConformerSetTests:test_get_ideal_conformer_by_descriptor_methods core:RingUtilityFunctionTests:test_is_atom_axial_or_equatorial core:RingUtilityFunctionTests:test_is_atom_axial_or_equatorial_to_ring core:RmsUtilTest:test_DLbundle_rmsd_aligned_unaligned core:RmsUtilTest:test_ca_rmsd_with_mapping core:RmsUtilTest:test_gdtsc core:RmsUtilTest:test_gdtsc_self core:RmsUtilTest:test_ligand_rms core:RmsUtilTest:test_mainchain_hevayatom_rmsd core:RmsUtilTest:test_superimpose_same core:RmsUtilTest:test_superimpose_self core:RotamerBuildingFunctionsTests:test_build_rotamers_from_rotamer_bins core:RotamerConstraintDun2002Tests:test_rescore_and_copy core:RotamerConstraintDun2002Tests:test_unbound_rot core:RotamerDotsTests:test_dotsphere_construction core:RotamerDotsTests:test_dotsphere_get_num_covered core:RotamerDotsTests:test_dotsphere_get_total_dots core:RotamerDotsTests:test_dotsphere_increment_count core:RotamerDotsTests:test_dotsphere_operators core:RotamerDotsTests:test_dotsphere_write_to_compact_array core:RotamerDotsTests:test_invrotamerdots core:RotamerDotsTests:test_invrotamerdots_overlap_is_buried core:RotamerDotsTests:test_invrotamerdots_overlap_is_buried_1FKB core:RotamerDotsTests:test_rotamerdots_construction core:RotamerDotsTests:test_rotamerdots_increment_and_decrement_from_cached core:RotamerDotsTests:test_rotamerdots_increment_and_decrement_from_cached_excl_hydrogens core:RotamerDotsTests:test_rotamerdots_increment_and_decrement_from_cached_expanded_polars core:RotamerDotsTests:test_rotamerdots_increment_both_and_cache core:RotamerDotsTests:test_rotamerdots_increment_both_and_cache_excl_hydrogens core:RotamerDotsTests:test_rotamerdots_increment_both_and_cache_expanded_polars core:RotamerDotsTests:test_rotamerdots_increment_self_overlap core:RotamerDotsTests:test_rotamerdots_increment_this_and_cache core:RotamerDotsTests:test_rotamerdots_increment_this_and_cache_expanded_polars core:RotamerDotsTests:test_rotamerdots_overlaps core:RotamerDotsTests:test_rotamerdotscache_construction core:RotamerSetsTests:test_rotamer_set_add_rotamer_into_existing_group1 core:RotamerSetsTests:test_rotamer_set_add_rotamer_into_existing_group2 core:RotamerSetsTests:test_rotamer_set_add_rotamer_into_existing_group3 core:RotamerSetsTests:test_rotamer_set_add_rotamer_into_existing_group4 core:RotamerSetsTests:test_rotamer_set_residue_type_offsets core:RotamerSetsTests:test_rotamer_sets core:RotamerSubsetsTest:test_rotamer_subset_constructor core:RotamerTrials:test_rotamer_trials core:RotamerUtils:test_residue_rotamer_recovery core:RotamerUtils:test_rotamer_recovery core:SCMinMinimizerMapTests:test_construct_SCMinMinimizerMap core:SCMinMultifuncTests:test_construct_SCMinMultifunc core:SOGFuncTests:test_func core:SOGFuncTests:test_serialize_SOGFunc core:SapConstraintEnergyTests:test_fast_partial_packing core:SapConstraintEnergyTests:test_helper_lightning core:SapConstraintEnergyTests:test_lightning_packing_partial core:SapConstraintEnergyTests:test_math_mover core:SapConstraintEnergyTests:test_mover core:SapConstraintEnergyTests:test_partial_packing core:SapConstraintEnergyTests:test_selectors core:SasaTests:test_calc_per_res_hydrophobic_sasa core:SasaTests:test_calc_total_sasa_glycine core:SasaTests:test_calc_total_sasa_smallprotein core:SasaTests:test_get_overlap core:ScTests:test_sc core:ScalarWeightedFuncTests:test_ScalarWeightedFunc core:ScalarWeightedFuncTests:test_serialize_ScalarWeightedFunc core:ScoreFunctionFactoryTest:test_beta_15_behavior core:ScoreFunctionFactoryTest:test_beta_15_behavior_noext core:ScoreFunctionFactoryTest:test_beta_15_returns core:ScoreFunctionFactoryTest:test_get_score_function_name core:ScoreFunctionFactoryTest:test_list_read_options_in_get_score_function_in_sync_w_get_score_function core:ScoreFunctionTest:test_ScoreFunction_ctor_actually_reads_option_collection core:ScoreFunctionTest:test_ScoreFunction_list_options_read_in_sync core:ScoreFunctionTest:test_add_weights_from_file core:ScoreFunctionTest:test_apply_patch_from_file core:ScoreFunctionTest:test_get_sub_score_exclude_res core:ScoreFunctionTest:test_get_sub_score_exclude_res_long_range_terms core:ScoreFunctionUtilityTest:test_find_weights_file core:ScoreTest:test_ScoreTest core:ScoringSchemeTests:test_pair_scoring_scheme core:ScoringSchemeTests:test_simple_scoring_scheme core:ScoringUtilTests:test_atomistic_energies core:SecondaryStructureSelectorTests:test_SecondaryStructureSelector_fail_bad_ss core:SecondaryStructureSelectorTests:test_SecondaryStructureSelector_fail_no_ss core:SecondaryStructureSelectorTests:test_SecondaryStructureSelector_fail_no_ss_C core:SecondaryStructureSelectorTests:test_SecondaryStructureSelector_overlap core:SecondaryStructureSelectorTests:test_SecondaryStructureSelector_parse_my_tag core:SelectedResidueCountMetricTests:test_with_selector core:SelectedResidueCountMetricTests:test_without_selector core:SelectorLogicParserTests:test_SelectorParser_and_combination core:SelectorLogicParserTests:test_SelectorParser_error_handling_with_illegal_varnames core:SelectorLogicParserTests:test_SelectorParser_missing_residue_selector core:SelectorLogicParserTests:test_SelectorParser_not_and_combination core:SelectorLogicParserTests:test_SelectorParser_not_or_combination core:SelectorLogicParserTests:test_SelectorParser_not_or_combination2 core:SelectorLogicParserTests:test_SelectorParser_or_combination core:SelectorLogicParserTests:test_combine_logic_within_all_selections core:SequenceAlignmentTests:test_alignment_functions core:SequenceAlignmentTests:test_alignment_io core:SequenceAlignmentTests:test_alignment_mapping core:SequenceAlignmentTests:test_equality_operator core:SequenceAlignmentTests:test_general_aln_io core:SequenceAlignmentTests:test_grishin_align_io core:SequenceAlignmentTests:test_mapping_to_alignment core:SequenceAlignmentTests:test_per_residue_scores core:SequenceAlignmentTests:test_simple_aligner core:SequenceMappingTests:test_constructor core:SequenceMappingTests:test_lengthevent_append core:SequenceMappingTests:test_lengthevent_append_end core:SequenceMappingTests:test_lengthevent_delete core:SequenceMappingTests:test_lengthevent_delete_end core:SequenceMappingTests:test_lengthevent_prepend core:SequenceMappingTests:test_lengthevent_prepend_end core:SequenceMappingTests:test_reverse core:SequenceMappingTests:test_transitive_mapping core:SequenceMetricTests:test_base_name core:SequenceMetricTests:test_full_name core:SequenceMetricTests:test_oneletter_code core:SequenceMetricTests:test_threeletter_code core:SequenceMotifUtilTests:test_split_sequence_motif core:SequenceProfileConstraintTests:test_serialize_SequenceProfileConstraint core:SequenceProfile_Tests:test_generate_from_sequence core:SequenceProfile_Tests:test_global_auto_rescale core:SequenceProfile_Tests:test_input core:SequenceProfile_Tests:test_prob_temp core:SequenceProfile_Tests:test_probs core:SequenceProfile_Tests:test_rescale core:SequenceProfile_Tests:test_sequence_entropy core:SequenceProfile_Tests:test_sequence_manipulation core:SequenceSimilarityMetricTests:test_selector core:SequenceSimilarityMetricTests:test_simple_case core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing_ncaa core:SequenceSymmetricAnnealerTests:test_chain_similarity_with_virtual_root core:SequenceSymmetricAnnealerTests:test_chain_similiarity_with_alternative_logic core:SequenceSymmetricAnnealerTests:test_different_accepted_restypes_for_linked_residues core:SequenceSymmetricAnnealerTests:test_fail_in_packing_from_no_common_res_types core:SequenceSymmetricAnnealerTests:test_fail_in_packing_from_no_common_res_types_L_and_D core:SequenceSymmetricAnnealerTests:test_index_residue_selectors core:SequenceSymmetricAnnealerTests:test_initialise_annealer_from_xml core:SequenceSymmetricAnnealerTests:test_overlapping_index_residue_selectors core:SequenceSymmetricAnnealerTests:test_recover_symmetry core:SequenceSymmetricAnnealerTests:test_xml_validation core:SequenceUtilTests:test_annotated_sequence core:SequenceUtilTests:test_mapping_into_sequence core:SequenceUtilTests:test_naive_alignment core:SequenceUtilTests:test_strip_spacers core:SigmoidFuncTests:test_serialize_SigmoidFunc core:SimpleInteractionGraphTests:test_instantiate_simple_ig core:SimpleInteractionGraphTests:test_simple_ig_neutral_compare core:SimpleMetricSelectorTests:test_selector core:SimpleMetricSelectorTests:test_xml core:SimpleMetricTests:test_composite_real_metric core:SimpleMetricTests:test_composite_string_metric core:SimpleMetricTests:test_glycan_layer_metric core:SimpleMetricTests:test_interaction_energy_metric core:SimpleMetricTests:test_per_residue_clash_metric core:SimpleMetricTests:test_per_residue_real_metric core:SimpleMetricTests:test_per_residue_string_metric core:SimpleMetricTests:test_real_metric core:SimpleMetricTests:test_residue_summary_metric core:SimpleMetricTests:test_sasa_metric core:SimpleMetricTests:test_seq_metric core:SimpleMetricTests:test_ss_metric core:SimpleMetricTests:test_string_metric core:SimpleMetricTests:test_utility_metrics core:SingleLigandRotamerLibraryTests:test_init_from_file_explicit_and_implicit 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core:SymmDLBetasTests:test_symm_DLBetas_omega core:SymmDLBetasTests:test_symm_DLBetas_p_aa_pp core:SymmDLBetasTests:test_symm_DLBetas_rama core:SymmDLBetasTests:test_symm_DLBetas_rama_prepro core:SymmDLBetasTests_beta:test_symm_DLBetas_default_scorefxn core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_atr core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_dun core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_elec core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_intra_rep core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_rep core:SymmDLBetasTests_beta:test_symm_DLBetas_fa_sol core:SymmDLBetasTests_beta:test_symm_DLBetas_hbonds core:SymmDLBetasTests_beta:test_symm_DLBetas_omega core:SymmDLBetasTests_beta:test_symm_DLBetas_p_aa_pp core:SymmDLBetasTests_beta:test_symm_DLBetas_rama core:SymmDLBetasTests_beta:test_symm_DLBetas_rama_prepro core:SymmDLMinTests:test_symm_DL_min_cart_bonded core:SymmDLMinTests:test_symm_DL_min_current_default_scorefxn core:SymmDLMinTests:test_symm_DL_min_dslf_fa13 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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:AddChainBreakTests:test_pose_manipulation protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_bounded protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_harmonic protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_scalar_weighted protocols:AddConstraintsToCurrentConformationMoverTests:test_coord_bounded protocols:AddConstraintsToCurrentConformationMoverTests:test_coord_harmonic protocols:AddConstraintsToCurrentConformationMoverTests:test_sc_tip protocols:AddFlankingVirtualResiduesMoverTests:test_AddFlankingVirtualResiduesMover 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:AddMHCEpitopeConstraintMoverTests:test_mhc_csts protocols:AddMPLigandMoverTest:test_membrane_invariant protocols:AddMPLigandMoverTest:test_membrane_plus_ligand_foldtree protocols:AddMembraneMoverTest:test_anchored_foldtree protocols:AddMembraneMoverTest:test_conformation_invariant protocols:AddMembraneMoverTest:test_default_membrane_position protocols:AddMembraneMoverTest:test_existing_membrane_rsd protocols:AddMembraneMoverTest:test_initial_foldtree protocols:AddMembraneMoverTest:test_initial_spans_setup protocols:AddMembraneMoverTest:test_membrane_jump_tracking protocols:AddMembraneMoverTest:test_membrane_rsd_tracking protocols:AddMembraneMoverTest:test_multi_mem_pose1 protocols:AddMembraneMoverTest:test_multi_mem_pose2 protocols:AddMembraneMoverTest:test_single_tm_span_pose protocols:AlignByResidueSelectorMoverTests:test_all_true protocols:AlignByResidueSelectorMoverTests:test_name protocols:AlignByResidueSelectorMoverTests:test_shift_aligned protocols:AlignPDBInfoToSequencesTests:test_SequenceSpecification protocols:AlignPDBInfoToSequencesTests:test_ctor_and_operators protocols:AlignPDBInfoToSequencesTests:test_dna_align protocols:AlignPDBInfoToSequencesTests:test_mode_enum protocols:AlignPDBInfoToSequencesTests:test_multiple protocols:AlignPDBInfoToSequencesTests:test_parse_target_tag protocols:AlignPDBInfoToSequencesTests:test_real_example protocols:AlignPDBInfoToSequencesTests:test_set_modes protocols:AlignPDBInfoToSequencesTests:test_single protocols:AlignPDBInfoToSequencesTests:test_throw_on_fail protocols:AlignPDBInfoToSequencesUtilTests:test_pad_sequence protocols:AlignResiduesMoverTests:test_align_theozyme protocols:AlignResiduesMoverTests:test_tomponent_cstfile protocols:AlignmentEnergyTests:test_deriv protocols:AlignmentEnergyTests:test_score_values protocols:AntibodyCDRGrafterTests:test_graft_classes protocols:AntibodyConstraintTests:test_constraints protocols:AntibodyDatabase:test_cdr_loading protocols:AntibodyDatabase:test_options_cdr_set protocols:AntibodyDesignOptions:test_native_seq protocols:AntibodyDesignOptions:test_options_graft_design protocols:AntibodyDesignOptions:test_options_seq_design protocols:AntibodyInfoTests:test_camelid protocols:AntibodyInfoTests:test_cdr_numbering_and_transform protocols:AntibodyInfoTests:test_info_functions protocols:AntibodyInfoTests:test_kink_functions protocols:AntibodyInfoTests:test_renumbering 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:ApplyChemistryMoverTests:test_apply_chemistry protocols:ApplyChemistryMoverTests:test_xml protocols:ApplyChemistryMoverTests:test_xml_nested protocols:ArithmeticTests:test_active_variables_max protocols:ArithmeticTests:test_active_variables_min protocols:ArithmeticTests:test_active_variables_min_complicated protocols:ArithmeticTests:test_active_variables_simple protocols:ArithmeticTests:test_add_derivative protocols:ArithmeticTests:test_addition_order protocols:ArithmeticTests:test_and_expession protocols:ArithmeticTests:test_combine_functions protocols:ArithmeticTests:test_equals_expression protocols:ArithmeticTests:test_function_order protocols:ArithmeticTests:test_function_precidence protocols:ArithmeticTests:test_gt_expression 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protocols:ArithmeticTests:test_parse_simple protocols:ArithmeticTests:test_parse_variables protocols:ArithmeticTests:test_precedence protocols:ArithmeticTests:test_sqrt 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:AtomicDistanceFilterTests:test_AtomicDistanceFilter protocols:BackrubMoverTest:test_BackrubMover protocols:BackrubProtocolTests:test_parse_pivots_from_residue_selector protocols:BackwardsProtocolsFeaturesReporterCreatorTests:test_all_creators_generate_correct_name_strings protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_analysis_PeptideDeriverFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_cyclic_peptide_OversaturatedHbondAcceptorFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_denovo_design_filters_ExposedHydrophobicsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_denovo_design_filters_PreProlineFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_denovo_design_filters_SSPredictionFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_denovo_design_filters_SSShapeComplementarityFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_DiffAtomSasaFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_EnzScoreFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_EnzdesScorefileFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_LigBurialFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_LigDSasaFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_LigInterfaceEnergyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_RemoveLigandFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_RepackWithoutLigandFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_enzdes_ResidueConformerFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_filters_CalculatorFilterCreator_name 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protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_FragQualFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_HSSTripletFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_HelixKinkFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_HelixPairingFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_InterlockingAromaFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_NcontactsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_ParallelBetaPairingPreferenceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_SecondaryStructureCountFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_SecondaryStructureFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_SecondaryStructureHasResidueFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_fldsgn_filters_SheetTopologyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_helical_bundle_BundleReporterFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_indexed_structure_store_filters_FragmentLookupFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_AtomCountFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_ChainExistsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_CompleteConnectionsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_HBondAcceptorFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_HBondDonorFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_HeavyAtomFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_MolarMassFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_ligand_docking_MolecularMassFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_loops_filters_LoopAnalyzerFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_matdes_ClashCheckFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_matdes_GetRBDOFValuesCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_matdes_InterfacePackingFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_matdes_OligomericAverageDegreeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_matdes_SymUnsatHbondFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_AtomicContactCountFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_AverageDegreeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_BindingStrainFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_BoltzmannFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_ClashWithTargetFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_DesignableResiduesFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_DisulfideFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_FNatFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_FilterScanFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_HbondsToAtomFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_HbondsToResidueFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_IRmsdFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_InterfaceHolesFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_LRmsdFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_RelativeSegmentFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_RmsdFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_RmsdSimpleFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_SSamountFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_SequenceRecoveryFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_SpecificResiduesNearInterfaceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_StubScoreFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_StubScoreLoopsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_protein_interface_design_filters_TorsionCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_AlaScanFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_AngleToVectorFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_AtomicContactFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_AtomicDistanceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_AveragePathLengthFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_BuriedUnsatHbondFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ConservedPosMutationFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ConstraintScoreFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_DdGScanCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_DdgFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_DeltaFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_DisulfideEntropyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_EnergyPerResidueFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ExpiryFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_FileExistFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_FileRemoveFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_GeometryFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_HolesFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_InterRepeatContactFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_InterfaceBindingEnergyDensityFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_InterfaceSasaFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_IntraRepeatContactFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_MotifScoreFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_MultipleSigmoidsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_MutationsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_NMerPSSMEnergyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_NMerSVMEnergyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_NeighborTypeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_NetChargeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_NonSequentialNeighborsFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_OperatorFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_PackStatFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_PoseCommentFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_PoseInfoFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_RangeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_RelativePoseFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_RepeatParameterFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ReportFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResidueCountFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResidueDepthFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResidueDistanceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResidueIEFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResidueSetChainEnergyFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ResiduesInInterfaceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_RotamerBoltzmannWeight2Creator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_RotamerBoltzmannWeightFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SSElementMotifContactFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SSMotifFinderFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SavePoseConstraintToFileFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SaveResfileToDiskFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ScoreCutoffFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ScoreTypeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_ShapeComplementarityFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SidechainRmsdFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SigmoidFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_StemFinderFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_SymmetricMotifFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_TaskAwareSASAFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_TaskAwareScoreTypeFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_TerminusDistanceFilterCreator_name protocols:BackwardsProtocolsFilterCreatorTests:test_protocols_simple_filters_TotalSasaFilterCreator_name protocols:BasePairConstraintTests:test_all_constraint_possibilities protocols:BasePairConstraintTests:test_bad_when_stretched_all_constraint_possibilities protocols:BetaAlphaDisulfideTests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov15_Tests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov16_Tests:test_mixed_disulf protocols:BetaSheetArchitectTests:test_simple protocols:BetaTurnDetectionFeaturesTest:test_ramachandran_hashes protocols:BetaTurnDetectionFeaturesTest:test_validate_ramachandran_hash protocols:BlockwiseAnalysisMoverTests:test_BlockwiseAnalysisMover protocols:BlockwisePoseCompMotifMetricTests:test_BWPCMM protocols:BlockwiseShapeCompMetricTests:test_BWSCM protocols:BluePrintTests:test_blueprint protocols:BranchAngleOptimizerTest:test_BranchAngleOptimizer protocols:BridgeChainsMoverTests:test_conn_chains protocols:BridgeChainsMoverTests:test_twohelix protocols:BridgeTests:test_bridge_size_three protocols:BridgeTests:test_bridge_size_zero protocols:BridgeTests:test_bridge_two_chain protocols:BuildManagerTests:test_compatibility_check protocols:BuildManagerTests:test_dependencies protocols:BuildManagerTests:test_modify protocols:BumpGridTests:test_bool3D_corners protocols:BumpGridTests:test_bool3D_corners2 protocols:BumpGridTests:test_bool3D_create_shifted_grid protocols:BumpGridTests:test_bool3D_grid_ctor protocols:BumpGridTests:test_bool3D_grid_ctor2 protocols:BumpGridTests:test_bool3D_grid_with_sphere protocols:BumpGridTests:test_bool3D_grid_with_sphere2 protocols:BumpGridTests:test_bool3D_grid_with_sphere_liberal protocols:BumpGridTests:test_bool3D_or_overlap protocols:BumpGridTests:test_bool3D_sphere_coverage protocols:BumpGridTests:test_bool3D_write_kinemage protocols:BumpGridTests:test_bumpgrid_for_pose protocols:CalculatorFilterTests:test_calculatorfilter protocols:CalculatorFilterTests:test_parsing protocols:ChromophoreDataReaderTests:test_access_to_nonexistent_residue protocols:ChromophoreDataReaderTests:test_initialize_from_file protocols:ChromophoreDataReaderTests:test_initialize_second_time protocols:ChromophoreDataReaderTests:test_nonexistent_file protocols:ChromophoreDataReaderTests:test_nothing_to_parse_comment_line protocols:ChromophoreDataReaderTests:test_nothing_to_parse_empty protocols:ChromophoreDataReaderTests:test_parse_correct_line protocols:ChromophoreDataReaderTests:test_parse_line_with_four_letter_atom_name protocols:ChromophoreDataReaderTests:test_parse_line_with_long_atom_name protocols:ChromophoreDataReaderTests:test_parse_line_with_wrong_number_of_columns protocols:ChromophoreDataReaderTests:test_parse_line_without_number_in_the_third_column protocols:ChunkTest:test_samples_in_range protocols:ChunkTest:test_start_stop protocols:ChunkTest:test_validity protocols:ClaimTests:test_tclaim_constructor_multi_pos protocols:ClaimTests:test_tclaim_constructor_single_pos protocols:ClassicGridTests:test_score_function protocols:ClearConstraintsMoverTests:test_it_clears_constraints protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features protocols:CoMTrack:test_com_init protocols:CoMTrack:test_com_reset protocols:CompoundArchitectTests:test_compound_architect_with_connection protocols:CompoundArchitectTests:test_gerard_case protocols:CompoundArchitectTests:test_simple_compound_architect protocols:ConcatenatePosesTests:test_concatenator protocols:ConnectRightTests:test_connection protocols:ConnectionArchitectTests:test_bridge_connection protocols:ConnectionArchitectTests:test_staple_connection protocols:ConsensusLoopDesignOperationTests:test_loop_info_and_task_manipulation protocols:ConsensusLoopDesignOperationTests:test_read_db protocols:ConservativeDesignOperationTests:test_task_op protocols:ConstraintGeneratorFactoryTests:test_register_one_creator_twice_with_ConstraintGeneratorFactory protocols:ConstraintGeneratorFactoryTests:test_register_one_creator_with_ConstraintGeneratorFactory protocols:ConstraintGeneratorFactoryTests:test_throw_on_unregistered_generator_name_ConstraintGeneratorFactory protocols:ConstraintScoreCutoffFilterTests:test_it_adds_scores protocols:ConstraintsManagerTests:test_pose_cache protocols:ConstraintsMetricTests:test_read_and_summarize protocols:ContactMapTests:test_apply protocols:ContactMapTests:test_contact protocols:ContactMapTests:test_contact_partner protocols:ContactMapTests:test_fill_contacts protocols:ContactMapTests:test_fill_contacts_ligand protocols:ContactMapTests:test_fill_two_region protocols:ContactMapTests:test_parse_region protocols:ContactMapTests:test_parse_tag protocols:ContainerMoversTest:test_CycleMover protocols:ContainerMoversTest:test_RepeatMover protocols:ContainerMoversTest:test_SequenceMover protocols:CoordSerializationTests:test_serialization 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:CopyRotamerMoverTests:test_copyrotamermover protocols:CoreScorerTests:test_corescorer protocols:CoupledMovesProtocolTests:test_apply protocols:CoupledMovesProtocolTests:test_bad_init protocols:CreateSequenceMotifOperationTests:test_task_op protocols:CrosslinkerMoverTests:test_tma_dihedral_fxn protocols:CstInfoMoverTests:test_it_adds_scores protocols:CycpepRigidBodyPermutationMoverTests:test_apply_setting protocols:CycpepSymmetryFilterTests:test_c2_symm protocols:CycpepSymmetryFilterTests:test_c2m_symm protocols:CycpepSymmetryFilterTests:test_c4m_symm protocols:DDGBindOptEDataTests:test_get_score protocols:DataLoaderTests:test_ConstraintGeneratorLoader protocols:DataLoaderTests:test_DataLoaderFactory protocols:DataLoaderTests:test_JumpSelectorLoader protocols:DataLoaderTests:test_LoopsDefinerLoader