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Functions
option.cc.gen.hh File Reference
#include <basic/options/option.hh>
#include <basic/options/option.cc.include.gen.hh>
#include <utility/options/OptionCollection.hh>

Functions

void add_rosetta_options_0 (utility::options::OptionCollection &option)
 
void add_rosetta_options_1 (utility::options::OptionCollection &option)
 
void add_rosetta_options_2 (utility::options::OptionCollection &option)
 
void add_rosetta_options_3 (utility::options::OptionCollection &option)
 
void add_rosetta_options_4 (utility::options::OptionCollection &option)
 
void add_rosetta_options_5 (utility::options::OptionCollection &option)
 
void add_rosetta_options_6 (utility::options::OptionCollection &option)
 
void add_rosetta_options_7 (utility::options::OptionCollection &option)
 
void add_rosetta_options_8 (utility::options::OptionCollection &option)
 
void add_rosetta_options_9 (utility::options::OptionCollection &option)
 
void add_rosetta_options_10 (utility::options::OptionCollection &option)
 
void add_rosetta_options_11 (utility::options::OptionCollection &option)
 
void add_rosetta_options_12 (utility::options::OptionCollection &option)
 
void add_rosetta_options_13 (utility::options::OptionCollection &option)
 
void add_rosetta_options_14 (utility::options::OptionCollection &option)
 
void add_rosetta_options_15 (utility::options::OptionCollection &option)
 
void add_all_rosetta_options (utility::options::OptionCollection &option)
 

Function Documentation

void add_all_rosetta_options ( utility::options::OptionCollection option)
inline
void add_rosetta_options_0 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::in::add_orbitals, basic::options::OptionKeys::out::file::alignment, basic::options::OptionKeys::in::file::alignment, basic::options::OptionKeys::in::file::alignment2, basic::options::OptionKeys::out::path::all, basic::options::OptionKeys::in::alternate_3_letter_codes, basic::options::OptionKeys::in::file::ambig_talos_cs_A, basic::options::OptionKeys::in::file::ambig_talos_cs_B, basic::options::OptionKeys::in::file::assign_gasteiger_atom_types, basic::options::OptionKeys::out::file::atom_tree_diff, basic::options::OptionKeys::in::file::atom_tree_diff, basic::options::OptionKeys::out::file::atom_tree_diff_bb, basic::options::OptionKeys::out::file::atom_tree_diff_bl, basic::options::OptionKeys::out::file::atom_tree_diff_sc, basic::options::OptionKeys::in::auto_detect_glycan_connections, basic::options::OptionKeys::in::auto_setup_metals, basic::options::OptionKeys::in::file::binary_chk, basic::options::OptionKeys::in::file::boinc_wu_zip, basic::options::OptionKeys::in::file::burial, basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::in::file::centroid_input, basic::options::OptionKeys::in::file::check_all_PDB_components, basic::options::OptionKeys::in::file::checkpoint, basic::options::OptionKeys::out::chname, basic::options::OptionKeys::out::chtimestamp, basic::options::OptionKeys::out::file::cif_extra_data_separate_file, basic::options::OptionKeys::inout::connect_info_cutoff, basic::options::OptionKeys::in::constraints_from_link_records, basic::options::OptionKeys::in::file::csa, basic::options::OptionKeys::in::Ctermini, basic::options::OptionKeys::in::file::d2h_sa_reweight, basic::options::OptionKeys::in::path::database, basic::options::OptionKeys::in::path::database_cache_dir, basic::options::OptionKeys::out::database_filter, basic::options::OptionKeys::inout::dbms::database_name, basic::options::OptionKeys::inout::dbms::database_partition, basic::options::OptionKeys::out::database_protocol_id, basic::options::OptionKeys::inout::dbms::dbms, basic::options::OptionKeys::in::dbms::dbms, basic::options::OptionKeys::in::file::dc, basic::options::OptionKeys::in::file::ddg_predictions_file, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::out::file::design_contrast, basic::options::OptionKeys::in::detect_disulf, basic::options::OptionKeys::in::detect_disulf_tolerance, basic::options::OptionKeys::in::detect_oops, basic::options::OptionKeys::out::file::do_not_autoassign_SS, basic::options::OptionKeys::out::file::dont_rewrite_dunbrack_database, basic::options::OptionKeys::out::dry_run, basic::options::OptionKeys::in::file::dssp, basic::options::OptionKeys::in::file::extended_pose, basic::options::OptionKeys::in::file::extra_patch_cen, basic::options::OptionKeys::in::file::extra_patch_fa, basic::options::OptionKeys::in::file::extra_res, basic::options::OptionKeys::in::file::extra_res_batch_path, basic::options::OptionKeys::in::file::extra_res_cen, basic::options::OptionKeys::in::file::extra_res_database, basic::options::OptionKeys::in::file::extra_res_database_mode, basic::options::OptionKeys::in::file::extra_res_database_resname_list, basic::options::OptionKeys::in::file::extra_res_fa, basic::options::OptionKeys::in::file::extra_res_mmCIF, basic::options::OptionKeys::in::file::extra_res_mol, basic::options::OptionKeys::in::file::extra_res_path, basic::options::OptionKeys::in::file::extra_res_pq_schema, basic::options::OptionKeys::in::file::extra_rot_lib_path, basic::options::OptionKeys::in::file::fail_on_bad_hbond, basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::in::fconfig, basic::options::OptionKeys::out::file::file, basic::options::OptionKeys::in::file::file, basic::options::OptionKeys::in::fix_disulf, basic::options::OptionKeys::in::file::fold_tree, basic::options::OptionKeys::inout::fold_tree_io, basic::options::OptionKeys::out::file::force_nonideal_structure, basic::options::OptionKeys::in::file::force_silent_bitflip_on_read, basic::options::OptionKeys::in::file::frag3, basic::options::OptionKeys::in::file::frag9, basic::options::OptionKeys::in::file::frag_files, basic::options::OptionKeys::out::file::frag_prefix, basic::options::OptionKeys::in::file::fragA, basic::options::OptionKeys::in::file::fragB, basic::options::OptionKeys::in::path::fragments, basic::options::OptionKeys::out::file::fullatom, basic::options::OptionKeys::in::file::fullatom, basic::options::OptionKeys::in::glycan_virtual_offset, basic::options::OptionKeys::in::guarantee_no_DNA, basic::options::OptionKeys::in::file::HDX, basic::options::OptionKeys::inout::dbms::host, basic::options::OptionKeys::in::file::hrf_ms_labeling, basic::options::OptionKeys::in::ignore_unrecognized_res, basic::options::OptionKeys::in::ignore_waters, basic::options::OptionKeys::in::in, basic::options::OptionKeys::in::include_lipids, basic::options::OptionKeys::in::include_sugars, basic::options::OptionKeys::in::include_surfaces, basic::options::OptionKeys::inout::inout, basic::options::OptionKeys::in::file::input_res, utility::options::Option::is_group(), basic::options::OptionKeys::in::file::job_definition_file, basic::options::OptionKeys::in::file::keep_input_scores, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::in::file::lazy_silent, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::out::level, basic::options::OptionKeys::out::levels, basic::options::OptionKeys::in::file::lipofile, basic::options::OptionKeys::in::file::list, basic::options::OptionKeys::in::file::load_PDB_components, basic::options::OptionKeys::in::maintain_links, basic::options::OptionKeys::in::max_bond_length, basic::options::OptionKeys::in::file::md_schfile, basic::options::OptionKeys::in::membrane, basic::options::OptionKeys::out::membrane_pdb, basic::options::OptionKeys::out::membrane_pdb_thickness, basic::options::OptionKeys::in::metals_angle_constraint_multiplier, basic::options::OptionKeys::in::metals_detection_LJ_multiplier, basic::options::OptionKeys::in::metals_distance_constraint_multiplier, basic::options::OptionKeys::in::min_bond_length, basic::options::OptionKeys::in::file::minimize_res, basic::options::OptionKeys::in::missing_density_to_jump, basic::options::OptionKeys::out::mmCIF, basic::options::OptionKeys::out::mmCIF_gz, basic::options::OptionKeys::out::mmtf, basic::options::OptionKeys::inout::mmtf_extra_data_io, basic::options::OptionKeys::out::mmtf_gz, basic::options::OptionKeys::inout::dbms::mode, basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::out::mover_controlled_output_name, basic::options::OptionKeys::out::mpi_tracer_to_file, basic::options::OptionKeys::out::mute, basic::options::OptionKeys::in::name3_property_codes, basic::options::OptionKeys::in::file::native, basic::options::OptionKeys::in::file::native_contacts, basic::options::OptionKeys::in::file::native_exclude_res, basic::options::OptionKeys::in::file::new_chain_order, basic::options::OptionKeys::in::file::no_binary_dunlib, basic::options::OptionKeys::out::file::no_chainend_ter, basic::options::OptionKeys::out::no_color, basic::options::OptionKeys::in::file::no_detect_pseudobonds, basic::options::OptionKeys::out::file::no_extra_sdf_data, basic::options::OptionKeys::in::no_fconfig, basic::options::OptionKeys::out::no_nstruct_label, basic::options::OptionKeys::out::file::no_output_cen, basic::options::OptionKeys::out::file::no_scores_in_pdb, basic::options::OptionKeys::out::nooutput, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::in::Ntermini, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::in::file::obey_ENDMDL, basic::options::OptionKeys::out::out, basic::options::OptionKeys::out::output, basic::options::OptionKeys::inout::output_alternate_atomids, basic::options::OptionKeys::out::file::output_ligands_as_separate_chains, basic::options::OptionKeys::out::file::output_only_asymmetric_unit, basic::options::OptionKeys::out::file::output_orbitals, basic::options::OptionKeys::out::file::output_pose_cache_data, basic::options::OptionKeys::out::file::output_pose_energies_table, basic::options::OptionKeys::out::file::output_pose_fold_tree, basic::options::OptionKeys::out::file::output_secondary_structure, basic::options::OptionKeys::out::output_tag, basic::options::OptionKeys::out::file::output_torsions, basic::options::OptionKeys::out::file::output_virtual, basic::options::OptionKeys::out::file::output_virtual_zero_occ, basic::options::OptionKeys::in::file::override_rot_lib_path, basic::options::OptionKeys::out::overwrite, basic::options::OptionKeys::inout::dbms::password, basic::options::OptionKeys::inout::dbms::path, basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::out::path::path, basic::options::OptionKeys::in::file::pca, basic::options::OptionKeys::in::file::PCS_frag_cst, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::in::path::pdb, basic::options::OptionKeys::out::path::pdb, basic::options::OptionKeys::out::file::pdb_comments, basic::options::OptionKeys::in::file::PDB_components_directory, basic::options::OptionKeys::in::file::PDB_components_overrides, basic::options::OptionKeys::out::pdb_gz, basic::options::OptionKeys::out::file::pdb_parents, basic::options::OptionKeys::out::file::per_chain_renumbering, basic::options::OptionKeys::inout::dbms::port, basic::options::OptionKeys::inout::dbms::pq_schema, basic::options::OptionKeys::out::prefix, basic::options::OptionKeys::in::preserve_crystinfo, basic::options::OptionKeys::in::prevent_auto_setup_metal_bb_variants, basic::options::OptionKeys::in::file::psipred_ss2, basic::options::OptionKeys::in::file::pssm, basic::options::OptionKeys::in::file::rama2b_map, basic::options::OptionKeys::out::file::raw, basic::options::OptionKeys::in::file::rdc, basic::options::OptionKeys::in::rdf::rdf, basic::options::OptionKeys::in::read_only_ATOM_entries, basic::options::OptionKeys::inout::dbms::readonly, basic::options::OptionKeys::in::file::remap_pdb_atom_names_for, basic::options::OptionKeys::in::remember_unrecognized_res, basic::options::OptionKeys::in::remember_unrecognized_water, basic::options::OptionKeys::out::file::renumber_pdb, basic::options::OptionKeys::in::file::repair_sidechains, basic::options::OptionKeys::in::replonly_loops, basic::options::OptionKeys::in::replonly_residues, basic::options::OptionKeys::in::file::rescore, basic::options::OptionKeys::out::file::residue_type_set, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::out::resume_batch, basic::options::OptionKeys::inout::dbms::retry_failed_reads, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::save_times, basic::options::OptionKeys::out::file::score_only, basic::options::OptionKeys::out::scorecut, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::out::file::scorefile_format, basic::options::OptionKeys::in::file::screening_job_file, basic::options::OptionKeys::in::file::screening_list, basic::options::OptionKeys::in::select_structures_from_database, basic::options::OptionKeys::in::rdf::sep_bb_ss, basic::options::OptionKeys::inout::dbms::separate_db_per_mpi_process, basic::options::OptionKeys::in::file::seq, basic::options::OptionKeys::out::file::set_pdb_author, basic::options::OptionKeys::out::sf, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::out::show_accessed_options, basic::options::OptionKeys::in::show_all_fixes, basic::options::OptionKeys::out::show_unused_options, basic::options::OptionKeys::out::shuffle_nstruct, basic::options::OptionKeys::in::file::shuffle_screening_jobs, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::in::file::silent_energy_cut, basic::options::OptionKeys::out::silent_gz, basic::options::OptionKeys::in::file::silent_list, basic::options::OptionKeys::out::file::silent_preserve_H, basic::options::OptionKeys::out::file::silent_print_all_score_headers, basic::options::OptionKeys::in::file::silent_read_through_errors, basic::options::OptionKeys::in::file::silent_renumber, basic::options::OptionKeys::in::file::silent_score_prefix, basic::options::OptionKeys::in::file::silent_scores_wanted, basic::options::OptionKeys::in::file::silent_select_random, basic::options::OptionKeys::in::file::silent_select_range_len, basic::options::OptionKeys::in::file::silent_select_range_mul, basic::options::OptionKeys::in::file::silent_select_range_start, basic::options::OptionKeys::out::file::silent_struct_type, basic::options::OptionKeys::in::file::silent_struct_type, basic::options::OptionKeys::in::skip_classic_cart_setup, basic::options::OptionKeys::inout::skip_connect_info, basic::options::OptionKeys::in::file::skip_failed_simulations, basic::options::OptionKeys::in::skip_new_cart_setup, basic::options::OptionKeys::in::file::spanfile, basic::options::OptionKeys::out::file::srlz, basic::options::OptionKeys::in::file::srlz, basic::options::OptionKeys::in::file::srlz_override, basic::options::OptionKeys::out::std_IO_exit_error_code, basic::options::OptionKeys::in::dbms::struct_ids, basic::options::OptionKeys::in::file::sucker_params, basic::options::OptionKeys::out::suffix, basic::options::OptionKeys::out::file::suppress_zero_occ_pdb_output, basic::options::OptionKeys::in::file::surface_vectors, basic::options::OptionKeys::in::file::t, basic::options::OptionKeys::in::file::tagfile, basic::options::OptionKeys::in::file::tags, basic::options::OptionKeys::in::file::talos_cs, basic::options::OptionKeys::in::file::talos_phi_psi, basic::options::OptionKeys::in::target_residues, basic::options::OptionKeys::in::file::template_pdb, basic::options::OptionKeys::in::file::template_silent, basic::options::OptionKeys::in::file::torsion_bin_probs, basic::options::OptionKeys::in::file::treat_residues_in_these_chains_as_separate_chemical_entities, basic::options::OptionKeys::out::unmute, basic::options::OptionKeys::inout::dbms::use_compact_residue_schema, basic::options::OptionKeys::out::use_database, basic::options::OptionKeys::in::use_database, basic::options::OptionKeys::out::file::use_occurrence_data, basic::options::OptionKeys::out::file::use_pdb_format_HETNAM_records, basic::options::OptionKeys::in::use_truncated_termini, basic::options::OptionKeys::inout::dbms::user, basic::options::OptionKeys::out::user_tag, basic::options::OptionKeys::in::file::user_tags, basic::options::OptionKeys::in::file::vall, basic::options::OptionKeys::in::water_type_if_unspecified, basic::options::OptionKeys::out::file::weight_silent_scores, basic::options::OptionKeys::inout::write_all_connect_info, basic::options::OptionKeys::out::file::write_glycan_pdb_codes, basic::options::OptionKeys::out::file::write_pdb_link_records, basic::options::OptionKeys::out::file::write_pdb_parametric_info, basic::options::OptionKeys::out::file::write_pdb_title_section_records, basic::options::OptionKeys::out::file::write_seqres_records, basic::options::OptionKeys::in::file::xyz, and basic::options::OptionKeys::in::file::zip.

