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Revisions №14847

branch: commits 「№14847」
Commited by: Rocco Moretti
GitHub commit link: 「dc03a49948584d71」
Commit date: 2020-03-02 23:49:46
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit build.cppcheck mpi mpi.serialization build.header build.levels build.ninja_debug graphics static beautification serialization code_quality.submodule_regression integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Beauty

Rosetta Benchmark 3 months
Tests for this revision was automatically canceled due to critical failure of test: linux.gcc.cxx11thread.serialization.build.debug
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Test: linux.gcc.cxx11thread.serialization.build.debug

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Test: mac.clang.unit

Failed sub-tests (click for more details):
apps:LigandDockTest:test_select_best_poses 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:AARepeatEnergyTests:test_energy_annealing core:AARepeatEnergyTests:test_energy_cases core:AARepeatEnergyTests:test_energy_eval core:ABEGOManagerTest:test_abego 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: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: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_serialize_AtomPairConstraint 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: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:BetaNov16WithAutoSetupMetalsTests:test_auto_setup_metals_with_ser_mn core:BinSelectorTests:test_binselector_abin core:BinarySilentMultiposeTests:test_save_multiple_poses_and_restore core:BinarySilentMultiposeTests:test_save_multiple_poses_with_resize_and_restore core:BinarySilentTests:test_read_badly_formatted_silent_file core:BinarySilentTests:test_save_and_restore core:BinarySilentTests:test_save_and_restore_centroid core:BinarySilentTests:test_save_and_restore_inserting_residues core:BuriedUnsatPenaltyGraphSymmetricTests:test_graph_setup core:BuriedUnsatPenaltyGraphSymmetricTests:test_smallpose_graph_setup core:BuriedUnsatPenaltyGraphTests:test_graph_setup core:BuriedUnsatPenaltyGraphTests:test_smallpose_graph_setup core:BuriedUnsatPenaltySymmetricTests:test_simple_symmetric_scoring core:BuriedUnsatPenaltySymmetricTests:test_simple_symmetric_scoring2 core:BuriedUnsatPenaltySymmetricTests:test_symmetric_packing core:BuriedUnsatPenaltySymmetricTests:test_symmetric_setup_for_packing core:BuriedUnsatPenaltyTests:test_packing core:BuriedUnsatPenaltyTests:test_packing_steps core:BuriedUnsatPenaltyTests:test_setup_for_packing core:BuriedUnsatPenaltyTests:test_simple_scoring core:CarbohydrateInfoTests:test_CarbohydrateInfo_branch_point 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: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: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: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 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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:CopyDofsTest:test_copy_dofs_into_extended 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 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core:ImplicitLipidInfo:test_f_hydration_gradient core:ImplicitLipidInfo:test_g_radius core:ImplicitLipidInfo:test_implicit_lipid_info_initialization core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_order_independence core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_parse_my_tag core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_parse_my_tag_fail_only_one_subselector core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_parse_my_tag_no_provided_grp1_data core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_parse_my_tag_no_provided_grp2_data core:InterGroupInterfaceByVectorSelectorTests:test_InterGroupInterfaceByVectorSelector_parse_my_tag_selectors_not_in_datamap core:InterGroupInterfaceByVectorSelectorTests:test_interface_vector_selector_from_resselector_on_test_in_pdb core:InterGroupInterfaceByVectorSelectorTests:test_interface_vector_selector_from_std_set_on_test_in_pdb core:InteractionGraphFactoryTests:test_DensePDInteractionGraph core:InteractionGraphFactoryTests:test_DoubleLazyInteractionGraph core:InteractionGraphFactoryTests:test_LazyInteractionGraph core:InteractionGraphFactoryTests:test_LinearMemoryInteractionGraph core:InteractionGraphFactoryTests:test_LinearMemorySurfaceInteractionGraph core:InteractionGraphFactoryTests:test_PDInteractionGraph core:InteractionGraphFactoryTests:test_PDSurfaceInteractionGraph core:InterchainJumpSelectorTests:test_InterchainJumpSelector_parse_my_tag core:InterchainJumpSelectorTests:test_interchain_jump_selector core:JumpDownstreamSelectorTests:test_JumpDownstreamSelector_parse_my_tag core:JumpDownstreamSelectorTests:test_NeighbohoodResidueSelector_fail_no_resnums core:JumpIndexSelectorTests:test_JumpIndexSelector_parse_my_tag core:JumpIndexSelectorTests:test_jump_index_jump_selector core:JumpUpstreamSelectorTests:test_JumpUpstreamSelector_parse_my_tag core:JumpUpstreamSelectorTests:test_NeighbohoodResidueSelector_fail_no_resnums core:LK_BallEnergyTests:test_lk_ball_bridge_rpe_matches_bbbb_bbsc_scscE core:LK_BallEnergyTests:test_lk_ball_rpe_matches_bbbb_bbsc_scscE core:LK_BallEnergyTests:test_lk_ball_setup_for_scoring core:LK_BallEnergyTests:test_lkball_numeric_deriv_check core:LK_BallEnergyTests:test_nblist_auto_update_derivatives_w_full_bb_flex core:LK_BallEnergyTests:test_nblist_auto_update_derivatives_w_partial_bb_flex core:LK_BallEnergyTests:test_start_func_matches_start_score_w_full_bbflex core:LK_BallEnergyTests:test_start_func_matches_start_score_w_partial_bbflex