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Rosetta Utilities
2014.16.56682
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Rosetta Utilities
2014.16.56682
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Functions | |
| BooleanOptionKey const | file ("in:file") |
| FileVectorOptionKey const | s ("in:file:s") |
| FileVectorOptionKey const | t ("in:file:t") |
| FileVectorOptionKey const | l ("in:file:l") |
| FileVectorOptionKey const | list ("in:file:list") |
| FileVectorOptionKey const | screening_list ("in:file:screening_list") |
| FileOptionKey const | screening_job_file ("in:file:screening_job_file") |
| BooleanOptionKey const | shuffle_screening_jobs ("in:file:shuffle_screening_jobs") |
| FileOptionKey const | native ("in:file:native") |
| FileOptionKey const | torsion_bin_probs ("in:file:torsion_bin_probs") |
| FileOptionKey const | PCS_frag_cst ("in:file:PCS_frag_cst") |
| FileOptionKey const | talos_phi_psi ("in:file:talos_phi_psi") |
| FileOptionKey const | talos_cs ("in:file:talos_cs") |
| FileOptionKey const | ambig_talos_cs_A ("in:file:ambig_talos_cs_A") |
| FileOptionKey const | ambig_talos_cs_B ("in:file:ambig_talos_cs_B") |
| IntegerVectorOptionKey const | native_exclude_res ("in:file:native_exclude_res") |
| StringVectorOptionKey const | tags ("in:file:tags") |
| StringVectorOptionKey const | user_tags ("in:file:user_tags") |
| FileOptionKey const | tagfile ("in:file:tagfile") |
| FileVectorOptionKey const | frag_files ("in:file:frag_files") |
| IntegerVectorOptionKey const | frag_sizes ("in:file:frag_sizes") |
| FileVectorOptionKey const | extra_res ("in:file:extra_res") |
| FileVectorOptionKey const | extra_res_fa ("in:file:extra_res_fa") |
| FileVectorOptionKey const | extra_res_mol ("in:file:extra_res_mol") |
| StringOptionKey const | extra_res_database ("in:file:extra_res_database") |
| StringOptionKey const | extra_res_pq_schema ("in:file:extra_res_pq_schema") |
| StringOptionKey const | extra_res_database_mode ("in:file:extra_res_database_mode") |
| FileOptionKey const | extra_res_database_resname_list ("in:file:extra_res_database_resname_list") |
| FileVectorOptionKey const | extra_res_cen ("in:file:extra_res_cen") |
| PathVectorOptionKey const | extra_res_path ("in:file:extra_res_path") |
| PathVectorOptionKey const | extra_res_batch_path ("in:file:extra_res_batch_path") |
| FileVectorOptionKey const | extra_patch_fa ("in:file:extra_patch_fa") |
| FileVectorOptionKey const | extra_patch_cen ("in:file:extra_patch_cen") |
| StringOptionKey const | frag3 ("in:file:frag3") |
| StringOptionKey const | frag9 ("in:file:frag9") |
| StringOptionKey const | fragA ("in:file:fragA") |
| StringOptionKey const | fragB ("in:file:fragB") |
| StringOptionKey const | surface_vectors ("in:file:surface_vectors") |
| StringOptionKey const | xyz ("in:file:xyz") |
| IntegerOptionKey const | fragA_size ("in:file:fragA_size") |
| BooleanOptionKey const | keep_input_scores ("in:file:keep_input_scores") |
| BooleanOptionKey const | lazy_silent ("in:file:lazy_silent") |
| FileVectorOptionKey const | silent ("in:file:silent") |
| FileVectorOptionKey const | atom_tree_diff ("in:file:atom_tree_diff") |
| StringOptionKey const | zip ("in:file:zip") |
| FileVectorOptionKey const | boinc_wu_zip ("in:file:boinc_wu_zip") |
| BooleanOptionKey const | fullatom ("in:file:fullatom") |
| BooleanOptionKey const | centroid_input ("in:file:centroid_input") |
| BooleanOptionKey const | centroid ("in:file:centroid") |
| StringOptionKey const | treat_residues_in_these_chains_as_separate_chemical_entities ("in:file:treat_residues_in_these_chains_as_separate_chemical_entities") |
| StringOptionKey const | residue_type_set ("in:file:residue_type_set") |
| FileOptionKey const | pca ("in:file:pca") |
| RealOptionKey const | silent_energy_cut ("in:file:silent_energy_cut") |
| FileVectorOptionKey const | silent_list ("in:file:silent_list") |
| BooleanOptionKey const | silent_renumber ("in:file:silent_renumber") |
| BooleanOptionKey const | silent_optH ("in:file:silent_optH") |
| StringOptionKey const | silent_struct_type ("in:file:silent_struct_type") |
| BooleanOptionKey const | silent_read_through_errors ("in:file:silent_read_through_errors") |
| StringOptionKey const | silent_score_prefix ("in:file:silent_score_prefix") |
| IntegerOptionKey const | silent_select_random ("in:file:silent_select_random") |
| IntegerOptionKey const | silent_select_range_start ("in:file:silent_select_range_start") |
| IntegerOptionKey const | silent_select_range_mul ("in:file:silent_select_range_mul") |
| IntegerOptionKey const | silent_select_range_len ("in:file:silent_select_range_len") |
| BooleanOptionKey const | skip_failed_simulations ("in:file:skip_failed_simulations") |