Referenced by add_all_rosetta_options().

void add_rosetta_options_1 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::score::aa_composition_setup_file, basic::options::OptionKeys::score::aa_repeat_energy_penalty_file, utility::options::OptionCollection::add(), basic::options::OptionKeys::run::PyMOLMover::address, basic::options::OptionKeys::score::analytic_etable_evaluation, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_assume_const_backbone, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_atomic_depth, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_probe_radius, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_burial_resolution, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_bonus_cross_chain, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_bonus_ser_to_helix_bb, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_hbond_energy_threshold, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_natural_corrections1, basic::options::OptionKeys::score::approximate_buried_unsat_penalty_oversat_penalty, basic::options::OptionKeys::run::archive, basic::options::OptionKeys::jd3::archive_on_disk, basic::options::OptionKeys::score::aspartimide_penalty_value, basic::options::OptionKeys::run::batches, basic::options::OptionKeys::run::benchmark, basic::options::OptionKeys::score::bonded_params, basic::options::OptionKeys::score::bonded_params_dir, basic::options::OptionKeys::jd2::buffer_flush_frequency, basic::options::OptionKeys::jd2::buffer_silent_output, basic::options::OptionKeys::score::buried_unsatisfied_penalty_burial_threshold, basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_angle_exponent, basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_angle_shift_factor, basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_dist_exponent, basic::options::OptionKeys::score::buried_unsatisfied_penalty_cone_dist_midpoint, basic::options::OptionKeys::score::buried_unsatisfied_penalty_hbond_energy_threshold, basic::options::OptionKeys::score::cart_bonded_skip_cutpoints, basic::options::OptionKeys::run::chain, basic::options::OptionKeys::jd3::checkpoint, basic::options::OptionKeys::run::checkpoint, basic::options::OptionKeys::jd3::checkpoint_directory, basic::options::OptionKeys::jd2::checkpoint_file, basic::options::OptionKeys::run::checkpoint_interval, basic::options::OptionKeys::jd3::checkpoint_period, basic::options::OptionKeys::jd3::compress_job_results, basic::options::OptionKeys::score::compute_mg_sol_for_hydrogens, basic::options::OptionKeys::score::conc, basic::options::OptionKeys::run::condor, basic::options::OptionKeys::run::constant_seed, basic::options::OptionKeys::jd3::continue_past_failed_checkpoint_restoration, basic::options::OptionKeys::score::count_pair_full, basic::options::OptionKeys::score::count_pair_hybrid, basic::options::OptionKeys::score::covalent_labeling_fa_input, basic::options::OptionKeys::score::covalent_labeling_input, basic::options::OptionKeys::run::crash_to_console, basic::options::OptionKeys::score::custom_atom_pair, basic::options::OptionKeys::run::cycles_inner, basic::options::OptionKeys::run::cycles_outer, basic::options::OptionKeys::out::path::db, basic::options::OptionKeys::jd2::dd_parser, basic::options::OptionKeys::run::debug, basic::options::OptionKeys::run::decoystats, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::run::delay, basic::options::OptionKeys::run::delete_checkpoints, basic::options::OptionKeys::jd2::delete_old_poses, basic::options::OptionKeys::score::disulf_matching_probe, basic::options::OptionKeys::jd3::do_not_archive_on_node0, basic::options::OptionKeys::score::docking_interface_score, basic::options::OptionKeys::run::dry_run, basic::options::OptionKeys::score::elec_context_minburial, basic::options::OptionKeys::score::elec_context_minstrength, basic::options::OptionKeys::score::elec_die, basic::options::OptionKeys::score::elec_group_extrafile, basic::options::OptionKeys::score::elec_group_file, basic::options::OptionKeys::score::elec_max_dis, basic::options::OptionKeys::score::elec_min_dis, basic::options::OptionKeys::score::elec_r_option, basic::options::OptionKeys::score::elec_representative_cp, basic::options::OptionKeys::score::elec_representative_cp_flip, basic::options::OptionKeys::score::elec_sigmoidal_die, basic::options::OptionKeys::score::elec_sigmoidal_die_D, basic::options::OptionKeys::score::elec_sigmoidal_die_D0, basic::options::OptionKeys::score::elec_sigmoidal_die_S, basic::options::OptionKeys::score::empty, basic::options::OptionKeys::jd2::enzdes_out, basic::options::OptionKeys::score::eval_intrares_elec_ST_only, basic::options::OptionKeys::score::exact_occ_pairwise, basic::options::OptionKeys::score::exact_occ_pairwise_by_res, basic::options::OptionKeys::score::exact_occ_radius_scaling, basic::options::OptionKeys::score::exact_occ_self_res_no_occ, basic::options::OptionKeys::score::exact_occ_skip_Hbonders, basic::options::OptionKeys::score::exact_occ_split_between_res, basic::options::OptionKeys::run::exit_if_missing_heavy_atoms, basic::options::OptionKeys::score::extra_improper_file, basic::options::OptionKeys::score::extra_mm_params_dir, demo.D060_Folding::f, basic::options::OptionKeys::score::fa_custom_pair_distance_file, basic::options::OptionKeys::score::fa_Hatr, basic::options::OptionKeys::score::fa_max_dis, basic::options::OptionKeys::score::fa_stack_base_base_only, basic::options::OptionKeys::score::fa_stack_include_rna_protein, basic::options::OptionKeys::score::fa_stack_lr_dist_cutoff, basic::options::OptionKeys::score::fa_stack_lr_prefactor, basic::options::OptionKeys::score::fa_stack_lr_stack_cutoff, basic::options::OptionKeys::score::fa_stack_sol_dist_cutoff, basic::options::OptionKeys::score::fa_stack_sol_prefactor, basic::options::OptionKeys::score::fa_stack_sol_stack_cutoff, basic::options::OptionKeys::jd2::failed_job_exception, basic::options::OptionKeys::score::find_neighbors_3dgrid, basic::options::OptionKeys::score::find_neighbors_stripehash, basic::options::OptionKeys::score::free_side_chain_bonus, basic::options::OptionKeys::score::gen_bonded_exclude_def_file, basic::options::OptionKeys::score::gen_bonded_params_file, basic::options::OptionKeys::score::genbonded_score_full, basic::options::OptionKeys::score::genbonded_score_hybrid, basic::options::OptionKeys::jd2::generic_job_name, basic::options::OptionKeys::score::geom_sol_interres_path_distance_cutoff, basic::options::OptionKeys::score::geom_sol_intrares_path_distance_cutoff, basic::options::OptionKeys::jd2::grid_ensemble, basic::options::OptionKeys::score::grp_cpfxn, basic::options::OptionKeys::score::grpelec_context_dependent, basic::options::OptionKeys::score::grpelec_cpfxn_weight, basic::options::OptionKeys::score::grpelec_fade_hbond, basic::options::OptionKeys::score::grpelec_fade_param1, basic::options::OptionKeys::score::grpelec_fade_param2, basic::options::OptionKeys::score::grpelec_fade_type, basic::options::OptionKeys::score::grpelec_max_qeps, basic::options::OptionKeys::score::hb_acc_strength, basic::options::OptionKeys::score::hb_don_strength, basic::options::OptionKeys::score::hb_max_energy, basic::options::OptionKeys::score::hbe_for_dH2O_aGEN_SP3SC_ssother, basic::options::OptionKeys::score::hbnet_bonus_function_ramping, basic::options::OptionKeys::score::hbnet_max_network_size, basic::options::OptionKeys::score::hbond_bb_per_residue_energy, basic::options::OptionKeys::score::hbond_disable_bbsc_exclusion_rule, basic::options::OptionKeys::score::hbond_params, basic::options::OptionKeys::jd2::HOSTNAME_in_jobname, basic::options::OptionKeys::score::hrf_dynamics_input, basic::options::OptionKeys::run::idealize_before_protocol, basic::options::OptionKeys::run::ignore_zero_occupancy, basic::options::OptionKeys::score::include_intra_res_protein, basic::options::OptionKeys::parser::inclusion_recursion_limit, basic::options::OptionKeys::parser::info, basic::options::OptionKeys::jd2::input_empty_pose, basic::options::OptionKeys::score::input_etables, basic::options::OptionKeys::run::interactive, basic::options::OptionKeys::run::intermediate_scorefiles, basic::options::OptionKeys::run::intermediate_structures, utility::options::Option::is_group(), basic::options::OptionKeys::jd2::jd2, basic::options::OptionKeys::jd3::jd3, basic::options::OptionKeys::jd3::job_definition_schema, basic::options::OptionKeys::jd3::job_definition_script_vars, basic::options::OptionKeys::run::jobdist_miscfile_ext, basic::options::OptionKeys::run::jran, basic::options::OptionKeys::jd3::keep_all_checkpoints, basic::options::OptionKeys::jd3::keep_checkpoint, basic::options::OptionKeys::run::keep_pymol_simulation_history, basic::options::OptionKeys::jd2::lazy_silent_file_reader, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::score::linear_bonded_potential, basic::options::OptionKeys::score::lk_polar_without_proline_N, basic::options::OptionKeys::jd3::load_input_poses_only_once, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::run::max_min_iter, basic::options::OptionKeys::jd2::max_nstruct_in_memory, basic::options::OptionKeys::run::PyMOLMover::max_packet_size, basic::options::OptionKeys::run::max_retry_job, basic::options::OptionKeys::run::maxruntime, basic::options::OptionKeys::run::maxruntime_bufferfactor, basic::options::OptionKeys::run::memory_test_cycles, basic::options::OptionKeys::score::min_score_score, basic::options::OptionKeys::run::min_tolerance, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::out::path::mmCIF, basic::options::OptionKeys::out::path::mmtf, basic::options::OptionKeys::jd3::mpi_fast_nonblocking_output, basic::options::OptionKeys::jd2::mpi_fast_nonblocking_output, basic::options::OptionKeys::jd2::mpi_file_buf_job_distributor, basic::options::OptionKeys::jd2::mpi_filebuf_jobdistributor, basic::options::OptionKeys::jd3::mpi_fraction_outputters, basic::options::OptionKeys::jd2::mpi_nowait_for_remaining_jobs, basic::options::OptionKeys::out::path::mpi_rank_dir, basic::options::OptionKeys::jd2::mpi_timeout_factor, basic::options::OptionKeys::jd3::mpi_work_partition_job_distributor, basic::options::OptionKeys::jd2::mpi_work_partition_job_distributor, basic::options::OptionKeys::run::multiple_processes_writing_to_one_directory, basic::options::OptionKeys::jd3::n_archive_nodes, basic::options::OptionKeys::run::n_cycles, basic::options::OptionKeys::run::n_replica, basic::options::OptionKeys::run::nblist_autoupdate, basic::options::OptionKeys::run::nblist_autoupdate_narrow, basic::options::OptionKeys::run::nblist_autoupdate_wide, basic::options::OptionKeys::score::no_lk_polar_desolvation, basic::options::OptionKeys::jd2::no_output, basic::options::OptionKeys::score::no_pro_close_ring_closure, basic::options::OptionKeys::run::no_prof_info_in_silentout, basic::options::OptionKeys::run::no_scorefile, basic::options::OptionKeys::score::no_smooth_etables, basic::options::OptionKeys::run::nodelay, basic::options::OptionKeys::run::nosignal, basic::options::OptionKeys::run::nproc, basic::options::OptionKeys::jd3::nthreads, basic::options::OptionKeys::jd2::ntrials, basic::options::OptionKeys::score::NV_lbound, basic::options::OptionKeys::score::NV_table, basic::options::OptionKeys::score::NV_ubound, basic::options::OptionKeys::score::optH_patch, basic::options::OptionKeys::score::optH_weights, basic::options::OptionKeys::run::other_pose_scorefile, basic::options::OptionKeys::run::other_pose_to_scorefile, basic::options::OptionKeys::score::output_etables, basic::options::OptionKeys::run::output_hbond_info, basic::options::OptionKeys::score::output_residue_energies, basic::options::OptionKeys::parser::output_schema, basic::options::OptionKeys::score::pack_weights, basic::options::OptionKeys::parser::parser, basic::options::OptionKeys::score::patch, basic::options::OptionKeys::parser::patchdock, basic::options::OptionKeys::parser::patchdock_random_entry, basic::options::OptionKeys::run::PyMOLMover::port, basic::options::OptionKeys::jd2::pose_input_stream, basic::options::OptionKeys::run::preserve_header, basic::options::OptionKeys::score::pro_close_planar_constraint, basic::options::OptionKeys::run::proc_id, basic::options::OptionKeys::run::profile, basic::options::OptionKeys::parser::protocol, basic::options::OptionKeys::run::protocol, basic::options::OptionKeys::score::put_intra_into_total, basic::options::OptionKeys::run::PyMOLMover::PyMOLMover, basic::options::OptionKeys::score::ramaneighbors, basic::options::OptionKeys::run::random_delay, basic::options::OptionKeys::run::randomize_missing_coords, basic::options::OptionKeys::run::rebuild_disulf, basic::options::OptionKeys::score::ref_offset, basic::options::OptionKeys::score::ref_offsets, basic::options::OptionKeys::run::reinitialize_mover_for_each_job, basic::options::OptionKeys::run::reinitialize_mover_for_new_input, basic::options::OptionKeys::run::remove_ss_length_screen, basic::options::OptionKeys::run::repack_rate, basic::options::OptionKeys::run::repeat, basic::options::OptionKeys::jd3::resource_definition_files, basic::options::OptionKeys::jd3::resource_definition_schema, basic::options::OptionKeys::jd3::restore_from_checkpoint, basic::options::OptionKeys::score::rg_local_span, basic::options::OptionKeys::score::ring_close_shadow_constraint, basic::options::OptionKeys::score::rms_target, basic::options::OptionKeys::run::rng, basic::options::OptionKeys::run::rng_seed_device, basic::options::OptionKeys::run::run, basic::options::OptionKeys::score::score, basic::options::OptionKeys::out::path::score, basic::options::OptionKeys::run::score_only, basic::options::OptionKeys::score::score_pose_cutpoint_variants, basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::parser::script_vars, basic::options::OptionKeys::score::secondary_seqdep_refene_fname, basic::options::OptionKeys::jd2::seed_ensemble, basic::options::OptionKeys::jd2::seed_ensemble_weights, basic::options::OptionKeys::jd2::seed_ensemble_weights_file, basic::options::OptionKeys::run::seed_offset, basic::options::OptionKeys::score::seqdep_refene_fname, basic::options::OptionKeys::jd2::sequential_mpi_job_distribution, basic::options::OptionKeys::score::set_weights, basic::options::OptionKeys::score::show_etable_contributions, basic::options::OptionKeys::run::show_simulation_in_pymol, basic::options::OptionKeys::view::show_virtual_residues, basic::options::OptionKeys::run::shuffle, basic::options::OptionKeys::score::sidechain_buried, basic::options::OptionKeys::score::sidechain_exposed, basic::options::OptionKeys::view::single_glycan_color, basic::options::OptionKeys::run::skip_set_reasonable_fold_tree, basic::options::OptionKeys::score::smooth_fa_elec, basic::options::OptionKeys::score::soft_wts, basic::options::OptionKeys::score::stack_elec_sigmoidal_die, basic::options::OptionKeys::run::suppress_checkpoints, basic::options::OptionKeys::score::symE_bonus, basic::options::OptionKeys::score::symE_units, basic::options::OptionKeys::score::symmetric_gly_tables, basic::options::OptionKeys::score::target_clash_pdb, basic::options::OptionKeys::run::test_cycles, basic::options::OptionKeys::run::timer, basic::options::OptionKeys::score::unmodifypot, basic::options::OptionKeys::run::update_pymol_on_conformation_changes_only, basic::options::OptionKeys::run::update_pymol_on_energy_changes_only, basic::options::OptionKeys::score::use_hb_env_dep, basic::options::OptionKeys::run::use_time_as_seed, basic::options::OptionKeys::parser::validate_and_exit, basic::options::OptionKeys::run::version, basic::options::OptionKeys::view::view, basic::options::OptionKeys::parser::view, basic::options::OptionKeys::score::water_hybrid_sf, basic::options::OptionKeys::score::weights, basic::options::OptionKeys::run::wide_nblist_extension, and basic::options::OptionKeys::run::write_failures.