protocols:DataLoaderTests:test_MonteCarloLoader protocols:DataLoaderTests:test_MoveMapBuilderLoader protocols:DataLoaderTests:test_MoveMapFactoryLoader protocols:DataLoaderTests:test_ResidueSelectorLoader protocols:DataLoaderTests:test_ScoreFunctionLoader protocols:DataLoaderTests:test_TaskOperationLoader protocols:DdGScan:test_calculate protocols:DdGScan:test_filter_parsing protocols:DdgFilter:test_filter_parsing protocols:DdgFilter:test_use_filter protocols:DeNovoArchitectTests:test_apply protocols:DeNovoArchitectTests:test_cloning protocols:DeNovoArchitectTests:test_parse_tag protocols:DeNovoMotifArchitectTests:test_apply protocols:DeNovoMotifArchitectTests:test_motif_base protocols:DeNovoMotifArchitectTests:test_parse_my_tag protocols:DesignAroundOperationTests:test_it_doesnt_restrict_for_big_enough_radius protocols:DesignAroundOperationTests:test_it_restricts_outside_design_radius protocols:DesignAroundOperationTests:test_it_restricts_outside_pack_radius protocols:DihedralConstraintGeneratorTests:test_generator protocols:DirectSegmentLookupTests:test_read_store protocols:DirectSegmentLookupTests:test_simple_mover protocols:DirectSegmentLookupTests:test_simple_sample protocols:DisulfideInsertionMoverTests:test_apply_function protocols:DisulfideInsertionMoverTests:test_cyclization_viability_function protocols:DisulfideInsertionMoverTests:test_rosettascripts_options protocols:DisulfidizeMoverTests:test_disulfidize protocols:DisulfidizeMoverTests:test_find_current_disulfides protocols:DisulfidizeMoverTests:test_multiplex protocols:DivideAndConquerorTests:test_ntf2 protocols:DivideAndConquerorTests:test_rossman 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:DsspDesignOperationTests:test_DsspDesignOperation protocols:DsspDesignOperationTests:test_copy_constructor protocols:DsspDesignOperationTests:test_get_restrictions protocols:DsspDesignOperationTests:test_set_restrictions_aa protocols:DsspDesignOperationTests:test_set_restrictions_append protocols:DsspDesignOperationTests:test_set_restrictions_exclude protocols:DsspDisulfideLabelerMoverTests:test_DSSPDisulfideLabelerMover protocols:DsspTests:test_dssp 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:EmbeddingDefTest:test_default_constructor protocols:EmbeddingDefTest:test_equals protocols:EmbeddingDefTest:test_from_span protocols:EmbeddingDefTest:test_standard_constructor protocols:EmbeddingDefTest:test_translate_by protocols:EmbeddingTest:test_constructor_from_topo_and_pose protocols:EmbeddingTest:test_constructor_from_topo_and_radius protocols:EnergyBasedClusteringTests:test_determine_ABOXYZ_bin protocols:EnergyBasedClusteringTests:test_get_circular_permutation_first_in_alphabetical_order protocols:EnergyBasedClusteringTests:test_num_asymmetric_binstrings protocols:EnergyBasedClusteringTests:test_num_asymmetric_binstrings_with_mirror_counterpart_represented protocols:EnergyBasedClusteringTests:test_permute_string protocols:EnergyBasedClusteringTests:test_storeposedata 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:EnsureExclusivelySharedJumpMoverTests:test_custom_foldtree1 protocols:EnsureExclusivelySharedJumpMoverTests:test_custom_foldtree2 protocols:EnsureExclusivelySharedJumpMoverTests:test_custom_foldtree3 protocols:EnsureExclusivelySharedJumpMoverTests:test_custom_foldtree4 protocols:EnsureExclusivelySharedJumpMoverTests:test_custom_foldtree5 protocols:EnsureExclusivelySharedJumpMoverTests:test_simple protocols:EnsureExclusivelySharedJumpMoverTests:test_simple_six_chains protocols:EnsureExclusivelySharedJumpMoverTests:test_simple_two_chain1 protocols:EnsureExclusivelySharedJumpMoverTests:test_simple_two_chain2 protocols:EnsureExclusivelySharedJumpMoverTests:test_simple_two_chain3 protocols:EnsureExclusivelySharedJumpMoverTests:test_simple_two_chain4 protocols:EntityCorrespondenceTests:test_correspondence_bad_instream_entity_range protocols:EntityCorrespondenceTests:test_correspondence_bad_instream_entity_type protocols:EntityCorrespondenceTests:test_correspondence_bad_instream_resid_type protocols:EntityCorrespondenceTests:test_correspondence_bad_instream_residue_range protocols:EntityCorrespondenceTests:test_correspondence_entity_index_out_of_bounds protocols:EntityCorrespondenceTests:test_correspondence_from_instream protocols:EntityCorrespondenceTests:test_correspondence_from_instream_ignoring_comments protocols:EntityCorrespondenceTests:test_correspondence_residue_index_out_of_bounds protocols:EntityCorrespondenceTests:test_entity_correspondence_ctor protocols:EntityTests:test_DummyElement_ctor protocols:EntityTests:test_Entity_assignment_operator protocols:EntityTests:test_Entity_copy_constructor protocols:EntityTests:test_Entity_equality protocols:EntityTests:test_Entity_fitness_lt_logic protocols:EntityTests:test_Entity_fitness_valid_logic protocols:EntityTests:test_Entity_from_string protocols:EntityTests:test_Entity_output protocols:EntityTests:test_Entity_with_dummy_elements protocols:EnvironmentJump:test_cache_persistence protocols:EnvironmentJump:test_cut_inheritance protocols:EnvironmentJump:test_jump_moves protocols:EnvironmentJump:test_pdb_info_persistence protocols:EnvironmentTorsion:test_dual_environment protocols:EnvironmentTorsion:test_empty_environment protocols:EnvironmentTorsion:test_single_phi_moves protocols:EnvironmentTorsion:test_torsion_can_exclusive_compatibility protocols:EnvironmentTorsion:test_torsion_init protocols:EnvironmentTorsion:test_torsion_must_can_coexist protocols:EnvironmentTorsion:test_torsion_must_exclusive_incompatibility protocols:EnzScoreFilterTests:test_auto_enzdes_csts protocols:EnzScoreFilterTests:test_resnum_enzdes_csts protocols:EnzScoreFilterTests:test_whole_pose_enzdes_csts protocols:EnzdesTaskOperations_Tests:test_ProteinLigandInterfaceUpweighter_gettersetter protocols:ExtendChainMoverTests:test_append protocols:ExtendChainMoverTests:test_input protocols:ExtendChainMoverTests:test_prepend protocols:ExtendedPoseBuilderTests:test_add_chain_from_segment protocols:ExtendedPoseBuilderTests:test_bridgechains_add_template_segment_functions protocols:ExtendedPoseBuilderTests:test_bridgechains_case protocols:ExtendedPoseBuilderTests:test_build_complicated protocols:ExtendedPoseBuilderTests:test_build_copy_multi_chain protocols:ExtendedPoseBuilderTests:test_build_copy_simple protocols:ExtendedPoseBuilderTests:test_build_pose_simple protocols:ExtendedPoseBuilderTests:test_build_pose_with_lower_template protocols:ExtendedPoseBuilderTests:test_build_pose_with_middle_template protocols:ExtendedPoseBuilderTests:test_build_pose_with_middle_template_and_cut protocols:ExtendedPoseBuilderTests:test_build_pose_with_upper_template protocols:ExtendedPoseBuilderTests:test_gerard_case protocols:ExtendedPoseBuilderTests:test_propeller_case protocols:ExternalGeomSamplerTests:test_external_geom_sampler_transforms protocols:ExternalGeomSamplerTests:test_sampler_ctor protocols:ExternalGeomSamplerTests:test_sampler_initialization protocols:ExtraThreadingMover_Tests:test_basic_threading 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_fastrelax_B3N protocols:FastRelaxTests:test_fastrelax_B3N_mod_termini protocols:FastRelaxTests:test_legacy_dualspace_script protocols:FastRelaxTests:test_legacy_script protocols:FastRelaxTests:test_local_script protocols:FastRelaxTests:test_nonexistent_local_script protocols:FavorSequenceProfileTests:test_global_scaling protocols:FavorSequenceProfileTests:test_no_scaling protocols:FavorSequenceProfileTests:test_use_BLOSUM62 protocols:FavorSequenceProfileTests:test_use_IDENTITY protocols:FavorSequenceProfileTests:test_use_PSSM protocols:FavorSequenceProfileTests:test_use_weight protocols:FeaturesReporterTests:test_identifier_generation protocols:FeaturesReporterTests:test_main protocols:FeaturesReporterTests:test_trajectory_report_to_db protocols:FilterFactoryTests:test_FilterFactory_all_Filter_all_attributes_have_descriptions protocols:FilterFactoryTests:test_FilterFactory_all_Filter_complexTypes_have_descriptions protocols:FilterFactoryTests:test_all_filters_define_valid_xsds protocols:FilterFactoryTests:test_confidence_usage protocols:FilterReportAsPoseExtraScoresMoverTests:test_FilterReportAsPoseExtraScoresMover protocols:FilterValueMetricTests:test_constructor protocols:FindConsensusSequenceTest:test_consensus_sequence protocols:FindConsensusSequenceTest:test_resfile_parsing protocols:FitnessFilterTest:test_FitnessFilter protocols:FlipChiralityMover:test_mirrored protocols:FlipChiralityMover:test_name_change protocols:FlipChiralityMover:test_size_range protocols:FlipMoverTest:test_constructor_from_jumpnum protocols:FlipMoverTest:test_constructor_from_jumpnum_and_angle protocols:FlipMoverTest:test_constructor_from_jumpnum_and_angle_mem protocols:FlipMoverTest:test_constructor_from_jumpnum_and_axis protocols:FlipMoverTest:test_constructor_from_jumpnum_and_axis_mem protocols:FlipMoverTest:test_constructor_from_jumpnum_axis_angle protocols:FlipMoverTest:test_constructor_from_jumpnum_axis_angle_mem protocols:FlipMoverTest:test_constructor_from_jumpnum_mem protocols:FlipMoverTest:test_default_constructor protocols:FlipMoverTest:test_flipmover_parse_my_tag_input protocols:FoldArchitectMoverTests:test_design protocols:FoldArchitectMoverTests:test_symmetry protocols:FoldGraphTests:test_create_fold_tree protocols:FoldGraphTests:test_create_loops protocols:FoldGraphTests:test_fold_tree_with_cutpoint protocols:FoldGraphTests:test_simple_fold_tree protocols:FoldTreeFromMotifTests:test_fold_tree_from_loops protocols:ForceDisulfidesMoverTests:test_keep_existing protocols:ForceDisulfidesMoverTests:test_original protocols:ForceDisulfidesMoverTests:test_parse protocols:ForceDisulfidesMoverTests:test_rearrange protocols:ForceDisulfidesMoverTests:test_remove_existing protocols:FragmentCMTest:test_fragment_insertion protocols:FragmentCMTest:test_xml protocols:FragmentCandidatesTests:test_DiversifyCrmsdByClustering protocols:FragmentCandidatesTests:test_DiversifyCrmsdSelector protocols:FragmentCandidatesTests:test_DiversifyDihedralsSelector protocols:FragmentCandidatesTests:test_read_vall2 protocols:FragmentCandidatesTests:test_read_vall_fragments protocols:FragmentLookupTests:test_binary_store protocols:FragmentLookupTests:test_read_store protocols:FragmentMoverTest:test_mover protocols:FragmentMoverTest:test_proposed_ss protocols:FragmentMoverTest:test_ss_check protocols:FragmentMoverTest:test_steal protocols:FragmentMoverTest:test_window_start 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:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_D protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_D_beforepro protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_beforepro protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_D protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_D_beforepro protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_beforepro 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:GlycosyltransferaseMoverTests:test_apply protocols:GraftSwitchMoverTests:test_graft_switch_mover_setup protocols:GraftingTest:test_graft_classes protocols:GraftingTest:test_utility_functions protocols:GreedyOptMutationMoverTests:test_GreedyOptMutationMover_ultrasimple protocols:GreenPackerTests:test_GreenPacker_ultrasimple protocols:GrowLeftTests:test_n_side_internal protocols:GrowLeftTests:test_n_term_extension protocols:GrowRightTests:test_c_side_internal protocols:GrowRightTests:test_c_term_extension protocols:GunnCostTest:test_cost protocols:HBNetMoverTests:test_hbnet_mover_setup protocols:HBPHelixAssignmentsTests:test_init_from_file protocols:HBondCalculatorsTest:test_hb_calculators protocols:HBondSelectorTests:test_HBondSelector_parse_my_tag protocols:HasDisulfideFilterTests:test_hasDisulfideFilter protocols:HasherTests:test_HitNeighborFinder_find_connected_components_1 protocols:HasherTests:test_HitNeighborFinder_find_connected_components_2 protocols:HasherTests:test_HitNeighborFinder_find_connected_components_3 protocols:HasherTests:test_HitNeighborFinder_find_connected_components_4 protocols:HasherTests:test_MatchCounter_three_geomcsts_expect_eight_matches protocols:HasherTests:test_MatchCounter_three_geomcsts_expect_four_matches protocols:HasherTests:test_MatchCounter_three_geomcsts_expect_one_match protocols:HasherTests:test_MatchCounter_three_geomcsts_expect_zero_matches protocols:HasherTests:test_MatchCounter_two_geomcsts_expect_one_match protocols:HasherTests:test_SixDCoordinateBinner_halfbin_index_euclid_offset protocols:HasherTests:test_SixDCoordinateBinner_halfbin_index_euler_offset protocols:HasherTests:test_SixDCoordinateBinner_halfbin_index_euler_phi_psi_offset protocols:HasherTests:test_SixDCoordinateBinner_halfbin_index_no_offset protocols:HasherTests:test_SixDCoordinateBinner_halfbin_index_theta_offset_euclid_offset protocols:HasherTests:test_SixDCoordinateBinner_offset_phi protocols:HasherTests:test_SixDCoordinateBinner_offset_psi protocols:HasherTests:test_SixDCoordinateBinner_offset_theta protocols:HasherTests:test_SixDCoordinateBinner_wrap_theta protocols:HasherTests:test_SixDCoordinateBinner_wrap_theta2 protocols:HasherTests:test_SixDCoordinateBinner_wrap_theta_and_phi protocols:HasherTests:test_boost_unordered_map protocols:HelicalBundlePDBInfoTests:test_pdbinfo_on_append protocols:HelixPairingFilterTests:test_pose_without_helices protocols:HelixPairingFilterTests:test_two_helix protocols:HighResEnsembleTests:test_spearman protocols:HighResEnsembleTests:test_vector_to_rank protocols:HotspotHashingTests:test_lsmsearchpattern protocols:HotspotHashingTests:test_placeresidueattransform protocols:HotspotHashingTests:test_placeresidueattransform_blankpose protocols:HotspotHashingTests:test_sicsearchpattern protocols:HotspotHashingTests:test_stubcentroid_transform protocols:HotspotHashingTests:test_stuborient_transform protocols:HotspotHashingTests:test_surfacesearchpattern_generation protocols:HybridizeProtocolTests:test_disulf_file_getter_setter protocols:HydrogenBondConstraintGeneratorTests:test_atoms protocols:HydrogenBondConstraintGeneratorTests:test_complicated protocols:HydrogenBondConstraintGeneratorTests:test_constraints_allresidues protocols:HydrogenBondConstraintGeneratorTests:test_constraints_hydrophobics protocols:IfThenFilterTests:test_elseonly protocols:IfThenFilterTests:test_floor protocols:IfThenFilterTests:test_invert protocols:IfThenFilterTests:test_multi protocols:IfThenFilterTests:test_oneif protocols:IfThenFilterTests:test_parse_invertweights protocols:IfThenFilterTests:test_parsing protocols:IfThenFilterTests:test_weights