| StringVectorOptionKey const | silent_scores_wanted ("in:file:silent_scores_wanted") |
| FileVectorOptionKey const | fasta ("in:file:fasta") |
| FileVectorOptionKey const | pssm ("in:file:pssm") |
| StringVectorOptionKey const | seq ("in:file:seq") |
| FileOptionKey const | checkpoint ("in:file:checkpoint") |
| FileOptionKey const | binary_chk ("in:file:binary_chk") |
| FileVectorOptionKey const | alignment ("in:file:alignment") |
| FileVectorOptionKey const | alignment2 ("in:file:alignment2") |
| FileOptionKey const | rama2b_map ("in:file:rama2b_map") |
| FileOptionKey const | psipred_ss2 ("in:file:psipred_ss2") |
| FileOptionKey const | dssp ("in:file:dssp") |
| BooleanOptionKey const | fail_on_bad_hbond ("in:file:fail_on_bad_hbond") |
| FileOptionKey const | movemap ("in:file:movemap") |
| BooleanOptionKey const | repair_sidechains ("in:file:repair_sidechains") |
| BooleanOptionKey const | no_binary_dunlib ("in:file:no_binary_dunlib") |
| IntegerOptionKey const | extended_pose ("in:file:extended_pose") |
| FileVectorOptionKey const | template_pdb ("in:file:template_pdb") |
| FileOptionKey const | template_silent ("in:file:template_silent") |
| FileVectorOptionKey const | rdc ("in:file:rdc") |
| FileVectorOptionKey const | csa ("in:file:csa") |
| FileVectorOptionKey const | dc ("in:file:dc") |
| FileVectorOptionKey const | burial ("in:file:burial") |
| FileVectorOptionKey const | vall ("in:file:vall") |
| BooleanOptionKey const | rescore ("in:file:rescore") |
| StringOptionKey const | spanfile ("in:file:spanfile") |
| StringOptionKey const | lipofile ("in:file:lipofile") |
| StringOptionKey const | embedfile ("in:file:embedfile") |
| StringOptionKey const | embedparams ("in:file:embedparams") |
| StringOptionKey const | membrane_chains ("in:file:membrane_chains") |
| StringOptionKey const | HDX ("in:file:HDX") |
| RealOptionKey const | d2h_sa_reweight ("in:file:d2h_sa_reweight") |
| FileOptionKey const | sucker_params ("in:file:sucker_params") |
| FileOptionKey const | fold_tree ("in:file:fold_tree") |
| BooleanOptionKey const | obey_ENDMDL ("in:file:obey_ENDMDL") |
| BooleanOptionKey const | new_chain_order ("in:file:new_chain_order") |
| FileOptionKey const | ddg_predictions_file ("in:file:ddg_predictions_file") |
| IntegerVectorOptionKey const | input_res ("in:file:input_res") |
| IntegerVectorOptionKey const | minimize_res ("in:file:minimize_res") |
| StringOptionKey const | md_schfile ("in:file:md_schfile") |
| BooleanOptionKey const | read_pdb_link_records ("in:file:read_pdb_link_records") |
| FileOptionKey const | native_contacts ("in:file:native_contacts") |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment | ( | "in:file:alignment" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2 | ( | "in:file:alignment2" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A | ( | "in:file:ambig_talos_cs_A" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B | ( | "in:file:ambig_talos_cs_B" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff | ( | "in:file:atom_tree_diff" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::binary_chk | ( | "in:file:binary_chk" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip | ( | "in:file:boinc_wu_zip" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::burial | ( | "in:file:burial" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::centroid | ( | "in:file:centroid" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input | ( | "in:file:centroid_input" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::checkpoint | ( | "in:file:checkpoint" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::csa | ( | "in:file:csa" | ) |
| RealOptionKey const basic::options::OptionKeys::in::file::d2h_sa_reweight | ( | "in:file:d2h_sa_reweight" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::dc | ( | "in:file:dc" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file | ( | "in:file:ddg_predictions_file" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::dssp | ( | "in:file:dssp" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::embedfile | ( | "in:file:embedfile" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::embedparams | ( | "in:file:embedparams" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose | ( | "in:file:extended_pose" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_cen | ( | "in:file:extra_patch_cen" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_fa | ( | "in:file:extra_patch_fa" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res | ( | "in:file:extra_res" | ) |
| PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_batch_path | ( | "in:file:extra_res_batch_path" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen | ( | "in:file:extra_res_cen" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database | ( | "in:file:extra_res_database" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database_mode | ( | "in:file:extra_res_database_mode" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::extra_res_database_resname_list | ( | "in:file:extra_res_database_resname_list" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa | ( | "in:file:extra_res_fa" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol | ( | "in:file:extra_res_mol" | ) |
| PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path | ( | "in:file:extra_res_path" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_pq_schema | ( | "in:file:extra_res_pq_schema" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond | ( | "in:file:fail_on_bad_hbond" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta | ( | "in:file:fasta" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::file | ( | "in:file" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::fold_tree | ( | "in:file:fold_tree" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::frag3 | ( | "in:file:frag3" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::frag9 | ( | "in:file:frag9" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files | ( | "in:file:frag_files" | ) |
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::frag_sizes | ( | "in:file:frag_sizes" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::fragA | ( | "in:file:fragA" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::fragA_size | ( | "in:file:fragA_size" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::fragB | ( | "in:file:fragB" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom | ( | "in:file:fullatom" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::HDX | ( | "in:file:HDX" | ) |
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::input_res | ( | "in:file:input_res" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores | ( | "in:file:keep_input_scores" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::l | ( | "in:file:l" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent | ( | "in:file:lazy_silent" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::lipofile | ( | "in:file:lipofile" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::list | ( | "in:file:list" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::md_schfile | ( | "in:file:md_schfile" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::membrane_chains | ( | "in:file:membrane_chains" | ) |
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::minimize_res | ( | "in:file:minimize_res" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::movemap | ( | "in:file:movemap" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::native | ( | "in:file:native" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::native_contacts | ( | "in:file:native_contacts" | ) |
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res | ( | "in:file:native_exclude_res" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order | ( | "in:file:new_chain_order" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib | ( | "in:file:no_binary_dunlib" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL | ( | "in:file:obey_ENDMDL" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::pca | ( | "in:file:pca" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst | ( | "in:file:PCS_frag_cst" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2 | ( | "in:file:psipred_ss2" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm | ( | "in:file:pssm" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map | ( | "in:file:rama2b_map" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc | ( | "in:file:rdc" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::read_pdb_link_records | ( | "in:file:read_pdb_link_records" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains | ( | "in:file:repair_sidechains" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::rescore | ( | "in:file:rescore" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set | ( | "in:file:residue_type_set" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::s | ( | "in:file:s" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::screening_job_file | ( | "in:file:screening_job_file" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::screening_list | ( | "in:file:screening_list" | ) |
| StringVectorOptionKey const basic::options::OptionKeys::in::file::seq | ( | "in:file:seq" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::shuffle_screening_jobs | ( | "in:file:shuffle_screening_jobs" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::silent | ( | "in:file:silent" | ) |
| RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut | ( | "in:file:silent_energy_cut" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list | ( | "in:file:silent_list" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_optH | ( | "in:file:silent_optH" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors | ( | "in:file:silent_read_through_errors" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber | ( | "in:file:silent_renumber" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix | ( | "in:file:silent_score_prefix" | ) |
| StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted | ( | "in:file:silent_scores_wanted" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random | ( | "in:file:silent_select_random" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_len | ( | "in:file:silent_select_range_len" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_mul | ( | "in:file:silent_select_range_mul" | ) |
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_start | ( | "in:file:silent_select_range_start" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type | ( | "in:file:silent_struct_type" | ) |
| BooleanOptionKey const basic::options::OptionKeys::in::file::skip_failed_simulations | ( | "in:file:skip_failed_simulations" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::spanfile | ( | "in:file:spanfile" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::sucker_params | ( | "in:file:sucker_params" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::surface_vectors | ( | "in:file:surface_vectors" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::t | ( | "in:file:t" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::tagfile | ( | "in:file:tagfile" | ) |
| StringVectorOptionKey const basic::options::OptionKeys::in::file::tags | ( | "in:file:tags" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::talos_cs | ( | "in:file:talos_cs" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi | ( | "in:file:talos_phi_psi" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb | ( | "in:file:template_pdb" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::template_silent | ( | "in:file:template_silent" | ) |
| FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs | ( | "in:file:torsion_bin_probs" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities | ( | "in:file:treat_residues_in_these_chains_as_separate_chemical_entities" | ) |
| StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags | ( | "in:file:user_tags" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::vall | ( | "in:file:vall" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::xyz | ( | "in:file:xyz" | ) |
| StringOptionKey const basic::options::OptionKeys::in::file::zip | ( | "in:file:zip" | ) |
| FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment("in:file:alignment") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::alignment2("in:file:alignment2") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_A("in:file:ambig_talos_cs_A") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::ambig_talos_cs_B("in:file:ambig_talos_cs_B") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::atom_tree_diff("in:file:atom_tree_diff") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::binary_chk("in:file:binary_chk") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::boinc_wu_zip("in:file:boinc_wu_zip") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::burial("in:file:burial") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::centroid("in:file:centroid") |
Referenced by add_rosetta_options_0(), and add_rosetta_options_1().
| BooleanOptionKey const basic::options::OptionKeys::in::file::centroid_input("in:file:centroid_input") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::checkpoint("in:file:checkpoint") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::csa("in:file:csa") |
Referenced by add_rosetta_options_0().
| RealOptionKey const basic::options::OptionKeys::in::file::d2h_sa_reweight("in:file:d2h_sa_reweight") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::dc("in:file:dc") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::ddg_predictions_file("in:file:ddg_predictions_file") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::dssp("in:file:dssp") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::embedfile("in:file:embedfile") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::embedparams("in:file:embedparams") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::extended_pose("in:file:extended_pose") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_cen("in:file:extra_patch_cen") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_patch_fa("in:file:extra_patch_fa") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res("in:file:extra_res") |
Referenced by add_rosetta_options_0().
| PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_batch_path("in:file:extra_res_batch_path") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_cen("in:file:extra_res_cen") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database("in:file:extra_res_database") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_database_mode("in:file:extra_res_database_mode") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::extra_res_database_resname_list("in:file:extra_res_database_resname_list") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_fa("in:file:extra_res_fa") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_mol("in:file:extra_res_mol") |
Referenced by add_rosetta_options_0().
| PathVectorOptionKey const basic::options::OptionKeys::in::file::extra_res_path("in:file:extra_res_path") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::extra_res_pq_schema("in:file:extra_res_pq_schema") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::fail_on_bad_hbond("in:file:fail_on_bad_hbond") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::fasta("in:file:fasta") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::file("in:file") |
Referenced by add_rosetta_options_0(), basic::options::start_files(), and options_class::writeToFile().
| FileOptionKey const basic::options::OptionKeys::in::file::fold_tree("in:file:fold_tree") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::frag3("in:file:frag3") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::frag9("in:file:frag9") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::frag_files("in:file:frag_files") |
Referenced by add_rosetta_options_0().
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::frag_sizes("in:file:frag_sizes") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::fragA("in:file:fragA") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::fragA_size("in:file:fragA_size") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::fragB("in:file:fragB") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::fullatom("in:file:fullatom") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::HDX("in:file:HDX") |
Referenced by add_rosetta_options_0().
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::input_res("in:file:input_res") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::keep_input_scores("in:file:keep_input_scores") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::l("in:file:l") |
Referenced by add_rosetta_options_0(), utility::BitVector< B >::BitVector(), utility::signals::SignalHub< ReturnType, Signal >::current_links(), utility::file::file_size(), Kernel::Kernel(), numeric::model_quality::maxsub(), utility::operator<<(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), basic::sampling::SphereSampler::read_sphere_data(), numeric::RemainderSelector< T, true >::remainder(), basic::sampling::SphereSampler::sanity_check(), utility::options::OptionCollection::show_all_hier(), utility::options::OptionCollection::show_table_text(), sigmoid_train(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), basic::options::start_files(), basic::svd::SVD_Solver::svdcmp(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_load_model(), svm_predict_values(), svm_save_model(), svm_train(), utility::options::OptionCollection::wrapped(), and basic::Emitter::write_raw().
| BooleanOptionKey const basic::options::OptionKeys::in::file::lazy_silent("in:file:lazy_silent") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::lipofile("in:file:lipofile") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::list("in:file:list") |
| StringOptionKey const basic::options::OptionKeys::in::file::md_schfile("in:file:md_schfile") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::membrane_chains("in:file:membrane_chains") |
Referenced by add_rosetta_options_0().
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::minimize_res("in:file:minimize_res") |
Referenced by add_rosetta_options_0(), and add_rosetta_options_3().
| FileOptionKey const basic::options::OptionKeys::in::file::movemap("in:file:movemap") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::native("in:file:native") |
| FileOptionKey const basic::options::OptionKeys::in::file::native_contacts("in:file:native_contacts") |
Referenced by add_rosetta_options_0().
| IntegerVectorOptionKey const basic::options::OptionKeys::in::file::native_exclude_res("in:file:native_exclude_res") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::new_chain_order("in:file:new_chain_order") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::no_binary_dunlib("in:file:no_binary_dunlib") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::obey_ENDMDL("in:file:obey_ENDMDL") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::pca("in:file:pca") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::PCS_frag_cst("in:file:PCS_frag_cst") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::psipred_ss2("in:file:psipred_ss2") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::pssm("in:file:pssm") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::rama2b_map("in:file:rama2b_map") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::rdc("in:file:rdc") |
Referenced by add_rosetta_options_0(), and add_rosetta_options_3().
