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Revisions №13655

branch: commits 「№13655」
Commited by: Vikram K. Mulligan
GitHub Pull Request link: 「№4225」
Merge: 「29f1d046a」「f52998199」  code diff
Scheduled at: 2019-09-16 23:08:33.144781
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit cppcheck mpi mpi.serialization build.header build.levels ninja graphics static beautification serialization 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

Pull Request №4225 master←vmullig/no_nbr_atom_error Merge: 29f1d046a74a32ff8637a99a12f858cecf11d78c←f52998199699a4f99400de5cca0e09b70ac940ca Adding check for NBR_ATOM and NBR_RADIUS lines in params files. ---------------- Merge commit message: Adding check for NBR_ATOM and NBR_RADIUS lines in params files.

Rosetta Benchmark 9 months
Tests for this revision was automatically canceled because newer set of tests for pull-request №4225 was submitted!
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Test: linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit

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Test: mac.clang.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments KillA2019 LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector OversaturatedHbondAcceptorFilter PDB_diagnostic PeptideCyclizeMover PeptideStubMover_prependRepeat ProQ RBOut ReadResfile_with_selector RescorePDDF ResidueDisorder SID_rescore SSElementSelector SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter ThreadingInputter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector abinitio add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_graft antibody_numbering_converter assemble_domains_jd2 autoNOE_rosetta autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot batch_relax beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins bridge_chains broker broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter buried_area_filter buried_unsat_kinemage buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa carbohydrates cart_min_glycans cartesianddg ccd_ends_graft_mover_rs centroid_disulfide_scores centroid_from_fullatom classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_filter composition_energy_layers constel contactMap copy_rotamer_mover coupled_moves create_clash-based_repack_shell create_sequence_motif crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io database_session_resource ddG_ensemble ddG_of_mutation ddG_scan density_denovo density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA distances disulfidize_beta_cys dna_interface_design dock_glycans docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_low_res docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal drrafter_error_estimation drrafter_run energy_based_clustering_alpha_aa energy_based_clustering_alpha_aa_bin_analysis energy_based_clustering_alpha_aa_dihedral entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution explicit_membrane extract_atomtree_diffs farfar_mrna farnesyl fast_relax fast_relax_scripts favor_native_residue features features_database_schema features_parallel features_pdb fiber_diffraction fiber_diffraction_fad fit_helixparams fit_helixparams_a3b fit_helixparams_rms fix_alignment_to_match_pdb fixbb flexpepdock flexpepdock_abinitio fold_and_dock fold_cst_new fold_from_loops fragment_picker fragmentpicker_integration_demo fuzzy ga_ligand_dock gen_apo_grids gen_lig_grids generate_6Dloopclose genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycan_tree_relax_build_single glycan_tree_relax_quench glycomutagenesis glycosylation grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbonds hbonds_sp2 hbondstoresidue_selector hbs_design helical_bundle helical_bundle_nonideal helical_bundle_predict helix_from_sequence homodimer_fnd_ref2015_memb hotspot_hashing hotspot_stub_constraints hshash_utils hybridization identify_cdr_clusters ig_dump interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design inverse_rotamer_remodel jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout jscore kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_modeling make_and_perturb_bundle_multirepeat make_exemplar make_mainchain_potential make_mainchain_potential_symm make_mainchain_potential_symm_preproline make_rot_lib make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml measure_lcaa_radii membrane_abinitio membrane_relax membrane_relax_hbond metal_setup metalloprotein_abrelax metalloprotein_broker mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mg_modeler mg_modeler_lores mhc_epitope mhc_epitope_nmer_preload min_pack_min minimize_6Dloopclose minimize_with_elec_dens mirror_symm mm_params mmtfIO_score_test motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_find_interface mp_interface_statistics mp_loadtime mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_range_relax mp_relax mp_relax_w_ligand mp_score_jd2 mp_span_ang_ref2015_memb mp_span_from_pdb mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols multistage_rosetta_scripts multistage_rosetta_scripts_clustering mutate ncaa_fixbb ncbb_packer_palette netcharge_design netcharge_design_symm next_generation_KIC noe_assignment non-canonical_connectivities nonideal_rtmin nucleobase_sample_around number_of_residuetypes oligourea_design oligourea_predict oop_create oop_design oop_dock_design orbitals pH_mode peptiderive per_residue_energies per_residue_sc_sasa pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate phosphorylation pmut_scan pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets polyaramid_test_trivial posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG protocol_metric pwsho pymol_cif r_pdb2top r_rmsf ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces read_polymeric_components readin_dna_rna_protein real_virt_mover recces_turner recon_design referencepose_mutateresidue relax_w_allatom_cst remodel remodel_disulfides remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax report_hbonds_for_plugin res_lipo_ref2015_memb residue_energy_breakdown resource_database_locator restype_converter rings rna_add_WC_stats rna_assemble rna_assemble_legacy rna_cluster rna_denovo rna_denovo_RNP_low_res rna_denovo_RNP_refine_native rna_denovo_base_pair_constraints rna_denovo_base_pair_setup rna_denovo_base_pair_setup_legacy rna_denovo_bps rna_denovo_bps_fixed_ends rna_denovo_bps_helix_ends rna_denovo_bps_helix_ends_legacy rna_denovo_bps_legacy rna_denovo_dna_bridge rna_denovo_fragment_homology_exclusion rna_denovo_grid_vdw rna_denovo_grid_vdw_legacy rna_denovo_lariat rna_denovo_legacy rna_denovo_new_FT_2in_dens rna_denovo_new_FT_5P_j12_leadzyme rna_denovo_new_FT_RNP_2prot_dens rna_denovo_new_FT_rna_two_chains rna_denovo_new_libs rna_denovo_symm_hack rna_design rna_farfar_block_stack rna_farfar_noncanonical_hairpin rna_farfar_syn_chi_res rna_helix rna_minimize rna_minimize_6D_loop_close rna_motif rna_predict_chem_map rna_puzzle11_H2H3H4_run3_connectU40 rna_puzzle12_P5P6P7_DMS rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation rna_puzzle5_p2_GAAA_mini