core:LinMemInteractionGraphTests:test_linmem_ig core:LinearChainbreakEnergyTests:test_linear_chainbreak_deriv_check core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_caching core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_chainbreak core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_external core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_matrix_scoring core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_overhangs core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_overhangs_multichain core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_packer core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_sym core:MHCEpitopeEnergyTests_Scoring:test_mhc_energy_uaa core:MMBondAngleEnergyTests:test_energy core:MMBondAngleEnergyTests:test_energy_original core:MMBondAngleEnergyTests:test_mmbond_angle_energy_start_score_start_func_match_w_total_flexibility core:MMTorsionEnergyTests:test_eval_intrares_energy core:MMTorsionEnergyTests:test_residue_pair_energy core:MPHelicalityTests:test_burial_sigmoid core:MPHelicalityTests:test_calc_energy core:MPHelicalityTests:test_calc_residue_burial core:MPHelicalityTests:test_cen_neighbors core:MPHelicalityTests:test_fa_neighbors core:MPHelicalityTests:test_residue_energy core:MPResidueLipophilicityTests:test_burial_sigmoid core:MPResidueLipophilicityTests:test_calc_energy core:MPResidueLipophilicityTests:test_calc_residue_burial core:MPResidueLipophilicityTests:test_cen_neighbors core:MPResidueLipophilicityTests:test_fa_neighbors core:MPSpanAngleEnergyTests:test_calc_span_score core:MPSpanAngleEnergyTests:test_compute core:MPSpanAngleEnergyTests:test_finalize_total_energy core:MPSpanAngleEnergyTests:test_find_helix_vector core:MPSpanInsertionEnergyTests:test_calc_span_score core:MPSpanInsertionEnergyTests:test_compute core:MPSpanInsertionEnergyTests:test_create_updated_spans core:MPSpanInsertionEnergyTests:test_finalize_total_energy core:MPSpanInsertionEnergyTests:test_spline_by_z core:MembraneInfoTest:test_atom_z_position core:MembraneInfoTest:test_conformation_invariant core:MembraneInfoTest:test_normal_center core:MembraneInfoTest:test_reasonable_foldtree core:MembraneInfoTest:test_reasonable_setup core:MembraneInfoTest:test_residue_z_position core:MembraneInfoTest:test_unreasonable_foldtree core:MinimizerTests:test_dfpmin core:MinimizerTests:test_dfpmin_armijo core:MinimizerTests:test_dfpmin_armijo_nonmonotone core:MinimizerTests:test_lbfgs_armijo core:MinimizerTests:test_lbfgs_armijo_nonmonotone core:MinimizerTests:test_linmin_iterated core:MinimizerTests:test_linmin_iterated_atol core:MinimizerTests:test_simple_min core:MirrorSymmetricConformationTests:test_aacomp core:MirrorSymmetricConformationTests:test_aacomp_design_subset core:MirrorSymmetricConformationTests:test_symmetric_conformation core:MolFileIODataTests:test_sdfreader core:MolFileIOReaderTests:test_build_rotamers core:MolFileIOReaderTests:test_read_rotamers core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v1 core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v2 core:MoveMapFactoryTests:test_MoveMapFactory_parse_my_tag_v3 core:MoveMapTest:test_backbone_range_protection core:MoveMapTest:test_show core:NCAADunbrackTests:test_score_with_ncaa core:NCAADunbrackTests_betanov15:test_score_with_ncaa core:NMRDummySpinlabelEnsembleTests:test_elaborate_clash_filter core:NMRDummySpinlabelEnsembleTests:test_instantiation_and_access core:NMRDummySpinlabelEnsembleTests:test_quick_clash_filter core:NMRSpinlabelTests:test_creation_and_access core:NMRSpinlabelTests:test_filter_spinlabel_ensemble_by_distance_check core:NMRSpinlabelTests:test_filter_spinlabel_ensemble_by_distance_check_and_clustering core:NMRSpinlabelTests:test_filter_spinlabel_ensemble_by_mask core:NMRSpinlabelTests:test_filter_spinlabel_ensemble_by_mask_and_clustering core:NMerSVMEnergyTests:test_eval_energy core:NPDHBondEnergyTests:test_hbonds_deriv_check_w_partial_torsional_flexibility core:NPDHBondEnergyTests:test_hbonds_w_sp2term_deriv_check_w_partial_torsional_flexibility core:NPDHBondEnergyTests:test_npd_hbond_symmetric_score_function_bad_symm_hbond_derivs core:NPDHBondEnergyTests:test_npd_hbonds_deriv_check_w_full_torsional_flexibility core:NPDHBondEnergyTests:test_npd_hbonds_deriv_check_w_full_torsional_flexibility_cyc_pep core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_dense_npdhb_ig core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_linmem_npdhb_ig core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_standard_npdhb_ig core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_w_bgnode_linmem_npdhb_ig_acc_network core:NPDHBondInteractionGraphTests:test_create_overcommitted_hbond_networks_w_bgnode_linmem_npdhb_ig_don_network core:NVscoreTests:test_eval_energy core:NamedAngleConstraintTests:test_angle_score core:NamedAngleConstraintTests:test_named_angle_constraint_clone core:NamedAngleConstraintTests:test_serialize_NamedAngleConstraint core:NamedAtomPairConstraintTests:test_atom_pair_score core:NamedAtomPairConstraintTests:test_named_atom_pair_constraint_clone core:NamedAtomPairConstraintTests:test_serialize_NamedAtomPairConstraint core:NeighborhoodResidueSelectorTests:test_NeighbohoodResidueSelector_fail_no_focus core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_code_level_acces core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_dont_include_focus_close core:NeighborhoodResidueSelectorTests:test_NeighborhoodResidueSelector_dont_include_focus_far 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: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: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 