protocols:InteractionGraphSummaryMetricTests:test_summary_from_trpcage_repack protocols:InterchainEnvEnergy:test_InterchainEnvEnergyTest protocols:InterchainEnvEnergy:test_OneChainEnvEnergyTest protocols:InterchainPairEnergy:test_InterchainPairEnergyTest protocols:InterchainPairEnergy:test_OneChainPairEnergyTest protocols:InterfaceBuilderLoaderTests:test_scoring_grid_loader_defines_valid_xsd protocols:InterfaceDdGMoverTests:test_8mer_unbind_by_single_chain_id protocols:InterfaceDdGMoverTests:test_dimer_unbind_chain1 protocols:InterfaceDdGMoverTests:test_dimer_unbind_chain2 protocols:InterfaceDdGMoverTests:test_dimer_unbind_chain3 protocols:InterfaceDdGMoverTests:test_dimer_unbind_chainA protocols:InterfaceDdGMoverTests:test_dimer_unbind_chainB protocols:InterfaceDdGMoverTests:test_dimer_unbind_chainC protocols:InterfaceDdGMoverTests:test_dimer_unbind_jump1 protocols:InterfaceDdGMoverTests:test_dimer_unbind_jump2 protocols:InterfaceDdGMoverTests:test_mut_pose_setter_and_getter protocols:InterfaceDdGMoverTests:test_mutation_list protocols:InterfaceDdGMoverTests:test_parse_my_tag protocols:InterfaceDdGMoverTests:test_uninitialized protocols:InterfaceDdGMoverTests:test_wt_pose_setter_and_getter protocols:InterfaceFeaturesTests:test_reporter protocols:InterfaceHbondsFilterTests:test_InterfaceHbondsFilter protocols:InterfaceHydrophobicResidueContactsFilterTests:test_InterfaceHydrophobicResidueContactsFilter_from_constructor_not_defaults protocols:InterfaceHydrophobicResidueContactsFilterTests:test_InterfaceHydrophobicResidueContactsFilter_from_xml_defaults protocols:InterfaceHydrophobicResidueContactsFilterTests:test_InterfaceHydrophobicResidueContactsFilter_from_xml_not_defaults protocols:InterfaceInfoTests:test_InterfaceInfoTest protocols:InterfaceInfoTests:test_OneChainInterfaceInfoTest protocols:InterfaceTest:test_InterfaceTest protocols:InterfaceTest:test_OneChainInterfaceTest protocols:InvrotTreeTest:test_invrot_tree protocols:JD3NodeManagersTests:test_node_manager protocols:JD3NodeManagersTests:test_segregated_node_manager protocols:JD3NodeManagersTests:test_simple1 protocols:JD3NodeManagersTests:test_single_node_manager_simple protocols:JD3NodeManagersTests:test_stop_early protocols:JD3NodeManagersTests:test_storage_matric_breadth_first protocols:JD3NodeManagersTests:test_storage_matric_breadth_first2 protocols:JD3NodeManagersTests:test_storage_matric_depth_first protocols:JD3NodeManagersTests:test_tokens protocols:JD3PDBPoseInputterTests:test_read_input_sources_from_listfile_attribute_in_tag protocols:JD3PDBPoseInputterTests:test_read_input_sources_from_listfile_attribute_in_tag_w_path protocols:JD3PDBPoseInputterTests:test_read_l_flag_four_pdbs protocols:JD3PDBPoseInputterTests:test_read_s_flag_one_pdb protocols:JD3PDBPoseInputterTests:test_read_s_flag_three_pdbs protocols:JacobiLoopClosureMoverTests:test_JacobiLoopClosureMover_copy_ctor protocols:JacobiLoopClosureMoverTests:test_JacobiLoopClosureMover_mover_factory protocols:JacobiLoopClosureMoverTests:test_default_constructor protocols:JacobiLoopClosureMoverTests:test_loop_reconstruction protocols:JacobiLoopClosureMoverTests:test_loop_refinement_basic protocols:JacobiLoopClosureMoverTests:test_loop_refinement_cut_middle protocols:JacobiLoopClosureMoverTests:test_loop_refinement_inverted protocols:JacobiLoopClosureMoverTests:test_loop_with_bad_foldtree protocols:JacobiLoopClosureMoverTests:test_loop_without_cut protocols:JobGenealogistTests:test_garbage_collection1 protocols:JobGenealogistTests:test_garbage_collection2 protocols:JobGenealogistTests:test_garbage_collection_with_multiple_results1 protocols:JobGenealogistTests:test_garbage_collection_with_multiple_results2 protocols:JobGenealogistTests:test_job_genealogist2_no_results_for_node1 protocols:JobGenealogistTests:test_job_genealogist2_one_result_for_node1 protocols:JobGenealogistTests:test_job_genealogist2_simple_test1 protocols:JobGenealogistTests:test_multiple_parents protocols:JobGenealogistTests:test_newick_tree protocols:JobOutputterTests:test_HOSTNAME_in_jobname protocols:JobOutputterTests:test_Observer_add_remove protocols:Json_based_cdr_detection_tests:test_cdr_regions_detection protocols:JumpingTest:test_SheetBuilder protocols:JumpingTest:test_jump_geometry protocols:JumpingTest:test_rt_library protocols:JumpingTest:test_save_and_restore_silentio_with_jumps protocols:JumpingTest:test_strand_fraction protocols:LabelPoseFromResidueSelectorMoverTests:test_label protocols:LabelPoseFromResidueSelectorMoverTests:test_name protocols:LabelPoseFromResidueSelectorMoverTests:test_unlabel protocols:LigInterfaceConstraintsTest:test_interface_constraints protocols:LigandAreaLoaderTests:test_ligand_area_loader_defines_valid_xsd protocols:LigandConformerTests:test_ligand_conformer_measure_global_coords protocols:LigandConformerTests:test_ligand_conformer_recover_input_coords protocols:LigandMetalContactSelectorTests:test_dist_cutoff_multiplier protocols:LigandMetalContactSelectorTests:test_parse_tag_embedded_selector protocols:LigandMetalContactSelectorTests:test_parse_tag_invalid protocols:LigandMetalContactSelectorTests:test_parse_tag_named_selector protocols:LigandMetalContactSelectorTests:test_parse_tag_resnum_list protocols:LigandScoresUtilTests:test_ligand_travel protocols:LigandScoresUtilTests:test_rmsds protocols:LimitAromaChi2OperationTests:test_limit_aroma_chi2 protocols:LocalBackboneMoverTests:test_free_peptide protocols:LocalBackboneMoverTests:test_free_peptide_move protocols:LocalBackboneMoverTests:test_free_peptide_movers protocols:LocalBackboneMoverTests:test_gap_closer protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withouttermini protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withselection protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withtermini protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withouttermini protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withselection protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withtermini protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withouttermini protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withselection protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withtermini protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withouttermini protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withselection protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withtermini 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:LoopLengthChangeTests:test_insert_one_then_three protocols:LoopModelerTests:test_apply protocols:LoopModelerTests:test_build_options protocols:LoopModelerTests:test_centroid_options protocols:LoopModelerTests:test_custom_centroid_movers protocols:LoopModelerTests:test_custom_fullatom_movers protocols:LoopModelerTests:test_custom_movers protocols:LoopModelerTests:test_default_config protocols:LoopModelerTests:test_empty_config protocols:LoopModelerTests:test_fast_option protocols:LoopModelerTests:test_fullatom_options protocols:LoopModelerTests:test_illegal_movers protocols:LoopModelerTests:test_loophash_kic protocols:LoopModelerTests:test_modeler_options protocols:LoopModelerTests:test_temp_cycles_regex protocols:LoopTest:test_increasing protocols:LoopTest:test_length protocols:LoopTest:test_midpoint protocols:LoophashTest:test_database protocols:LoopsFileIOTest:test_LoopsFileIO_read_JSON_loops_file protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_cutpoint protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_extended protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_skiprate protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_extended protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_extended_old_format protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_w_cutpoint protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_w_skip_rate protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_one_loop protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_one_loop_w_comments protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_two_loops protocols:LoopsFileLoaderTest:test_create_LoopsFileData_from_LoopsFileLoder protocols:LoopsFoldTreeTest:test_CTerminalLoopFoldTree protocols:LoopsFoldTreeTest:test_CTerminalLoopFoldTreeWithStupidCutpoint protocols:LoopsFoldTreeTest:test_MultiLoopFoldTree protocols:LoopsFoldTreeTest:test_Multichain_CtermLoop protocols:LoopsFoldTreeTest:test_Multichain_NandCtermLoop protocols:LoopsFoldTreeTest:test_Multichain_NtermLoop protocols:LoopsFoldTreeTest:test_NTerminalLoopFoldTree protocols:LoopsFoldTreeTest:test_NTerminalLoopFoldTreeWithStupidCutpoint protocols:LoopsFoldTreeTest:test_SingleLoopFoldTree protocols:LoopsTest:test_center_of_mass protocols:LoopsTest:test_invert_between protocols:LoopsTest:test_invert_empty protocols:LoopsTest:test_invert_preceding protocols:LoopsTest:test_invert_trailing protocols:LoopsTest:test_loop_size protocols:LoopsTest:test_loop_size_empty protocols:LoopsUtilTest:testSafeExtendLoopsAndIdealize protocols:LoopsUtilTest:test_loop_picking_aligned protocols:LoopsUtilTest:test_loop_picking_chainbreak protocols:MPDockingSetupMoverTest:test_parse_my_tag_input protocols:MPFastRelaxFoldTreeTest:test_double_chain_com_anchored_foldtree protocols:MPFastRelaxFoldTreeTest:test_single_chain_com_anchored_foldtree protocols:MPIWorkPoolJobDistributorTests:test_MPIWorkPoolJobDistributor_master_node_vanilla_end_to_end_all_successes protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_archive_output_result_from_other_archive protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_archive_two_rounds_one_archive_no_archiving_on_node_0 protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_jd_checkpoint_archive_node protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_jd_checkpoint_master_node protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_manager_deallocation_messages_sent_to_remote_nodes protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_manager_two_rounds_no_archive protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_manager_two_rounds_no_archive_last_job_fails protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_manager_two_rounds_one_archive_no_archiving_on_node_0 protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_manager_two_rounds_one_archive_one_outputter_no_archiving_on_node_0 protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_worker_deallocation_messages_sent_to_remote_nodes protocols:MPIWorkPoolJobDistributorTests:test_jd3_workpool_worker_two_rounds_one_archive_no_archiving_on_node_0 protocols:MPIWorkPoolJobDistributorTests:test_master_node_response_to_failure_to_retrieve_job_result_from_archive protocols:MPIWorkPoolJobDistributorTests:test_master_node_response_to_failure_to_retrieve_job_result_from_archive_job_previously_output protocols:MPIWorkPoolJobDistributorTests:test_master_node_response_to_failure_to_retrieve_job_result_from_archive_job_result_discarded protocols:MPIWorkPoolJobDistributorTests:test_send_bad_message_to_master_node_should_never_happen protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_archive_asked_for_result_it_doesnt_have protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_job_digraph_updater_and_job_node_w_zero_jobs protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_manager_asked_for_result_it_doesnt_have protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_master_node_fails_to_deserialize_undeserializable_job_summary protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_master_tries_to_serialize_larval_job_w_unserializable_data protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_worker_tries_to_deserialize_job_result_w_undeserializable_data protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_worker_tries_to_deserialize_larval_job_w_undeserializable_data protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_worker_tries_to_serialize_job_result_w_unserializable_data protocols:MPIWorkPoolJobDistributorTests:test_work_pool_jd_worker_tries_to_serialize_job_summary_w_unserializable_data protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_master_node_job_failed_bad_input protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_master_node_job_failed_do_not_retry protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_master_node_job_failed_w_exception protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_master_node_job_failed_w_retry_limit_exceeded protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_and_outputter_node_vanilla_end_to_end_all_successes protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_node_job_failed_bad_input protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_node_job_failed_do_not_retry protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_node_job_failed_w_bad_inputs_exception protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_node_job_failed_w_exception protocols:MPIWorkPoolJobDistributorTests:test_workpool_jd3_worker_node_job_failed_w_retry_limit_exceeded protocols:MPLipidAccessibilityTest:test_mp_lipid_accessibility protocols:MPLipidAccessibilityTest:test_parse_my_tag_input protocols:MPRangeRelaxMover:test_mprangerelaxmover_parse_my_tag_input protocols:MRSClusteringTests:test_factory protocols:MRSClusteringTests:test_jump_serialization protocols:MRSClusteringTests:test_sequence_serialization protocols:MRSJobQueenTests:test_MRSJobQueen_with_good_input protocols:MRSJobQueenTests:test_incorrect_attribute_value protocols:MRSJobQueenTests:test_not_enough_job_results_for_next_node protocols:MRSJobQueenTests:test_tag_for_nonmover_nonfilter protocols:MRSJobQueenTests:test_typo_in_score_function protocols:MSDMoverTest:test_correct_constraints protocols:MSDMoverTest:test_keeps_constraints protocols:MSDMoverTest:test_resfile_parsing protocols:MakeCanonicalHelixTest:test_default_dihedral_angles protocols:MatchConsolidatorTests:test_BestMatchesCollection_full protocols:MatchConsolidatorTests:test_BestMatchesCollection_not_full protocols:MatchConstraintFileInfoTest:test_interface_constraints protocols:MembraneEnergyLandscapeSamplerTest:test_axis_center_of_alpha_helix protocols:MembraneEnergyLandscapeSamplerTest:test_axis_center_of_protein protocols:MembranePositionFromTopologyMoverTest:test_initial_membrane_position_move 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:MetalContactsConstraintGeneratorTests:test_default_values protocols:MetalContactsConstraintGeneratorTests:test_invalid_tags protocols:MetalContactsConstraintGeneratorTests:test_set_contacts protocols:MetalContactsConstraintGeneratorTests:test_set_ligand protocols:MetalContactsConstraintGeneratorTests:test_set_options_in_tag