rna_puzzle6_U75G76A77_on_thread1 rna_puzzle6_j67_into_p6p7rigidbody_thread1 rna_ribosome_tether rna_score rna_screen_phosphates rna_suitename rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_jd3 rosetta_scripts_loops rotamer_recovery rotamer_recovery_compare_two_structures rs_loophash sasa_metric_options score_jd2 score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI select_best_unique_ligand_poses selected_residue_count_metric sequence_profile_constraints sequence_recovery sequence_tolerance set_torsion shobuns silent2frag simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_per_residue site_constraint small_molecule_lattice_dock smallmover_resselector splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter startfrom_file stepwise_lores stored_residue_subset struc_set_fragment_picker super_aln supercharge surface_docking swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_cluster swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swa_rna_erraser swa_rna_gagu_01_append swa_rna_gagu_02_prepend swa_rna_gagu_03_append_to_silent swa_rna_gagu_04_clustering swa_rna_gagu_05_prepend_to_5primeterminus swa_rna_gagu_06_append_to_3primeterminus swa_rna_gagu_07_prepend_dinucleotide swa_rna_gagu_08_append_dinucleotide swa_rna_gagu_09_sample_virtual_ribose swa_rna_gagu_10_prepend_and_ccd_close swa_rna_gagu_11_append_and_ccd_close swa_rna_gagu_12_helix_addition swa_rna_gagu_13_chunk_combination_and_closure swa_rna_gagu_14_combine_long_loop_filtering swa_rna_gagu_15_combine_long_loop_sampling swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide swa_rna_gagu_17_append_floating_base swa_rna_gagu_18_rebuild_bulge swa_rna_gagu_19_prepend_floating_base_by_jump swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump swa_rna_gagu_22_prepend_and_kic_close swa_rna_gagu_23_append_and_kic_close swa_rna_loop_clusterer swa_rna_loop_sampler sweep_respair_energies swm_add_rosettascripts swm_beta_peptide_loop swm_build_full_model swm_dna_bridge swm_dna_loop swm_l_rna swm_protein_CCDmove swm_protein_from_scratch swm_protein_loop_sampler swm_protein_move_inside_coiledcoil_by_bond swm_protein_move_inside_helix_by_bond swm_protein_preminimize swm_rna_base_pair_constraints swm_rna_checkpoint_partition swm_rna_fourwayjunction swm_rna_loop_design swm_rna_move_align_dock swm_rna_move_inside_helix_by_bond swm_rna_move_inside_helix_by_jump swm_rna_move_two_strands swm_rna_nickedhelix swm_rna_protonated_adenosine swm_rna_singleloop swm_rna_srl_triplet symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetric_docking symmetrical_residue_selector symmetry_data_resource symmetry_multicomponent task_selector tcrmodel template_features test1_benchmark test_computed_saxs_spectrum test_d_l_readin test_idealize thermal_sampler threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling unfolded_state_energy_calc validate_database vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
Test: linux.clang.performance

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Test: linux.clang.scripts.rosetta.parse

Failed sub-tests (click for more details):
pilot.cyclic_peptide_design.cis_peptide_design_backbone_generation.KIC pilot.enzymedesign.design_threading.relax_deimm_designs pilot.enzymedesign.proenzyme_design.cpg2_proenzyme_disulfidize pilot.enzymedesign.proenzyme_design.cpg2_proenzyme_interface_saltbridges pilot.enzymedesign.proenzyme_design.cpg2_proenzyme_prodomain_energylandscape pilot.metal_binding.zinc_dependent_hydrolase.05_symmetrize_matcheZn_rb_min pilot.metal_binding.zinc_dependent_hydrolase.05_symmetrize_matchechi_min_match pilot.metal_binding.zinc_dependent_hydrolase.15_relax_w_zadd_zn pilot.protein_binding_energy_estimation.h3h4_designs.fastrelax3x_h3h4_fullrelax pilot.protein_design.backrub_disulfidize_monte_carlo.backrub_disulfidize_monte_carlo pilot.protein_design.de_novo_heterodimers.heterodimer_LSAS_final_design_close_loops_only pilot.protein_design.scotts_scripts.invrot_rem_itest pilot.protein_design.scotts_scripts.mutate_minimize_w_cst pilot.protein_interface_design.edge_strand_mediated_interface_design.multidomain_1_bpb pilot.protein_interface_design.edge_strand_mediated_interface_design.multidomain_1_sel_bpb pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_add_2nd_helix_back_designs_bpb2_csts pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_add_2nd_helix_back_designs_c_pass_ba.bp_pass__20161129210609.pdb.bp_20161219173455_0001_0002_bpb2 pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_add_2nd_helix_back_designs_c_pass_gba.bp_pass__20161129210228.pdb.bp_20161219172446_0001_0001_bpb2 pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_add_2nd_helix_back_designs_c_pass_gba.bp_pass__20161129210254.pdb.bp_20161219172548_0001_0003_bpb2 pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_add_2nd_helix_back_designs_c_pass_gba.bp_pass__20161129210726.pdb.bp_20161219173002_0001_0001_bpb2 pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_extend_cter_bpb pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_DeNovo_scaffolds_DeNovoStrands_motif15aa_l3_off-1_rosman_2kpo_renumber pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_bulge_processed_renumber pilot.protein_interface_design.edge_strand_mediated_interface_design.relaxed_tfr_retry_nonrelaxed_large_sheet_bulge_bulge_processed_renumber pilot.protein_interface_design.edge_strand_mediated_interface_design.rif_rifdock_HHHscafs_sel_designs_bpb pilot.scoring.fast_relax_and_score.fast_relax_and_score pilot.symmetry.symm public.analysis.interface.analyze_electrostatics_in_helix_trimer public.analysis.interface.custom_interface_filter1 public.analysis.interface.delete_chain_then_interface_analyzer public.docking.terrible_analyze_mutations_at_interface public.homology_modeling.relax_into_density.relax_into_density public.loop_modeling.simple_loop_grower.simple_loop_grower public.protein_hacking.helix_extend_with_threading public.protein_hacking.helix_extender public.sewing.refinement.HR1B_refinement public.sewing.refinement.HR1B_refinement_remove_partner public.sewing.refinement.refine_C-terminal_binding_helix public.visualize_protocol.template_pymol_mover