| BooleanOptionKey const basic::options::OptionKeys::in::file::read_pdb_link_records("in:file:read_pdb_link_records") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::repair_sidechains("in:file:repair_sidechains") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::rescore("in:file:rescore") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::residue_type_set("in:file:residue_type_set") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::s("in:file:s") |
Referenced by add_rosetta_options_0(), basic::Tracer::calculate_tracer_level(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::can_hold_another(), numeric::kinematic_closure::chainXYZ(), numeric::kinematic_closure::radians::chainXYZ(), utility::query::Filter_And< T >::description(), utility::query::Filter_Or< T >::description(), utility::query::Filter_Not< T >::description(), utility::query::Metric_Neg< T >::description(), utility::down_cast(), basic::Emitter::escape_string(), fastsin(), utility::sql_database::DatabaseSessionManager::get_session_mysql(), utility::sql_database::DatabaseSessionManager::get_session_postgres(), utility::sql_database::DatabaseSessionManager::get_session_sqlite3(), basic::Tracer::in(), numeric::jacobi(), numeric::jacobi_rotation(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::legal_string(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::legal_string(), numeric::kinematic_closure::numchanges(), numeric::kinematic_closure::numroots(), utility::options::operator+(), utility::operator+(), utility::operator-(), utility::operator|(), utility::options::OptionCollection::prefix(), basic::Tracer::prepend_channel_name(), basic::database::schema_generator::Index::print(), numeric::BodyPosition< typename >::q_refresh(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::remainder_conversion(), utility::signals::SignalHub< ReturnType, Signal >::send(), basic::Emitter::set_indent(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::shortd(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::shortd(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), utility::keys::ClassKeyVector< K, T, C >::sort(), utility::options::OptionCollection::space_prefixed(), basic::options::start_files(), utility::options::OptionCollection::suffix(), basic::svd::SVD_Solver::svbksb(), basic::svd::SVD_Solver::svdcmp(), basic::TracerToFile::t_flush(), basic::ComparingTracer::t_flush(), basic::Tracer::TracerProxy::t_flush(), utility::options::OptionCollection::tab_prefixed(), numeric::kinematic_closure::torsion(), numeric::kinematic_closure::radians::torsion(), utility::options::OptionCollection::trim(), utility::options::OptionCollection::trimmed(), and utility::options::OptionCollection::wrapped().
| FileOptionKey const basic::options::OptionKeys::in::file::screening_job_file("in:file:screening_job_file") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::screening_list("in:file:screening_list") |
Referenced by add_rosetta_options_0(), and basic::options::start_files().
| StringVectorOptionKey const basic::options::OptionKeys::in::file::seq("in:file:seq") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::shuffle_screening_jobs("in:file:shuffle_screening_jobs") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::silent("in:file:silent") |
Referenced by add_rosetta_options_0().
| RealOptionKey const basic::options::OptionKeys::in::file::silent_energy_cut("in:file:silent_energy_cut") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::silent_list("in:file:silent_list") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_optH("in:file:silent_optH") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_read_through_errors("in:file:silent_read_through_errors") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::silent_renumber("in:file:silent_renumber") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::silent_score_prefix("in:file:silent_score_prefix") |
Referenced by add_rosetta_options_0().
| StringVectorOptionKey const basic::options::OptionKeys::in::file::silent_scores_wanted("in:file:silent_scores_wanted") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_random("in:file:silent_select_random") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_len("in:file:silent_select_range_len") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_mul("in:file:silent_select_range_mul") |
Referenced by add_rosetta_options_0().
| IntegerOptionKey const basic::options::OptionKeys::in::file::silent_select_range_start("in:file:silent_select_range_start") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::silent_struct_type("in:file:silent_struct_type") |
Referenced by add_rosetta_options_0().