protocols:MinimumInterAlphaDistanceMetricTests:test_MIADM protocols:MonteCarloTests:test_interface_mc protocols:MonteCarloTests:test_vanilla_mc protocols:MotifGraftMoverTests:test_self_graft_recovery_oneFragment_using_end2endMatching protocols:MotifGraftMoverTests:test_self_graft_recovery_oneFragment_using_fixBBmatching protocols:MotifGraftMoverTests:test_self_graft_recovery_twoFragment_using_end2endMatching protocols:MotifGraftMoverTests:test_self_graft_recovery_twoFragment_using_fixBBmatching protocols:MoveMapBuilderLoaderTests:test_movemap_builder_loader_defines_valid_xsd protocols:MoverFactoryTests:test_MoverFactory_all_Mover_all_attributes_have_descriptions protocols:MoverFactoryTests:test_MoverFactory_all_Mover_complexTypes_have_descriptions protocols:MoverFactoryTests:test_all_movers_define_valid_xsds protocols:MoverJobTests:test_basic_mover_job protocols:MoverJobTests:test_seq_mover_job protocols:MoversTest:test_AllMovers protocols:MultiThreadedJobDistributorTests:test_dummy_in_tss_one_thread protocols:MultiThreadedJobDistributorTests:test_tss_in_threads 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:MultistateFitnessFunctionTest:test_top_entity_set_handle_ties protocols:MultistateFitnessFunctionTest:test_top_entity_set_keep_four protocols:MutateResidueTests:test_mutate_disulfide protocols:MutateResidueTests:test_mutate_residue protocols:NMethylationTests:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov15:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov16:test_linear_nmethyl_peptide protocols:NativeSelectorTests:test_native_is_too_large protocols:NativeSelectorTests:test_native_is_too_small protocols:NativeSelectorTests:test_serialize_simple1 protocols:NativeSelectorTests:test_serialize_simple2 protocols:NativeSelectorTests:test_simple1 protocols:NativeSelectorTests:test_simple2 protocols:Neighbor_CalculatorsTests:test_InterGroupNeighborsCalculator protocols:Neighbor_CalculatorsTests:test_NeighborHoodDistanceCalculators protocols:Neighbor_CalculatorsTests:test_NeighborsByDistanceCalculators protocols:NewSEWINGHasherTests:test_alignment_generator protocols:NewSEWINGHasherTests:test_can_hash protocols:NewSEWINGHasherTests:test_find_aligned_atoms protocols:NewSEWINGHasherTests:test_generate_key protocols:NewSEWINGHasherTests:test_hash_segments protocols:NewSEWINGHasherTests:test_transform_segments protocols:NonlocalUtilTest:test_compute_jump_rmsd_identity protocols:NonlocalUtilTest:test_compute_jump_rmsd_with_no_jumps protocols:NonlocalUtilTest:test_limit_chunk_size protocols:NonlocalUtilTest:test_random_position protocols:NonlocalUtilTest:test_remove_virtual_residues 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:OccupiedSpaceHashTests:test_occupied_space_hash_ctor protocols:OccupiedSpaceHashTests:test_occupied_space_hash_note_hit_geometry protocols:OccupiedSpaceHashTests:test_occupied_space_hash_note_hit_geometry2 protocols:OmnibusDisulfideAnalysisLabelerMoverTests:testOmnibusDisulfideAnalysisLabelerMover protocols:OopPuckMoverTest:test_OopPuckMoverMinus protocols:OopPuckMoverTest:test_OopPuckMoverPlus protocols:OopPuckMoverTest:test_OopPuckMoverSmall protocols:OptimizeMembranePositionMoverTest:test_default_constructor protocols:OptimizeMembranePositionMoverTest:test_parse_my_tag_input protocols:OptimizeProteinEmbeddingMoverTest: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:PCSEnergyTests:test_PCSEnergy_instantiation protocols:PCSEnergyTests:test_PCSEnergy_score_calculation protocols:PCSEnergyTests:test_PCSEnergy_score_calculation_scaled_data protocols:PCSEnergyTests:test_PCSEnergy_show_info protocols:PCSEnergyTests:test_PCSEnergy_show_info_scaled_data protocols:PCSMultiGridTest:test_PCSMultiGrid_creation protocols:PCSMultiGridTest:test_PCSMultiGrid_scoring protocols:PCSMultiGridTest:test_PCSMultiGrid_update protocols:PCSSingleGridTest:test_PCSSingleGrid_creation protocols:PCSSingleGridTest:test_PCSSingleGrid_scoring protocols:PCSSingleGridTest:test_PCSSingleGrid_update protocols:PCSTensorOptimizerTests:test_PCSTensorOptimizer_error_function protocols:PCSTensorOptimizerTests:test_PCSTensorOptimizer_instantiation protocols:PCSTensorOptimizerTests:test_minimization_with_PCSTensorOptimizer_ protocols:PDBPoseOutputterTests:test_mmTF_output protocols:PDBPoseOutputterTests:test_output_path_handling_1 protocols:PDBPoseOutputterTests:test_output_path_handling_2 protocols:PDBPoseOutputterTests:test_output_path_handling_3 protocols:PDBPoseOutputterTests:test_output_path_handling_4 protocols:PDBPoseOutputterTests:test_output_path_handling_prefix_suffix protocols:PDBPoseOutputterTests:test_output_path_handling_priority_1 protocols:PDBPoseOutputterTests:test_output_path_tag_dir protocols:PDBPoseOutputterTests:test_output_path_tag_prefix_suffix protocols:PREEnergyTests:test_PREEnergy_instantiation protocols:PREEnergyTests:test_score_calculation_with_spinlabel_bump_energy_filter protocols:PREEnergyTests:test_score_calculation_with_spinlabel_distance_filter protocols:PREEnergyTests:test_show_info protocols:PREMoverTests:test_PREMover_apply_function protocols:PREMoverTests:test_PREMover_instantiation_through_ctor protocols:PREMoverTests:test_PREMover_instantiation_through_factory protocols:PREMoverTests:test_PREMover_parse_my_tag_function protocols:PREMoverTests:test_PREMover_setters_and_getters protocols:PackDaemonTest:test_DenseIGRepacker_create_dense_ig protocols:PackDaemonTest:test_DoubleDenseIGRepacker_create_double_dense_ig protocols:PackDaemonTest:test_daemon_set_setup protocols:PackDaemonTest:test_pack_daemon_ctor protocols:PackDaemonTest:test_pack_daemon_repack protocols:PairedSheetResidueSelectorTests:test_paired_res protocols:ParamsDataStorageTests:test_params_data_copying protocols:ParamsDataStorageTests:test_params_data_storage protocols:ParamsDataStorageTests:test_params_residue_storage protocols:ParsedProtocolTests:test_filter_reporting protocols:ParsedProtocolTests:test_filter_reporting_commandline protocols:PatchChemistryTests:test_apply_patch protocols:PatchChemistryTests:test_xml protocols:PatchChemistryTests:test_xsd 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:PeptideInternalHbondsMetricTests:test_generate_allowed_partners protocols:PeptideInternalHbondsMetricTests:test_peptide_internal_hbonds_filter protocols:PeptideInternalHbondsMetricTests:test_peptide_internal_hbonds_metric protocols:PeptideStubMoverTests:test_append protocols:PeptideStubMoverTests:test_append2 protocols:PeptideStubMoverTests:test_append_NME_and_prepend_ACE protocols:PeptideStubMoverTests:test_append_chainA protocols:PeptideStubMoverTests:test_append_repeat protocols:PeptideStubMoverTests:test_complicated_labeling protocols:PeptideStubMoverTests:test_multi_append protocols:PeptideStubMoverTests:test_multi_prepend protocols:PeptideStubMoverTests:test_prepend protocols:PeptideStubMoverTests:test_prepend2 protocols:PeptideStubMoverTests:test_prepend_chainB protocols:PeptideStubMoverTests:test_prepend_fail protocols:PeptideStubMoverTests:test_prepend_repeat protocols:PerturbBundleTests:test_perturb_r0_uniform protocols:PlainSilentFileJobDistributorTest:test_next_job 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:PoseFromSequenceMoverTests:test_apply protocols:PoseFromSequenceMoverTests:test_ctor protocols:PoseFromSequenceMoverTests:test_parse_my_tag protocols:PoseManipulationTests:test_linear_rigid_body_moves protocols:PoseManipulationTests:test_repack_functions protocols:PoseManipulationTests:test_rotation_rigid_body_moves protocols:PreProlineFilterTests:test_compute protocols:PreProlineFilterTests:test_spline protocols:PredockRotCenterTest:test_predock_rotcenter protocols:ProtLigEnsembleTests:test_process_line protocols:ProtLigEnsembleTests:test_sort_by_binding protocols:ProtectedConf:test_replace_residue protocols:ProteinInterfaceDesignOperationTests:test_ProteinInterfaceDesignOperation protocols:ProteinInterfaceDesignOperationTests:test_ProteinInterfaceDesignOperation_all protocols:ProteinInterfaceDesignTests:test_AtomicContactCount_filter protocols:ProteinMPNNTest:test_ProteinMPNNOptions_init protocols:ProteinMPNNTest:test_ProteinMPNN_sample_deterministic_always_same protocols:ProteinMPNNTest:test_ProteinMPNN_sample_deterministic_matches_python protocols:ProteinMPNNTest:test_ProteinMPNN_sample_seq_recovery_at_least_40_pct protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_bias_AAs_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_chain_mask_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_coord_mask_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_pos_mask_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_sequence_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_invalid_tied_positions_option_throws_exception protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_omit_AA_pos_restricts_types protocols:ProteinMPNNTest:test_ProteinMPNN_sample_sequence_pos_mask_fixes_residues protocols:ProteinMPNNTest:test_ProteinMPNN_sample_shape_unchanged protocols:ProteinMPNNTest:test_ProteinMPNN_sample_with_opts_seq_recovery_at_least_40_pct protocols:ProteinMPNNTest:test_ProteinMPNN_sample_with_opts_shape_unchanged protocols:ProteinProteinInterfaceUpweighterTests:test_packing_4SER protocols:ProteinSCSamplerTests:test_sc_sampler_ctor protocols:ProteinSCSamplerTests:test_sc_sampler_desymmeterize protocols:ProteinSilentReportTests:test_main protocols:ProteinUpstreamBuilderTests:test_FullChiSampleSet_exflags_dryrun_vs_regular protocols:ProteinUpstreamBuilderTests:test_FullChiSampleSet_semirotameric_dryrun_vs_regular protocols:ProteinUpstreamBuilderTests:test_FullChiSampleSet_step_wi_sdrange_dryrun_vs_regular protocols:ProteinUpstreamBuilderTests:test_ProteinUpstreamBuilder_build protocols:ProteinUpstreamBuilderTests:test_ProteinUpstreamBuilder_build_w_pre_chitip_transform protocols:ProteinUpstreamBuilderTests:test_ProteinUpstreamBuilder_recover_hit protocols:ProteinUpstreamBuilderTests:test_ProteinUpstreamBuilder_recover_hits protocols:ProteinUpstreamBuilderTests:test_build_set_ctor protocols:ProteinUpstreamBuilderTests:test_full_sample_set_ctor protocols:ProteinUpstreamBuilderTests:test_sc_upstream_geom_coords protocols:ProteinUpstreamBuilderTests:test_sc_upstream_geom_map_atoms_to_controlling_chi 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:PyMOLMoverTest:test_cmdline_01 protocols:PyMOLMoverTest:test_link protocols:PyMOLMoverTest:test_new_pose_has_no_observer protocols:PyMOLMoverTest:test_pose_clone_has_no_observer protocols:PyMOLMoverTest:test_pose_has_observer protocols:PyMOLMoverTest:test_replaced_pose_keeps_observer protocols:QueryDatabaseTests:test_pair_query protocols:QueryDatabaseTests:test_single_query protocols:RDCEnergyTests:test_PCSEnergy_show_info protocols:RDCEnergyTests:test_RDCEnergy_instantiation protocols:RDCEnergyTests:test_RDCEnergy_score_calculation protocols:RNA_DeNovoOptimizerTest:test_sarcin_ricin_loop_buildup protocols:RNA_DeNovoProtocolTest:test_save_times_option protocols:RRComparerTests:test_RRComparerAutomorphicRMSD_main protocols:RRComparerTests:test_RRComparerRotBins_main protocols:RRReporterSQLiteTests:test_RRReporterSQLite_features protocols:RRReporterSQLiteTests:test_RRReporterSQLite_full protocols:RRReporterTests:test_RRReporterSimple_main protocols:RamaMutationSelectorTests:test_select_by_aib protocols:RamaMutationSelectorTests:test_select_by_dproline protocols:RamaMutationSelectorTests:test_select_by_native protocols:RamaMutationSelectorTests:test_select_by_proline protocols:RamaMutationSelectorTests:test_select_by_valine protocols:RandomizeBBByRamaPreProTests:test_rama_distribution_d_ala protocols:RandomizeBBByRamaPreProTests:test_rama_distribution_l_ala protocols:ReadPoseExtraScoreFilter:test_use_filter protocols:ReadResidueCoordinatesFromPDBTests:test_no_coordinates protocols:ReadResidueCoordinatesFromPDBTests:test_read_from_file protocols:ReadResidueCoordinatesFromPDBTests:test_read_from_file_nonexistent_residue protocols:ReadResidueCoordinatesFromPDBTests:test_read_from_file_one_residue_do_not_exist protocols:ReadResidueCoordinatesFromPDBTests:test_read_from_nonexistent_file protocols:ReadResidueCoordinatesFromPDBTests:test_read_from_stream protocols:ReadResidueCoordinatesFromPDBTests:test_try_save_residue_information_twice protocols:RegExManager_tests:test_cdr_regex_parsing protocols:Regex_based_cdr_detection_tests:test_cdr_regions_detection protocols:RegionTest:test_getters protocols:RegionTest:test_length protocols:RelativeConnectRightTests:test_connection protocols:RemodelConstraintGeneratorTest:test_sheet_constraints protocols:RemoveMetalConnectionsMoverTests:test_mover protocols:RemoveMetalConnectionsMoverTests:test_mover_his63_cu_only protocols:RemoveMetalConnectionsMoverTests:test_mover_not_his63 protocols:RepackingRefinerTests:test_repacking_refiner_options protocols:ReplicateFilterTests:test_basic protocols:ReplicateFilterTests:test_parsing protocols:ReplicateFilterTests:test_thresholding protocols:ResfileAutoRemapTest:test_resfile_auto_remap protocols:ResidueCountFilterTests:test_residue_count_filter_manual protocols:ResidueCountFilterTests:test_residue_count_report protocols:ResidueCountFilterTests:test_residue_count_with_types_and_properties protocols:ResidueProbDesignOperationTests:test_task_op protocols:ResidueTorsionRestraintsTest:test_randomize_with_constraints protocols:ResidueTypeConstraintGeneratorTests:test_change_favor_native_bonus protocols:ResidueTypeConstraintGeneratorTests:test_constraints_full_pose_native protocols:ResidueTypeConstraintGeneratorTests:test_constraints_full_ref_pose protocols:ResidueTypeConstraintGeneratorTests:test_constraints_ref_pose_with_selector protocols:ResidueTypeConstraintGeneratorTests:test_constraints_residue_selector protocols:ResidueTypeConstraintGeneratorTests:test_constraints_set_type_full_pose protocols:ResidueTypeConstraintGeneratorTests:test_constraints_set_type_with_selector protocols:ResidueTypeConstraintGeneratorTests:test_two_constraints_same_residue protocols:ResidueTypeConstraintMoverTests:test_it_adds_constraints protocols:RestrictNonSurfaceToRepackingOperationTests:test_RestrictNonSurfaceToRepackingOperation protocols:RestrictOperationsTests:test_RestrictByCalculatorsOperation protocols:RestrictOperationsTests:test_RestrictInterGroupVectorOperation protocols:RestrictOperationsTests:test_RestrictToInterfaceOperation protocols:RestrictOperationsTests:test_RestrictToInterfaceVectorOperation protocols:RestrictOperationsTests:test_RestrictToMoveMapChiOperation protocols:RestrictOperationsTests:test_RestrictToNeighborhoodOperation protocols:RestrictToCDRH3LoopTest:test_RestrictToCDRH3Loop