Test: linux.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:AACompositionEnergyTests_consttail:test_tailfunctions_const_lin core:AACompositionEnergyTests_interpolate_linear:test_interpolation_linear_tails core:AACompositionEnergyTests_linconsttail:test_tailfunctions_lin_const core:AACompositionEnergyTests_packer:test_energy_annealing core:AACompositionEnergyTests_quadratail:test_tailfunctions_quadratic core:AACompositionEnergyTests_quadratic_interpolation:test_interpolation_quadratic_tails core:AARepeatEnergyTests:test_energy_annealing core:AARepeatEnergyTests:test_energy_cases core:AARepeatEnergyTests:test_energy_eval core:ABEGOManagerTest:test_abego core:AndJumpSelectorTests:test_AndJumpSelector_fail_parse_subtag core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag_no_provided_selectors core:AndJumpSelectorTests:test_AndJumpSelector_parse_my_tag_selectors_not_in_datamap core:AndJumpSelectorTests:test_AndJumpSelector_parse_subtag_v1 core:AndJumpSelectorTests:test_AndJumpSelector_parse_subtag_v2 core:AndJumpSelectorTests:test_and_jump_selector_odd_1mod5_lots_of_jumps core:AndJumpSelectorTests:test_and_jump_selector_odd_1mod5_no_jumps core:AndResidueSelectorTests:test_AndResidueSelector_fail_parse_subtag core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag_no_provided_selectors core:AndResidueSelectorTests:test_AndResidueSelector_parse_my_tag_selectors_not_in_datamap core:AndResidueSelectorTests:test_AndResidueSelector_parse_subtag core:AndResidueSelectorTests:test_and_residue_selector_odd_1mod5 core:AngleConstraintTests:test_angle_constraint_clone core:AngleConstraintTests:test_angle_constraint_equality_operator core:AngleConstraintTests:test_angle_derivatives core:AngleConstraintTests:test_angle_score core:AngleConstraintTests:test_serialize_AngleConstraint core:AnnotatedSequenceTests:test_make_pose_from_saccharide_sequence core:AnnotatedSequenceTests:test_residue_types_from_saccharide_sequence core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_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 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core:IsopeptideBondTests:test_rama_prepro 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:LoopGraphTest:test_loop_cycles core:MHCEpitopeConstraintTests:test_mhc_constraints 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_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_extra_data core:MolFileIODataTests:test_sdfreader 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:NetChargeEnergyTests_packer:test_energy_annealing core:NetChargeEnergyTests_packer_symm:test_energy_annealing_symmetric core:NetChargeEnergyTests_tailfxns:test_constant_tailfxns core:NetChargeEnergyTests_tailfxns:test_linear_tailfxns core:NetChargeEnergyTests_tailfxns:test_quadratic_tailfxns core: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_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:P_AA_pp_Energy_SymGlyTests:test_eval_symm_energy 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:PeptoidResidueTypeTests:test_lower_connect_dependence core:PhiSelectorTests:test_phiselector_negativephi core:PhiSelectorTests:test_phiselector_negativephi_no_ignore_unconnected_upper core:PhiSelectorTests:test_phiselector_positivephi core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_meta_ala core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_ortho_ala core:PolyaramidBackboneMinimizeTests:test_min_phi_succeeds_para_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_meta_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_ortho_ala core:PolyaramidBackboneMinimizeTests:test_min_psi_succeeds_para_ala core:PolylinearInterpolationTests:test_1D core:PolylinearInterpolationTests:test_1D_wraparound core:PolylinearInterpolationTests:test_polylinear_interpolation_2D_derivs core:PolylinearInterpolationTests:test_polylinear_interpolation_3D_derivs core:PolylinearInterpolationTests:test_polylinear_interpolation_3D_derivs_wraparound core:PolylinearInterpolationTests:test_polylinear_interpolation_lysine_derivs core:PoseFromPDBLoaderTests:test_PoseFromPDBLoader core:PoseFromSFRBuilderTests:test_1rgr core:PoseFromSFRBuilderTests:test_build_trpcage_pdb core:PoseFromSFRBuilderTests:test_read_cyclic_peptide_with_link_record core:PoseFromSFRBuilderTests:test_read_in_acylated_nterm_residue core:PoseFromSFRBuilderTests:test_read_in_res_both_acetylated_and_cterm core:PoseResidueTypeSetTests:test_addition core:PoseResidueTypeSetTests:test_local_vs_default core:PoseTests:test_Pose_mainchain_torsions core:PoseTests:test_Pose_observer core:PoseTests:test_append_pose_by_jump core:PoseTests:test_cutpoint_bond_rotation core:PoseTests:test_serialize_pose core:PoseTests:test_update_cutpoint_virtual_atoms_if_connected core:PoseTests:test_update_cutpoint_virtual_atoms_when_bond_declared core:PoseTests:test_update_cutpoint_virtual_atoms_when_cutpoint_variant_added core:PoseTests:test_update_residue_neighbors core:PoseToStructFileRepConverterTests:test_assignment_of_new_chainIDs_for_ligands core:PoseToStructFileRepConverterTests:test_conect_records core:PoseToStructFileRepConverterTests:test_foldtree_records core:PoseToStructFileRepConverterTests:test_membrane_hetatm core:PoseToStructFileRepConverterTests:test_title_section_records core:PoseToStructFileRepConverterTests:test_torsion_records core:PoseUtilTests:test_chain_designations core:PoseUtilTests:test_chainid_functions core:PoseUtilTests:test_chainletter_functions core:PoseUtilTests:test_compare_atom_coordinates core:PoseUtilTests:test_conformation_sha1 core:PoseUtilTests:test_fix_pdbinfo_damaged_by_insertion core:PoseUtilTests:test_jump_functions core:PoseUtilTests:test_pose_float_map core:PoseUtilTests:test_pose_string_map core:PoseUtilTests:test_reasonable_foldtree core:PoseUtilTests:test_renumber_pdbinfo_based_on_conf_chains core:PoseUtilTests:test_unique_chains core: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:RNA_FA_ElecEnergyTests:test_rnaelec_deriv_check_w_full_torsional_flexibility_smoothed_wo_ddd core:RNA_FA_ElecEnergyTests:test_rnaelec_nblist_autoupdate_no_smoothing core:RNA_FA_ElecEnergyTests:test_score_rna_pdb core: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:RamaPreProTests_oligourea:test_random_tors_canonical core:RamaPreProTests_oligourea:test_random_tors_canonical_d_aa core:RamaPreProTests_oligourea:test_random_tors_canonical_d_aa_prepro core:RamaPreProTests_oligourea:test_random_tors_canonical_prepro core:RamaPreProTests_symmgly:test_random_phipsi_gly core:RamaPreProTests_symmgly:test_random_phipsi_gly_invert core:RamaPreProTests_symmgly:test_random_phipsi_gly_prepro core:RamaPreProTests_symmgly:test_random_phipsi_gly_prepro_invert core:RamachandranEnergyTests:test_rama_deriv_check core:RamachandranEnergyTests:test_setup_for_minimizing_with_rama_and_full_bb_flex core:RamachandranEnergyTests:test_setup_for_minimizing_with_rama_and_partial_bbflex core:RamachandranEnergy_SymGlyTests:test_eval_symm_energy core:RamachandranPowerTest:test_eval_rama_score_residue core:RamachandranTest:test_eval_rama_score_residue core:RamachandranTest:test_phipsi_in_allowed_rama core:RamachandranTest:test_rama_cdf_creation core:RamachandranTest:test_rama_cdf_creation_for_ppo_torbin_A core:RamachandranTest:test_random_phipsi_from_rama core:RamachandranTest:test_random_phipsi_from_rama_by_torsion_bin core:RamachandranTest:test_uniform_phipsi_from_allowed_rama core:RandomResidueSelectorTests:test_RandomResidueSelector_parse_my_tag core: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:ResidueTest:test_fill_missing_atoms core:ResidueTest:test_fill_missing_atoms_polymer core:ResidueTest:test_isDNA core:ResidueTest:test_isLigand core:ResidueTest:test_recursive_identification_of_connection_dependencies core:ResidueTest:test_recursive_identification_of_connection_dependencies_peptoid core:ResidueTest:test_residue_serialization core:ResidueTypeBloatTests:test_number_of_residue_types