core:OrResidueSelectorTests:test_or_residue_selector_odd_1mod5 core:OrbitalsEnergyTests:test_make_compiler_happy core:OrbitalsEnergyTests:test_orbital_deriv_check_w_partial_flexibility core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_all core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_orbitals_hpol_bb core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_cation_pi core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_hbond core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_pi_pi core:OrbitalsEnergyTests:test_orbital_deriv_check_w_total_flexibility_pci_salt_bridge core:OrbitalsEnergyTests:test_orbital_scoring_function_values core:OrbitalsEnergyTests:test_orbital_start_score_start_func_match_w_total_flexibility core:OrderedFragSetTest:test_frag_iterator core:PCSDataSymmetryTests:test_PCSData_score_calculation_all_tags_automatic_symmetry_deduction core:PCSDataSymmetryTests:test_PCSData_score_calculation_all_tags_manual_symmetry_handling core:PCSDataTests:test_PCSData_creation_by_NMRDataFactory core:PCSDataTests:test_PCSData_instantiation core:PCSDataTests:test_PCSData_score_calculation_with_gridsearch core:PCSDataTests:test_PCSData_score_calculation_with_spinlabel core:PCSDataTests:test_scaled_PCSData_score_calculation core:PCSMultiSetTests:test_PCSMultiSet_instantiation_and_getters core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_from_fixed_tensor core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_with_gridsearch core:PCSMultiSetTests:test_PCSMultiSet_score_calculation_with_spinlabel core:PCSSingleSetSymmetryTests:test_calc_tensor_and_score_nls_automatic_symmetry_deduction 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 core:PDBInfoTests:test_PDBInfo_from_input_pdb core:PDBInfoTests:test_PDBInfo_from_input_pdb_PDBPoseMap core:PDBInfoTests:test_PDBInfo_observe_append core:PDBInfoTests:test_PDBInfo_observe_attach_detach core:PDBInfoTests:test_PDBInfo_observe_delete core:PDBInfoTests:test_PDBInfo_observe_prepend core:PDBInfoTests:test_PDBInfo_observe_replace core:PDBInfoTests:test_PDBInfo_prepend_residue core:PDBInfoTests:test_PDBInfo_resize core:PDBInfoTests:test_PDBInfo_silent_files core:PDBInfoTests:test_PDBInfo_single_residue_chain_mutator core:PDBInfoTests:test_PDBInfo_single_residue_icode_mutator core:PDBInfoTests:test_PDBInfo_single_residue_number_mutator core:PDBInfoTests:test_PDBInfo_single_residue_resinfo_mutator 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 core:PREDataTests:test_pre_score_calculation_with_metal_ion_gridsearch core:PREMultiSetTests:test_PREMultiSet_instantiation_and_data_scaling core:PREMultiSetTests:test_PREMultiSet_instantiation_and_getters_and_setters core:PREMultiSetTests:test_find_spinlabel_position_and_pre_score_calculation core:PREMultiSetTests:test_pre_r2_score_calculation_with_spinlabel core:PREMultiSetTests:test_pre_score_calculation_with_gridsearch core:P_AA_EnergyTests:test_eval_energy core:P_AA_pp_EnergyTests:test_paapp_deriv_check core:PackerTaskTests:test_PackerTask_init_from_options_actually_reads_option_collection core:PackerTaskTests:test_PackerTask_initialize_from_options_and_list_options_read_are_in_sync core:PackerTaskTests:test_ResidueLevelTask_init_from_options_actually_reads_option_collection core:PackerTaskTests:test_ResidueLevelTask_initialize_from_options_and_list_options_read_are_in_sync 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 core:PairEnergyTests:test_pairE_start_score_start_func_match_w_partial_flexibility core:PairEnergyTests:test_pairE_start_score_start_func_match_w_total_flexibility core:PeptoidDesignTests:test_design_001_601_602 core:PeptoidDesignTests:test_design_hydrophobic_aa_001_601_602 core:PhiSelectorTests:test_phiselector_negativephi core:PhiSelectorTests:test_phiselector_negativephi_no_ignore_unconnected_upper core:PhiSelectorTests:test_phiselector_positivephi 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: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: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:RG_Energy_Tests:test_eval_energy 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:RamaPreProTests:test_correct_score_stored 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: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:RandomResidueSelectorTests:test_RandomResidueSelector_parse_my_tag core:ReferencePoseTests:test_ReferencePoseSet_deleting core:ReferencePoseTests:test_ReferencePoseSet_setup core:ReferencePoseTests:test_ReferencePose_string_parsing 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:ResiduePropertySelectorTests:test_selector core:ResiduePropertySelectorTests:test_xml_interface 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_serialize_ResidueTypeLinkingConstraint 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: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: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_superimpose_same core:RmsUtilTest:test_superimpose_self 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: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: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:ScoreTest:test_ScoreTest 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_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: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:SequenceSimilarityMetricTests:test_selector core:SequenceSimilarityMetricTests:test_simple_case core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing core:SequenceSymmetricAnnealerTests:test_chain_similarity_after_packing_cli