protocols:RestrictToLoopsTests:test_copy_constructor protocols:RestrictToLoopsTests:test_restrict_design_to_loops protocols:RestrictToLoopsTests:test_set_design_loops protocols:RestrictToLoopsTests:test_set_loops protocols:RestrictToLoopsTests:test_set_loops_from_file 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:RigidChunkTest:test_apply_to_template protocols:RigidChunkTest:test_chunk protocols:RigidChunkTest:test_two_chunk protocols:RigidChunkTest:test_two_part_chunk 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:RingPlaneFlipMoverTests:test_RingPlaneFlipMover protocols:RmsdFromResidueSelectorFilterTests:test_all_true protocols:RmsdFromResidueSelectorFilterTests:test_name protocols:RmsdFromResidueSelectorFilterTests:test_selection_aligned protocols:RmsdFromResidueSelectorFilterTests:test_selection_non_aligned protocols:RosettaScriptsJobQueenTests:test_read_resources_from_xml_file protocols:RosettaScriptsParserTests:test_all_attributes_in_xsd_have_descriptions protocols:RosettaScriptsParserTests:test_allowed_multiple_dependencies protocols:RosettaScriptsParserTests:test_multiple_includes protocols:RosettaScriptsParserTests:test_output_scoring 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:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_random protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_range protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_single protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_underspecified_jump protocols:SandwichFeaturesTests:test_main protocols:ScaffoldBuildPointTests:test_scaffold_build_point_ctor protocols:ScoreFileOutputterTests:test_output_path_handling_1 protocols:ScoreFileOutputterTests:test_output_path_handling_2 protocols:ScoreFileOutputterTests:test_output_path_handling_3 protocols:ScoreFileOutputterTests:test_output_path_handling_4a protocols:ScoreFileOutputterTests:test_output_path_handling_4b protocols:ScoreFileOutputterTests:test_output_path_handling_5a protocols:ScoreFileOutputterTests:test_output_path_handling_5b protocols:ScoreFileOutputterTests:test_output_path_handling_6 protocols:ScoreFileOutputterTests:test_output_path_handling_7 protocols:ScoreFileOutputterTests:test_output_path_handling_8 protocols:ScoreFileOutputterTests:test_output_path_handling_priority_1 protocols:ScoreFileOutputterTests:test_output_path_handling_priority_2 protocols:ScoreFileOutputterTests:test_output_path_handling_priority_3 protocols:ScoreFileOutputterTests:test_output_path_handling_priority_4 protocols:ScoreNormalizationTest:test_all_atom_normalization protocols:ScoreNormalizationTest:test_chi_angle_normalization protocols:ScoreNormalizationTest:test_get_score_normalization_function protocols:ScoreNormalizationTest:test_heavy_atom_normalization protocols:ScoreNormalizationTest:test_mol_weight_normalization protocols:ScoreTest:test_Score12 protocols:ScoringGridLoaderTests:test_scoring_grid_loader_defines_valid_xsd protocols:Scs_functor_filtering_tests:test_filter_by_OCD protocols:Scs_functor_filtering_tests:test_filter_by_alignment_length protocols:Scs_functor_filtering_tests:test_filter_by_outlier protocols:Scs_functor_filtering_tests:test_filter_by_pdbid protocols:Scs_functor_filtering_tests:test_filter_by_proline protocols:Scs_functor_filtering_tests:test_filter_by_sequence_identity protocols:Scs_functor_filtering_tests:test_filter_by_sequence_length protocols:Scs_functor_filtering_tests:test_filter_by_template_bfactor protocols:Scs_functor_filtering_tests:test_filter_by_template_resolution protocols:SecondaryStructureFilterTests:test_convert_impossible_pairings protocols:SegmentInsertTests:test_C_side_connection_simple_internal protocols:SegmentInsertTests:test_C_side_connection_simple_internal_pure protocols:SegmentInsertTests:test_C_side_connection_simple_n_term protocols:SegmentInsertTests:test_N_side_connection_no_left_flanking_region protocols:SegmentInsertTests:test_N_side_connection_no_right_flanking_region protocols:SegmentInsertTests:test_N_side_connection_simple_c_term protocols:SegmentInsertTests:test_N_side_connection_simple_internal protocols:SegmentInsertTests:test_N_side_connection_simple_internal_pure protocols:SegmentPairingTests:test_bulge_strandpairing protocols:SegmentPairingTests:test_helix_pairing_str protocols:SegmentPairingTests:test_hss_triplet_str protocols:SegmentPairingTests:test_strand_pairing protocols:SegmentRebuildTests:test_continuous_segment_internal_contract protocols:SegmentRebuildTests:test_continuous_segment_internal_expand protocols:SegmentRebuildTests:test_continuous_segment_internal_identity protocols:SegmentRebuildTests:test_cut2_segment_contract protocols:SegmentRebuildTests:test_cut2_segment_expand protocols:SegmentRebuildTests:test_cut2_segment_identity protocols:SegmentRebuildTests:test_cut_segment_contract protocols:SegmentRebuildTests:test_cut_segment_expand protocols:SegmentRebuildTests:test_cut_segment_identity protocols:SegmentRebuildTests:test_multi_chain_cterm_chain1 protocols:SegmentRebuildTests:test_multi_chain_cterm_chain2 protocols:SegmentRebuildTests:test_multi_chain_nterm_chain1 protocols:SegmentRebuildTests:test_multi_chain_nterm_chain2 protocols:SegmentSequenceProfileTests:test_simple_profile protocols:SegmentSwapTests:test_continuous_complex_swap1 protocols:SegmentSwapTests:test_continuous_complex_swap2 protocols:SegmentSwapTests:test_continuous_swap protocols:SegmentTests:test_cutpoint_residues protocols:SegmentTests:test_motif_str_parse protocols:SegmentTests:test_numbering protocols:SegmentTests:test_segment_lookups protocols:SegmentedAtomPairConstraintGeneratorTests:test_constraints_defaults_allresidues protocols:SegmentedAtomPairConstraintGeneratorTests:test_constraints_defaults_inner protocols:SegmentedAtomPairConstraintGeneratorTests:test_constraints_defaults_outer protocols:SequenceRecoveryMetricTests:test_average protocols:SequenceRecoveryMetricTests:test_basic protocols:SequenceRecoveryMetricTests:test_delta protocols:SequenceRecoveryMetricTests:test_pssm protocols:SequenceRecoveryMetricTests:test_subsection protocols:SetMembranePositionTest:test_membrane_position_rotation protocols:SetMembranePositionTest:test_membrane_position_translation protocols:SetMembranePositionTest:test_uniform_rotation_translation protocols:SetSecStructEnergiesMoverTests:test_modify_score_function protocols:SetupDockingFoldTree:test_autodetct_vs_specifing_first_jump protocols:SetupDockingFoldTree:test_residue_selector_based_setup protocols:SetupMetalsMoverTests:test_contact_selection protocols:SetupMetalsMoverTests:test_default_options protocols:SetupMetalsMoverTests:test_parse_invalid_tag protocols:SetupMetalsMoverTests:test_parse_tag_all_metals protocols:SetupMetalsMoverTests:test_parse_tag_named_selector protocols:SetupMetalsMoverTests:test_parse_tag_resnum_list protocols:SewAnythingTests:test_empty protocols:SewingHasherTests:test_5_ss_model_generation_from_db protocols:SewingHasherTests:test_key_generation protocols:SewingHasherTests:test_scoring protocols:SewingHasherTests:test_serialization protocols:SewingHasherTests:test_transform_coords protocols:ShearMoverTest:test_ShearMover protocols:ShearMoverTest:test_ShearMover_w_sugar protocols:ShearMoverTest:test_one_shear_move protocols:SheetConstraintGeneratorTests:test_bulge_strandpairing protocols:SheetConstraintGeneratorTests:test_spair_strings protocols:SheetConstraintGeneratorTests:test_user_secstruct protocols:SheetTopologyFilterTest:test_bad_topology protocols:SheetTopologyFilterTest:test_residue_count_no_rgstr_shift protocols:ShowConstraintsFilterTests:test_it_accepts_a_pose_with_constraints protocols:ShowConstraintsFilterTests:test_it_accepts_a_pose_with_no_constraints protocols:SilentFilePoseInputterTests:test_read_in_file_silent_flag protocols:SilentFilePoseInputterTests:test_read_in_from_cmdline_without_pose_input_sources_call protocols:SilentFilePoseOutputterTests:test_output_path_handling_1a protocols:SilentFilePoseOutputterTests:test_output_path_handling_1b protocols:SilentFilePoseOutputterTests:test_output_path_handling_1c protocols:SilentFilePoseOutputterTests:test_output_path_handling_2 protocols:SilentFilePoseOutputterTests:test_output_path_handling_3 protocols:SilentFilePoseOutputterTests:test_output_path_handling_4 protocols:SilentFilePoseOutputterTests:test_output_path_handling_5 protocols:SilentFilePoseOutputterTests:test_output_path_handling_6 protocols:SilentFilePoseOutputterTests:test_output_path_handling_7 protocols:SilentFilePoseOutputterTests:test_output_path_handling_priority_1 protocols:SilentFilePoseOutputterTests:test_output_path_handling_with_tag 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_basename protocols:SimpleThreadingMoverTests:test_basic_class protocols:SimpleThreadingMoverTests:test_fullname protocols:SimpleThreadingMoverTests:test_oneletter protocols:SimpleThreadingMoverTests:test_threeletter protocols:SiteGridTests:test_score_function protocols:SixDoFGridDockMoverTests:test_lex_position protocols:SixDoFGridDockMoverTests:test_parse_range protocols:SixDoFGridDockMoverTests:test_pdb_geometries protocols:SixDoFGridDockMoverTests:test_xyz_orthogonality protocols:SmallMoverTest:test_SmallMover protocols:SmallMoverTest:test_SmallMover_w_sugar protocols:SmallMoverTest:test_one_small_move protocols:SmallMoverTests:test_perturb_oligourea protocols:SmartAssemblyTests:test_assemblies_are_continuous protocols:SmartAssemblyTests:test_auto_detect_contacts protocols:SmartAssemblyTests:test_basis_pair_calculations_recursive_unchimerize_c_term protocols:SmartAssemblyTests:test_basis_pair_calculations_recursive_unchimerize_n_term protocols:SmartAssemblyTests:test_can_make_chimera1 protocols:SmartAssemblyTests:test_can_make_chimera2 protocols:SmartAssemblyTests:test_can_make_chimera3 protocols:SmartAssemblyTests:test_do_not_delete_vital_segments_cterm protocols:SmartAssemblyTests:test_do_not_delete_vital_segments_nterm protocols:SmartAssemblyTests:test_do_not_hash_the_unhashable protocols:SmartAssemblyTests:test_double_chimerize_single_helix_two_triplets_cterm_first protocols:SmartAssemblyTests:test_double_chimerize_single_helix_two_triplets_nterm_first protocols:SmartAssemblyTests:test_double_unchimerize_single_helix_two_triplets_cterm protocols:SmartAssemblyTests:test_double_unchimerize_single_helix_two_triplets_nterm protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_basic protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_chimaera_cterm_first protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_chimaera_nterm_first protocols:SmartAssemblyTests:test_maintain_contact_cterm_chimerization protocols:SmartAssemblyTests:test_maintain_contact_double_chimerization_cterm_first protocols:SmartAssemblyTests:test_maintain_contact_double_chimerization_nterm_first protocols:SmartAssemblyTests:test_maintain_contact_nterm_chimerization protocols:SmartAssemblyTests:test_maintain_contact_recurse_revert_cterm protocols:SmartAssemblyTests:test_maintain_contact_recurse_revert_nterm protocols:SmartAssemblyTests:test_maintain_contact_unchimerize_cterm protocols:SmartAssemblyTests:test_maintain_contact_unchimerize_nterm protocols:SmartAssemblyTests:test_reverting_double_unchimerize_cterm protocols:SmartAssemblyTests:test_reverting_double_unchimerize_nterm protocols:SmartAssemblyTests:test_set_starting_segment protocols:SmartAssemblyTests:test_simple_assembly_length protocols:SmartAssemblyTests:test_simple_assembly_parent_connectivity protocols:SmartAssemblyTests:test_simple_assembly_size protocols:SmartAssemblyTests:test_simple_delete_cterm protocols:SmartAssemblyTests:test_simple_delete_nterm protocols:SmartAssemblyTests:test_simple_switch_cterm protocols:SmartAssemblyTests:test_simple_switch_nterm protocols:SnugDockProtocol_setup_ab_ag_foldtree_tests:test_place_VRT_at_residue_COM protocols:SnugDockProtocol_setup_ab_ag_foldtree_tests:test_setup_ab_ag_foldtree protocols:SpartaTest:test_ANN_INPUT protocols:SpartaTest:test_ANN_PARAMETERS protocols:SpartaTest:test_BLOSUM62 protocols:SpartaTest:test_PDB protocols:SpartaTest:test_PRED_SUM protocols:SpartaTest:test_scores protocols:SpartaTest:test_sparta_foldit protocols:SpinAroundPartnerMoverTest:test_constructor_from_jumpnum protocols:SpinAroundPartnerMoverTest:test_spinaroundpartner_parse_my_tag_input protocols:StandardJobQueenOverrideInputterTests:test_sjq_add_unregistered_inputter_read_cl protocols:StandardJobQueenOverrideInputterTests:test_sjq_add_unregistered_inputter_read_jobdef_file protocols:StandardJobQueenOverrideInputterTests:test_sjq_add_unregistered_inputter_read_jobdef_file2 protocols:StandardJobQueenOverrideInputterTests:test_sjq_add_unregistered_inputter_xsd_correct protocols:StandardJobQueenOverrideInputterTests:test_sjq_allow_only_non_factory_registered_inputter_read_cl protocols:StandardJobQueenOverrideInputterTests:test_sjq_allow_only_non_factory_registered_inputter_read_jobdef_file protocols:StandardJobQueenOverrideInputterTests:test_sjq_allow_only_non_factory_registered_inputter_read_jobdef_file_bad_inputter protocols:StandardJobQueenOverrideInputterTests:test_sjq_allow_only_non_factory_registered_inputter_xsd_correct protocols:StandardJobQueenOverrideOutputterTests:test_sjq_add_unregistered_outputter_read_cl_get_default_outputter protocols:StandardJobQueenOverrideOutputterTests:test_sjq_add_unregistered_outputter_read_cl_get_requested_dummy_outputter protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_cl protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_jobdef_file protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_jobdef_file_bad_outputter protocols:StandardJobQueenTests:test_job_definition_file_xsd protocols:StandardJobQueenTests:test_job_options_initialization protocols:StandardJobQueenTests:test_preliminary_job_node_job_index_ranges protocols:StandardJobQueenTests:test_read_jobs_from_xml_file protocols:StandardJobQueenTests:test_read_jobs_from_xml_file2 protocols:StandardJobQueenTests:test_sjq_remote_node_mature_larval_job protocols:StandardJobQueenTests:test_standard_job_queen_pose_deallocation_messages protocols:StandardJobQueenTests:test_standard_job_queen_pose_deallocation_messages_and_preserve_input_poses protocols:StandardJobQueenTests:test_standard_job_queen_pose_deallocation_messages_no_preserve_poses protocols:StandardPoseJobSummaryTests:test_basic_pose_job_summary protocols:StartFromTests:test_PDB_file protocols:StartFromTests:test_PDB_file_atom_name protocols:StartFromTests:test_hash_tag protocols:StartFromTests:test_json_file protocols:StartFromTests:test_multiple_positions protocols:StartFromTests:test_pdb_tag protocols:StartFromTests:test_specified_position