Referenced by add_all_rosetta_options().

void add_rosetta_options_10 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::mh::match::aa, basic::options::OptionKeys::mh::match::aa1, basic::options::OptionKeys::mh::filter::aa1, basic::options::OptionKeys::mh::match::aa2, basic::options::OptionKeys::mh::filter::aa2, utility::options::OptionCollection::add(), basic::options::OptionKeys::magnesium::montecarlo::add_delete_frequency, basic::options::OptionKeys::mh::harvest::agg_with_max, basic::options::OptionKeys::matdes::mutalyze::ala_scan, basic::options::OptionKeys::magnesium::all_hydration_frames, basic::options::OptionKeys::ms::anchor_offset, basic::options::OptionKeys::mh::score::anti_polar_weight, basic::options::OptionKeys::motifs::aromatic_motifs, basic::options::OptionKeys::mh::score::background_weight, basic::options::OptionKeys::mean_field::bb_average_weight, basic::options::OptionKeys::mean_field::bb_boltz_probs, basic::options::OptionKeys::mean_field::bb_list, basic::options::OptionKeys::mean_field::biased_dist_all_gen, basic::options::OptionKeys::mh::path::biounit, basic::options::OptionKeys::mh::path::biounit_ideal, basic::options::OptionKeys::ms::Boltz_temp, basic::options::OptionKeys::motifs::BPData, basic::options::OptionKeys::motifs::build_residue_file, basic::options::OptionKeys::mh::score::ca_cb_clash_weight, basic::options::OptionKeys::matdes::mutalyze::calc_rot_boltz, basic::options::OptionKeys::ms::checkpoint::checkpoint, basic::options::OptionKeys::motifs::clear_bprots, basic::options::OptionKeys::motifs::close_enough, basic::options::OptionKeys::mc::convergence_check_frequency, basic::options::OptionKeys::mh::filter::coorderr, basic::options::OptionKeys::nmr::rdc::correct_sign, basic::options::OptionKeys::mh::score::coverage_pow, basic::options::OptionKeys::magnesium::montecarlo::cycles, basic::options::OptionKeys::motifs::data_file, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::mh::filter::dssp1, basic::options::OptionKeys::mh::filter::dssp2, basic::options::OptionKeys::motifs::dtest, basic::options::OptionKeys::magnesium::montecarlo::dump, basic::options::OptionKeys::mh::harvest::dump, basic::options::OptionKeys::mh::dump::dump, basic::options::OptionKeys::mh::dump_input_pdb, basic::options::OptionKeys::mh::dump_matching_motifs, basic::options::OptionKeys::mh::dump_motif_pdbs, basic::options::OptionKeys::motifs::dump_motifs, basic::options::OptionKeys::mean_field::dump_transfac, basic::options::OptionKeys::motifs::duplicate_angle_cutoff, basic::options::OptionKeys::motifs::duplicate_dist_cutoff, basic::options::OptionKeys::motifs::duplicate_motif_cutoff, basic::options::OptionKeys::motifs::elec_max_threshold, basic::options::OptionKeys::motifs::elec_min_threshold, basic::options::OptionKeys::motifs::eliminate_weak_motifs, basic::options::OptionKeys::mc::excluded_residues_from_rmsd, basic::options::OptionKeys::motifs::expand_motifs, basic::options::OptionKeys::mh::explicit_motif_score, basic::options::OptionKeys::mh::filter::faatr, basic::options::OptionKeys::mh::filter::faatr_or_hb, basic::options::OptionKeys::mh::filter::faatr_or_hbbb, basic::options::OptionKeys::motifs::file_prefix, basic::options::OptionKeys::mh::filter::filter, basic::options::OptionKeys::mh::filter::filter_harvest, basic::options::OptionKeys::mh::filter::filter_io, basic::options::OptionKeys::magnesium::fixup, basic::options::OptionKeys::motifs::flex_sugar, basic::options::OptionKeys::ms::fraction_by_recombination, basic::options::OptionKeys::mean_field::ga_pack_detect_interface, basic::options::OptionKeys::mh::gen_reverse_motifs_on_load, basic::options::OptionKeys::ms::generations, basic::options::OptionKeys::ms::checkpoint::gz, basic::options::OptionKeys::mh::harvest::harvest, basic::options::OptionKeys::mh::harvest_motifs, basic::options::OptionKeys::mh::harvest_motifs_min_hh_ends, basic::options::OptionKeys::mh::harvest_scores, basic::options::OptionKeys::mh::harvest::hash_angle_resl, basic::options::OptionKeys::mh::harvest::hash_cart_resl, basic::options::OptionKeys::mh::filter::hb_bb, basic::options::OptionKeys::mh::filter::hb_bb_sc, basic::options::OptionKeys::mh::filter::hb_sc, basic::options::OptionKeys::motifs::hb_score_cutoff, basic::options::OptionKeys::motifs::hbond_max_threshold, basic::options::OptionKeys::motifs::hbond_min_threshold, basic::options::OptionKeys::mc::heat_convergence_check, basic::options::OptionKeys::mc::hierarchical_pool, basic::options::OptionKeys::magnesium::hydrate, basic::options::OptionKeys::mh::harvest::idealize, basic::options::OptionKeys::mh::ignore_io_errors, basic::options::OptionKeys::mean_field::include_all_aa, basic::options::OptionKeys::nmr::pcs::input_file, basic::options::OptionKeys::nmr::rdc::input_file, basic::options::OptionKeys::nmr::pre::input_file, basic::options::OptionKeys::magnesium::integration_test, basic::options::OptionKeys::mh::match::interface_only, basic::options::OptionKeys::ms::checkpoint::interval, utility::options::Option::is_group(), basic::options::OptionKeys::motifs::keep_motif_xtal_location, basic::options::OptionKeys::mc::known_structures, basic::options::OptionKeys::magnesium::leave_other_waters, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::mh::filter::lig, basic::options::OptionKeys::motifs::ligand_motif_sphere, basic::options::OptionKeys::magnesium::ligand_res, basic::options::OptionKeys::mh::dump::limit_per_pair, basic::options::OptionKeys::motifs::list_dnaconformers, basic::options::OptionKeys::motifs::list_motifs, basic::options::OptionKeys::mc::log_scores_in_MC, basic::options::OptionKeys::magnesium::lores_scan, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::magnesium::magnesium, basic::options::OptionKeys::mh::match::match, basic::options::OptionKeys::mh::dump::max_ca_dis, basic::options::OptionKeys::mh::score::max_cb_dis, basic::options::OptionKeys::mh::score::max_contact_pairs, basic::options::OptionKeys::motifs::max_depth, basic::options::OptionKeys::mh::dump::max_per_res, basic::options::OptionKeys::mh::harvest::max_res, basic::options::OptionKeys::mh::dump::max_rms, basic::options::OptionKeys::mh::harvest::max_rmsd, basic::options::OptionKeys::mc::max_rmsd_against_known_structures, basic::options::OptionKeys::mh::filter::max_seqsep, basic::options::OptionKeys::mh::filter::maxdist2, basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::mean_field::mean_field, basic::options::OptionKeys::mh::merge_motifs, basic::options::OptionKeys::mh::merge_motifs_one_per_bin, basic::options::OptionKeys::mh::merge_scores, basic::options::OptionKeys::mh::merge_similar_motifs, basic::options::OptionKeys::magnesium::mg_res, basic::options::OptionKeys::mh::mh, basic::options::OptionKeys::mh::harvest::min_bin_val, basic::options::OptionKeys::mh::score::min_contact_pairs, basic::options::OptionKeys::mh::score::min_cover_fraction, basic::options::OptionKeys::matdes::mutalyze::min_rb, basic::options::OptionKeys::mh::filter::mindist2, basic::options::OptionKeys::magnesium::minimize, basic::options::OptionKeys::motifs::minimize, basic::options::OptionKeys::motifs::minimize_dna, basic::options::OptionKeys::magnesium::minimize_during_scoring, basic::options::OptionKeys::magnesium::minimize_mg_coord_constraint_distance, basic::options::OptionKeys::magnesium::monte_carlo, basic::options::OptionKeys::magnesium::montecarlo::montecarlo, basic::options::OptionKeys::motifs::motif_build_defs, basic::options::OptionKeys::motifs::motif_build_positions, basic::options::OptionKeys::motifs::motif_filename, basic::options::OptionKeys::motifs::motif_flexible_loop_file, basic::options::OptionKeys::mh::motif_match_radius, basic::options::OptionKeys::mh::motif_out_file, basic::options::OptionKeys::motifs::motif_output_directory, basic::options::OptionKeys::mh::filter::motif_type, basic::options::OptionKeys::motifs::motifs, basic::options::OptionKeys::mh::path::motifs, basic::options::OptionKeys::mh::path::motifs_BB_BB, basic::options::OptionKeys::mh::path::motifs_BB_PH, basic::options::OptionKeys::mh::path::motifs_BB_PO, basic::options::OptionKeys::mh::path::motifs_PH_PO, basic::options::OptionKeys::mh::path::motifs_SC_BB, basic::options::OptionKeys::mh::path::motifs_SC_SC, basic::options::OptionKeys::ms::ms, basic::options::OptionKeys::mh::harvest::multiplier, basic::options::OptionKeys::nmr::pcs::multiset_weights, basic::options::OptionKeys::nmr::rdc::multiset_weights, basic::options::OptionKeys::matdes::mutalyze::mutalyze, basic::options::OptionKeys::mutate::mutant_file, basic::options::OptionKeys::mutate::mutate, basic::options::OptionKeys::ms::mutate_rate, basic::options::OptionKeys::mutate::mutation, basic::options::OptionKeys::nmr::pcs::nls_repeats, basic::options::OptionKeys::nmr::rdc::nls_repeats, basic::options::OptionKeys::nmr::pre::nls_repeats, basic::options::OptionKeys::nmr::nmr, basic::options::OptionKeys::mh::filter::no_hb_bb, basic::options::OptionKeys::motifs::no_rotamer_bump, basic::options::OptionKeys::mh::filter::nodisulf, basic::options::OptionKeys::mh::score::nohelix, basic::options::OptionKeys::mh::score::noloops, basic::options::OptionKeys::mh::filter::noloops, basic::options::OptionKeys::nmr::rdc::normalization_type, basic::options::OptionKeys::nmr::pcs::normalize_data, basic::options::OptionKeys::mh::normalize_score_ncontact, basic::options::OptionKeys::mh::score::nosheets, basic::options::OptionKeys::mh::filter::not_restype, basic::options::OptionKeys::mh::filter::not_restype_one, basic::options::OptionKeys::ms::num_packs, basic::options::OptionKeys::motifs::num_repacks, basic::options::OptionKeys::ms::numresults, basic::options::OptionKeys::mh::filter::occupancy, basic::options::OptionKeys::mh::filter::oneloop, basic::options::OptionKeys::nmr::pcs::optimize_tensor, basic::options::OptionKeys::motifs::output_file, basic::options::OptionKeys::motifs::pack_max_threshold, basic::options::OptionKeys::motifs::pack_min_threshold, basic::options::OptionKeys::motifs::pack_score_cutoff, basic::options::OptionKeys::magnesium::pack_water_hydrogens, basic::options::OptionKeys::mh::path::path, basic::options::OptionKeys::nmr::pcs::pcs, basic::options::OptionKeys::mh::path::pdb, basic::options::OptionKeys::mh::filter::pdb, basic::options::OptionKeys::motifs::place_adduct_waters, basic::options::OptionKeys::ms::pop_from_ss, basic::options::OptionKeys::ms::pop_size, basic::options::OptionKeys::magnesium::pose_ligand_res, basic::options::OptionKeys::nmr::pre::pre, basic::options::OptionKeys::ms::checkpoint::prefix, basic::options::OptionKeys::motifs::preminimize_motif_pdbs, basic::options::OptionKeys::motifs::preminimize_motif_pdbs_sconly, basic::options::OptionKeys::mh::print_motifs, basic::options::OptionKeys::mh::print_scores, basic::options::OptionKeys::motifs::quick_and_dirty, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::nmr::rdc::rdc, basic::options::OptionKeys::mc::read_structures_into_pool, basic::options::OptionKeys::mh::remove_duplicates, basic::options::OptionKeys::ms::checkpoint::rename, basic::options::OptionKeys::motifs::rerun_motifsearch, basic::options::OptionKeys::mh::dump::resfile_dump, basic::options::OptionKeys::mh::dump::resfile_min_pair_score, basic::options::OptionKeys::mh::dump::resfile_min_tot_score, basic::options::OptionKeys::motifs::residue_trim_file, basic::options::OptionKeys::motifs::restrict_to_wt, basic::options::OptionKeys::mh::filter::restype, basic::options::OptionKeys::mh::filter::restype1, basic::options::OptionKeys::mh::filter::restype2, basic::options::OptionKeys::mh::filter::restype_one, basic::options::OptionKeys::matdes::mutalyze::revert_scan, basic::options::OptionKeys::mean_field::rf_peptide, basic::options::OptionKeys::mean_field::rot_norm_weight, basic::options::OptionKeys::motifs::rotlevel, basic::options::OptionKeys::motifs::rots2add, basic::options::OptionKeys::motifs::run_motifs, basic::options::OptionKeys::mh::filter::sasa, basic::options::OptionKeys::magnesium::scan, basic::options::OptionKeys::mh::score::score, basic::options::OptionKeys::mh::filter::score, basic::options::OptionKeys::mh::score_across_chains_only, basic::options::OptionKeys::magnesium::score_cut, basic::options::OptionKeys::magnesium::score_cut_PDB, basic::options::OptionKeys::mh::score_pdbs, basic::options::OptionKeys::magnesium::scored_hydrogen_sampling, basic::options::OptionKeys::mh::path::scores, basic::options::OptionKeys::mh::path::scores_BB_BB, basic::options::OptionKeys::mh::path::scores_BB_PH, basic::options::OptionKeys::mh::path::scores_BB_PO, basic::options::OptionKeys::mh::path::scores_frags, basic::options::OptionKeys::mh::path::scores_PH_PO, basic::options::OptionKeys::mh::path::scores_SC_BB, basic::options::OptionKeys::mh::path::scores_SC_SC, basic::options::OptionKeys::mh::harvest::sep_aa, basic::options::OptionKeys::mh::harvest::sep_aa1, basic::options::OptionKeys::mh::harvest::sep_aa2, basic::options::OptionKeys::mh::harvest::sep_bfac, basic::options::OptionKeys::mh::harvest::sep_dist, basic::options::OptionKeys::mh::harvest::sep_dssp, basic::options::OptionKeys::mh::harvest::sep_hb, basic::options::OptionKeys::mh::harvest::sep_lj, basic::options::OptionKeys::mh::harvest::sep_nbrs, basic::options::OptionKeys::mh::harvest::sep_ss, basic::options::OptionKeys::mh::filter::seqsep, basic::options::OptionKeys::mh::sequence_recovery, basic::options::OptionKeys::nmr::pcs::show_info, basic::options::OptionKeys::nmr::rdc::show_info, basic::options::OptionKeys::mh::harvest::smoothing_factor, basic::options::OptionKeys::mean_field::spec_profile, basic::options::OptionKeys::motifs::special_rotweight, basic::options::OptionKeys::mh::score::spread_ss_element, basic::options::OptionKeys::mh::match::ss, basic::options::OptionKeys::mh::match::ss1, basic::options::OptionKeys::mh::filter::ss1, basic::options::OptionKeys::mh::match::ss2, basic::options::OptionKeys::mh::filter::ss2, basic::options::OptionKeys::mh::score::strand_pair_weight, basic::options::OptionKeys::mh::dump::symmetric_motifs, basic::options::OptionKeys::motifs::target_aa, basic::options::OptionKeys::motifs::target_dna_defs, basic::options::OptionKeys::magnesium::montecarlo::temperature, basic::options::OptionKeys::magnesium::tether_to_closest_res, basic::options::OptionKeys::mh::filter::uniformfrag, utility::options::ScalarOption_T_< K, T >::upper(), basic::options::OptionKeys::mh::score::use_aa1, basic::options::OptionKeys::mh::score::use_aa2, basic::options::OptionKeys::mh::score::use_log, basic::options::OptionKeys::mh::score::use_ss1, basic::options::OptionKeys::mh::score::use_ss2, basic::options::OptionKeys::nmr::pcs::use_symmetry_calc, basic::options::OptionKeys::nmr::rdc::use_symmetry_calc, basic::options::OptionKeys::motifs::water_score_cutoff, basic::options::OptionKeys::mh::harvest::weight_by_energy, basic::options::OptionKeys::magnesium::xyz_step, basic::options::OptionKeys::motifs::z1, and basic::options::OptionKeys::motifs::z2.