core:SequenceSymmetricAnnealerTests:test_chain_similarity_with_virtual_root core:SequenceSymmetricAnnealerTests:test_recover_symmetry core:SequenceSymmetricAnnealerTests:test_residue_selectors core:SequenceSymmetricAnnealerTests:test_unequal_chain_lengths core:SimpleInteractionGraphTests:test_instantiate_simple_ig core:SimpleInteractionGraphTests:test_simple_ig_neutral_compare 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:SpanningTopologyTest:test_concatenate_topology core:SpanningTopologyTest:test_from_pdb1 core:SpanningTopologyTest:test_from_pdb2 core:SpanningTopologyTest:test_from_pdb3 core:SpanningTopologyTest:test_from_pdb4 core:SpanningTopologyTest:test_from_spanfile core:SpanningTopologyTest:test_is_valid core:SpanningTopologyTest:test_res_in_membrane core:SpanningTopologyTest:test_spanning_membrane core:StructFileRepTests:test_extra_res_fa_flag core:StructFileRepTests:test_generate_secondary_structure_informations core:StructFileRepTests:test_generate_secondary_structure_informations_twochains core:StructFileRepTests:test_get_connectivity_annotation_info core:SurfacePotentialTests:test_average_residue_hASA core:SurfacePotentialTests:test_compute_pose_hpatch_energy core:SurfacePotentialTests:test_compute_pose_surface_energy_fragment core:SurfacePotentialTests:test_compute_pose_surface_energy_smallprotein core:SurfacePotentialTests:test_compute_pose_with_HETATM_hpatch_energy core:SurfacePotentialTests:test_compute_residue_surface_energy core:SurfacePotentialTests:test_hASA_patch_energy core:SurfacePotentialTests:test_hpatch_score 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 core:SymmDLMinTests:test_symm_DL_min_fa_atr core:SymmDLMinTests:test_symm_DL_min_fa_dun core:SymmDLMinTests:test_symm_DL_min_fa_elec core:SymmDLMinTests:test_symm_DL_min_fa_intra_rep core:SymmDLMinTests:test_symm_DL_min_fa_rep core:SymmDLMinTests:test_symm_DL_min_fa_sol core:SymmDLMinTests:test_symm_DL_min_hbonds core:SymmDLMinTests:test_symm_DL_min_omega core:SymmDLMinTests:test_symm_DL_min_p_aa_pp core:SymmDLMinTests:test_symm_DL_min_pro_close core:SymmDLMinTests:test_symm_DL_min_rama core:SymmDLMinTests:test_symm_DL_min_rama_prepro core:SymmDLMinTests:test_symm_DL_min_rama_prepro2 core:SymmDLMinTests:test_symm_DL_min_talaris2014 core:SymmDLMinTests:test_symm_DL_min_yhh_planarity core:SymmDLMin_betanov15_Tests:test_symm_DL_min_beta_nov15 core:SymmDLMin_betanov15_Tests:test_symm_DL_min_cart_bonded core:SymmDLMin_betanov15_Tests:test_symm_DL_min_current_default_scorefxn core:SymmDLMin_betanov15_Tests:test_symm_DL_min_dslf_fa13 core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_atr core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_dun core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_elec core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_intra_rep core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_intra_sol_xover4 core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_rep core:SymmDLMin_betanov15_Tests:test_symm_DL_min_fa_sol core:SymmDLMin_betanov15_Tests:test_symm_DL_min_hbonds core:SymmDLMin_betanov15_Tests:test_symm_DL_min_lk_ball_wtd core:SymmDLMin_betanov15_Tests:test_symm_DL_min_omega core:SymmDLMin_betanov15_Tests:test_symm_DL_min_p_aa_pp core:SymmDLMin_betanov15_Tests:test_symm_DL_min_pro_close core:SymmDLMin_betanov15_Tests:test_symm_DL_min_rama core:SymmDLMin_betanov15_Tests:test_symm_DL_min_rama_prepro core:SymmDLMin_betanov15_Tests:test_symm_DL_min_rama_prepro2 core:SymmDLMin_betanov15_Tests:test_symm_DL_min_yhh_planarity core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_cart_bonded core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_current_default_scorefxn core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_dslf_fa13 core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_atr core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_dun core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_elec core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_intra_rep core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_rep core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_fa_sol core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_hbonds core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_omega core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_p_aa_pp core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_pro_close core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_rama core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_rama_prepro core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_rama_prepro2 core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_talaris2014 core:SymmDLMin_nmethyl_Tests:test_symm_DL_min_yhh_planarity core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_beta_sfxn core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_cart_bonded core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_current_default_scorefxn core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_dslf_fa13 core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_atr core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_dun core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_elec core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_intra_rep core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_intra_sol_xover4 core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_rep core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_fa_sol core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_hbonds core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_lk_ball_wtd