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Revisions №20659

branch: rosetta:commits 「№20659」
Commited by: Rocco Moretti
GitHub Pull Request link: 「№356」
Merge: 「029c6a159」← 「ac45f690b」  code diff
Scheduled at: 2025-03-13 16:31:55.501249
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
mac.clang.python38.PyRosetta.unit ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit mpi mpi.serialization build.header build.levels build.ninja_debug beautification code_quality.cppcheck code_quality.merge_size serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration.torch integration performance profile linux.clang.score linux.gcc.score mac.clang.score scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify util.apps windows.build.debug windows.build.release

Pull Request №356 RosettaCommons/rosetta/main ← roccomoretti/rosetta/better_mmcif_loading Merge: 029c6a159b896477003a14f78f472d4cd2cead46←ac45f690b673004939d3a4daf3098a721343b38a Better debugging on CIF file read in. ---------------- Merge commit message: Fix compilation

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AnchorFinder AnchoredDesign AnchoredPDBCreator BFactorSelector CCS_PARCS ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FavorSequenceProfileMover FilterReportAsPoseExtraScoresMover FloppyTail HDXEnergy InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_metrics InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments LoopAnalyzer LoopLengthChange PDB_diagnostic ProQ RBOut RescorePDDF ResidueDisorder RunSimpleMetric_b_factor_test SID_ERMS_prediction SID_rescore SSElementSelector SnugDock ThreadingInputter UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm abinitio add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data ambiguous_nmr_distance_constraint angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter assemble_domains_jd2 auto-drrafter_setup_run_R1 auto-drrafter_setup_run_R2 auto-drrafter_setup_run_R3 autosetup_metals_centroid backrub backrub_interface_ddG backrub_pilot balancedKIC batch_relax beta_strand_homodimer binselector binselector_probins broker broker_membrane buried_unsat_kinemage buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa cart_min_glycans cartesianddg ccd_ends_graft_mover_rs centroid_disulfide_scores centroid_from_fullatom cl_complex_rescore classic_relax_1a19 cleanAlignment cluster_alns cmaes_minimizer combine_silent constel constraints_metric contactMap control_flow_rs coupled_moves create_clash-based_repack_shell create_sequence_motif crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter database_jd2_compact_io database_jd2_io database_session_resource ddG_ensemble ddG_of_mutation ddG_scan density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dgdp_aio dgdp_script dihedral_constraint_generator distances 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 energy_based_clustering_alpha_aa_scorefile entropy_correction enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution exclusively_shared_jumps farfar_mrna farnesyl fast_relax favor_coupling_tensor favor_native_residue features_pdb fiber_diffraction 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 ga_ligand_dock_amino_acid ga_ligand_dock_macrocycle gen_lig_grids genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycopeptidedocking glycopeptidedocking_diglyco_long grid_scores_features hbnet_use_input_rot hbonds hbonds_sp2 hbs_design helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design iphold 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_cholesterol ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_motif_discovery ligand_motif_identification ligand_water_docking loop_creation loop_grower_N_term_symm loop_hash loop_modeling make_exemplar make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml membrane_abinitio metal_setup metalloprotein_abrelax 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_with_elec_dens mixed_monte_carlo motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_ensemble mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_f19_relax mp_find_interface mp_interface_statistics mp_ligand_interface mp_loadtime mp_mutate_relax mp_mutate_repack 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 mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols mutate ncaa_fixbb ncbb_packer_palette netcharge_design netcharge_design_symm next_generation_KIC non-canonical_connectivities nonideal_rtmin 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 phiselector phosphonate place_simultaneously pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets pose_sewing 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 ralford_dump_rotamers range_relax_w_cst rb_recces rdkit_metrics readin_dna_rna_protein real_virt_mover recon_design relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens report_hbonds_for_plugin res_lipo_ref2015_memb residue_energy_breakdown rna_assemble rna_denovo rna_denovo_RNP_low_res rna_denovo_RNP_refine_native rna_denovo_bps rna_denovo_bps_fixed_ends rna_denovo_bps_helix_ends rna_denovo_dna_bridge rna_denovo_fragment_homology_exclusion rna_denovo_grid_vdw 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_design rna_farfar_noncanonical_hairpin rna_minimize rna_motif rna_predict_chem_map rna_puzzle11_H2H3H4_run3_connectU40 rna_puzzle12_P5P6P7_DMS rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation rna_puzzle6_U75G76A77_on_thread1 rna_puzzle6_j67_into_p6p7rigidbody_thread1 rna_ribosome_tether rna_score rna_screen_phosphates rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_include rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sample_seq_from_probs sasa_metric_options score12_docking score_jd2 score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_tolerance shobuns sim_cryo simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_glycosylation simple_glycosylation_alternate_AAs simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_b_factor simple_metrics_in_protocols simple_metrics_per_residue site_constraint small_molecule_lattice_dock 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 swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus 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_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_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_sampler 