core: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:ResidueTypeSetTests:test_get_mirror_type core:ResidueTypeSetTests:test_residue_type_sets core:ResidueTypeTests:test_atom_add core:ResidueTypeTests:test_chi_assignment core:ResidueTypeTests:test_icoor_reassignment core:ResidueTypeTests:test_odd_proline_ring_detection core:ResidueTypeTests:test_residue_type_initialization core:ResidueTypeTests:test_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:RingUtilityFunctionTests:test_is_atom_axial_or_equatorial core:RingUtilityFunctionTests:test_is_atom_axial_or_equatorial_to_ring core:RmsUtilTest:test_DLbundle_rmsd_aligned_unaligned core:RmsUtilTest:test_ca_rmsd_with_mapping core:RmsUtilTest:test_gdtsc core:RmsUtilTest:test_gdtsc_self core:RmsUtilTest:test_ligand_rms core:RmsUtilTest:test_superimpose_same core:RmsUtilTest:test_superimpose_self core:RotamerBuildingFunctionsTests:test_build_rotamers_from_rotamer_bins 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:ScoreFunctionFactoryTest:test__list_read_options_in_get_score_function__in_sync_w__get_score_function core:ScoreFunctionTest:test_ScoreFunction_ctor_actually_reads_option_collection core:ScoreFunctionTest:test_ScoreFunction_list_options_read_in_sync core:ScoreFunctionTest:test_add_weights_from_file core:ScoreFunctionTest:test_apply_patch_from_file core:ScoreFunctionTest:test_get_sub_score_exclude_res core:ScoreFunctionTest:test_get_sub_score_exclude_res_long_range_terms core: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:SequenceMetricTests:test_base_name core:SequenceMetricTests:test_full_name core:SequenceMetricTests:test_oneletter_code core:SequenceMetricTests:test_threeletter_code 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_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:SingleLigandRotamerLibraryTests:test_init_from_file_explicit_and_implicit core:SingleLigandRotamerLibraryTests:test_init_from_stream core:SingleNCAARotamerLibraryTests:test_B3C_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_B3N_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_DAB_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_DPP_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_ORN_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_d_nme_trp_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_equivalence_independent_of_rotamer_order core:SingleNCAARotamerLibraryTests:test_nme_trp_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_peptoid_001_off_rotamer_scoring core:SingleNCAARotamerLibraryTests:test_peptoid_001_off_rotamer_scoring_2 core:SingleNCAARotamerLibraryTests:test_peptoid_001_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_peptoid_001_spikes_in_dunbrack_landscape core:SingleNCAARotamerLibraryTests:test_peptoid_001_spikes_in_dunbrack_landscape_2 core:SingleNCAARotamerLibraryTests:test_peptoid_601_rotamer_well_scoring core:SingleNCAARotamerLibraryTests:test_peptoid_602_rotamer_well_scoring core:SingleNCAARotamerLibraryTests_Dun02:test_equivalent_derivatives_to_canonical core:SingleNCAARotamerLibraryTests_Dun02:test_equivalent_rotlib_values_to_canonical core:SingleNCAARotamerLibraryTests_Dun02:test_equivalent_scoring_to_canonical core:SingleNCAARotamerLibraryTests_Dun02_no_voronoi:test_equivalent_derivatives_to_canonical core:SingleNCAARotamerLibraryTests_Dun02_no_voronoi:test_equivalent_rotlib_values_to_canonical core:SingleNCAARotamerLibraryTests_Dun02_no_voronoi:test_equivalent_scoring_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_no_voronoi:test_equivalent_derivatives_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_no_voronoi:test_equivalent_rotlib_values_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_no_voronoi:test_equivalent_scoring_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_voronoi:test_equivalent_derivatives_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_voronoi:test_equivalent_rotlib_values_to_canonical core:SingleNCAARotamerLibraryTests_equivalency_voronoi:test_equivalent_scoring_to_canonical core:SingleNCAARotamerLibraryTests_oligourea:test_OU3_PRO_rotamer_well_scoring core:SingleNCAARotamerLibraryTests_oligourea:test_OU3_VAL_rotamer_well_scoring core:SingleResidueRotamerLibraryTests:test_expand_proton_chis core:SingleResidueRotamerLibraryTests:test_extra_chi_expansion 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:SplitUnfoldedReferenceEnergyTests:test_residue_energy_default_file_weights core:SplitUnfoldedReferenceEnergyTests:test_residue_energy_emap_weights core:SplitUnfoldedReferenceEnergyTests:test_residue_energy_no_weights core:SplitUnfoldedTwoBodyPotentialTests:test_get_restype_emap core:StoredRotamerLibrarySpecificationTests:test_add_conformers core:StoredRotamerLibrarySpecificationTests:test_add_rotamer 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 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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 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protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_AIB_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_GLY_before_proline protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine protocols:AchiralResidueTypeTests_betanov16:test_symmetric_rama_prepro_scoring_sarcosine_before_proline protocols:AddChainBreakTests:test_pose_manipulation protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_bounded protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_harmonic protocols:AddConstraintsToCurrentConformationMoverTests:test_atompair_scalar_weighted protocols:AddConstraintsToCurrentConformationMoverTests:test_coord_bounded protocols:AddConstraintsToCurrentConformationMoverTests:test_coord_harmonic protocols:AddHelixSequenceConstraintsMoverTests:test_detect_helices protocols:AddHelixSequenceConstraintsMoverTests:test_limit_ala protocols:AddHelixSequenceConstraintsMoverTests:test_limit_val protocols:AddHelixSequenceConstraintsMoverTests:test_limit_val_by_hydrophobicity protocols:AddHelixSequenceConstraintsMoverTests:test_negative_nterm protocols:AddHelixSequenceConstraintsMoverTests:test_positive_cterm protocols:AddMHCEpitopeConstraintMoverTests:test_mhc_csts protocols:AddMPLigandMoverTest:test_membrane_invariant protocols:AddMPLigandMoverTest:test_membrane_plus_ligand_foldtree protocols:AddMembraneMoverTest:test_anchored_foldtree protocols:AddMembraneMoverTest:test_conformation_invariant protocols:AddMembraneMoverTest:test_default_membrane_position protocols:AddMembraneMoverTest:test_existing_membrane_rsd protocols:AddMembraneMoverTest:test_initial_foldtree protocols:AddMembraneMoverTest:test_initial_spans_setup protocols:AddMembraneMoverTest:test_membrane_jump_tracking protocols:AddMembraneMoverTest:test_membrane_rsd_tracking protocols:AddMembraneMoverTest:test_multi_mem_pose1 protocols:AddMembraneMoverTest:test_multi_mem_pose2 protocols:AddMembraneMoverTest:test_single_tm_span_pose protocols:AlignByResidueSelectorMoverTests:test_all_true protocols:AlignByResidueSelectorMoverTests:test_name protocols:AlignByResidueSelectorMoverTests:test_shift_aligned