core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_omega core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_p_aa_pp core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_pro_close core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_rama core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_rama_prepro core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_rama_prepro2 core:SymmDLMin_nmethyl_beta_Tests:test_symm_DL_min_yhh_planarity core:SymmDLMin_peptoid_Tests:test_symm_DL_min_cart_bonded core:SymmDLMin_peptoid_Tests:test_symm_DL_min_current_default_scorefxn core:SymmDLMin_peptoid_Tests:test_symm_DL_min_dslf_fa13 core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_atr core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_dun core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_elec core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_intra_rep core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_rep core:SymmDLMin_peptoid_Tests:test_symm_DL_min_fa_sol core:SymmDLMin_peptoid_Tests:test_symm_DL_min_hbonds core:SymmDLMin_peptoid_Tests:test_symm_DL_min_omega core:SymmDLMin_peptoid_Tests:test_symm_DL_min_p_aa_pp core:SymmDLMin_peptoid_Tests:test_symm_DL_min_pro_close core:SymmDLMin_peptoid_Tests:test_symm_DL_min_rama core:SymmDLMin_peptoid_Tests:test_symm_DL_min_rama_prepro core:SymmDLMin_peptoid_Tests:test_symm_DL_min_rama_prepro2 core:SymmDLMin_peptoid_Tests:test_symm_DL_min_talaris2014 core:SymmDLMin_peptoid_Tests:test_symm_DL_min_yhh_planarity core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_beta_sfxn core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_cart_bonded core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_current_default_scorefxn core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_dslf_fa13 core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_atr core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_dun core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_elec core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_intra_rep core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_intra_sol_xover4 core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_rep core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_fa_sol core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_hbonds core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_lk_ball_wtd core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_omega core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_p_aa_pp core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_pro_close core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_rama core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_rama_prepro core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_rama_prepro2 core:SymmDLMin_peptoid_beta_Tests:test_symm_DL_min_yhh_planarity core:SymmDLTests:test_symm_DL_cart_bonded core:SymmDLTests:test_symm_DL_default_scorefxn core:SymmDLTests:test_symm_DL_dslf_fa13 core:SymmDLTests:test_symm_DL_fa_atr core:SymmDLTests:test_symm_DL_fa_dun core:SymmDLTests:test_symm_DL_fa_elec core:SymmDLTests:test_symm_DL_fa_intra_rep core:SymmDLTests:test_symm_DL_fa_rep core:SymmDLTests:test_symm_DL_fa_sol core:SymmDLTests:test_symm_DL_hbonds core:SymmDLTests:test_symm_DL_omega core:SymmDLTests:test_symm_DL_p_aa_pp core:SymmDLTests:test_symm_DL_pro_close core:SymmDLTests:test_symm_DL_rama core:SymmDLTests:test_symm_DL_rama_prepro core:SymmDLTests:test_symm_DL_rama_prepro2 core:SymmDLTests:test_symm_DL_talaris2014 core:SymmDLTests:test_symm_DL_yhh_planarity core:SymmDL_betanov15_Tests:test_symm_DL_beta core:SymmDL_betanov15_Tests:test_symm_DL_cart_bonded core:SymmDL_betanov15_Tests:test_symm_DL_default_scorefxn core:SymmDL_betanov15_Tests:test_symm_DL_dslf_fa13 core:SymmDL_betanov15_Tests:test_symm_DL_fa_atr core:SymmDL_betanov15_Tests:test_symm_DL_fa_dun core:SymmDL_betanov15_Tests:test_symm_DL_fa_elec core:SymmDL_betanov15_Tests:test_symm_DL_fa_intra_rep core:SymmDL_betanov15_Tests:test_symm_DL_fa_intra_sol_xover4 core:SymmDL_betanov15_Tests:test_symm_DL_fa_rep core:SymmDL_betanov15_Tests:test_symm_DL_fa_sol core:SymmDL_betanov15_Tests:test_symm_DL_hbonds core:SymmDL_betanov15_Tests:test_symm_DL_lk_ball_wtd core:SymmDL_betanov15_Tests:test_symm_DL_omega core:SymmDL_betanov15_Tests:test_symm_DL_p_aa_pp core:SymmDL_betanov15_Tests:test_symm_DL_pro_close core:SymmDL_betanov15_Tests:test_symm_DL_rama core:SymmDL_betanov15_Tests:test_symm_DL_rama_prepro core:SymmDL_betanov15_Tests:test_symm_DL_rama_prepro2 core:SymmDL_betanov15_Tests:test_symm_DL_yhh_planarity core:SymmDL_nmethyl_Tests:test_symm_DL_cart_bonded core:SymmDL_nmethyl_Tests:test_symm_DL_default_scorefxn core:SymmDL_nmethyl_Tests:test_symm_DL_dslf_fa13 core:SymmDL_nmethyl_Tests:test_symm_DL_fa_atr core:SymmDL_nmethyl_Tests:test_symm_DL_fa_dun core:SymmDL_nmethyl_Tests:test_symm_DL_fa_elec core:SymmDL_nmethyl_Tests:test_symm_DL_fa_intra_rep core:SymmDL_nmethyl_Tests:test_symm_DL_fa_rep core:SymmDL_nmethyl_Tests:test_symm_DL_fa_sol core:SymmDL_nmethyl_Tests:test_symm_DL_hbonds core:SymmDL_nmethyl_Tests:test_symm_DL_omega core:SymmDL_nmethyl_Tests:test_symm_DL_p_aa_pp core:SymmDL_nmethyl_Tests:test_symm_DL_pro_close core:SymmDL_nmethyl_Tests:test_symm_DL_rama core:SymmDL_nmethyl_Tests:test_symm_DL_rama_prepro core:SymmDL_nmethyl_Tests:test_symm_DL_rama_prepro2 core:SymmDL_nmethyl_Tests:test_symm_DL_talaris2014 core:SymmDL_nmethyl_Tests:test_symm_DL_yhh_planarity core:SymmDL_peptoid_Tests:test_peptoid_mirroring core:SymmDL_peptoid_Tests:test_symm_DL_cart_bonded core:SymmDL_peptoid_Tests:test_symm_DL_default_scorefxn core:SymmDL_peptoid_Tests:test_symm_DL_dslf_fa13 core:SymmDL_peptoid_Tests:test_symm_DL_fa_atr core:SymmDL_peptoid_Tests:test_symm_DL_fa_dun core:SymmDL_peptoid_Tests:test_symm_DL_fa_elec core:SymmDL_peptoid_Tests:test_symm_DL_fa_intra_rep core:SymmDL_peptoid_Tests:test_symm_DL_fa_rep core:SymmDL_peptoid_Tests:test_symm_DL_fa_sol core:SymmDL_peptoid_Tests:test_symm_DL_hbonds core:SymmDL_peptoid_Tests:test_symm_DL_omega core:SymmDL_peptoid_Tests:test_symm_DL_p_aa_pp core:SymmDL_peptoid_Tests:test_symm_DL_pro_close core:SymmDL_peptoid_Tests:test_symm_DL_rama core:SymmDL_peptoid_Tests:test_symm_DL_rama_prepro core:SymmDL_peptoid_Tests:test_symm_DL_rama_prepro2 core:SymmDL_peptoid_Tests:test_symm_DL_talaris2014 core:SymmDL_peptoid_Tests:test_symm_DL_yhh_planarity core:SymmLinMemInteractionGraphTests:test_sym_linmem_ig_with_asu_in_middle core:SymmLinMemInteractionGraphTests:test_symm_minimalist_ig core:SymmMinimalistInteractionGraphTests:test_symm_minimalist_ig core:SymmetricConformationTests:test_symmetric_conformation core:SymmetricMinimizerTests:test_c2_symm_score core:SymmetricMinimizerTests:test_c3_symm_score core:SymmetricMinimizerTests:test_cs_symm_score core:SymmetricMinimizerTests:test_fibril_symm_score core:SymmetricRotamerTrials:test_symmetric_rotamer_trials core:SymmetricScoreTest:test_SymmetricScoreTest core:Symmetric_Binary_Protein_Silent_File_Tests:test_save_and_restore core:SymmetryUtilTests:test_make_score_function_consistent core:SymmetryUtilTests:test_symmetrize_fold_tree core:TableVsAnalyticEtableTests:test_etable_analytic_derivatives core:TableVsAnalyticEtableTests:test_etable_analytic_lk_individual core:TaskOperationsTests:test_DisallowIfNonnativeTaskOperation core:TaskOperationsTests:test_ProhibitResidueProperties core:TaskOperationsTests:test_ProhibitSpecifiedBaseResidueTypes core:TaskOperationsTests:test_ReplicateTaskTaskOperation core:TaskOperationsTests:test_RestrictToResidueProperties core:TaskOperationsTests:test_RestrictToSpecifiedBaseResidueTypes core:TestAsymmetricUnitSelector:test_select_master_subunit_selector core:TestAutoDetectGlycanConnections:test_auto_detect_mmtf_readwrite core:TestAutoDetectGlycanConnections:test_auto_detect_pdb_read core:VDW_EnergyTests:test_vdw_trie_vs_trie core:VirtualResidueScoreTest:test_centroid_vrt_scores core:VirtualResidueScoreTest:test_fa_vrt_scores core:VoidsPenaltyEnergyTests:test_packing_success core:VoidsPenaltyVoxelGridTests:test_compute_bounding_box core:VoidsPenaltyVoxelGridTests:test_voxel_grid core:VoidsPenaltyVoxelGridTests_rotamer_setup:test_rotamer_setup core:VoidsPenaltyVoxelGridTests_rotamer_setup_2:test_rotamer_setup_2 core:WaterMediatedHbondMetricTests:test_basic_functions core:WaterMediatedHbondMetricTests:test_depth_one core:WaterMediatedHbondMetricTests:test_depth_one_with_self core:WaterMediatedHbondMetricTests:test_depth_two core:WaterMediatedHbondMetricTests:test_only_depth_two core:WaterMediatedHbondMetricTests:test_sele1_to_sele2 core:YHHPlanarityEnergyTests:test_yhh_planarity_deriv_check_w_total_flexibility core:YHHPlanarityEnergyTests:test_yhh_planarity_start_score_start_func_match_w_partial_flexibility core:YHHPlanarityEnergyTests:test_yhh_planarity_start_score_start_func_match_w_total_flexibility core:component_reading_Tests:test_load_components core:conformation_stored_restypes_tests:test_cartmin_restype_noset core:conformation_stored_restypes_tests:test_load_pdb core:conformation_stored_restypes_tests:test_load_pdb_with_pose_copy core:conformation_stored_restypes_tests:test_load_restype_conf core:conformation_stored_restypes_tests:test_min_restype_noset core:conformation_stored_restypes_tests:test_pack_restype_noset core:conformation_stored_restypes_tests:test_score_restype_noset core:conformation_stored_restypes_tests:test_serialization core:metalloprotein_import:test_metalloprotein_import core:mmcif_IO:test_mmcif_input core:mmcif_IO:test_mmcif_output core:mmcif_IO:test_mmcif_vs_pdb_input core:mmcif_IO:test_multimodel_cif core:mmtf_IO:test_add_link_and_ss_information core:mmtf_IO:test_add_or_read_extra_data core:mmtf_IO:test_aiPose_from_sfr core:mmtf_IO:test_bond_info_io core:mmtf_IO:test_mmtf_model_io core:mmtf_IO:test_mmtf_noncanonicals core:mmtf_IO:test_mmtf_roundtrip core:mmtf_IO:test_mmtf_simple_metric_IO core:mmtf_IO:test_mmtf_string_float_map_IO core:mmtf_IO:test_mmtf_testsuite core:residue_support_Tests:test_make_centroid core:residue_support_Tests:test_make_centroid_no_crash core:residue_support_Tests:test_possible_nbr core:residue_support_Tests:test_recharging core:residue_support_Tests:test_renaming core:residue_support_Tests:test_rigid_matrix core:residue_support_Tests:test_shortest_path core:rtmin_setup_Tests:test_noop_test core:rtmin_setup_Tests:test_rtmin_setup core:single_mol_loading_Tests:test_file_positioning devel:BuildSheetTests:test_flat_sheet_grid devel:CoreResiduesPerElementFilterTests:test_bad_struct devel:CoreResiduesPerElementFilterTests:test_good_struct devel:FoldabilityFilterTests:test_foldability devel:MMTDriverTests:test_MMTDriver_end_to_end devel:MMTMinPackingJobTests:test_initialize_minpacking_job devel:MMTMinPackingJobTests:test_run_quick_minpacking devel:ZnHashTests:test_ZnCoordConstraint_score_two_matches devel:ZnHashTests:test_ZnCoordinateConstraint_transform_coordinates devel:ZnHashTests:test_score_zn_constraint_in_pose numeric:MinimalClashHashTest:test_that_it_works numeric:bridgeObjectsTests:test_nonredundant_bridgeObject numeric:bridgeObjectsTests:test_symm_solutions