Referenced by add_all_rosetta_options().

void add_rosetta_options_11 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::pepspec::add_buffer_res, basic::options::OptionKeys::fingerprint::add_esp, basic::options::OptionKeys::pepspec::anchor_type, basic::options::OptionKeys::pb_potential::apbs_debug, basic::options::OptionKeys::pb_potential::apbs_path, basic::options::OptionKeys::optE::approximate_decoy_entropy, basic::options::OptionKeys::fingerprint::atom_radius_buffer, basic::options::OptionKeys::fingerprint::atom_radius_scale, basic::options::OptionKeys::ProQ::basename, basic::options::OptionKeys::pepspec::binding_score, basic::options::OptionKeys::nmr::spinlabel::boltzmann_kt, basic::options::OptionKeys::patterson::Bsol, basic::options::OptionKeys::pH::calc_pka::calc_pka, basic::options::OptionKeys::pepspec::calc_sasa, basic::options::OptionKeys::pb_potential::calcenergy, basic::options::OptionKeys::fingerprint::cap_e_potential, basic::options::OptionKeys::packstat::cavity_burial_probe_radius, basic::options::OptionKeys::pepspec::cen_wts, basic::options::OptionKeys::pocket_grid::central_relax_pdb_num, basic::options::OptionKeys::optE::centroid_rot, basic::options::OptionKeys::optE::centroid_rot_min, basic::options::OptionKeys::pepspec::cg_res_type, basic::options::OptionKeys::pb_potential::charged_chains, basic::options::OptionKeys::nonlocal::chunks, basic::options::OptionKeys::pepspec::clash_cutoff, basic::options::OptionKeys::gen_pharmacophore::clash_distance_cutoff, basic::options::OptionKeys::packstat::cluster_min_volume, basic::options::OptionKeys::pH::cognate_partners, basic::options::OptionKeys::pH::cognate_pdb, basic::options::OptionKeys::optE::component_weights, basic::options::OptionKeys::optE::constant_logic_taskops_file, basic::options::OptionKeys::optE::constrain_weights, basic::options::OptionKeys::optE::rescore::context_round, basic::options::OptionKeys::fingerprint::darc_components, basic::options::OptionKeys::fingerprint::darc_elsts_only, basic::options::OptionKeys::fingerprint::darc_shape_only, basic::options::OptionKeys::optE::data_in, basic::options::OptionKeys::optE::data_out, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::fingerprint::delphi_grid, basic::options::OptionKeys::optE::design_first, basic::options::OptionKeys::optE::design_with_fast_design, basic::options::OptionKeys::optE::design_with_minpack, basic::options::OptionKeys::optE::design_with_offrotpack, basic::options::OptionKeys::fingerprint::dist_cut_off, basic::options::OptionKeys::pepspec::diversify_lvl, basic::options::OptionKeys::pepspec::diversify_pep_seqs, basic::options::OptionKeys::optE::dont_use_reference_energies, basic::options::OptionKeys::patterson::dont_use_symm_in_pcalc, basic::options::OptionKeys::pepspec::dump_cg_bb, basic::options::OptionKeys::pocket_grid::dump_connollySurface, basic::options::OptionKeys::pocket_grid::dump_espGrid, basic::options::OptionKeys::pocket_grid::dump_Grid, basic::options::OptionKeys::pocket_grid::dump_pocketGrid, basic::options::OptionKeys::pocket_grid::eggshell_dist, basic::options::OptionKeys::nmr::spinlabel::elaborate_rotamer_clash_check, basic::options::OptionKeys::pocket_grid::esp_buffer_dist, basic::options::OptionKeys::fingerprint::esp_protein_wt, basic::options::OptionKeys::fingerprint::esp_surface_wt, basic::options::OptionKeys::fingerprint::esp_weight, basic::options::OptionKeys::optE::exclude_badrep_ddGs, basic::options::OptionKeys::pocket_grid::extend_eggshell, basic::options::OptionKeys::pocket_grid::extend_eggshell_dist, basic::options::OptionKeys::pocket_grid::extra_eggshell_dist, basic::options::OptionKeys::fingerprint::fingerprint, basic::options::OptionKeys::optE::fit_reference_energies_to_aa_profile_recovery, basic::options::OptionKeys::optE::fix, basic::options::OptionKeys::optE::fixed, basic::options::OptionKeys::optE::free, basic::options::OptionKeys::patterson::Fsol, basic::options::OptionKeys::pepspec::gen_pep_bb_sequential, basic::options::OptionKeys::gen_pharmacophore::gen_pharmacophore, basic::options::OptionKeys::nmr::spinlabel::highres_conformer_filter_type, basic::options::OptionKeys::pepspec::homol_csts, basic::options::OptionKeys::fingerprint::include_extrashell_to_set_origin, basic::options::OptionKeys::fingerprint::include_hydrogens, basic::options::OptionKeys::optE::include_intra_res_protein, basic::options::OptionKeys::packstat::include_water, basic::options::OptionKeys::fingerprint::inp_lig, basic::options::OptionKeys::pepspec::input_seq, basic::options::OptionKeys::pepspec::interface_cutoff, basic::options::OptionKeys::optE::inv_kT_nataa, basic::options::OptionKeys::optE::inv_kT_natrot, basic::options::OptionKeys::optE::inv_kT_natstruct, utility::options::Option::is_group(), basic::options::OptionKeys::pH::keep_input_protonation_state, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::optE::limit_bad_scores, basic::options::OptionKeys::optE::load_from_silent, basic::options::OptionKeys::nmr::spinlabel::max_ensemble_size, basic::options::OptionKeys::optE::max_rms_from_native, basic::options::OptionKeys::optE::rescore::measure_sequence_recovery, basic::options::OptionKeys::packstat::min_cav_ball_radius, basic::options::OptionKeys::packstat::min_cluster_overlap, basic::options::OptionKeys::optE::min_decoy_rms_to_native, basic::options::OptionKeys::gen_pharmacophore::min_num_ring, basic::options::OptionKeys::packstat::min_surface_accessibility, basic::options::OptionKeys::patterson::model_B, basic::options::OptionKeys::optE::mpi_weight_minimization, basic::options::OptionKeys::fingerprint::multiple_origin, basic::options::OptionKeys::nmr::pre::multiset_weights, basic::options::OptionKeys::pepspec::n_anchor_dock_std_devs, basic::options::OptionKeys::pepspec::n_append, basic::options::OptionKeys::pepspec::n_build_loop, basic::options::OptionKeys::pepspec::n_cgrelax_loop, basic::options::OptionKeys::optE::n_design_cycles, basic::options::OptionKeys::pepspec::n_dock_loop, basic::options::OptionKeys::pepspec::n_peptides, basic::options::OptionKeys::pepspec::n_prepend, basic::options::OptionKeys::optE::n_top_natives_to_optimize, basic::options::OptionKeys::pepspec::native_align, basic::options::OptionKeys::pepspec::native_pep_anchor, basic::options::OptionKeys::pepspec::native_pep_chain, basic::options::OptionKeys::pepspec::no_cen, basic::options::OptionKeys::pepspec::no_cen_rottrials, basic::options::OptionKeys::pepspec::no_design, basic::options::OptionKeys::optE::no_design, basic::options::OptionKeys::optE::no_design_pdb_output, basic::options::OptionKeys::patterson::no_ecalc, basic::options::OptionKeys::optE::no_hb_env_dependence, basic::options::OptionKeys::optE::no_hb_env_dependence_DNA, basic::options::OptionKeys::pepspec::no_prepack_prot, basic::options::OptionKeys::nonlocal::nonlocal, basic::options::OptionKeys::PCS::normalization_id, basic::options::OptionKeys::PCSTS2::normalization_id, basic::options::OptionKeys::PCSTS3::normalization_id, basic::options::OptionKeys::PCSTS4::normalization_id, basic::options::OptionKeys::PCSTS1::normalization_id, basic::options::OptionKeys::nmr::pre::normalize_data, basic::options::OptionKeys::optE::normalize_decoy_score_spread, basic::options::OptionKeys::patterson::nshells, basic::options::OptionKeys::optE::number_of_swarm_cycles, basic::options::OptionKeys::optE::number_of_swarm_particles, basic::options::OptionKeys::optE::optE, basic::options::OptionKeys::optE::optE_no_protein_fa_elec, basic::options::OptionKeys::optE::optE_soft_rep, basic::options::OptionKeys::optE::optimize_ddG_bind_correlation, basic::options::OptionKeys::optE::optimize_ddGmutation, basic::options::OptionKeys::optE::optimize_ddGmutation_boltzman_average, basic::options::OptionKeys::optE::optimize_ddGmutation_straight_mean, basic::options::OptionKeys::optE::optimize_decoy_discrimination, basic::options::OptionKeys::optE::optimize_dGbinding, basic::options::OptionKeys::optE::optimize_ligand_discrimination, basic::options::OptionKeys::optE::optimize_ligand_rot, basic::options::OptionKeys::optE::optimize_nat_aa, basic::options::OptionKeys::optE::optimize_nat_rot, basic::options::OptionKeys::nmr::pre::optimize_para_ion_position, basic::options::OptionKeys::optE::optimize_pssm, basic::options::OptionKeys::optE::optimize_starting_free_weights, basic::options::OptionKeys::fingerprint::origin_res_num, basic::options::OptionKeys::optE::rescore::outlog, basic::options::OptionKeys::nmr::score::output_exp_calc, basic::options::OptionKeys::pH::output_raw_scores, basic::options::OptionKeys::nmr::score::output_tensor_info, basic::options::OptionKeys::optE::output_top_n_new_decoys, basic::options::OptionKeys::packstat::oversample, basic::options::OptionKeys::pepspec::p_homol_csts, basic::options::OptionKeys::fingerprint::packing_weight, basic::options::OptionKeys::packstat::packstat, basic::options::OptionKeys::packstat::packstat_pdb, basic::options::OptionKeys::optE::parse_tagfile, basic::options::OptionKeys::patterson::patterson, basic::options::OptionKeys::pb_potential::pb_potential, basic::options::OptionKeys::PCS::PCS, basic::options::OptionKeys::PCSTS1::PCSTS1, basic::options::OptionKeys::PCSTS2::PCSTS2, basic::options::OptionKeys::PCSTS3::PCSTS3, basic::options::OptionKeys::PCSTS4::PCSTS4, basic::options::OptionKeys::pepspec::pdb_list, basic::options::OptionKeys::pepspec::pep_anchor, basic::options::OptionKeys::pepspec::pep_chain, basic::options::OptionKeys::pepspec::pepspec, basic::options::OptionKeys::pH::pH, basic::options::OptionKeys::pH::pH_mode, basic::options::OptionKeys::pH::calc_pka::pH_neighbor_pack, basic::options::OptionKeys::pH::calc_pka::pH_prepack, basic::options::OptionKeys::pH::calc_pka::pH_relax, basic::options::OptionKeys::pH::pH_unbound, basic::options::OptionKeys::pH::calc_pka::pka_all, basic::options::OptionKeys::pH::calc_pka::pka_for_chainno, basic::options::OptionKeys::pH::calc_pka::pka_for_resnos, basic::options::OptionKeys::pH::calc_pka::pka_rad, basic::options::OptionKeys::pocket_grid::pocket_buried_dist, basic::options::OptionKeys::pocket_grid::pocket_buried_score, basic::options::OptionKeys::pocket_grid::pocket_debug_output, basic::options::OptionKeys::pocket_grid::pocket_dump_exemplars, basic::options::OptionKeys::pocket_grid::pocket_dump_pdbs, basic::options::OptionKeys::pocket_grid::pocket_dump_rama, basic::options::OptionKeys::pocket_grid::pocket_exemplar_vdw_pen, basic::options::OptionKeys::pocket_grid::pocket_filter_by_exemplar, basic::options::OptionKeys::pocket_grid::pocket_grid, basic::options::OptionKeys::pocket_grid::pocket_grid_size, basic::options::OptionKeys::pocket_grid::pocket_grid_size_x, basic::options::OptionKeys::pocket_grid::pocket_grid_size_y, basic::options::OptionKeys::pocket_grid::pocket_grid_size_z, basic::options::OptionKeys::pocket_grid::pocket_grid_spacing, basic::options::OptionKeys::pocket_grid::pocket_ignore_buried, basic::options::OptionKeys::pocket_grid::pocket_limit_exemplar_color, basic::options::OptionKeys::pocket_grid::pocket_limit_small_exemplars, basic::options::OptionKeys::pocket_grid::pocket_max_size, basic::options::OptionKeys::pocket_grid::pocket_max_spacing, basic::options::OptionKeys::pocket_grid::pocket_min_size, basic::options::OptionKeys::pocket_grid::pocket_ntrials, basic::options::OptionKeys::pocket_grid::pocket_num_angles, basic::options::OptionKeys::pocket_grid::pocket_only_buried, basic::options::OptionKeys::pocket_grid::pocket_probe_radius, basic::options::OptionKeys::pocket_grid::pocket_psp, basic::options::OptionKeys::pocket_grid::pocket_restrict_size, basic::options::OptionKeys::pocket_grid::pocket_search13, basic::options::OptionKeys::pocket_grid::pocket_side, basic::options::OptionKeys::pocket_grid::pocket_sps, basic::options::OptionKeys::pocket_grid::pocket_static_grid, basic::options::OptionKeys::pocket_grid::pocket_surface_dist, basic::options::OptionKeys::pocket_grid::pocket_surface_score, basic::options::OptionKeys::pb_potential::potential_cap, basic::options::OptionKeys::pH::pre_process, basic::options::OptionKeys::pepspec::prep_align_prot_to, basic::options::OptionKeys::pepspec::prep_rot_std_dev, basic::options::OptionKeys::pepspec::prep_trans_std_dev, basic::options::OptionKeys::pepspec::prep_use_ref_rotamers, basic::options::OptionKeys::optE::pretend_no_ddG_repulsion, basic::options::OptionKeys::fingerprint::print_eggshell, basic::options::OptionKeys::ProQ::ProQ, basic::options::OptionKeys::patterson::radius_cutoffs, basic::options::OptionKeys::optE::ramp_nativeness, basic::options::OptionKeys::nonlocal::randomize_missing, basic::options::OptionKeys::optE::randomly_perturb_starting_free_weights, basic::options::OptionKeys::packstat::raw_stats, basic::options::OptionKeys::optE::recover_nat_rot, basic::options::OptionKeys::pocket_grid::reduce_rays, basic::options::OptionKeys::fingerprint::ref_lig, basic::options::OptionKeys::pepspec::ref_pdb_list, basic::options::OptionKeys::pepspec::remove_input_bb, basic::options::OptionKeys::optE::repack_and_minimize_decoys, basic::options::OptionKeys::optE::repack_and_minimize_input_structures, basic::options::OptionKeys::optE::repeat_swarm_optimization_until_fitness_improves, basic::options::OptionKeys::optE::rescore::rescore, basic::options::OptionKeys::packstat::residue_scores, basic::options::OptionKeys::patterson::resolution_cutoffs, basic::options::OptionKeys::fingerprint::return_zero_darc_score, basic::options::OptionKeys::pb_potential::revamp_near_chain, basic::options::OptionKeys::gen_pharmacophore::ring_atm_dist_cutoff, basic::options::OptionKeys::gen_pharmacophore::ring_ring_dist_cutoff, basic::options::OptionKeys::gen_pharmacophore::ring_sasa_cutoff, basic::options::OptionKeys::patterson::rmsd, basic::options::OptionKeys::pepspec::rmsd_analysis, basic::options::OptionKeys::pH::calc_pka::rotamer_prot_stats, basic::options::OptionKeys::pocket_grid::round_pocketGrid_center, basic::options::OptionKeys::pepspec::run_sequential, basic::options::OptionKeys::pepspec::save_all_pdbs, basic::options::OptionKeys::pepspec::save_low_pdbs, basic::options::OptionKeys::patterson::sc_scaling, basic::options::OptionKeys::nmr::score::score, basic::options::OptionKeys::pepspec::seq_align, basic::options::OptionKeys::fingerprint::set_origin, basic::options::OptionKeys::fingerprint::set_protein_esp_to_zero, basic::options::OptionKeys::fingerprint::set_surface_esp_to_zero, basic::options::OptionKeys::nmr::pre::show_info, basic::options::OptionKeys::pb_potential::sidechain_only, basic::options::OptionKeys::pepspec::soft_wts, basic::options::OptionKeys::nmr::spinlabel::spinlabel, basic::options::OptionKeys::optE::sqrt_pssm, basic::options::OptionKeys::fingerprint::square_score, basic::options::OptionKeys::pepspec::ss_type, basic::options::OptionKeys::optE::starting_refEs, basic::options::OptionKeys::packstat::surface_accessibility, basic::options::OptionKeys::ProQ::svmmodel, basic::options::OptionKeys::packstat::threads, basic::options::OptionKeys::pb_potential::tolerance, basic::options::OptionKeys::pepspec::upweight_interface, basic::options::OptionKeys::fingerprint::use_DARC_gpu, basic::options::OptionKeys::pepspec::use_input_bb, basic::options::OptionKeys::patterson::use_on_repack, basic::options::OptionKeys::patterson::use_spline_interpolation, basic::options::OptionKeys::nmr::pre::use_symmetry_calc, basic::options::OptionKeys::pH::value_pH, basic::options::OptionKeys::nmr::score::verbose, basic::options::OptionKeys::patterson::weight, basic::options::OptionKeys::optE::weights, basic::options::OptionKeys::optE::rescore::weights, basic::options::OptionKeys::optE::wrap_dof_optimization, basic::options::OptionKeys::PCSTS1::write_extra, basic::options::OptionKeys::PCSTS2::write_extra, basic::options::OptionKeys::PCS::write_extra, basic::options::OptionKeys::PCSTS4::write_extra, and basic::options::OptionKeys::PCSTS3::write_extra.