protocols:StartFromTests:test_specified_position_nbr protocols:StartFromTests:test_spurious_items protocols:StepWiseMinimizerTest:test_num_pose_minimize protocols:StepWiseMonteCarloTest:test_force_submotif_without_intervening_bulge protocols:StepWiseMonteCarloTest:test_skip_preminimize protocols:StepWiseMoveSelectorTest:test_reverse_of_FROM_SCRATCH_move protocols:StepWiseMoveSelectorTest:test_submotif_split protocols:StepWisePoseAlignerTest:test_rna_dna_match protocols:StepWisePoseAlignerTest:test_superimpose_res_in_root_partition protocols:StochasticFilterTests:test_apply protocols:StochasticFilterTests:test_subfilter_apply_false protocols:StochasticFilterTests:test_subfilter_apply_true protocols:StoredResidueSubsetSelectorTests:test_StoreResidueSubsetMover_parse_my_tag protocols:StoredResidueSubsetSelectorTests:test_StoredResidueSubsetSelector_parse_my_tag protocols:StoredResidueSubsetSelectorTests:test_store_and_retrieve_subset protocols:StructureDataFactoryTests:test_silent_io protocols:StructureDataFactoryTests:test_structuredata_io protocols:StructureDataFactoryTests:test_symmetry protocols:StructureDataFactoryTests:test_xml_io protocols:StructureDataObserverTests:test_attachment protocols:StructureDataObserverTests:test_residue_deletion protocols:StructureDataTests:test_delete_segment protocols:StructureDataTests:test_enzdes_remarks protocols:StructureDataTests:test_move_segments protocols:StructureDataTests:test_non_peptidic_bonds protocols:StructureDataTests:test_slice protocols:StructureStoreTests:test_convert_stores protocols:StructureStoreTests:test_read_h5_store protocols:StructureStoreTests:test_read_stores protocols:StructureStoreTests:test_store_cache protocols:SurfaceVectorLoaderTest:test_create_SurfaceParameters_from_SurfaceVectorLoader protocols:SwitchChainOrderMoverTests:test_pdbinfo_labels protocols:SymmetricAddMembraneMoverTest:test_appropriate_foldtree protocols:SymmetricAddMembraneMoverTest:test_membrane_jump_tracking protocols:SymmetricAddMembraneMoverTest:test_preserved_symmetry protocols:SymmetricAddMembraneMoverTest:test_symm_add_postconditions protocols:SymmetricCycpepAlignTests:test_align_c4m_to_origin protocols:SymmetricCycpepAlignTests:test_align_c4m_to_zaxis protocols:SymmetricCycpepAlignTests:test_detect_asymm protocols:SymmetricCycpepAlignTests:test_detect_c3_symmetry_tbmb protocols:SymmetricCycpepAlignTests:test_detect_c4m_symmetry protocols:SymmetricCycpepAlignTests:test_trim_c3_tbmb_to_repeat_two protocols:SymmetricCycpepAlignTests:test_trim_c4m_to_repeat_two protocols:TCRmodelGraftingTests:test_tcr_grafting protocols:TCRmodelSeqParserTests:test_tcr_seq_parsing protocols:TaskAwareMinMoverTests:test_TaskAwareMinMover protocols:TaskSelectorTests:test_TaskSelector_parse_my_tag protocols:TautomerizeAnomerMoverTests:test_TautomerizeAnomerMover protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_closes protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_copy_ctor protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_exceptions protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_mover_factory protocols:Thioether_Helper_Tests:test_build_ala_thioether protocols:Thioether_Helper_Tests:test_build_b3a_thioether protocols:Thioether_Helper_Tests:test_build_gly_thioether protocols:ThreadingMover_Tests:test_basic_threading protocols:TiltMoverTest:test_constructor_from_jumpnum_and_angle protocols:TiltMoverTest:test_tiltmover_parse_my_tag_input protocols:TorsionBinIOTests:test_read_file protocols:TorsionSamplingKinematicPerturberTests:test_TorsionSamplingKinematicPerturber protocols:TotalSasaFilterTests:test_calc_per_res_hydrophobic_sasa protocols:TotalSasaFilterTests:test_calc_total_sasa_glycine protocols:TotalSasaFilterTests:test_calc_total_sasa_smallprotein 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:TransformTests:test_conformer_change protocols:TransformTests:test_randomize_ligand protocols:TransformTests:test_score_constraints protocols:TranslationRotationMoverTest:test_rotation protocols:TranslationRotationMoverTest:test_rotation_translation protocols:TranslationRotationMoverTest:test_translation protocols:TypesetMoversTests:test_TypesetMovers protocols:UniformRigidBody:test_uniform_rb protocols:VarSolDRotamerDotsTest:test_radii_setting protocols:VarSolDRotamerDotsTest:test_residue_pair_overlap protocols:VarSolDRotamerDotsTest:test_self_overlap protocols:VarSolDRotamerDotsTest:test_shells_evenly_spaced protocols:VicinitySamplingKinematicPerturberTests:test_VicinitySamplingKinematicPerturber protocols:VoxelSetIteratorTests:test_bounding_box_edge_x protocols:VoxelSetIteratorTests:test_bounding_box_edge_y protocols:VoxelSetIteratorTests:test_bounding_box_edge_z protocols:VoxelSetIteratorTests:test_center_iteration protocols:VoxelSetIteratorTests:test_center_iterations_pos protocols:VoxelSetIteratorTests:test_wrap_phi_at_360 protocols:VoxelSetIteratorTests:test_wrap_psi_at_360 protocols:VoxelSetIteratorTests:test_wrap_theta_at_0 protocols:VoxelSetIteratorTests:test_wrap_theta_at_180 protocols:WindowPoseCompMotifMetricTests:test_WPCMM protocols:WobbleMoverTest:test_wobble protocols:XmlObjectsTests:test_file_instantiation protocols:XmlObjectsTests:test_includes protocols:XmlObjectsTests:test_parsed_protocol protocols:XmlObjectsTests:test_static_instantiation_filter protocols:XmlObjectsTests:test_static_instantiation_mover protocols:XmlObjectsTests:test_static_instantiation_residue_selector protocols:XmlObjectsTests:test_static_instantiation_score_function protocols:XmlObjectsTests:test_static_instantiation_simple_metric protocols:XmlObjectsTests:test_static_instantiation_taskop protocols:XmlObjectsTests:test_string_instantiation 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 protocols:fold_tree_functions_Tests:test_remove_cutpoints protocols:hybridization_TMalign_Tests:test_align_pose1_onto_pose2 protocols:orphan_restypes_tests:test_cartmin_restype_noset protocols:orphan_restypes_tests:test_load_restype_noset protocols:orphan_restypes_tests:test_min_restype_noset protocols:orphan_restypes_tests:test_pack_restype_noset protocols:orphan_restypes_tests:test_score_restype_noset protocols:pHVariantTaskOperationTest:test_pHVariantTaskOp protocols:packer_palette_compatibility_global_tests:test_different_interchange_group protocols:packer_palette_compatibility_global_tests:test_same_interchange_group protocols:packer_palette_compatibility_tests:test_inpose_custom_palette protocols:packer_palette_compatibility_tests:test_inpose_different_interchange_group protocols:packer_palette_compatibility_tests:test_inpose_highresdocker protocols:packer_palette_compatibility_tests:test_inpose_same_interchange_group protocols:packer_palette_compatibility_tests:test_orphan_different_interchange_group protocols:packer_palette_compatibility_tests:test_orphan_same_interchange_group protocols:stepwise_modeler_rna_util_test:test_virtualize_free_rna_moieties utility:ArrayPoolTests:test_allocate_one_array utility:ArrayPoolTests:test_allocate_one_block utility:ArrayPoolTests:test_allocate_two_blocks utility:ArrayPoolTests:test_pool_1argument_ctor utility:ArrayPoolTests:test_pool_2argument_ctor utility:ArrayPoolTests:test_pool_default_ctor utility:ArrayPoolTests:test_reuse_space utility:AutoKeyTests:test_AutoKey_general utility:BinaryUtilTests:test_decode6bit_avoid_buffer_overrun utility:BitSetTests:test_BitSet_assignment utility:BitSetTests:test_BitSet_constructor utility:BitSetTests:test_BitSet_method utility:BitVectorTests:test_BitVector_assignment utility:BitVectorTests:test_BitVector_constructor utility:BitVectorTests:test_BitVector_method utility:BufferedSignalHubTests:test_BufferedSignalHub_buffering utility:DatabaseSessionManagerTests:test_cppdb_interface utility:DatabaseSessionManagerTests:test_db_session utility:DatabaseSessionManagerTests:test_multiple_selections utility:DatingUtilitiesTests:test_get_current_date utility:DeepCopyOPTests:test_conversion utility:DeepCopyOPTests:test_copying utility:DeepCopyVector1Tests:test_assignment utility:DeepCopyVector1Tests:test_construct utility:DeepCopyVector1Tests:test_copying utility:DeepCopyVector1Tests:test_move_semantics utility:DenseBoolMapTests:test_dense_bool_map utility:DisjointSetsTests:test_disjoint_sets_example1 utility:FactoryTests:test_Factory_general utility:FileContentsMapTests:test_FileContentsMap_delete_contents_at_nread_limit_1_read utility:FileContentsMapTests:test_FileContentsMap_delete_contents_at_nread_limit_2_read utility:FileContentsMapTests:test_FileContentsMap_get_file_contents utility:FileContentsMapTests:test_FileContentsMap_get_file_contents_ref utility:FileContentsMapTests:test_FileContentsMap_refuse_file_failure utility:FileContentsMapTests:test_FileContentsMap_refuse_file_success utility:FileNameTests:test_path utility:FileNameTests:test_vol utility:FileSysUtilTests:test_create_directory_recursive utility:GraphTests:test_add_edge utility:GraphTests:test_copy_constructor utility:GraphTests:test_drop_all_edges_for_node utility:GraphTests:test_find_edge utility:GraphTests:test_get_node utility:GraphTests:test_loops utility:GraphTests:test_memory_usage utility:GraphTests:test_num_neighbors_including_self utility:GraphTests:test_operator_assignment utility:GraphTests:test_serialize_graph utility:GraphTests:test_serialize_graph_pointer utility:GraphTests:test_set_num_nodes utility:IZStreamTests:test_alternate_paths utility:IZStreamTests:test_getline utility:IZStreamTests:test_izstream_directory_read utility:IZStreamTests:test_izstream_read_from_zipped_file utility:IterUtilTest:test_find_closest_largest utility:IterUtilTest:test_find_closest_rounding utility:IterUtilTest:test_find_closest_smallest utility:IterUtilTest:test_find_closest_value_excluded utility:IterUtilTest:test_find_closest_value_included utility:Key4TupleTests:test_Key4Tuple_general utility:Key4VectorTests:test_Key4Vector_general utility:KeyMapTests:test_ClassKeyMap_general utility:KeyMapTests:test_ClassKeyMap_swap utility:KeyVectorTests:test_ClassKeyVector_int utility:KeyVectorTests:test_ClassKeyVector_long utility:KeyVectorTests:test_ClassKeyVector_swap utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_at_end utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_constructor utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_continue_at_dim utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_increment utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_num_states_total utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_reset_state utility:LexicographicalIteratorTests:test_FixedSizeLexicographicalIterator_set_dim_sizes utility:LexicographicalIteratorTests:test_LexicographicalIterator_at_end utility:LexicographicalIteratorTests:test_LexicographicalIterator_constructor utility:LexicographicalIteratorTests:test_LexicographicalIterator_continue_at_dim utility:LexicographicalIteratorTests:test_LexicographicalIterator_increment utility:LexicographicalIteratorTests:test_LexicographicalIterator_num_states_total utility:LexicographicalIteratorTests:test_LexicographicalIterator_reset_state utility:LowMemGraphTests:test_add_edge utility:LowMemGraphTests:test_copy_constructor utility:LowMemGraphTests:test_deletion_space_savings utility:LowMemGraphTests:test_drop_all_edges_for_node utility:LowMemGraphTests:test_find_edge utility:LowMemGraphTests:test_get_node utility:LowMemGraphTests:test_iterators utility:LowMemGraphTests:test_iterators_w_deleted_data utility:LowMemGraphTests:test_operator_assignment utility:MinMaxTest:test_argmax_std_vector utility:MinMaxTest:test_argmax_std_vector_empty_input utility:MinMaxTest:test_argmax_vector1 utility:MinMaxTest:test_argmax_vector1_empty_input utility:MinMaxTest:test_argmin_std_vector utility:MinMaxTest:test_argmin_std_vector_empty_input utility:MinMaxTest:test_argmin_vector1 utility:MinMaxTest:test_argmin_vector1_empty_input utility:OptionCollectionTests:test_check_specs utility:OrderedTupleTests:test_OrderedTuple_compare_fsa utility:OrderedTupleTests:test_OrderedTuple_data_assignment_fsa utility:OrderedTupleTests:test_OrderedTuple_data_assignment_list utility:OrderedTupleTests:test_OrderedTuple_data_assignment_v1 utility:PathNameTests:test_parent utility:PathNameTests:test_path utility:PathNameTests:test_vol utility:PausableSignalHubTests:test_PausableSignalHub_pausing utility:ReadWriteMutexTests:test_empty utility:ReadWriteMutexTests:test_thread_waits_for_reading_to_finish_to_write utility:ReadWriteMutexTests:test_two_threads_read_together utility:ReadWriteMutexTests:test_write_lock_prevents_reading utility:RecentHistoryQueueTests:test_bump_an_element_from_the_history utility:RecentHistoryQueueTests:test_bump_an_element_from_the_history_after_resent_queue_end utility:RecentHistoryQueueTests:test_recent_history_queue_fill_queue utility:RecentHistoryQueueTests:test_reset_recent_history_queue_head utility:RecentHistoryQueueTests:test_reset_recent_history_queue_middle utility:RecentHistoryQueueTests:test_reset_recent_history_queue_tail utility:RingDetectionTests:test_benzene_annotation utility:RingDetectionTests:test_benzene_sizes utility:RingDetectionTests:test_cubane_sizes 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utility:SmallVector1_Tests:test_vector1_swap utility:SortFunctionsTest:test_argsort utility:SortFunctionsTest:test_fractional_rank utility:StringUtilTests:test_contains utility:StringUtilTests:test_file_basename utility:StringUtilTests:test_filename utility:StringUtilTests:test_make_segtag utility:StringUtilTests:test_pad_atom_name utility:StringUtilTests:test_padding utility:StringUtilTests:test_pathname utility:StringUtilTests:test_quoted_split utility:StringUtilTests:test_real_format utility:StringUtilTests:test_remove_from_string utility:StringUtilTests:test_reschain_to_string utility:StringUtilTests:test_reschainseg_to_string utility:StringUtilTests:test_same_ignoring_spaces utility:StringUtilTests:test_slurp utility:StringUtilTests:test_string2uint utility:StringUtilTests:test_string_to_res_and_segid utility:StringUtilTests:test_string_to_reschain utility:StringUtilTests:test_string_to_sha1 utility:StringUtilTests:test_trims utility:TagTests:test_17 utility:TagTests:test_18 