| BooleanOptionKey const basic::options::OptionKeys::in::file::skip_failed_simulations("in:file:skip_failed_simulations") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::spanfile("in:file:spanfile") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::sucker_params("in:file:sucker_params") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::surface_vectors("in:file:surface_vectors") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::t("in:file:t") |
Referenced by add_rosetta_options_0(), utility::options::OptionCollection::cleaned(), numeric::model_quality::erfcc(), numeric::statistics::erfcx_y100(), basic::sampling::orientations::Quaternion::euler(), utility::from_string(), numeric::hsv_to_rgb(), numeric::jacobi(), numeric::jacobi_rotation(), numeric::fourier::kf_bfly2(), numeric::fourier::kf_bfly_generic(), numeric::model_quality::maxsub(), utility::options::OptionCollection::merged(), multiclass_probability(), basic::sampling::orientations::Quaternion::Normalize(), utility::json_spirit::Value_impl< Config >::Variant_converter_visitor::operator()(), numeric::sphericalVector< typename >::operator*=(), numeric::xyzTriple< typename >::operator*=(), numeric::xyzVector< T >::operator*=(), numeric::xyzMatrix< T >::operator*=(), numeric::sphericalVector< typename >::operator+=(), numeric::xyzTriple< typename >::operator+=(), numeric::xyzVector< T >::operator+=(), numeric::xyzMatrix< T >::operator+=(), numeric::sphericalVector< typename >::operator-=(), numeric::xyzTriple< typename >::operator-=(), numeric::xyzVector< T >::operator-=(), numeric::xyzMatrix< T >::operator-=(), numeric::operator<<(), utility::io::ocstream::operator<<(), utility::io::orstream::operator<<(), utility::io::ozstream::operator<<(), utility::io::mpi_stream::basic_mpi_ostream< Elem, Tr, ElemA, ByteT, ByteAT >::operator<<(), numeric::sphericalVector< typename >::operator=(), numeric::xyzTriple< typename >::operator=(), numeric::xyzVector< T >::operator=(), numeric::xyzMatrix< T >::operator=(), numeric::operator>>(), utility::io::icstream::operator>>(), utility::io::irstream::operator>>(), utility::io::izstream::operator>>(), powi(), basic::prof_show(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), basic::YamlEmitter::quote_string(), basic::JsonEmitter::quote_string(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::read_row(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), Solver::select_working_set(), Solver_NU::select_working_set(), sigmoid_train(), numeric::xyzTriple< typename >::square(), numeric::xyzVector< T >::square(), utility::string_split(), swap(), numeric::Quaternion< T >::swap(), basic::T(), numeric::kinematic_closure::test_point_value2(), basic::gpu::Timer::Timer(), utility::lua::LuaObject::to(), utility::to_string(), numeric::geometry::BoundingBox< Vector >::translate(), and numeric::statistics::w_im_y100().
| FileOptionKey const basic::options::OptionKeys::in::file::tagfile("in:file:tagfile") |
Referenced by add_rosetta_options_0().
| StringVectorOptionKey const basic::options::OptionKeys::in::file::tags("in:file:tags") |
Referenced by add_rosetta_options_0(), and utility::get_resnum_and_chain().
| FileOptionKey const basic::options::OptionKeys::in::file::talos_cs("in:file:talos_cs") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::talos_phi_psi("in:file:talos_phi_psi") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::template_pdb("in:file:template_pdb") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::template_silent("in:file:template_silent") |
Referenced by add_rosetta_options_0().
| FileOptionKey const basic::options::OptionKeys::in::file::torsion_bin_probs("in:file:torsion_bin_probs") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities("in:file:treat_residues_in_these_chains_as_separate_chemical_entities") |
Referenced by add_rosetta_options_0().
| StringVectorOptionKey const basic::options::OptionKeys::in::file::user_tags("in:file:user_tags") |
Referenced by add_rosetta_options_0().
| FileVectorOptionKey const basic::options::OptionKeys::in::file::vall("in:file:vall") |
Referenced by add_rosetta_options_0().
| StringOptionKey const basic::options::OptionKeys::in::file::xyz("in:file:xyz") |
| StringOptionKey const basic::options::OptionKeys::in::file::zip("in:file:zip") |
Referenced by add_rosetta_options_0().
1.8.7