Referenced by add_all_rosetta_options().

void add_rosetta_options_12 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::remodel::staged_sampling::all_3mer_cycles, basic::options::OptionKeys::remodel::staged_sampling::all_3mer_score_file, basic::options::OptionKeys::remodel::staged_sampling::all_9mer_cycles, basic::options::OptionKeys::remodel::staged_sampling::all_9mer_score_file, basic::options::OptionKeys::remodel::design::allow_rare_aro_chi, basic::options::OptionKeys::remodel::RemodelLoopMover::allowed_closure_attempts, basic::options::OptionKeys::relax::range::angle_max, basic::options::OptionKeys::rescore::assign_ss, basic::options::OptionKeys::hydrate::attempt_all_polar, basic::options::OptionKeys::relax::bb_move, basic::options::OptionKeys::hydrate::bias_design_search_to_native, basic::options::OptionKeys::remodel::blueprint, basic::options::OptionKeys::remodel::RemodelLoopMover::boost_closure_cycles, basic::options::OptionKeys::remodel::boundary_cutoff, basic::options::OptionKeys::remodel::boundaryAA, basic::options::OptionKeys::remodel::build_disulf, basic::options::OptionKeys::remodel::RemodelLoopMover::bypass_closure, basic::options::OptionKeys::remodel::bypass_fragments, basic::options::OptionKeys::relax::cartesian, basic::options::OptionKeys::remodel::cbeta, basic::options::OptionKeys::remodel::cen_minimize, basic::options::OptionKeys::remodel::cen_sfxn, basic::options::OptionKeys::remodel::cenpack, basic::options::OptionKeys::relax::centroid::centroid, basic::options::OptionKeys::relax::centroid_mode, basic::options::OptionKeys::relax::chainbreak_weight, basic::options::OptionKeys::remodel::check_scored_centroid, basic::options::OptionKeys::remodel::checkpoint, basic::options::OptionKeys::relax::chi_move, basic::options::OptionKeys::relax::classic, basic::options::OptionKeys::remodel::cluster_on_entire_pose, basic::options::OptionKeys::remodel::cluster_radius, basic::options::OptionKeys::remodel::COM_sd, basic::options::OptionKeys::remodel::COM_tolerance, basic::options::OptionKeys::relax::constrain_relax_segments, basic::options::OptionKeys::relax::constrain_relax_to_native_coords, basic::options::OptionKeys::relax::constrain_relax_to_start_coords, basic::options::OptionKeys::relax::coord_constrain_sidechains, basic::options::OptionKeys::relax::coord_cst_stdev, basic::options::OptionKeys::relax::coord_cst_width, basic::options::OptionKeys::remodel::core_cutoff, basic::options::OptionKeys::remodel::coreAA, basic::options::OptionKeys::rdc::correct_NH_length, basic::options::OptionKeys::remodel::cst_fa_only, basic::options::OptionKeys::RBSegmentRelax::cst_seqwidth, basic::options::OptionKeys::remodel::cstfile, basic::options::OptionKeys::remodel::cstfilter, basic::options::OptionKeys::relax::cycle_ratio, basic::options::OptionKeys::relax::range::cycles, basic::options::OptionKeys::relax::cyclic_peptide, basic::options::OptionKeys::remodel::RemodelLoopMover::cyclic_peptide, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::RBSegmentRelax::default_movement_params, basic::options::OptionKeys::relax::default_repeats, basic::options::OptionKeys::remodel::design::design, basic::options::OptionKeys::remodel::design::design_all, basic::options::OptionKeys::remodel::design_around_ligand, basic::options::OptionKeys::remodel::design::design_neighbors, basic::options::OptionKeys::hydrate::display_water_hb_network, basic::options::OptionKeys::remodel::disulf_landing_range, basic::options::OptionKeys::relax::dna_move, basic::options::OptionKeys::relax::centroid::do_final_repack, basic::options::OptionKeys::remodel::domainFusion::domainFusion, basic::options::OptionKeys::hydrate::dont_hydrate_hb_engaged_bb_O, basic::options::OptionKeys::remodel::dr_cycles, basic::options::OptionKeys::relax::dualspace, basic::options::OptionKeys::rdc::dump_weight_trajectory, basic::options::OptionKeys::relax::energycut, basic::options::OptionKeys::remodel::staged_sampling::fa_mode, basic::options::OptionKeys::remodel::staged_sampling::fa_relax_moves, basic::options::OptionKeys::relax::fast, basic::options::OptionKeys::remodel::filter_omega, basic::options::OptionKeys::remodel::filter_radius, basic::options::OptionKeys::remodel::filter_rise, basic::options::OptionKeys::relax::filter_stage2_beginning, basic::options::OptionKeys::relax::filter_stage2_end, basic::options::OptionKeys::relax::filter_stage2_half, basic::options::OptionKeys::relax::filter_stage2_quarter, basic::options::OptionKeys::remodel::design::find_neighbors, basic::options::OptionKeys::rdc::fit_method, basic::options::OptionKeys::rdc::fix_normAzz, basic::options::OptionKeys::relax::fix_omega, basic::options::OptionKeys::rdc::fixDa, basic::options::OptionKeys::rdc::fixR, basic::options::OptionKeys::remodel::RemodelLoopMover::force_cutting_index, basic::options::OptionKeys::remodel::RemodelLoopMover::force_cutting_N, basic::options::OptionKeys::hydrate::force_enforce_all_waters, basic::options::OptionKeys::remodel::free_relax, basic::options::OptionKeys::remodel::generic_aa, basic::options::OptionKeys::qsar::grid_dir, basic::options::OptionKeys::remodel::hb_lrbb, basic::options::OptionKeys::remodel::hb_srbb, basic::options::OptionKeys::hydrate::hbond_entropy_threshold, basic::options::OptionKeys::hydrate::hbond_threshold, basic::options::OptionKeys::RBSegmentRelax::helical_movement_params, basic::options::OptionKeys::remodel::helical_omega, basic::options::OptionKeys::remodel::helical_radius, basic::options::OptionKeys::remodel::helical_rise, basic::options::OptionKeys::hydrate::hydrate, basic::options::OptionKeys::hydrate::hydrate_all, basic::options::OptionKeys::hydrate::hyfile, basic::options::OptionKeys::relax::range::idealize, basic::options::OptionKeys::hydrate::ignore_fa_sol_at_positions, basic::options::OptionKeys::remodel::design::include_current, basic::options::OptionKeys::relax::centroid::increase_vdw_radii, basic::options::OptionKeys::remodel::RemodelLoopMover::independent_cycles, basic::options::OptionKeys::RBSegmentRelax::input_pdb, basic::options::OptionKeys::remodel::domainFusion::insert_segment2_from_pdb, basic::options::OptionKeys::remodel::domainFusion::insert_segment_from_pdb, utility::options::Option::is_group(), basic::options::OptionKeys::rdc::iterate_reset, basic::options::OptionKeys::rdc::iterate_tol, basic::options::OptionKeys::rdc::iterate_weights, basic::options::OptionKeys::relax::jump_move, basic::options::OptionKeys::resample::jumps, basic::options::OptionKeys::hydrate::just_score, basic::options::OptionKeys::hydrate::keep_non_buried_waters, basic::options::OptionKeys::relax::range::kT, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::remodel::lh_cbreak_selection, basic::options::OptionKeys::remodel::lh_closure_filter, basic::options::OptionKeys::remodel::lh_ex_limit, basic::options::OptionKeys::remodel::lh_filter_string, basic::options::OptionKeys::relax::limit_aroma_chi2, basic::options::OptionKeys::relax::linear_chainbreak_weight, basic::options::OptionKeys::remodel::staged_sampling::loop_3mer_cycles, basic::options::OptionKeys::remodel::staged_sampling::loop_3mer_score_file, basic::options::OptionKeys::remodel::staged_sampling::loop_9mer_cycles, basic::options::OptionKeys::remodel::staged_sampling::loop_9mer_score_file, basic::options::OptionKeys::remodel::staged_sampling::loop_btw_parametric_components, basic::options::OptionKeys::remodel::RemodelLoopMover::loophash_cycles, basic::options::OptionKeys::remodel::match_rt_limit, basic::options::OptionKeys::qsar::max_grid_cache_size, basic::options::OptionKeys::remodel::RemodelLoopMover::max_linear_chainbreak, basic::options::OptionKeys::ProQ::membrane, basic::options::OptionKeys::hydrate::min_backbone_file, basic::options::OptionKeys::relax::range::min_cycles, basic::options::OptionKeys::resample::min_max_start_seq_sep, basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::relax::min_type, basic::options::OptionKeys::relax::mini, basic::options::OptionKeys::hydrate::minimize_bb_where_packing, basic::options::OptionKeys::relax::minimize_bond_angles, basic::options::OptionKeys::relax::minimize_bond_lengths, basic::options::OptionKeys::relax::minimize_bondangle_subset, basic::options::OptionKeys::relax::minimize_bondlength_subset, basic::options::OptionKeys::relax::minirelax_repeats, basic::options::OptionKeys::relax::minirelax_sdev, basic::options::OptionKeys::remodel::move_ligand, basic::options::OptionKeys::relax::movemap_disables_packing_of_fixed_chi_positions, basic::options::OptionKeys::hydrate::near_water_threshold, basic::options::OptionKeys::rdc::nlsrepeat, basic::options::OptionKeys::relax::range::nmoves, basic::options::OptionKeys::remodel::design::no_design, basic::options::OptionKeys::remodel::no_jumps, basic::options::OptionKeys::ProQ::normalize, basic::options::OptionKeys::RBSegmentRelax::nrbmoves, basic::options::OptionKeys::RBSegmentRelax::nrboutercycles, basic::options::OptionKeys::remodel::num_trajectory, basic::options::OptionKeys::hydrate::only_remove_non_buried_waters, basic::options::OptionKeys::ProQ::output_feature_vector, basic::options::OptionKeys::ProQ::output_local_prediction, basic::options::OptionKeys::relax::overlap_chainbreak_weight, basic::options::OptionKeys::hydrate::pack_nloop, basic::options::OptionKeys::relax::centroid::parameters, basic::options::OptionKeys::hydrate::partial_hydrate_dew, basic::options::OptionKeys::rbe::poll_frequency, basic::options::OptionKeys::hydrate::pre_bump_check, basic::options::OptionKeys::remodel::staged_sampling::pre_centroid, basic::options::OptionKeys::ProQ::prefix, basic::options::OptionKeys::rdc::print_rdc_values, basic::options::OptionKeys::ProQ::prof_bug, basic::options::OptionKeys::hydrate::protein_flexibility, basic::options::OptionKeys::qsar::qsar, basic::options::OptionKeys::relax::quick, basic::options::OptionKeys::remodel::quick_and_dirty, basic::options::OptionKeys::remodel::rama, basic::options::OptionKeys::relax::ramady, basic::options::OptionKeys::relax::ramady_cutoff, basic::options::OptionKeys::relax::ramady_force, basic::options::OptionKeys::relax::ramady_max_rebuild, basic::options::OptionKeys::relax::ramady_rms_limit, basic::options::OptionKeys::relax::ramp_constraints, basic::options::OptionKeys::relax::centroid::ramp_rama, basic::options::OptionKeys::relax::centroid::ramp_vdw, basic::options::OptionKeys::remodel::RemodelLoopMover::randomize_loops, basic::options::OptionKeys::relax::range::range, basic::options::OptionKeys::remodel::rank_by_bsasa, basic::options::OptionKeys::RBSegmentRelax::rb_file, basic::options::OptionKeys::RBSegmentRelax::rb_scorefxn, basic::options::OptionKeys::rbe::rbe, basic::options::OptionKeys::RBSegmentRelax::RBSegmentRelax, basic::options::OptionKeys::rdc::rdc, basic::options::OptionKeys::rdc::reduced_couplings, basic::options::OptionKeys::relax::relax, basic::options::OptionKeys::remodel::remodel, basic::options::OptionKeys::remodel::RemodelLoopMover::RemodelLoopMover, basic::options::OptionKeys::relax::range::repack_again, basic::options::OptionKeys::remodel::repeat_structure, basic::options::OptionKeys::remodel::staged_sampling::require_frags_match_blueprint, basic::options::OptionKeys::remodel::reroot_tree, basic::options::OptionKeys::resample::resample, basic::options::OptionKeys::remodel::resclass_by_sasa, basic::options::OptionKeys::rescore::rescore, basic::options::OptionKeys::remodel::staged_sampling::residues_to_sample, basic::options::OptionKeys::relax::respect_resfile, basic::options::OptionKeys::remodel::rg, basic::options::OptionKeys::remodel::rg_local, basic::options::OptionKeys::remodel::rsigma, basic::options::OptionKeys::remodel::run_confirmation, basic::options::OptionKeys::remodel::staged_sampling::sample_over_loops, basic::options::OptionKeys::remodel::save_top, basic::options::OptionKeys::relax::sc_cst_maxdist, basic::options::OptionKeys::relax::script, basic::options::OptionKeys::relax::script_max_accept, basic::options::OptionKeys::rdc::segment_file, basic::options::OptionKeys::rdc::segment_scoring_mode, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::relax::sequence_file, basic::options::OptionKeys::rbe::server_port, basic::options::OptionKeys::rbe::server_url, basic::options::OptionKeys::remodel::RemodelLoopMover::set_segment, basic::options::OptionKeys::relax::range::set_tm_helical, basic::options::OptionKeys::hydrate::short_residence_time_mode, basic::options::OptionKeys::hydrate::show_derivatives_check, basic::options::OptionKeys::hydrate::show_pre_filtered_water_rotamers_count, basic::options::OptionKeys::hydrate::show_pre_post_filter_water_rotamers, basic::options::OptionKeys::hydrate::show_residues_near_water, basic::options::OptionKeys::hydrate::show_rotamer_count, basic::options::OptionKeys::resample::silent, basic::options::OptionKeys::remodel::RemodelLoopMover::simultaneous_cycles, basic::options::OptionKeys::hydrate::single_away_rotamer, basic::options::OptionKeys::rescore::skip, basic::options::OptionKeys::RBSegmentRelax::skip_fragment_moves, basic::options::OptionKeys::remodel::design::skip_partial, basic::options::OptionKeys::RBSegmentRelax::skip_rb_moves, basic::options::OptionKeys::relax::range::skip_relax, basic::options::OptionKeys::RBSegmentRelax::skip_seqshift_moves, basic::options::OptionKeys::remodel::staged_sampling::small_moves, basic::options::OptionKeys::relax::range::spherical_wave, basic::options::OptionKeys::remodel::ss_pair, basic::options::OptionKeys::resample::stage1, basic::options::OptionKeys::relax::stage1_ramp_cycles, basic::options::OptionKeys::relax::stage1_ramp_inner_cycles, basic::options::OptionKeys::resample::stage2, basic::options::OptionKeys::relax::stage2_cycles, basic::options::OptionKeys::relax::stage2_repack_period, basic::options::OptionKeys::relax::stage3_cycles, basic::options::OptionKeys::remodel::staged_sampling::staged_sampling, basic::options::OptionKeys::remodel::staged_sampling::start_w_ideal_helices, basic::options::OptionKeys::remodel::staged_sampling::starting_non_canonical, basic::options::OptionKeys::remodel::staged_sampling::starting_pdb, basic::options::OptionKeys::remodel::staged_sampling::starting_sequence, basic::options::OptionKeys::RBSegmentRelax::strand_movement_params, basic::options::OptionKeys::relax::superimpose_to_file, basic::options::OptionKeys::relax::superimpose_to_native, basic::options::OptionKeys::remodel::surfaceAA, basic::options::OptionKeys::remodel::swap_refine_confirm_protocols, basic::options::OptionKeys::remodel::staged_sampling::sym_move, basic::options::OptionKeys::resample::tag, basic::options::OptionKeys::remodel::RemodelLoopMover::temperature, basic::options::OptionKeys::rdc::tensor_weight, basic::options::OptionKeys::relax::thorough, basic::options::OptionKeys::remodel::RemodelLoopMover::threshold_for_boost_closure, basic::options::OptionKeys::rdc::total_weight, basic::options::OptionKeys::remodel::two_chain_tree, basic::options::OptionKeys::remodel::use_blueprint_sequence, basic::options::OptionKeys::remodel::use_cart_relax, basic::options::OptionKeys::remodel::use_clusters, basic::options::OptionKeys::relax::use_explicit_water, basic::options::OptionKeys::ProQ::use_gzip, basic::options::OptionKeys::remodel::RemodelLoopMover::use_loop_hash, basic::options::OptionKeys::remodel::use_pose_relax, basic::options::OptionKeys::remodel::use_same_length_fragments, basic::options::OptionKeys::remodel::vdw, basic::options::OptionKeys::rescore::verbose, basic::options::OptionKeys::hydrate::water_angular_resolution, basic::options::OptionKeys::hydrate::water_desolvation, basic::options::OptionKeys::hydrate::water_energy_threshold, basic::options::OptionKeys::hydrate::water_packing_radius, basic::options::OptionKeys::hydrate::water_rotamers_cap, basic::options::OptionKeys::hydrate::water_space_resolution, basic::options::OptionKeys::qsar::weights, basic::options::OptionKeys::rdc::weights, basic::options::OptionKeys::relax::centroid::weights, and basic::options::OptionKeys::relax::wobblemoves.