protocols:AlignResiduesMoverTests:test_align_theozyme protocols:AlignResiduesMoverTests:test_tomponent_cstfile protocols:AlignmentEnergyTests:test_deriv protocols:AlignmentEnergyTests:test_score_values protocols:AntibodyCDRGrafterTests:test_graft_classes protocols:AntibodyConstraintTests:test_constraints protocols:AntibodyDatabase:test_cdr_loading protocols:AntibodyDatabase:test_options_cdr_set protocols:AntibodyDesignOptions:test_native_seq protocols:AntibodyDesignOptions:test_options_graft_design protocols:AntibodyDesignOptions:test_options_seq_design protocols:AntibodyInfoTests:test_camelid protocols:AntibodyInfoTests:test_cdr_numbering_and_transform protocols:AntibodyInfoTests:test_info_functions protocols:AntibodyInfoTests:test_kink_functions protocols:AntibodyInfoTests:test_renumbering protocols:AntibodyResidueSelectorsTest:test_selectors protocols:AntibodySeqDesign:test_graft_tf_generation1 protocols:AntibodySeqDesign:test_graft_tf_generation2 protocols:AntibodySeqDesign:test_normal_tf_generation protocols:AntibodySeqDesign:test_task_ops protocols:AntibodySeqDesign:test_utility_functions protocols:AntibodyTaskOps:test_AddCDRProfileSetsOperation protocols:AntibodyTaskOps:test_AddCDRProfilesOperation protocols:AntibodyTaskOps:test_DisableAntibodyRegionOperation protocols:AntibodyTaskOps:test_DisableCDRsOperation protocols:AntibodyTaskOps:test_RestrictToCDRsAndNeighbors protocols: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:BackrubProtocolTests:test_parse_pivots_from_residue_selector protocols:BasePairConstraintTests:test_all_constraint_possibilities protocols:BasePairConstraintTests:test_bad_when_stretched_all_constraint_possibilities protocols:BetaAlphaDisulfideTests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov15_Tests:test_mixed_disulf protocols:BetaAlphaDisulfide_betanov16_Tests:test_mixed_disulf protocols:BranchAngleOptimizerTest:test_BranchAngleOptimizer protocols:BridgeChainsMoverTests:test_conn_chains protocols:BridgeChainsMoverTests:test_twohelix protocols:BridgeTests:test_bridge_size_three protocols:BridgeTests:test_bridge_size_zero protocols:BridgeTests:test_bridge_two_chain protocols:BuildDeNovoBackboneMoverTests:test_design protocols:BuildDeNovoBackboneMoverTests:test_symmetry protocols:BuildManagerTests:test_compatibility_check protocols:BuildManagerTests:test_dependencies protocols:BuildManagerTests:test_modify protocols:BumpGridTests:test_bool3D_corners protocols:BumpGridTests:test_bool3D_corners2 protocols:BumpGridTests:test_bool3D_create_shifted_grid protocols:BumpGridTests:test_bool3D_grid_ctor protocols:BumpGridTests:test_bool3D_grid_ctor2 protocols:BumpGridTests:test_bool3D_grid_with_sphere protocols:BumpGridTests:test_bool3D_grid_with_sphere2 protocols:BumpGridTests:test_bool3D_grid_with_sphere_liberal protocols:BumpGridTests:test_bool3D_or_overlap protocols:BumpGridTests:test_bool3D_sphere_coverage protocols:BumpGridTests:test_bool3D_write_kinemage protocols:BumpGridTests:test_bumpgrid_for_pose protocols:CM_Util_Tests:test_loop_picking_aligned protocols:CM_Util_Tests:test_loop_picking_chainbreak protocols:CalculatorFilterTests:test_calculatorfilter protocols:CalculatorFilterTests:test_parsing protocols:ClaimTests:test_tclaim_constructor_multi_pos protocols:ClaimTests:test_tclaim_constructor_single_pos protocols:ClassicGridTests:test_score_function protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features protocols:CoMTrack:test_com_init protocols:CoMTrack:test_com_reset protocols:CompoundArchitectTests:test_compound_architect_with_connection protocols:CompoundArchitectTests:test_gerard_case protocols:CompoundArchitectTests:test_simple_compound_architect protocols:ConcatenatePosesTests:test_concatenator protocols:ConnectRightTests:test_connection protocols:ConnectionArchitectTests:test_bridge_connection protocols:ConnectionArchitectTests:test_staple_connection protocols:ConsensusLoopDesignOperationTests:test_loop_info_and_task_manipulation protocols:ConsensusLoopDesignOperationTests:test_read_db protocols:ConservativeDesignOperationTests:test_task_op protocols: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:CoordSerializationTests:test_serialization protocols:CoordinateConstraintGeneratorTests:test_constraints_allresidues protocols:CoordinateConstraintGeneratorTests:test_constraints_subset protocols:CoordinateConstraintGeneratorTests:test_input_bounded_default protocols:CoordinateConstraintGeneratorTests:test_input_harmonic_default protocols:CoordinateConstraintGeneratorTests:test_input_harmonic_sidechain protocols:CoordinateConstraintGeneratorTests:test_integration_native protocols:CoordinateConstraintGeneratorTests:test_native_harmonic_default protocols:CoordinateConstraintGeneratorTests:test_native_harmonic_sidechain protocols:CopyRotamerMoverTests:test_copyrotamermover protocols:CoupledMovesProtocolTests:test_apply protocols:CoupledMovesProtocolTests:test_bad_init protocols:CreateSequenceMotifOperationTests:test_task_op protocols:CrosslinkerMoverTests:test_tma_dihedral_fxn 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:DirectSegmentLookupTests:test_read_store protocols:DirectSegmentLookupTests:test_simple_mover protocols:DirectSegmentLookupTests:test_simple_sample protocols:DisulfideInsertionMoverTests:test_apply_function protocols:DisulfideInsertionMoverTests:test_cyclization_viability_function protocols:DisulfideInsertionMoverTests:test_rosettascripts_options protocols:DisulfidizeMoverTests:test_disulfidize protocols:DisulfidizeMoverTests:test_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:EnergyBasedClusteringTests:test_determine_ABOXYZ_bin protocols:EnergyBasedClusteringTests:test_get_circular_permutation_first_in_alphabetical_order protocols:EnergyBasedClusteringTests:test_num_asymmetric_binstrings protocols:EnergyBasedClusteringTests:test_num_asymmetric_binstrings_with_mirror_counterpart_represented protocols:EnergyBasedClusteringTests:test_permute_string protocols:EnergyBasedClusteringTests:test_storeposedata protocols:EnergyBasedClusteringTests_alpha_aa:test_cartesian_cluster_cyclic_alpha_aa protocols:EnergyBasedClusteringTests_alpha_aa:test_dihedral_cluster_cyclic_alpha_aa protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea protocols:EnergyBasedClusteringTests_oligourea:test_cartesian_cluster_cyclic_oligourea_s2_symm protocols:EnergyBasedClusteringTests_oligourea:test_dihedral_cluster_cyclic_oligourea protocols:EnergyJobSummaryTests:test_basic_energy_job_summary protocols: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:EnvironmentJump:test_cache_persistence protocols:EnvironmentJump:test_cut_inheritance protocols:EnvironmentJump:test_jump_moves protocols:EnvironmentJump:test_pdb_info_persistence protocols:EnvironmentTorsion:test_dual_environment protocols:EnvironmentTorsion:test_empty_environment protocols:EnvironmentTorsion:test_single_phi_moves protocols:EnvironmentTorsion:test_torsion_can_exclusive_compatibility protocols:EnvironmentTorsion:test_torsion_init protocols:EnvironmentTorsion:test_torsion_must_can_coexist