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"passed" }, "core:MolFileIOReaderTests:test_build_rotamers": { "log": "", "state": "passed" }, "core:MolFileIOReaderTests:test_read_rotamers": { "log": "", "state": "passed" }, "core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v1": { "log": "", "state": "passed" }, "core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v2": { "log": "", "state": "passed" }, "core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v3": { "log": "", "state": "passed" }, "core:MoveMapTest:test_backbone_range_protection": { "log": "", "state": "passed" }, "core:MoveMapTest:test_show": { "log": "", "state": "passed" }, "core:NCAACentroidResidueTypeTests:test_centroid_aib_orn_dab_dap": { "log": "", "state": "passed" }, "core:NCAADunbrackTests:test_score_with_ncaa": { "log": "", "state": "passed" }, "core:NCAADunbrackTests_betanov15:test_score_with_ncaa": { "log": "", "state": "passed" }, "core:NMRDummySpinlabelEnsembleTests:test_elaborate_clash_filter": { "log": "", "state": "passed" }, 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"core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_w_bgnode_linmem_npdhb_ig_acc_network": { "log": "", "state": "passed" }, "core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_w_bgnode_linmem_npdhb_ig_don_network": { "log": "", "state": "passed" }, "core:NVlookupTests:test_lookup_values": { "log": "", "state": "passed" }, "core:NVscoreTests:test_eval_energy": { "log": "", "state": "passed" }, "core:NamedAngleConstraintTests:test_angle_score": { "log": "", "state": "passed" }, "core:NamedAngleConstraintTests:test_named_angle_constraint_clone": { "log": "", "state": "passed" }, "core:NamedAngleConstraintTests:test_serialize_NamedAngleConstraint": { "log": "", "state": "passed" }, "core:NamedAtomPairConstraintTests:test_atom_pair_score": { "log": "", "state": "passed" }, "core:NamedAtomPairConstraintTests:test_named_atom_pair_constraint_clone": { "log": "", "state": "passed" }, "core:NamedAtomPairConstraintTests:test_serialize_NamedAtomPairConstraint": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighbohoodResidueSelector_fail_no_focus": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_code_level_acces": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_dont_include_focus_close": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_dont_include_focus_far": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_parse_my_tag_selector": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_parse_my_tag_str": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_uninitialized_pose": { "log": "", "state": "passed" }, "core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_use_last_provided_source_of_focus": { "log": "", "state": "passed" }, "core:NetChargeEnergyTests_packer:test_energy_annealing": { "log": "", "state": "passed" }, "core:NetChargeEnergyTests_packer_symm:test_energy_annealing_symmetric": { "log": "", "state": "passed" }, "core:NetChargeEnergyTests_tailfxns:test_constant_tailfxns": { "log": "", "state": "passed" }, "core:NetChargeEnergyTests_tailfxns:test_linear_tailfxns": { "log": "", "state": "passed" }, "core:NetChargeEnergyTests_tailfxns:test_quadratic_tailfxns": { "log": "", "state": "passed" }, "core:NomenclatureManagerTestsWCL:test_default_mainchain_connectivity_from_pdb_code": { "log": "", "state": "passed" }, "core:NomenclatureManagerTestsWCL:test_nomenclature_manager_test_w_command_line_alt_codes": { "log": "", "state": "passed" }, "core:NomenclatureManagerTestsWCL:test_nomenclature_manager_three_name_conflicts": { "log": "", "state": "passed" }, "core:NomenclatureManagerTestsWCL:test_pdb_code_from_rosetta_name": { "log": "", "state": "passed" }, "core:NomenclatureManagerTestsWOCL:test_rosetta_names_from_pdb_code": { "log": "", "state": "passed" }, "core:NonResidueTypeConstraintTests:test_serialize_NonResidueTypeConstraint": { "log": "", "state": "passed" }, "core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag": { "log": "", "state": "passed" }, "core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag_no_provided_selectors": { "log": "", "state": "passed" }, "core:NotJumpSelectorTests:test_NotJumpSelector_parse_my_tag_selectors_not_in_datamap": { "log": "", "state": "passed" }, "core:NotJumpSelectorTests:test_not_jump_selector_odd_lots_of_jumps": { "log": "", "state": "passed" }, "core:NotJumpSelectorTests:test_not_jump_selector_odd_no_jumps": { "log": "", "state": "passed" }, "core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag": { "log": "", "state": "passed" }, "core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag_no_provided_selectors": { "log": "", "state": "passed" }, "core:NotResidueSelectorTests:test_NotResidueSelector_parse_my_tag_selectors_not_in_datamap": { "log": "", "state": "passed" }, "core:NotResidueSelectorTests:test_not_residue_selector_odd": { "log": "", "state": "passed" }, "core:NumNeighborsSelectorTests:test_num_neighbors_selector_1": { "log": "", "state": "passed" }, "core:NumNeighborsSelectorTests:test_num_neighbors_selector_parse_my_tag": { "log": "", "state": "passed" }, "core:NumNeighborsSelectorTests:test_num_neighbors_selector_parse_my_tag_w_defaults": { "log": "", "state": "passed" }, "core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_deriv_check_w_partial_flexibility": { "log": "", "state": "passed" }, "core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_deriv_check_w_total_flexibility": { "log": "", "state": "passed" }, "core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_start_score_start_func_match_w_partial_flexibility": { "log": "", "state": "passed" }, "core:OccludedHbondSolEnergyTests:test_occ_sol_fitted_start_score_start_func_match_w_total_flexibility": { "log": "", "state": "passed" }, "core:OmegaPreferencesFunctionTests:test_omega_preferences_derivatives": { "log": "", "state": "passed" }, "core:OmegaPreferencesFunctionTests:test_omega_preferences_function": { "log": "", "state": "passed" }, "core:OmegaTetherTests:test_alpha_aa_omega": { "log": "", "state": "passed" }, "core:OmegaTetherTests:test_beta_aa_omega_min": { "log": "", "state": "passed" }, "core:OmegaTetherTests:test_oligourea_omega": { "log": "", "state": "passed" }, "core:OmegaTetherTests:test_oligourea_omega_min": { "log": "", "state": "passed" }, "core:OperateOnResidueSubsetTests:test_disable_odd_residues_init_by_ctor": { "log": "", "state": "passed" }, "core:OperateOnResidueSubsetTests:test_disable_odd_residues_init_w_functions": { "log": "", "state": "passed" }, "core:OperateOnResidueSubsetTests:test_oors_parse_tag_1": { "log": "", "state": "passed" }, "core:OperateOnResidueSubsetTests:test_oors_parse_tag_2": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_fail_parse_subtag": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag_no_provided_selectors": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_parse_my_tag_selectors_not_in_datamap": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_parse_subtag_v1": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_OrJumpSelector_parse_subtag_v2": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_and_jump_selector_odd_1mod5_lots_of_jumps": { "log": "", "state": "passed" }, "core:OrJumpSelectorTests:test_and_jump_selector_odd_1mod5_no_jumps": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_AndResidueSelector_parse_my_tag_selectors_not_in_datamap": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_OrResidueSelector_fail_parse_subtag": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_OrResidueSelector_parse_my_tag": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_OrResidueSelector_parse_my_tag_no_provided_selectors": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_OrResidueSelector_parse_subtag": { "log": "", "state": "passed" }, "core:OrResidueSelectorTests:test_or_residue_selector_odd_1mod5": { "log": "", "state": "passed" }, "core:OrbitalTests:test_orbital_initialization": { "log": "", "state": "passed" }, "core:OrbitalTests:test_orbital_setters": { "log": "", "state": "passed" }, "core:OrbitalTypeSetTests:test_operator_brackets": { "log": "", "state": "passed" }, "core:OrbitalTypeSetTests:test_orbital_type_index": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_make_compiler_happy": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_partial_flexibility": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_all": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_orbitals_hpol_bb": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_cation_pi": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_hbond": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_pi_pi": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_salt_bridge": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_scoring_function_values": { "log": "", "state": "passed" }, "core:OrbitalsEnergyTests:test_orbital_start_score_start_func_match_w_total_flexibility": { "log": "", "state": "passed" }, "core:OrderedFragSetTest:test_frag_iterator": { "log": "", "state": "passed" }, "core:PCSDataSymmetryTests:test_PCSData_score_calculation_all_tags_automatic_symmetry_deduction": { "log": "", "state": "passed" }, "core:PCSDataSymmetryTests:test_PCSData_score_calculation_all_tags_manual_symmetry_handling": { "log": "", "state": "passed" }, "core:PCSDataTests:test_PCSData_creation_by_NMRDataFactory": { "log": "", "state": "passed" }, "core:PCSDataTests:test_PCSData_instantiation": { "log": "", "state": "passed" }, "core:PCSDataTests:test_PCSData_score_calculation_with_gridsearch": { "log": "", "state": "passed" }, "core:PCSDataTests:test_PCSData_score_calculation_with_spinlabel": { "log": "", "state": "passed" }, "core:PCSDataTests:test_scaled_PCSData_score_calculation": { "log": "", "state": "passed" }, "core:PCSMultiSetTests:test_PCSMultiSet_instantiation_and_getters": { "log": "", "state": "passed" }, "core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_from_fixed_tensor": { "log": "", "state": "passed" }, "core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_with_gridsearch": { "log": "", "state": "passed" }, "core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_with_spinlabel": { "log": "", "state": "passed" }, "core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_nls_automatic_symmetry_deduction": { "log": "", "state": "passed" }, "core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_nls_manual_symmetry_handling": { "log": "", "state": "passed" }, "core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_svd_automatic_symmetry_deduction": { "log": "", "state": "passed" }, "core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_svd_manual_symmetry_handling": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_PCSSingleSet_instantiation_and_getters": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_PCSSingleSet_instantiation_and_scaling": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_calc_tensor_and_score_nls": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_calc_tensor_and_score_nls_fixed_XaxXrh": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_calc_tensor_and_score_nls_svd_different_weightings": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_calc_tensor_and_score_svd": { "log": "", "state": "passed" }, "core:PCSSingleSetTests:test_calc_tensor_and_score_svd_on_scaled_data": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_append_residue": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_chain_sequences": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_delete_residue": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_detach_on_destroy": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_en_masse_residue_mutators": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_from_input_pdb": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_from_input_pdb_PDBPoseMap": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_observe_append": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_observe_attach_detach": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_observe_delete": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_observe_prepend": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_observe_replace": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_prepend_residue": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_resize": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_silent_files": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_single_residue_chain_mutator": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_single_residue_icode_mutator": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_single_residue_number_mutator": { "log": "", "state": "passed" }, "core:PDBInfoTests:test_PDBInfo_single_residue_resinfo_mutator": { "log": "", "state": "passed" }, "core:PDBPoseMapTests:test_PDBPoseMap_erase": { "log": "", "state": "passed" }, "core:PDBPoseMapTests:test_PDBPoseMap_find": { "log": "", "state": "passed" }, "core:PDBPoseMapTests:test_PDBPoseMap_insert": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_chain_sequence_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_cis_peptide_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_formula_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_heterogen_name_record_in_sfr_and_store_base_residue_type_name_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_heterogen_synonym_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_link_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_mod_res_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_ssbond_record_in_sfr": { "log": "", "state": "passed" }, "core:PDBReaderTests:test_store_unknown_records_in_sfr": { "log": "", "state": "passed" }, "core:PDBSilentStruct_Tests:test_pdb_silent_disulfide": { "log": "", "state": "passed" }, "core:PDBSilentStruct_Tests:test_save_and_restore": { "log": "", "state": "passed" }, "core:PDB_IO:test_pdb_io": { "log": "", "state": "passed" }, "core:PDB_IO:test_pdb_io_seqres": { "log": "", "state": "passed" }, "core:PDB_IO:test_pdb_read_d_aa": { "log": "", "state": "passed" }, "core:PDB_IO:test_pdb_read_partial_residues": { "log": "", "state": "passed" }, "core:PDB_w_glycans_IO:test_glycan_fragment": { "log": "", "state": "passed" }, "core:PDB_w_glycans_IO:test_pdb_io": { "log": "cd build/test/debug/linux/3.10/64/x86/gcc/4.8/default && /usr/bin/python /home/benchmark/rosetta/source/test/timelimit.py 18 ./core.test PDB_w_glycans_IO --database /home/benchmark/rosetta/database -mute all -no_fconfig 1>&2\nRunning core.test:PDB_w_glycans_IO unit tests...\nRunning one suite: PDB_w_glycans_IO\nTest suite: PDB_w_glycans_IO (test/core/io/PDB_w_glycans_IO.cxxtest.hh)\n\nIn PDB_w_glycans_IO::test_pdb_io:\n./test/core/io/PDB_w_glycans_IO.cxxtest.hh:153: Error: Test failed: Files are not equal!\nLine1: ATOM 1115 1HD2 ASN B 611 38.441 53.073 33.243 1.00 0.00 H \nLine2: ATOM 1115 2HD2 ASN B 611 38.026 51.401 33.072 1.00 0.00 H \n\n./test/core/io/PDB_w_glycans_IO.cxxtest.hh:153: Error: Test failed: Files 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