Referenced by add_all_rosetta_options().

void add_rosetta_options_13 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::stepwise::align_pdb, basic::options::OptionKeys::stepwise::alignment_anchor_res, basic::options::OptionKeys::rna::denovo::allow_bulge, basic::options::OptionKeys::rna::denovo::allow_consecutive_bulges, basic::options::OptionKeys::rna::denovo::allow_fragment_moves_in_bps, basic::options::OptionKeys::rna::denovo::allowed_bulge_res, basic::options::OptionKeys::sample_around::alpha_increment, basic::options::OptionKeys::rotamerdump::annealer, basic::options::OptionKeys::legacy_sewing::assembly_type, basic::options::OptionKeys::stepwise::atr_rep_screen, basic::options::OptionKeys::stepwise::atr_rep_screen_for_docking, basic::options::OptionKeys::rna::erraser::attempt_pyrimidine_flip, basic::options::OptionKeys::rna::denovo::autofilter, basic::options::OptionKeys::stepwise::backbone_only1, basic::options::OptionKeys::stepwise::backbone_only2, basic::options::OptionKeys::legacy_sewing::base_native_bonus, basic::options::OptionKeys::rna::denovo::out::binary_output, basic::options::OptionKeys::sewing::box_length, basic::options::OptionKeys::legacy_sewing::box_length, basic::options::OptionKeys::rna::denovo::db::bps_database, basic::options::OptionKeys::rna::denovo::bps_moves, basic::options::OptionKeys::legacy_sewing::calcium_motif_score_weight, basic::options::OptionKeys::rna::denovo::center_jumps_in_single_stranded, basic::options::OptionKeys::rna::denovo::chain_connection, basic::options::OptionKeys::stepwise::choose_random, basic::options::OptionKeys::sicdock::clash_dis, basic::options::OptionKeys::rna::denovo::close_loops, basic::options::OptionKeys::rna::denovo::close_loops_after_each_move, basic::options::OptionKeys::rna::erraser::constrain_P, basic::options::OptionKeys::sicdock::contact_dis, basic::options::OptionKeys::rna::denovo::convert_protein_CEN, basic::options::OptionKeys::rna::corrected_geo, basic::options::OptionKeys::sample_around::cosbeta_increment, basic::options::OptionKeys::rna::denovo::cst_gap, basic::options::OptionKeys::rna::cut_at_rna_chainbreak, basic::options::OptionKeys::rna::denovo::cycles, basic::options::OptionKeys::rna::data_file, basic::options::OptionKeys::rna::denovo::db::db, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::rna::denovo::denovo, basic::options::OptionKeys::rna::denovo::minimize::deriv_check, basic::options::OptionKeys::rna::denovo::disallow_bps_at_extra_min_res, basic::options::OptionKeys::legacy_sewing::disregard_num_segment_matches, basic::options::OptionKeys::legacy_sewing::do_not_remove_connection_inconsistencies, basic::options::OptionKeys::rna::denovo::dock_chunks, basic::options::OptionKeys::rna::denovo::dock_each_chunk, basic::options::OptionKeys::rna::denovo::dock_each_chunk_per_chain, basic::options::OptionKeys::rna::denovo::dock_into_density, basic::options::OptionKeys::rna::denovo::dock_into_density_legacy, basic::options::OptionKeys::rna::denovo::docking_move_size, basic::options::OptionKeys::stepwise::dump, basic::options::OptionKeys::rna::denovo::out::dump, basic::options::OptionKeys::legacy_sewing::dump_every_model, basic::options::OptionKeys::legacy_sewing::dump_pdbs, basic::options::OptionKeys::rna::denovo::dump_stems, basic::options::OptionKeys::sewing::edge_file_name, basic::options::OptionKeys::stepwise::enumerate, basic::options::OptionKeys::rna::erraser::erraser, basic::options::OptionKeys::rna::evaluate_base_pairs, basic::options::OptionKeys::rna::denovo::exclude_fragment_files, basic::options::OptionKeys::rna::denovo::exclude_fragments, basic::options::OptionKeys::rna::denovo::exclude_native_fragments, basic::options::OptionKeys::rna::denovo::exclusion_match_type, basic::options::OptionKeys::rna::denovo::exhaustive_fragment_insertion, basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_chi_res, basic::options::OptionKeys::rna::denovo::minimize::extra_minimize_res, basic::options::OptionKeys::rna::denovo::filter_chain_closure, basic::options::OptionKeys::rna::denovo::filter_chain_closure_distance, basic::options::OptionKeys::rna::denovo::filter_chain_closure_halfway, basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs, basic::options::OptionKeys::rna::denovo::filter_lores_base_pairs_early, basic::options::OptionKeys::stepwise::fixed_res, basic::options::OptionKeys::rna::erraser::fixed_res, basic::options::OptionKeys::rna::denovo::fixed_stems, basic::options::OptionKeys::rna::denovo::fold_tree_from_silent_file_tag, basic::options::OptionKeys::SSrbrelax::frag_files, basic::options::OptionKeys::rna::denovo::frag_size, basic::options::OptionKeys::SSrbrelax::frag_sizes, basic::options::OptionKeys::rna::denovo::fragment_homology_rmsd, basic::options::OptionKeys::rna::denovo::ft_close_chains, basic::options::OptionKeys::rna::denovo::fuzz_fragments, basic::options::OptionKeys::sample_around::gamma_increment, basic::options::OptionKeys::rna::denovo::get_fold_tree_from_silent_file, basic::options::OptionKeys::rna::denovo::gradual_constraints, basic::options::OptionKeys::rna::denovo::grid_vdw_weight, basic::options::OptionKeys::sicdock::hash_2D_vs_3D, basic::options::OptionKeys::legacy_sewing::hash_tag_only_terminal_Es, basic::options::OptionKeys::rna::denovo::heat, basic::options::OptionKeys::rna::denovo::helical_substructs, basic::options::OptionKeys::rna::denovo::ignore_secstruct, basic::options::OptionKeys::rna::denovo::initial_structures, basic::options::OptionKeys::stepwise::input_res1, basic::options::OptionKeys::stepwise::input_res2, basic::options::OptionKeys::rna::denovo::input_silent_res, utility::options::Option::is_group(), basic::options::OptionKeys::rna::denovo::jump_change_frequency, basic::options::OptionKeys::rna::denovo::db::jump_database, basic::options::OptionKeys::rna::denovo::out::jump_histogram_binwidth, basic::options::OptionKeys::rna::denovo::out::jump_histogram_binwidth_rotvector, basic::options::OptionKeys::rna::denovo::out::jump_histogram_boxsize, basic::options::OptionKeys::rna::denovo::jump_library_file, basic::options::OptionKeys::legacy_sewing::keep_model_residues, basic::options::OptionKeys::legacy_sewing::keep_source_segments, basic::options::OptionKeys::legacy_sewing::leave_antiparallel_way_H_bonded_models_by_terminal_strands, basic::options::OptionKeys::legacy_sewing::leave_certain_model_ids, basic::options::OptionKeys::legacy_sewing::leave_models_by_ss_num, basic::options::OptionKeys::legacy_sewing::leave_models_with_E_terminal_ss, basic::options::OptionKeys::legacy_sewing::leave_models_with_H_terminal_ss, basic::options::OptionKeys::legacy_sewing::leave_parallel_way_H_bonded_models_by_terminal_strands, basic::options::OptionKeys::legacy_sewing::leave_these_model_ids, basic::options::OptionKeys::legacy_sewing::legacy_sewing, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::rna::denovo::lores_scorefxn, basic::options::OptionKeys::sewing::match_segments, basic::options::OptionKeys::legacy_sewing::match_segments, basic::options::OptionKeys::sewing::max_clash_score, basic::options::OptionKeys::legacy_sewing::max_clash_score, basic::options::OptionKeys::legacy_sewing::max_helix_length, basic::options::OptionKeys::legacy_sewing::max_loop_length, basic::options::OptionKeys::legacy_sewing::max_models, basic::options::OptionKeys::legacy_sewing::max_ss_num, basic::options::OptionKeys::legacy_sewing::max_strand_length, basic::options::OptionKeys::stepwise::max_tries_multiplier_for_ccd, basic::options::OptionKeys::legacy_sewing::may_add_already_added_model, basic::options::OptionKeys::sewing::min_hash_score, basic::options::OptionKeys::legacy_sewing::min_hash_score, basic::options::OptionKeys::legacy_sewing::min_helix_length, basic::options::OptionKeys::legacy_sewing::min_lh_fragments, basic::options::OptionKeys::legacy_sewing::min_loop_length, basic::options::OptionKeys::legacy_sewing::min_motif_score, basic::options::OptionKeys::legacy_sewing::min_strand_length, basic::options::OptionKeys::rna::denovo::minimize::min_type, basic::options::OptionKeys::rna::denovo::minimize::minimize, basic::options::OptionKeys::rna::denovo::minimize::minimize_all_protein, basic::options::OptionKeys::rna::denovo::minimize::minimize_bps, basic::options::OptionKeys::rna::denovo::minimize::minimize_max_iter, basic::options::OptionKeys::rna::denovo::minimize::minimize_nblist_auto_update, basic::options::OptionKeys::rna::denovo::minimize::minimize_protein_sc, basic::options::OptionKeys::rna::denovo::minimize_rna, basic::options::OptionKeys::rna::denovo::minimize::minimize_rounds, basic::options::OptionKeys::rna::denovo::minimize::minimize_use_nblist, basic::options::OptionKeys::stepwise::minimize_waters, basic::options::OptionKeys::stepwise::minimizer_mode, basic::options::OptionKeys::rna::denovo::minimize::minimizer_use_coordinate_constraints, basic::options::OptionKeys::legacy_sewing::mode, basic::options::OptionKeys::legacy_sewing::model_file_name, basic::options::OptionKeys::sewing::model_file_name, basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_E, basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_E_at_terminal_segment, basic::options::OptionKeys::legacy_sewing::model_should_have_at_least_1_H, basic::options::OptionKeys::legacy_sewing::model_should_have_this_num_of_ss, basic::options::OptionKeys::legacy_sewing::models_to_dump, basic::options::OptionKeys::stepwise::move, basic::options::OptionKeys::rna::denovo::move_first_rigid_body, basic::options::OptionKeys::legacy_sewing::neighbor_cutoff, basic::options::OptionKeys::stepwise::new_align_pdb, basic::options::OptionKeys::rna::denovo::new_fold_tree_initializer, basic::options::OptionKeys::legacy_sewing::new_model_file_name, basic::options::OptionKeys::stepwise::new_move_selector, basic::options::OptionKeys::rna::denovo::no_filters, basic::options::OptionKeys::legacy_sewing::num_edges_to_follow, basic::options::OptionKeys::legacy_sewing::num_models_to_dump, basic::options::OptionKeys::stepwise::num_pose_minimize, basic::options::OptionKeys::legacy_sewing::num_procs, basic::options::OptionKeys::stepwise::num_random_samples, basic::options::OptionKeys::legacy_sewing::num_repeats, basic::options::OptionKeys::legacy_sewing::num_segments_to_match, basic::options::OptionKeys::rna::denovo::obligate_pair, basic::options::OptionKeys::rna::denovo::obligate_pair_explicit, basic::options::OptionKeys::rna::denovo::offset, basic::options::OptionKeys::legacy_sewing::offset_bump_dsq, basic::options::OptionKeys::rotamerdump::one_body, basic::options::OptionKeys::rna::denovo::out::out, basic::options::OptionKeys::legacy_sewing::output_alignments_to_file, basic::options::OptionKeys::rna::denovo::output_filters, basic::options::OptionKeys::rna::denovo::out::output_histogram_file, basic::options::OptionKeys::rna::denovo::out::output_jump_chainbreak, basic::options::OptionKeys::rna::denovo::out::output_jump_o3p_to_o5p, basic::options::OptionKeys::rna::denovo::out::output_jump_reference_RT, basic::options::OptionKeys::rna::denovo::out::output_jump_res, basic::options::OptionKeys::rna::denovo::out::output_lores_silent_file, basic::options::OptionKeys::rna::denovo::output_res_num, basic::options::OptionKeys::rna::denovo::out::output_rotation_vector, basic::options::OptionKeys::rna::denovo::out::output_score_file, basic::options::OptionKeys::rna::denovo::out::output_score_frequency, basic::options::OptionKeys::rna::denovo::override_refine_pose_rounds, basic::options::OptionKeys::legacy_sewing::partner_pdb, basic::options::OptionKeys::sewing::pose_segment_ends, basic::options::OptionKeys::legacy_sewing::pose_segment_ends, basic::options::OptionKeys::sewing::pose_segment_starts, basic::options::OptionKeys::legacy_sewing::pose_segment_starts, basic::options::OptionKeys::stepwise::preminimize, basic::options::OptionKeys::rna::denovo::minimize::protein_pack_all, basic::options::OptionKeys::rna::denovo::minimize::protein_packing, basic::options::OptionKeys::rna::denovo::minimize::protein_packing_distance, basic::options::OptionKeys::rna::denovo::ramp_rnp_vdw, basic::options::OptionKeys::rna::denovo::randomize_init_rnp, basic::options::OptionKeys::legacy_sewing::rank, basic::options::OptionKeys::SSrbrelax::rb_file, basic::options::OptionKeys::SSrbrelax::rb_param_file, basic::options::OptionKeys::rna::erraser::ready_set_only, basic::options::OptionKeys::sewing::recursive_depth, basic::options::OptionKeys::rna::denovo::refine_native, basic::options::OptionKeys::rna::denovo::refine_native_get_good_FT, basic::options::OptionKeys::rna::denovo::refine_silent_file, basic::options::OptionKeys::rna::denovo::refine_silent_number_of_poses, basic::options::OptionKeys::rna::denovo::refine_silent_tags, basic::options::OptionKeys::rna::denovo::relax_rna, basic::options::OptionKeys::legacy_sewing::remove_all_dssp, basic::options::OptionKeys::legacy_sewing::remove_any_dssp, basic::options::OptionKeys::rna::denovo::remove_obligate_pair, basic::options::OptionKeys::rna::denovo::remove_pair, basic::options::OptionKeys::legacy_sewing::repeat, basic::options::OptionKeys::stepwise::rmsd_screen, basic::options::OptionKeys::rna::rna, basic::options::OptionKeys::rna::denovo::rna_lores_chainbreak_weight, basic::options::OptionKeys::rna::denovo::rna_lores_linear_chainbreak_weight, basic::options::OptionKeys::rna::erraser::rna_prot_erraser, basic::options::OptionKeys::rna::denovo::rna_protein_docking, basic::options::OptionKeys::rna::denovo::rna_protein_docking_freq, basic::options::OptionKeys::rna::denovo::rna_protein_docking_legacy, basic::options::OptionKeys::rna::denovo::rnp_high_res_cycles, basic::options::OptionKeys::rna::denovo::rnp_high_res_relax, basic::options::OptionKeys::rna::denovo::rnp_min_first, basic::options::OptionKeys::rna::denovo::rnp_pack_first, basic::options::OptionKeys::rna::denovo::rnp_ramp_rep, basic::options::OptionKeys::rna::denovo::root_at_first_rigid_body, basic::options::OptionKeys::rotamerdump::rotamerdump, basic::options::OptionKeys::rna::denovo::rounds, basic::options::OptionKeys::stepwise::s1, basic::options::OptionKeys::stepwise::s2, basic::options::OptionKeys::sample_around::sample_around, basic::options::OptionKeys::stepwise::sampler_silent_file, basic::options::OptionKeys::rna::denovo::out::save_jump_histogram, basic::options::OptionKeys::sewing::score_between_opposite_terminal_segments, basic::options::OptionKeys::legacy_sewing::score_between_opposite_terminal_segments, basic::options::OptionKeys::legacy_sewing::score_file_name, basic::options::OptionKeys::rna::denovo::secstruct, basic::options::OptionKeys::rna::denovo::secstruct_file, basic::options::OptionKeys::rna::denovo::secstruct_general, basic::options::OptionKeys::rna::denovo::secstruct_general_file, basic::options::OptionKeys::rna::denovo::secstruct_legacy, basic::options::OptionKeys::rna::denovo::sequence, basic::options::OptionKeys::rna::denovo::set_lores_weights, basic::options::OptionKeys::sewing::sewing, basic::options::OptionKeys::sicdock::sicdock, basic::options::OptionKeys::stepwise::silent1, basic::options::OptionKeys::stepwise::silent2, basic::options::OptionKeys::rna::denovo::simple_relax, basic::options::OptionKeys::rna::denovo::minimize::skip_coord_constraints, basic::options::OptionKeys::legacy_sewing::skip_filters, basic::options::OptionKeys::legacy_sewing::skip_loop_generation, basic::options::OptionKeys::stepwise::skip_minimize, basic::options::OptionKeys::rna::erraser::skip_minimize, basic::options::OptionKeys::rna::denovo::minimize::skip_o2prime_trials, basic::options::OptionKeys::stepwise::skip_preminimize, basic::options::OptionKeys::legacy_sewing::skip_refinement, basic::options::OptionKeys::stepwise::slice_res1, basic::options::OptionKeys::stepwise::slice_res2, basic::options::OptionKeys::rna::denovo::small_docking_moves, basic::options::OptionKeys::SSrbrelax::SSrbrelax, basic::options::OptionKeys::rna::denovo::staged_constraints, basic::options::OptionKeys::legacy_sewing::starting_model, basic::options::OptionKeys::stepwise::stepwise, basic::options::OptionKeys::stepwise::superimpose_over_all, basic::options::OptionKeys::rna::denovo::suppress_bp_constraint, basic::options::OptionKeys::rna::denovo::symm_hack_arity, basic::options::OptionKeys::rna::denovo::tag, basic::options::OptionKeys::stepwise::tags1, basic::options::OptionKeys::stepwise::tags2, basic::options::OptionKeys::rna::denovo::out::target_xyz, basic::options::OptionKeys::rna::denovo::temperature, basic::options::OptionKeys::stepwise::test_all_moves, basic::options::OptionKeys::stepwise::test_encapsulation, basic::options::OptionKeys::rotamerdump::two_body, basic::options::OptionKeys::rna::denovo::use_1jj2_torsions, basic::options::OptionKeys::stepwise::use_green_packer, basic::options::OptionKeys::rna::denovo::use_legacy_setup, basic::options::OptionKeys::rna::denovo::vall_torsions, basic::options::OptionKeys::rna::vary_geometry, basic::options::OptionKeys::rna::denovo::VDW_rep_screen_include_sidechains, basic::options::OptionKeys::stepwise::VERBOSE, basic::options::OptionKeys::rna::denovo::virtual_anchor, basic::options::OptionKeys::stepwise::virtualize_packable_moieties_in_screening_pose, basic::options::OptionKeys::rna::denovo::working_native, and basic::options::OptionKeys::rotamerdump::xyz.

Referenced by add_all_rosetta_options().