protocols:EnvironmentTorsion:test_torsion_must_exclusive_incompatibility protocols:EnzScoreFilterTests:test_auto_enzdes_csts protocols:EnzScoreFilterTests:test_resnum_enzdes_csts protocols:EnzScoreFilterTests:test_whole_pose_enzdes_csts protocols: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:FilterFactoryTests:test_FilterFactory_all_Filter_all_attributes_have_descriptions protocols:FilterFactoryTests:test_FilterFactory_all_Filter_complexTypes_have_descriptions protocols:FilterFactoryTests:test_all_filters_define_valid_xsds protocols:FilterFactoryTests:test_confidence_usage protocols:FilterReportAsPoseExtraScoresMoverTests:test_FilterReportAsPoseExtraScoresMover protocols: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:FragmentCMTest:test_fragment_insertion protocols:FragmentCMTest:test_xml protocols:FragmentCandidatesTests:test_DiversifyCrmsdByClustering protocols:FragmentCandidatesTests:test_DiversifyCrmsdSelector protocols:FragmentCandidatesTests:test_DiversifyDihedralsSelector protocols:FragmentCandidatesTests:test_read_vall2 protocols:FragmentCandidatesTests:test_read_vall_fragments protocols:FragmentLookupTests:test_binary_store protocols:FragmentLookupTests:test_read_store protocols:FragmentMoverTest:test_mover protocols:FragmentMoverTest:test_proposed_ss protocols:FragmentMoverTest:test_ss_check protocols:FragmentMoverTest:test_steal protocols:FragmentMoverTest:test_window_start protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_L_alpha_backbone protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_L_alpha_backbone_lowmem protocols:GeneralizedKIC_Tests:test_GeneralizedKIC_mixed_DL_alpha_backbone protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_D protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_D_beforepro protocols:GeneralizedKIC_Tests_ramaprepro:test_GeneralizedKIC_ramaprepro_perturbation_canonical_beforepro protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_D protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_D_beforepro protocols:GeneralizedKIC_Tests_ramaprepro_NCAA:test_GeneralizedKIC_ramaprepro_perturbation_noncanonical_beforepro protocols:GenerateMainchainPotentialTests:test_full_run_ALA protocols:GenerateMainchainPotentialTests:test_full_run_B3N protocols:GenerateMainchainPotentialTests:test_full_run_GLY_asymm protocols:GenerateMainchainPotentialTests:test_full_run_GLY_symm protocols:GenerateMainchainPotentialTests:test_full_run_VAL protocols:GenerateMainchainPotentialTests:test_full_run_VAL_prepro protocols:GenerateMainchainPotentialTests:test_pose_generation protocols:GenerateMainchainPotentialTests:test_pose_generation_prepro protocols:GenericSimulatedAnnealerTests:test_acceptance protocols:GenericSimulatedAnnealerTests:test_boltzmann protocols:GenericSimulatedAnnealerTests:test_checkpointing protocols:GlycosyltransferaseMoverTests:test_apply protocols:GraftSwitchMoverTests:test_graft_switch_mover_setup protocols:GraftingTest:test_graft_classes protocols:GraftingTest:test_utility_functions protocols:GrowLeftTests:test_n_side_internal protocols:GrowLeftTests:test_n_term_extension protocols:GrowRightTests:test_c_side_internal protocols:GrowRightTests:test_c_term_extension protocols:GunnCostTest:test_cost protocols:HBNetMoverTests:test_hbnet_mover_setup protocols:HBondCalculatorsTest:test_hb_calculators protocols:HBondSelectorTests:test_HBondSelector_parse_my_tag 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:LigandConformerTests:test_ligand_conformer_measure_global_coords protocols:LigandConformerTests:test_ligand_conformer_recover_input_coords protocols:LigandMetalContactSelectorTests:test_dist_cutoff_multiplier protocols:LigandMetalContactSelectorTests:test_parse_tag_embedded_selector protocols:LigandMetalContactSelectorTests:test_parse_tag_invalid protocols:LigandMetalContactSelectorTests:test_parse_tag_named_selector protocols:LigandMetalContactSelectorTests:test_parse_tag_resnum_list protocols:LigandScoresUtilTests:test_ligand_travel protocols:LigandScoresUtilTests:test_rmsds protocols:LimitAromaChi2OperationTests:test_limit_aroma_chi2 protocols:LocalBackboneMoverTests:test_free_peptide protocols:LocalBackboneMoverTests:test_free_peptide_move protocols:LocalBackboneMoverTests:test_free_peptide_movers protocols:LocalBackboneMoverTests:test_gap_closer protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withouttermini protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withselection protocols:LongestContinuousApolarSegmentFilterTests:test_multichain_pose_withtermini protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withouttermini protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withselection protocols:LongestContinuousApolarSegmentFilterTests:test_singlechain_pose_withtermini protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withouttermini protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withselection protocols:LongestContinuousPolarSegmentFilterTests:test_multichain_pose_withtermini protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withouttermini protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withselection protocols:LongestContinuousPolarSegmentFilterTests:test_singlechain_pose_withtermini protocols:LoopAnalyzerMoverTests:test_Cterm_adjacent protocols:LoopAnalyzerMoverTests:test_Nterm_adjacent protocols:LoopAnalyzerMoverTests:test_at_Nterm protocols:LoopAnalyzerMoverTests:test_internal_termini protocols:LoopAnalyzerMoverTests:test_internal_terminiCterm protocols:LoopAnalyzerMoverTests:test_simple_loop protocols:LoopLengthChangeTests:test_insert_one_then_three protocols:LoopModelerTests:test_apply protocols:LoopModelerTests:test_build_options protocols:LoopModelerTests:test_centroid_options protocols:LoopModelerTests:test_custom_centroid_movers protocols:LoopModelerTests:test_custom_fullatom_movers protocols:LoopModelerTests:test_custom_movers protocols:LoopModelerTests:test_default_config protocols:LoopModelerTests:test_empty_config protocols:LoopModelerTests:test_fast_option protocols:LoopModelerTests:test_fullatom_options protocols:LoopModelerTests:test_illegal_movers protocols:LoopModelerTests:test_loophash_kic protocols:LoopModelerTests:test_modeler_options protocols:LoopModelerTests:test_temp_cycles_regex protocols:LoophashTest:test_database protocols:LoopsFileIOTest:test_LoopsFileIO_read_JSON_loops_file protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_cutpoint protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_extended protocols:LoopsFileIOTest:test_LoopsFileIO_read_loopstream_from_pose_numbered_file_w_skiprate protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_extended protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_extended_old_format protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_w_cutpoint protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_loop_w_skip_rate protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_one_loop protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_one_loop_w_comments protocols:LoopsFileIOTest:test_PoseNumberedLoopFileReader_two_loops protocols: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:MakeCanonicalHelixTest:test_default_dihedral_angles protocols:MatchConstraintFileInfoTest:test_interface_constraints 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:NMethylationTests:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov15:test_linear_nmethyl_peptide protocols:NMethylationTests_betanov16:test_linear_nmethyl_peptide protocols:NativeSelectorTests:test_native_is_too_large protocols:NativeSelectorTests:test_native_is_too_small protocols:NativeSelectorTests:test_serialize_simple1 protocols:NativeSelectorTests:test_serialize_simple2 protocols:NativeSelectorTests:test_simple1 protocols:NativeSelectorTests:test_simple2 protocols: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:ParamsDataStorageTests:test_params_data_copying protocols:ParamsDataStorageTests:test_params_data_storage protocols:ParamsDataStorageTests:test_params_residue_storage 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:PerturbBundleTests:test_perturb_r0_uniform 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:ProtectedConf:test_replace_residue 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:RNA_DeNovoOptimizerTest:test_sarcin_ricin_loop_buildup protocols:RNA_DeNovoProtocolTest:test_sarcin_ricin_loop_fixed protocols:RNA_DeNovoProtocolTest:test_sarcin_ricin_loop_free_with_base_pair_steps protocols:RNA_DeNovoProtocolTest:test_save_times_option protocols:RRReporterSQLiteTests:test_RRReporterSQLite_features protocols:RRReporterSQLiteTests:test_RRReporterSQLite_full protocols:RRReporterTests:test_RRReporterSimple_main protocols:RamaMutationSelectorTests:test_select_by_aib protocols:RamaMutationSelectorTests:test_select_by_dproline protocols:RamaMutationSelectorTests:test_select_by_native protocols:RamaMutationSelectorTests:test_select_by_proline protocols:RamaMutationSelectorTests:test_select_by_valine protocols:RandomizeBBByRamaPreProTests:test_rama_distribution_d_ala protocols:RandomizeBBByRamaPreProTests:test_rama_distribution_l_ala protocols:RelativeConnectRightTests:test_connection protocols:RemodelConstraintGeneratorTest:test_sheet_constraints protocols:RepackingRefinerTests:test_repacking_refiner_options protocols:ReplicateFilterTests:test_basic protocols:ReplicateFilterTests:test_parsing protocols:ReplicateFilterTests:test_thresholding protocols:ResfileAutoRemapTest:test_resfile_auto_remap protocols:ResidueCountFilterTests:test_residue_count_filter_manual protocols:ResidueCountFilterTests:test_residue_count_report protocols:ResidueCountFilterTests:test_residue_count_with_types_and_properties protocols:ResidueProbDesignOperationTests:test_task_op protocols:ResidueTorsionRestraintsTest:test_randomize_with_constraints protocols:ResidueTypeConstraintGeneratorTests:test_change_favor_native_bonus protocols:ResidueTypeConstraintGeneratorTests:test_constraints_full_pose_native protocols:ResidueTypeConstraintGeneratorTests:test_constraints_full_ref_pose protocols:ResidueTypeConstraintGeneratorTests:test_constraints_ref_pose_with_selector protocols:ResidueTypeConstraintGeneratorTests:test_constraints_residue_selector protocols:ResidueTypeConstraintGeneratorTests:test_constraints_set_type_full_pose protocols:ResidueTypeConstraintGeneratorTests:test_constraints_set_type_with_selector protocols:ResidueTypeConstraintGeneratorTests:test_two_constraints_same_residue protocols:ResidueTypeConstraintMoverTests:test_it_adds_constraints protocols:RestrictNonSurfaceToRepackingOperationTests:test_RestrictNonSurfaceToRepackingOperation protocols:RestrictOperationsTests:test_RestrictByCalculatorsOperation protocols:RestrictOperationsTests:test_RestrictInterGroupVectorOperation protocols:RestrictOperationsTests:test_RestrictToInterfaceOperation protocols:RestrictOperationsTests:test_RestrictToInterfaceVectorOperation protocols:RestrictOperationsTests:test_RestrictToMoveMapChiOperation protocols:RestrictOperationsTests:test_RestrictToNeighborhoodOperation protocols:RestrictToCDRH3LoopTest:test_RestrictToCDRH3Loop protocols:RestrictToLoopsTests:test_copy_constructor protocols:RestrictToLoopsTests:test_restrict_design_to_loops protocols:RestrictToLoopsTests:test_set_design_loops protocols:RestrictToLoopsTests:test_set_loops protocols:RestrictToLoopsTests:test_set_loops_from_file protocols:RigidBodyMoverTests:test_RigidBodyPerturbMover_int protocols:RigidBodyMoverTests:test_RigidBodyPerturbMover_no_int protocols:RigidBodyMoverTests:test_RigidBodyPerturbNoCenterMover protocols:RigidBodyMoverTests:test_RigidBodyRandomizeMover protocols:RigidBodyMoverTests:test_RigidBodySpinMover protocols:RigidBodyMoverTests:test_RigidBodyTransMover protocols:RigidBodyMoverTests:test_RigidBodyTransMover_parse protocols:RigidChunkTest:test_apply_to_template protocols:RigidChunkTest:test_chunk protocols:RigidChunkTest:test_two_chunk protocols:RigidChunkTest:test_two_part_chunk protocols:RigidLigandBuilderTests:test_downstream_placement_from_sinisas_param_file protocols:RigidLigandBuilderTests:test_lig_downstream_geom protocols:RigidLigandBuilderTests:test_rigid_ligand_ds_builder_recover_input_coords protocols:RingPlaneFlipMoverTests:test_RingPlaneFlipMover protocols:RmsdFromResidueSelectorFilterTests:test_all_true protocols:RmsdFromResidueSelectorFilterTests:test_name protocols:RmsdFromResidueSelectorFilterTests:test_selection_aligned protocols:RmsdFromResidueSelectorFilterTests:test_selection_non_aligned protocols:RosettaScriptsJobQueenTests:test_read_resources_from_xml_file protocols:RosettaScriptsParserTests:test_all_attributes_in_xsd_have_descriptions protocols:RosettaScriptsParserTests:test_allowed_multiple_dependencies protocols:RosettaScriptsParserTests:test_multiple_includes protocols:RosettaScriptsParserTests:test_output_scoring protocols:RosettaScriptsParserTests:test_prohibit_circular_dependencies protocols:RosettaScriptsParserTests:test_report_at_end protocols:RotamerBoltzmannWeight2Tests:test_calculator_ids protocols:RotamerBoltzmannWeight2Tests:test_rbw2_vs_rbw protocols:RotamerRecoveryTests:test_RotamerRecovery_main protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_random protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_range protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_single protocols:RotateJumpAxisMoverTests:test_RotateJumpAxisMover_underspecified_jump protocols:SandwichFeaturesTests:test_main protocols:ScaffoldBuildPointTests:test_scaffold_build_point_ctor protocols:ScoreNormalizationTest:test_all_atom_normalization protocols:ScoreNormalizationTest:test_chi_angle_normalization protocols:ScoreNormalizationTest:test_get_score_normalization_function protocols:ScoreNormalizationTest:test_heavy_atom_normalization protocols:ScoreNormalizationTest:test_mol_weight_normalization protocols:SecondaryStructureFilterTests:test_convert_impossible_pairings protocols:SegmentInsertTests:test_C_side_connection_simple_internal protocols:SegmentInsertTests:test_C_side_connection_simple_internal_pure protocols:SegmentInsertTests:test_C_side_connection_simple_n_term