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_rotamer_boltzmann symmetric_docking symmetry_multicomponent target_clash tcrmodel template_features test1_benchmark test_computed_saxs_spectrum test_d_l_readin thermal_sampler threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling vip write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AnchorFinder AnchoredDesign AnchoredPDBCreator BFactorSelector CCS_PARCS ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FavorSequenceProfileMover FilterReportAsPoseExtraScoresMover FloppyTail HDXEnergy InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_metrics InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments LoopAnalyzer LoopLengthChange PDB_diagnostic ProQ RBOut RescorePDDF ResidueDisorder RunSimpleMetric_b_factor_test SID_ERMS_prediction SID_rescore SSElementSelector SnugDock ThreadingInputter UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm abinitio add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data ambiguous_nmr_distance_constraint angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter assemble_domains_jd2 auto-drrafter_setup_run_R1 auto-drrafter_setup_run_R2 auto-drrafter_setup_run_R3 autosetup_metals_centroid backrub backrub_interface_ddG backrub_pilot balancedKIC batch_relax beta_strand_homodimer binselector binselector_probins broker broker_membrane buried_unsat_kinemage buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa cart_min_glycans cartesianddg ccd_ends_graft_mover_rs centroid_disulfide_scores centroid_from_fullatom cl_complex_rescore classic_relax_1a19 cleanAlignment cluster_alns cmaes_minimizer combine_silent constel constraints_metric contactMap control_flow_rs coupled_moves create_clash-based_repack_shell create_sequence_motif crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_rdkit_metric cycpep_rigid_body_permutation_mover cycpep_symmetry_filter database_jd2_compact_io database_jd2_io database_session_resource ddG_ensemble ddG_of_mutation ddG_scan density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA dgdp_aio dgdp_script dihedral_constraint_generator distances 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 energy_based_clustering_alpha_aa_scorefile entropy_correction enumerative_sampling enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution exclusively_shared_jumps farfar_mrna farnesyl fast_relax favor_coupling_tensor favor_native_residue features_pdb fiber_diffraction 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 ga_ligand_dock_amino_acid ga_ligand_dock_macrocycle gen_lig_grids genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycopeptidedocking glycopeptidedocking_diglyco_long grid_scores_features hbnet_use_input_rot hbonds hbonds_sp2 hbs_design helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design iphold 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_cholesterol ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_motif_discovery ligand_motif_identification ligand_water_docking loop_creation loop_grower_N_term_symm loop_hash loop_modeling make_exemplar make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml membrane_abinitio membrane_relax membrane_relax_hbond metal_setup metalloprotein_abrelax 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_with_elec_dens mixed_monte_carlo motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_ensemble mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_f19_relax mp_find_interface mp_interface_statistics mp_ligand_interface 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 mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols mutate ncaa_fixbb ncbb_packer_palette netcharge_design netcharge_design_symm next_generation_KIC non-canonical_connectivities nonideal_rtmin 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 phiselector phosphonate place_simultaneously pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets pose_sewing 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 ralford_dump_rotamers range_relax_w_cst rb_recces rdkit_metrics readin_dna_rna_protein real_virt_mover recon_design relax_w_allatom_cst remodel remodel_disulfides remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens report_hbonds_for_plugin res_lipo_ref2015_memb residue_energy_breakdown rna_assemble rna_denovo rna_denovo_RNP_low_res rna_denovo_RNP_refine_native rna_denovo_bps rna_denovo_bps_fixed_ends rna_denovo_bps_helix_ends rna_denovo_dna_bridge rna_denovo_fragment_homology_exclusion rna_denovo_grid_vdw 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_design rna_farfar_noncanonical_hairpin rna_minimize rna_motif rna_predict_chem_map rna_puzzle11_H2H3H4_run3_connectU40 rna_puzzle12_P5P6P7_DMS rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation rna_puzzle6_U75G76A77_on_thread1 rna_puzzle6_j67_into_p6p7rigidbody_thread1 rna_ribosome_tether rna_score rna_screen_phosphates rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_include rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sample_seq_from_probs sasa_metric_options score12_docking score_jd2 score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI selected_residue_count_metric sequence_tolerance shobuns sim_cryo simple_cycpep_predict simple_cycpep_predict_1_4_bbmb simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_glycosylation simple_glycosylation_alternate_AAs simple_grafting_movers simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_b_factor simple_metrics_in_protocols simple_metrics_per_residue site_constraint small_molecule_lattice_dock 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 swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus 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_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_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_sampler 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_rotamer_boltzmann symmetric_docking symmetry_multicomponent target_clash tcrmodel template_features test1_benchmark test_computed_saxs_spectrum test_d_l_readin thermal_sampler threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling vip write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup