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Revisions №14607

branch: commits 「№14607」
Commited by: bcov77
GitHub Pull Request link: 「№4385」
Merge: 「64dae26f3」「b1bb79833」  code diff
Scheduled at: 2020-01-30 11:35:42.728038
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit mac.PyRosetta.unit cppcheck ubuntu.gcc.build.cppcheck mpi mpi.serialization build.header build.levels build.ninja_debug graphics static beautification serialization code_quality.submodule_regression integration.mpi integration.release_debug integration performance profile linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify

Pull Request №4385 master←bcov/PDBInfoPSSM2 Merge: 64dae26f31e6b62cec936d57aae85c1da1eaf933←b1bb79833145bfbe468eb99cbe8ad8db0f9046a0 AddPSSMFromPDBInfoMover for PSSMs from PDBInfo labels ---------------- Merge commit message: Whitespace

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Test: linux.clang.build.cppcheck

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Test: linux.clang.code_quality.submodule_regression

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HOW_TO_MAKE_TESTS 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 RescoreSAXS 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 Werror_check 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_cc antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter app_exception_handling 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 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 burial_measure_centroid 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 case_sensitive_filenames ccd_ends_graft_mover_rs central_class_modification centroid_disulfide_scores centroid_from_fullatom classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_calibur cluster_filter code_template_tests_app code_template_tests_src code_template_tests_unit combine_silent composition_energy_layers constel contactMap copy_rotamer_mover count_cycpep_sequences coupled_moves create_clash-based_repack_shell create_sequence_motif crossaln 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 dock_with_hotspot_place_simultaneously 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 drrafter_setup drrafter_setup_build_missing drrafter_setup_protein_dock drrafter_setup_real_test_H drrafter_setup_real_test_H_no_init drrafter_setup_ribosome_test drrafter_setup_simple duplicate_header_guards 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 extract_pdbs farfar_mrna farnesyl fast_relax fast_relax_scripts favor_native_residue features features_database_schema features_parallel features_pdb features_pdb_mpi features_postgres features_scientific_benchmark 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 header_using_check helical_bundle helical_bundle_nonideal helical_bundle_predict helix_from_sequence hierarchical_clustering homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump include_cc_check interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout jrelax jscore kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_ensemble 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_hash 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 metal_setup metalloprotein_abrelax metalloprotein_broker metropolis_hastings 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 molfile_to_params 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 mp_quick_relax_ref2015_memb mp_range_relax mp_relax 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 mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols multistage_rosetta_scripts multistage_rosetta_scripts_clustering multithreaded_fastdesign multithreaded_fixbb multithreaded_interaction_graph_accuracy multithreaded_interaction_graph_accuracy_symm multithreaded_packrotamersmover 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 pepspec_anchor_dock peptiderive per_residue_energies per_residue_sc_sasa per_residue_solvent_exposure 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 place_simultaneously 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 ppk 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 recon_design_mpi referencepose_mutateresidue relax_w_allatom_cst 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_setup rnp_ddg_calc_wt rnp_ddg_finalize rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rnp_ddg_relax_finalize rnp_ddg_relax_setup rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_aln 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_general_polymer_sampler 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 tensorflow_connection_test tensorflow_simple_model_load_and_evaluate test1_benchmark test_computed_saxs_spectrum test_d_l_readin test_energy_method_options test_idealize test_rosetta_thread_manager_advanced_API test_rosetta_thread_manager_basic_API thermal_sampler thread_local_tracers_check 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: mac.clang.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HOW_TO_MAKE_TESTS 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 RescoreSAXS 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 Werror_check 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_cc antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter app_exception_handling 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 burial_measure_centroid 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 case_sensitive_filenames ccd_ends_graft_mover_rs central_class_modification centroid_disulfide_scores centroid_from_fullatom classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_calibur cluster_filter code_template_tests_app code_template_tests_src code_template_tests_unit combine_silent composition_energy_layers constel contactMap continuous_sewing_hasher copy_rotamer_mover count_cycpep_sequences coupled_moves create_clash-based_repack_shell create_sequence_motif crossaln 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 discontinuous_sewing_hasher distances disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously 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 drrafter_setup drrafter_setup_build_missing drrafter_setup_protein_dock drrafter_setup_real_test_H drrafter_setup_real_test_H_no_init drrafter_setup_ribosome_test drrafter_setup_simple duplicate_header_guards 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 extract_pdbs farfar_mrna farnesyl fast_relax fast_relax_scripts favor_native_residue features features_database_schema features_parallel features_pdb features_pdb_mpi features_postgres features_scientific_benchmark 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 header_using_check helical_bundle helical_bundle_nonideal helical_bundle_predict helix_from_sequence hierarchical_clustering homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump include_cc_check 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 jrelax jscore kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_ensemble 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_hash 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 metropolis_hastings 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 molfile_to_params 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 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 mpi_simple_cycpep_predict mpi_simple_cycpep_predict_4level mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols multistage_rosetta_scripts multistage_rosetta_scripts_clustering multithreaded_fastdesign multithreaded_fixbb multithreaded_interaction_graph_accuracy multithreaded_interaction_graph_accuracy_symm multithreaded_packrotamersmover 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 pepspec pepspec_anchor_dock peptiderive per_residue_energies per_residue_sc_sasa per_residue_solvent_exposure 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 place_simultaneously 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 ppk 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 recon_design_mpi 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_setup rnp_ddg_calc_wt rnp_ddg_finalize rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rnp_ddg_relax_finalize rnp_ddg_relax_setup rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_aln 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_general_polymer_sampler 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 tensorflow_connection_test tensorflow_simple_model_load_and_evaluate test1_benchmark test_computed_saxs_spectrum test_d_l_readin test_energy_method_options test_idealize test_rosetta_thread_manager_advanced_API test_rosetta_thread_manager_basic_API thermal_sampler thread_local_tracers_check 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