void add_rosetta_options_14 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::recces::a_form_range, basic::options::OptionKeys::recces::accept_no_op_moves, utility::options::OptionCollection::add(), basic::options::OptionKeys::stepwise::monte_carlo::add_delete_frequency, basic::options::OptionKeys::stepwise::monte_carlo::add_proposal_density_factor, basic::options::OptionKeys::stepwise::rna::add_virt_root, basic::options::OptionKeys::stepwise::rna::alignment_res, basic::options::OptionKeys::stepwise::rna::allow_base_pair_only_centroid_screen, basic::options::OptionKeys::stepwise::rna::allow_bulge_at_chainbreak, basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP, basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves, basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_local_moves, basic::options::OptionKeys::full_model::allow_jump_in_numbering, basic::options::OptionKeys::stepwise::monte_carlo::allow_skip_bulge, basic::options::OptionKeys::stepwise::monte_carlo::allow_split_off, basic::options::OptionKeys::stepwise::monte_carlo::allow_submotif_split, basic::options::OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry, basic::options::OptionKeys::stepwise::rna::allow_virtual_o2prime_hydrogens, basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, basic::options::OptionKeys::recces::thermal_sampling::angle_range_bb, basic::options::OptionKeys::recces::thermal_sampling::angle_range_chi, basic::options::OptionKeys::recces::thermal_sampling::angle_range_free_bb, basic::options::OptionKeys::recces::thermal_sampling::angle_range_free_chi, basic::options::OptionKeys::stepwise::monte_carlo::csa::annealing, basic::options::OptionKeys::recces::base_pair::base_pair, basic::options::OptionKeys::recces::thermal_sampling::bb_stdev, basic::options::OptionKeys::recces::base_pair::block_stack, basic::options::OptionKeys::full_model::rna::block_stack_above_res, basic::options::OptionKeys::full_model::rna::block_stack_below_res, basic::options::OptionKeys::stepwise::boltzmann_choice_post_enumerated_minimize, basic::options::OptionKeys::stepwise::polar_hydrogens::bond_angle_sd_polar_hydrogen, basic::options::OptionKeys::stepwise::polar_hydrogens::bond_torsion_sd_polar_hydrogen, basic::options::OptionKeys::stepwise::protein::bridge_res, basic::options::OptionKeys::full_model::rna::bulge_res, basic::options::OptionKeys::full_model::calc_rms_res, basic::options::OptionKeys::stepwise::protein::cart_min, basic::options::OptionKeys::stepwise::protein::ccd_close, basic::options::OptionKeys::stepwise::protein::centroid_output, basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut, basic::options::OptionKeys::stepwise::rna::centroid_screen, basic::options::OptionKeys::stepwise::protein::centroid_screen, basic::options::OptionKeys::stepwise::protein::centroid_weights, basic::options::OptionKeys::templates::change_movemap, basic::options::OptionKeys::stepwise::monte_carlo::checkpointing_frequency, basic::options::OptionKeys::recces::thermal_sampling::chi_stdev, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file, basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode, basic::options::OptionKeys::templates::config, basic::options::OptionKeys::stepwise::monte_carlo::continue_until_none_missing, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_bank_size, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_output_rounds, basic::options::OptionKeys::stepwise::monte_carlo::csa::csa_rmsd, basic::options::OptionKeys::templates::cst::cst, basic::options::OptionKeys::full_model::cutpoint_closed, basic::options::OptionKeys::full_model::cutpoint_open, basic::options::OptionKeys::stepwise::monte_carlo::cycles, basic::options::OptionKeys::full_model::cyclize, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::stepwise::definitely_virtualize, basic::options::OptionKeys::stepwise::monte_carlo::designing_with_noncanonicals, basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff, basic::options::OptionKeys::stepwise::polar_hydrogens::disallow_pack_polar_hydrogens, basic::options::OptionKeys::stepwise::polar_hydrogens::disallow_vary_geometry_proton_chi, basic::options::OptionKeys::stepwise::rna::distinguish_pucker, basic::options::OptionKeys::stepwise::protein::disulfide_file, basic::options::OptionKeys::full_model::disulfide_res, basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar, basic::options::OptionKeys::stepwise::monte_carlo::docking_frequency, basic::options::OptionKeys::recces::dump_freq, basic::options::OptionKeys::recces::dump_pdb, basic::options::OptionKeys::recces::dump_silent, basic::options::OptionKeys::stepwise::rna::erraser, basic::options::OptionKeys::stepwise::monte_carlo::exclude_submotifs, basic::options::OptionKeys::stepwise::protein::expand_loop_takeoff, basic::options::OptionKeys::full_model::extra_min_jump_res, basic::options::OptionKeys::full_model::extra_min_res, basic::options::OptionKeys::wum::extra_scorefxn, basic::options::OptionKeys::wum::extra_scorefxn_ref_structure, basic::options::OptionKeys::wum::extra_scorefxn_relax, basic::options::OptionKeys::strand_assembly::extract_native_only, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, basic::options::OptionKeys::stepwise::rna::filter_output_filename, basic::options::OptionKeys::stepwise::rna::filter_user_alignment_res, basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure, basic::options::OptionKeys::full_model::fiveprime_cap, basic::options::OptionKeys::templates::fix_aligned_residues, basic::options::OptionKeys::stepwise::polar_hydrogens::fix_angles, basic::options::OptionKeys::templates::fix_frag_file, basic::options::OptionKeys::stepwise::polar_hydrogens::fix_lengths, basic::options::OptionKeys::templates::fix_margin, basic::options::OptionKeys::stepwise::polar_hydrogens::fix_torsions, basic::options::OptionKeys::stepwise::rna::floating_base, basic::options::OptionKeys::stepwise::rna::floating_base_anchor_res, basic::options::OptionKeys::full_model::rna::force_anti_chi_res_list, basic::options::OptionKeys::stepwise::rna::force_centroid_interaction, basic::options::OptionKeys::stepwise::force_moving_res_for_erraser, basic::options::OptionKeys::templates::force_native_topology, basic::options::OptionKeys::full_model::rna::force_north_sugar_list, basic::options::OptionKeys::stepwise::rna::force_phosphate_instantiation, basic::options::OptionKeys::full_model::rna::force_south_sugar_list, basic::options::OptionKeys::stepwise::monte_carlo::force_submotif_without_intervening_bulge, basic::options::OptionKeys::full_model::rna::force_syn_chi_res_list, basic::options::OptionKeys::stepwise::rna::force_user_defined_jumps, basic::options::OptionKeys::templates::fragsteal::fragsteal, basic::options::OptionKeys::recces::thermal_sampling::free_residues, basic::options::OptionKeys::stepwise::monte_carlo::from_scratch_frequency, basic::options::OptionKeys::full_model::full_model, basic::options::OptionKeys::stepwise::monte_carlo::full_model_constraints, basic::options::OptionKeys::stepwise::protein::ghost_loops, basic::options::OptionKeys::stepwise::protein::global_optimize, basic::options::OptionKeys::stepwise::rna::global_sample_res_list, basic::options::OptionKeys::full_model::global_seq_file, basic::options::OptionKeys::templates::helix_pairings, basic::options::OptionKeys::recces::histogram_max, basic::options::OptionKeys::recces::histogram_min, basic::options::OptionKeys::recces::histogram_spacing, basic::options::OptionKeys::stepwise::rna::integration_test, basic::options::OptionKeys::stepwise::monte_carlo::intermolecular_frequency, utility::options::Option::is_group(), basic::options::OptionKeys::stepwise::rna::job_queue_ID, basic::options::OptionKeys::stepwise::rna::jump_point_pairs, basic::options::OptionKeys::full_model::jump_res, basic::options::OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::stepwise::monte_carlo::local_redock_only, basic::options::OptionKeys::recces::thermal_sampling::loop_residues, basic::options::OptionKeys::stepwise::lores, basic::options::OptionKeys::stepwise::monte_carlo::make_movie, basic::options::OptionKeys::templates::max_align_pos, basic::options::OptionKeys::strand_assembly::max_num_strands_to_deal, basic::options::OptionKeys::strand_assembly::max_O_N_dis, basic::options::OptionKeys::strand_assembly::max_res_in_strand, basic::options::OptionKeys::strand_assembly::max_sheet_angle, basic::options::OptionKeys::strand_assembly::max_sheet_dis, basic::options::OptionKeys::strand_assembly::max_sheet_torsion, basic::options::OptionKeys::templates::max_shrink, basic::options::OptionKeys::wum::memory_limit, basic::options::OptionKeys::templates::min_align_pos, basic::options::OptionKeys::templates::min_frag_size, basic::options::OptionKeys::templates::min_nr_large_frags, basic::options::OptionKeys::templates::min_nr_small_frags, basic::options::OptionKeys::strand_assembly::min_num_strands_to_deal, basic::options::OptionKeys::strand_assembly::min_O_N_dis, basic::options::OptionKeys::templates::min_padding, basic::options::OptionKeys::strand_assembly::min_res_in_strand, basic::options::OptionKeys::strand_assembly::min_sheet_angle, basic::options::OptionKeys::strand_assembly::min_sheet_dis, basic::options::OptionKeys::strand_assembly::min_sheet_torsion, basic::options::OptionKeys::strand_assembly::min_shortest_dis_sidechain_inter_sheet, basic::options::OptionKeys::stepwise::min_tolerance, basic::options::OptionKeys::stepwise::min_type, basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose, basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar, basic::options::OptionKeys::stepwise::rna::minimize_res, basic::options::OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency, basic::options::OptionKeys::stepwise::rna::minimizer_rename_tag, basic::options::OptionKeys::stepwise::rna::missing_res, basic::options::OptionKeys::stepwise::rna::missing_res2, basic::options::OptionKeys::stepwise::monte_carlo::monte_carlo, basic::options::OptionKeys::full_model::motif_mode, basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains, basic::options::OptionKeys::recces::n_cycle, basic::options::OptionKeys::recces::n_intermediate_dump, basic::options::OptionKeys::wum::n_masters, basic::options::OptionKeys::stepwise::protein::n_sample, basic::options::OptionKeys::wum::n_slaves_per_master