protocols:SegmentInsertTests:test_N_side_connection_no_left_flanking_region protocols:SegmentInsertTests:test_N_side_connection_no_right_flanking_region protocols:SegmentInsertTests:test_N_side_connection_simple_c_term protocols:SegmentInsertTests:test_N_side_connection_simple_internal protocols:SegmentInsertTests:test_N_side_connection_simple_internal_pure protocols:SegmentRebuildTests:test_continuous_segment_internal_contract protocols:SegmentRebuildTests:test_continuous_segment_internal_expand protocols:SegmentRebuildTests:test_continuous_segment_internal_identity protocols:SegmentRebuildTests:test_cut2_segment_contract protocols:SegmentRebuildTests:test_cut2_segment_expand protocols:SegmentRebuildTests:test_cut2_segment_identity protocols:SegmentRebuildTests:test_cut_segment_contract protocols:SegmentRebuildTests:test_cut_segment_expand protocols:SegmentRebuildTests:test_cut_segment_identity protocols:SegmentRebuildTests:test_multi_chain_cterm_chain1 protocols:SegmentRebuildTests:test_multi_chain_cterm_chain2 protocols:SegmentRebuildTests:test_multi_chain_nterm_chain1 protocols:SegmentRebuildTests:test_multi_chain_nterm_chain2 protocols:SegmentSequenceProfileTests:test_simple_profile protocols:SegmentSwapTests:test_continuous_complex_swap1 protocols:SegmentSwapTests:test_continuous_complex_swap2 protocols:SegmentSwapTests:test_continuous_swap protocols: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:SilentFilePoseInputterTests:test_read_in_file_silent_flag protocols:SilentFilePoseInputterTests:test_read_in_from_cmdline_without_pose_input_sources_call 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:SmallMoverTests:test_perturb_oligourea protocols:SmartAssemblyTests:test_assemblies_are_continuous protocols:SmartAssemblyTests:test_auto_detect_contacts protocols:SmartAssemblyTests:test_basis_pair_calculations_recursive_unchimerize_c_term protocols:SmartAssemblyTests:test_basis_pair_calculations_recursive_unchimerize_n_term protocols:SmartAssemblyTests:test_can_make_chimera1 protocols:SmartAssemblyTests:test_can_make_chimera2 protocols:SmartAssemblyTests:test_can_make_chimera3 protocols:SmartAssemblyTests:test_do_not_delete_vital_segments_cterm protocols:SmartAssemblyTests:test_do_not_delete_vital_segments_nterm protocols:SmartAssemblyTests:test_do_not_hash_the_unhashable protocols:SmartAssemblyTests:test_double_chimerize_single_helix_two_triplets_cterm_first protocols:SmartAssemblyTests:test_double_chimerize_single_helix_two_triplets_nterm_first protocols:SmartAssemblyTests:test_double_unchimerize_single_helix_two_triplets_cterm protocols:SmartAssemblyTests:test_double_unchimerize_single_helix_two_triplets_nterm protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_basic protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_chimaera_cterm_first protocols:SmartAssemblyTests:test_iterate_over_basis_pairs_chimaera_nterm_first protocols:SmartAssemblyTests:test_maintain_contact_cterm_chimerization protocols:SmartAssemblyTests:test_maintain_contact_double_chimerization_cterm_first protocols:SmartAssemblyTests:test_maintain_contact_double_chimerization_nterm_first protocols:SmartAssemblyTests:test_maintain_contact_nterm_chimerization protocols:SmartAssemblyTests:test_maintain_contact_recurse_revert_cterm protocols:SmartAssemblyTests:test_maintain_contact_recurse_revert_nterm protocols:SmartAssemblyTests:test_maintain_contact_unchimerize_cterm protocols:SmartAssemblyTests:test_maintain_contact_unchimerize_nterm protocols:SmartAssemblyTests:test_reverting_double_unchimerize_cterm protocols:SmartAssemblyTests:test_reverting_double_unchimerize_nterm protocols:SmartAssemblyTests:test_set_starting_segment protocols:SmartAssemblyTests:test_simple_assembly_length protocols:SmartAssemblyTests:test_simple_assembly_parent_connectivity protocols:SmartAssemblyTests:test_simple_assembly_size protocols:SmartAssemblyTests:test_simple_delete_cterm protocols:SmartAssemblyTests:test_simple_delete_nterm protocols:SmartAssemblyTests:test_simple_switch_cterm protocols:SmartAssemblyTests:test_simple_switch_nterm protocols:SnugDockProtocol_setup_ab_ag_foldtree_tests:test_place_VRT_at_residue_COM protocols:SnugDockProtocol_setup_ab_ag_foldtree_tests:test_setup_ab_ag_foldtree protocols:SpartaTest:test_ANN_INPUT protocols:SpartaTest:test_ANN_PARAMETERS protocols:SpartaTest:test_BLOSUM62 protocols:SpartaTest:test_PDB protocols:SpartaTest:test_PRED_SUM protocols:SpartaTest:test_scores protocols:SpartaTest:test_sparta_foldit protocols:SpinAroundPartnerMoverTest:test_constructor_from_jumpnum protocols:SpinAroundPartnerMoverTest:test_spinaroundpartner_parse_my_tag_input protocols:StandardJobQueenOverrideOutputterTests:test_sjq_add_unregistered_outputter_read_cl_get_default_outputter protocols:StandardJobQueenOverrideOutputterTests:test_sjq_add_unregistered_outputter_read_cl_get_requested_dummy_outputter protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_cl protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_jobdef_file protocols:StandardJobQueenOverrideOutputterTests:test_sjq_allow_only_non_factory_registered_outputter_read_jobdef_file_bad_outputter protocols:StandardPoseJobSummaryTests:test_basic_pose_job_summary protocols:StartFromTests:test_PDB_file protocols:StartFromTests:test_PDB_file_atom_name protocols:StartFromTests:test_hash_tag protocols:StartFromTests:test_json_file protocols:StartFromTests:test_multiple_positions protocols:StartFromTests:test_pdb_tag protocols:StartFromTests:test_specified_position protocols:StartFromTests:test_specified_position_nbr protocols:StartFromTests:test_spurious_items protocols:StepWiseMinimizerTest:test_num_pose_minimize protocols:StepWiseMonteCarloTest:test_force_submotif_without_intervening_bulge protocols:StepWiseMonteCarloTest:test_skip_preminimize protocols:StepWiseMoveSelectorTest:test_reverse_of_FROM_SCRATCH_move protocols:StepWiseMoveSelectorTest:test_submotif_split protocols:StepWisePoseAlignerTest:test_rna_dna_match protocols:StepWisePoseAlignerTest:test_superimpose_res_in_root_partition protocols:StochasticFilterTests:test_apply protocols:StochasticFilterTests:test_subfilter_apply_false protocols:StochasticFilterTests:test_subfilter_apply_true protocols:StoredResidueSubsetSelectorTests:test_StoreResidueSubsetMover_parse_my_tag protocols:StoredResidueSubsetSelectorTests:test_StoredResidueSubsetSelector_parse_my_tag protocols:StoredResidueSubsetSelectorTests:test_store_and_retrieve_subset protocols:StructureDataFactoryTests:test_silent_io protocols:StructureDataFactoryTests:test_structuredata_io protocols:StructureDataFactoryTests:test_symmetry protocols:StructureDataFactoryTests:test_xml_io protocols:StructureDataObserverTests:test_attachment protocols:StructureDataObserverTests:test_residue_deletion protocols:StructureDataTests:test_delete_segment protocols:StructureDataTests:test_enzdes_remarks protocols:StructureDataTests:test_move_segments protocols:StructureDataTests:test_non_peptidic_bonds protocols:StructureDataTests:test_slice protocols:StructureStoreTests:test_convert_stores