protocols:AchiralResidueTypeTests:test_import_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_import_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov15:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_import_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_mirror_symmetry_sarcosine_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols: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: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: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:AlignResiduesMoverTests:test_align_theozyme protocols:AlignResiduesMoverTests:test_tomponent_cstfile 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: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:BackrubMoverTest:test_BackrubMover protocols:BetaAlphaDisulfideTests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov15_Tests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov16_Tests:test_mixed_disulf protocols:BranchAngleOptimizerTest:test_BranchAngleOptimizer protocols:BridgeChainsMoverTests:test_conn_chains protocols:BridgeChainsMoverTests:test_twohelix protocols:BuildDeNovoBackboneMoverTests:test_design protocols:BuildDeNovoBackboneMoverTests:test_symmetry 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:CM_Util_Tests:test_loop_picking_aligned protocols:CM_Util_Tests:test_loop_picking_chainbreak protocols:CalculatorFilterTests:test_calculatorfilter protocols:CalculatorFilterTests:test_parsing protocols:ClassicGridTests:test_score_function protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features protocols:CompoundArchitectTests:test_compound_architect_with_connection protocols:CompoundArchitectTests:test_gerard_case protocols:CompoundArchitectTests:test_simple_compound_architect protocols:ConcatenatePosesTests:test_concatenator 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:ConstraintsManagerTests:test_pose_cache 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: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:CoupledMovesProtocolTests:test_apply protocols:CoupledMovesProtocolTests:test_bad_init protocols:CreateSequenceMotifOperationTests:test_task_op 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: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:DisulfideInsertionMoverTests:test_apply_function protocols:DisulfideInsertionMoverTests:test_cyclization_viability_function protocols:DisulfideInsertionMoverTests:test_rosettascripts_options protocols:DisulfidizeMoverTests:test_disulfidize protocols:DisulfidizeMoverTests:test_multiplex protocols:DockingTest:test_DockingPacking protocols:DockingTest:test_DockingProtocolFunctions protocols:DockingTest:test_DockingProtocol_clone protocols:DockingTest:test_DockingRigidBodyMinimize protocols:DockingTest:test_DockingSlideIntoContact protocols:DockingTest:test_EllipsoidalRandomizationMover protocols: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: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:EnergyJobSummaryTests:test_basic_energy_job_summary 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:EnzScoreFilterTests:test_auto_enzdes_csts protocols:EnzScoreFilterTests:test_resnum_enzdes_csts protocols:EnzScoreFilterTests:test_whole_pose_enzdes_csts 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: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:FilterReportAsPoseExtraScoresMoverTests:test_FilterReportAsPoseExtraScoresMover 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:ForceDisulfidesMoverTests:test_keep_existing protocols:ForceDisulfidesMoverTests:test_original protocols:ForceDisulfidesMoverTests:test_parse protocols:ForceDisulfidesMoverTests:test_rearrange protocols:ForceDisulfidesMoverTests:test_remove_existing 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: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:GunnCostTest:test_cost protocols:HBNetMoverTests:test_hbnet_mover_setup protocols:HBondCalculatorsTest:test_hb_calculators protocols:HelicalBundlePDBInfoTests:test_pdbinfo_on_append protocols:HelixPairingFilterTests:test_pose_without_helices protocols:HelixPairingFilterTests:test_two_helix 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: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: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:InvrotTreeTest:test_invrot_tree 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: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: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: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: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: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:MPDockingSetupMoverTest:test_parse_my_tag_input protocols:MPFastRelaxFoldTreeTest:test_double_chain_com_anchored_foldtree protocols:MPFastRelaxFoldTreeTest:test_single_chain_com_anchored_foldtree protocols:MPLipidAccessibilityTest:test_mp_lipid_accessibility protocols:MPLipidAccessibilityTest:test_parse_my_tag_input protocols:MPRangeRelaxMover:test_mprangerelaxmover_parse_my_tag_input 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: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: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:MoverJobTests:test_basic_mover_job protocols:MoverJobTests:test_seq_mover_job protocols:MoversTest:test_AllMovers 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:MutateResidueTests:test_mutate_residue 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: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: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:PairedSheetResidueSelectorTests:test_paired_res 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:PeptideStubMoverTests:test_append protocols:PeptideStubMoverTests:test_append2 protocols:PeptideStubMoverTests:test_append_repeat protocols:PeptideStubMoverTests:test_multi_append protocols:PeptideStubMoverTests:test_multi_prepend protocols:PeptideStubMoverTests:test_prepend protocols:PeptideStubMoverTests:test_prepend2 protocols:PeptideStubMoverTests:test_prepend_fail protocols:PeptideStubMoverTests:test_prepend_repeat protocols:PointMutScanDriverTests:test_calculate_neighbor_table protocols:PointMutScanDriverTests:test_fill_mutations_list protocols:PointMutScanDriverTests:test_fill_mutations_list_double_mutant_scan protocols:PointMutScanDriverTests:test_fill_mutations_list_single_mutant_scan protocols:PointMutScanDriverTests:test_make_specific_mutant protocols:PointMutScanDriverTests:test_make_specific_mutant_insertion_code protocols:PoseManipulationTests:test_linear_rigid_body_moves protocols:PoseManipulationTests:test_repack_functions protocols:PoseManipulationTests:test_rotation_rigid_body_moves protocols:PreProlineFilterTests:test_compute protocols:PreProlineFilterTests:test_spline protocols:PredockRotCenterTest:test_predock_rotcenter protocols:ProteinInterfaceDesignOperationTests:test_ProteinInterfaceDesignOperation protocols:ProteinInterfaceDesignOperationTests:test_ProteinInterfaceDesignOperation_all protocols:ProteinInterfaceDesignTests:test_AtomicContactCount_filter protocols:ProteinProteinInterfaceUpweighterTests:test_packing_4SER protocols:ProteinSCSamplerTests:test_sc_sampler_ctor protocols:ProteinSCSamplerTests:test_sc_sampler_desymmeterize protocols:ProteinSilentReportTests:test_main protocols:PruneBuriedUnsatsOperationTests:test_burial_sanity_check protocols:PruneBuriedUnsatsOperationTests:test_pruning_arg_and_two_ser protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_bb protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_satisfied_bb protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_satisfied_ser protocols:PruneBuriedUnsatsOperationTests:test_pruning_asn_to_ser protocols:PseudocontactShiftTests:test_eval_abinitio_pcs_only protocols:PseudocontactShiftTests:test_eval_pcs_energy_on_abinitio_output protocols:PseudocontactShiftTests:test_eval_pcs_energy_on_native protocols: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: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:RemodelConstraintGeneratorTest:test_sheet_constraints 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:RestrictToCDRH3LoopTest:test_RestrictToCDRH3Loop 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: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: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:SecondaryStructureFilterTests:test_convert_impossible_pairings protocols:SegmentSequenceProfileTests:test_simple_profile 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: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:SimpleCycpepPredictApplicationTests:test_designfile_read protocols:SimpleCycpepPredictApplicationTests:test_mergesort protocols:SimpleCycpepPredictApplicationTests:test_mergesort_edgecases protocols:SimpleCycpepPredictApplicationTests:test_mergesort_rmsd protocols:SimpleCycpepPredictApplicationTests:test_quicksort protocols:SimpleCycpepPredictApplicationTests:test_quicksort_cis_peptide_bonds protocols:SimpleCycpepPredictApplicationTests:test_quicksort_rmsd protocols:SimpleCycpepPredictApplicationTests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_betanov15_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_Tests:test_simple_cycpep_predict_withfile protocols:SimpleCycpepPredictApplication_design_betanov15_Tests:test_simple_cycpep_predict protocols:SimpleCycpepPredictApplication_design_betanov15_Tests:test_simple_cycpep_predict_withfile protocols:SimpleMetricProtocolsTests:test_composite_real_metric protocols:SimpleMetricProtocolsTests:test_composite_string_metric protocols:SimpleMetricProtocolsTests:test_composite_total_energy_metric protocols:SimpleMetricProtocolsTests:test_dihedral_metric protocols:SimpleMetricProtocolsTests:test_protocol_settings_metric protocols:SimpleMetricProtocolsTests:test_real_metric protocols:SimpleMetricProtocolsTests:test_rmsd_metric protocols:SimpleMetricProtocolsTests:test_string_metric protocols:SimpleMetricProtocolsTests:test_total_energy_metric protocols:SimpleThreadingMoverTests:test_basic_class protocols:SiteGridTests:test_score_function protocols:SmallMoverTest:test_SmallMover protocols:SmallMoverTest:test_SmallMover_w_sugar protocols:SmallMoverTest:test_one_small_move 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: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: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: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: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:TaskAwareMinMoverTests:test_TaskAwareMinMover protocols:TaskSelectorTests:test_TaskSelector_parse_my_tag protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_closes protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_copy_ctor protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_exceptions protocols:TestCCDLoopClosureMover:test_CCDLoopClosureMover_mover_factory protocols:ThreadingMover_Tests:test_basic_threading protocols:TiltMoverTest:test_constructor_from_jumpnum_and_angle protocols:TiltMoverTest:test_tiltmover_parse_my_tag_input 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: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: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:hybridization_TMalign_Tests:test_align_pose1_onto_pose2 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