, basic::options::OptionKeys::stepwise::rna::native_alignment_res, basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff, basic::options::OptionKeys::stepwise::rna::native_virtual_res, basic::options::OptionKeys::templates::no_culling, basic::options::OptionKeys::templates::no_pick_fragments, basic::options::OptionKeys::templates::nr_large_copies, basic::options::OptionKeys::templates::nr_small_copies, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, basic::options::OptionKeys::stepwise::rna::o2prime_legacy_mode, basic::options::OptionKeys::full_model::other_poses, basic::options::OptionKeys::recces::out_prefix, basic::options::OptionKeys::recces::out_torsions, basic::options::OptionKeys::stepwise::output_cluster_size, basic::options::OptionKeys::stepwise::rna::output_extra_RMSDs, basic::options::OptionKeys::recces::output_min_pose, basic::options::OptionKeys::stepwise::output_minimized_pose_list, basic::options::OptionKeys::stepwise::pack_protein_side_chains, basic::options::OptionKeys::templates::pairings, basic::options::OptionKeys::stepwise::rna::parin_favorite_output, basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure, basic::options::OptionKeys::templates::pick_multiple_sizes, basic::options::OptionKeys::stepwise::polar_hydrogens::polar_hydrogens, basic::options::OptionKeys::templates::prefix, basic::options::OptionKeys::stepwise::protein::protein, basic::options::OptionKeys::stepwise::protein::protein_prepack, basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list, basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode, basic::options::OptionKeys::recces::base_pair::recces, basic::options::OptionKeys::stepwise::monte_carlo::recover_low, basic::options::OptionKeys::TailSegment::refine_cycles, basic::options::OptionKeys::TailSegment::refine_repack_cycles, basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions, basic::options::OptionKeys::stepwise::rna::rm_virt_phosphate, basic::options::OptionKeys::recces::base_pair::rmsd_cutoff, basic::options::OptionKeys::stepwise::rna::rmsd_res, basic::options::OptionKeys::full_model::rna::rna, basic::options::OptionKeys::stepwise::rna::rna, basic::options::OptionKeys::full_model::root_res, basic::options::OptionKeys::recces::base_pair::rotation_mag, basic::options::OptionKeys::stepwise::rna::sample_all_chi, basic::options::OptionKeys::stepwise::protein::sample_beta, basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer, basic::options::OptionKeys::recces::base_pair::sample_jump, basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar, basic::options::OptionKeys::full_model::sample_res, basic::options::OptionKeys::recces::thermal_sampling::sample_residues, basic::options::OptionKeys::full_model::rna::sample_sugar_res, basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine, basic::options::OptionKeys::stepwise::rna::sampler_assert_no_virt_sugar_sampling, basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_extra_chi_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_extra_epsilon_rotamer, basic::options::OptionKeys::stepwise::rna::sampler_include_torsion_value_in_tag, basic::options::OptionKeys::stepwise::rna::sampler_max_centroid_distance, basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept, basic::options::OptionKeys::stepwise::rna::sampler_perform_phosphate_pack, basic::options::OptionKeys::stepwise::rna::sampler_try_sugar_instantiation, basic::options::OptionKeys::recces::save_score_terms, basic::options::OptionKeys::stepwise::protein::score_diff_cut, basic::options::OptionKeys::recces::seq1, basic::options::OptionKeys::recces::seq2, basic::options::OptionKeys::recces::thermal_sampling::setup_base_pair_constraints, basic::options::OptionKeys::templates::shrink_pos_step, basic::options::OptionKeys::templates::shrink_step, basic::options::OptionKeys::stepwise::rna::simple_append_map, basic::options::OptionKeys::stepwise::monte_carlo::skip_bulge_frequency, basic::options::OptionKeys::stepwise::protein::skip_coord_constraints, basic::options::OptionKeys::stepwise::monte_carlo::skip_deletions, basic::options::OptionKeys::unfolded_state::split_unfolded_energies_atom_type, basic::options::OptionKeys::unfolded_state::split_unfolded_energies_file, basic::options::OptionKeys::recces::st_weights, basic::options::OptionKeys::recces::thermal_sampling::standard_bb_stdev, basic::options::OptionKeys::strand_assembly::strand_assembly, basic::options::OptionKeys::templates::strand_constraint, basic::options::OptionKeys::stepwise::monte_carlo::submotif_frequency, basic::options::OptionKeys::stepwise::monte_carlo::switch_focus_frequency, basic::options::OptionKeys::TailSegment::TailSegment, basic::options::OptionKeys::stepwise::monte_carlo::temperature, basic::options::OptionKeys::templates::templates, basic::options::OptionKeys::recces::temps, basic::options::OptionKeys::full_model::rna::terminal_res, basic::options::OptionKeys::stepwise::rna::tether_jump, basic::options::OptionKeys::recces::thermal_sampling::thermal_sampling, basic::options::OptionKeys::templates::cst::topN, basic::options::OptionKeys::templates::fragsteal::topN, basic::options::OptionKeys::templates::topology_rank_cutoff, basic::options::OptionKeys::recces::base_pair::translation_mag, basic::options::OptionKeys::wum::trim_proportion, basic::options::OptionKeys::stepwise::rna::turn_off_rna_chem_map_during_optimize, basic::options::OptionKeys::full_model::twoprime, basic::options::OptionKeys::unfolded_state::unfolded_energies_file, basic::options::OptionKeys::unfolded_state::unfolded_state, basic::options::OptionKeys::stepwise::monte_carlo::use_first_jump_for_submotif, basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials, basic::options::OptionKeys::stepwise::monte_carlo::use_precomputed_library, basic::options::OptionKeys::templates::vary_frag_size, basic::options::OptionKeys::stepwise::monte_carlo::vary_loop_length_frequency, basic::options::OptionKeys::stepwise::polar_hydrogens::vary_polar_hydrogen_geometry, basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen, basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF, basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res, basic::options::OptionKeys::stepwise::rna::VDW_rep_optimize_memory_usage, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_info, basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff, basic::options::OptionKeys::stepwise::verbose_sampler, basic::options::OptionKeys::stepwise::monte_carlo::verbose_scores, basic::options::OptionKeys::full_model::virtual_res, basic::options::OptionKeys::stepwise::rna::virtual_sugar_do_minimize, basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed, basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode, basic::options::OptionKeys::full_model::virtual_sugar_res, basic::options::OptionKeys::stepwise::virtualize_free_moieties_in_native, basic::options::OptionKeys::templates::cst::wExtern, basic::options::OptionKeys::templates::fragsteal::wExtern, basic::options::OptionKeys::full_model::working_res, basic::options::OptionKeys::templates::cst::wTopol, basic::options::OptionKeys::templates::fragsteal::wTopol, and basic::options::OptionKeys::wum::wum.

Referenced by add_all_rosetta_options().

void add_rosetta_options_15 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, basic::options::OptionKeys::tcrmodel::ab_template_db_path, basic::options::OptionKeys::smhybrid::abinitio_cycles, basic::options::OptionKeys::smhybrid::abinitio_design, basic::options::OptionKeys::evolution::action, utility::options::OptionCollection::add(), basic::options::OptionKeys::smhybrid::add_atom_at_cen, basic::options::OptionKeys::smhybrid::add_cavities, basic::options::OptionKeys::smhybrid::add_metal_at_0, basic::options::OptionKeys::smhybrid::add_res_after, basic::options::OptionKeys::smhybrid::add_res_before, basic::options::OptionKeys::smhybrid::add_ss_after, basic::options::OptionKeys::smhybrid::add_ss_before, basic::options::OptionKeys::ralford::dump_rotamers::all_positions, basic::options::OptionKeys::tcrmodel::alpha_cdr1_template_id, basic::options::OptionKeys::tcrmodel::alpha_cdr1_template_pdb, basic::options::OptionKeys::tcrmodel::alpha_cdr2_template_id, basic::options::OptionKeys::tcrmodel::alpha_cdr2_template_pdb, basic::options::OptionKeys::tcrmodel::alpha_cdr3_template_id, basic::options::OptionKeys::tcrmodel::alpha_cdr3_template_pdb, basic::options::OptionKeys::tcrmodel::alpha_framework_template_id, basic::options::OptionKeys::tcrmodel::alpha_framework_template_pdb, basic::options::OptionKeys::tcrmodel::alpha_germline_template_id, basic::options::OptionKeys::tcrmodel::alpha_germline_template_pdb, basic::options::OptionKeys::tcrmodel::alpha_orientation_template_id, basic::options::OptionKeys::tcrmodel::alpha_orientation_template_pdb, basic::options::OptionKeys::tcrmodel::anarci_path, basic::options::OptionKeys::tcrmodel::assign_cdr, basic::options::OptionKeys::tcrmodel::assign_cdr1a, basic::options::OptionKeys::tcrmodel::assign_cdr1b, basic::options::OptionKeys::tcrmodel::assign_cdr2a, basic::options::OptionKeys::tcrmodel::assign_cdr2b, basic::options::OptionKeys::tcrmodel::assign_cdr3a, basic::options::OptionKeys::tcrmodel::assign_cdr3b, basic::options::OptionKeys::james::atom_names, basic::options::OptionKeys::smhybrid::attach_as_sc, basic::options::OptionKeys::smhybrid::attach_as_sc_sub, basic::options::OptionKeys::smhybrid::attach_atom, basic::options::OptionKeys::smhybrid::attach_rsd, basic::options::OptionKeys::ufv::insert::attached_pdb, basic::options::OptionKeys::tcrmodel::beta_cdr1_template_id, basic::options::OptionKeys::tcrmodel::beta_cdr1_template_pdb, basic::options::OptionKeys::tcrmodel::beta_cdr2_template_id, basic::options::OptionKeys::tcrmodel::beta_cdr2_template_pdb, basic::options::OptionKeys::tcrmodel::beta_cdr3_template_id, basic::options::OptionKeys::tcrmodel::beta_cdr3_template_pdb, basic::options::OptionKeys::tcrmodel::beta_framework_template_id, basic::options::OptionKeys::tcrmodel::beta_framework_template_pdb, basic::options::OptionKeys::tcrmodel::beta_germline_template_id, basic::options::OptionKeys::tcrmodel::beta_germline_template_pdb, basic::options::OptionKeys::tcrmodel::beta_orientation_template_id, basic::options::OptionKeys::tcrmodel::beta_orientation_template_pdb, basic::options::OptionKeys::tcrmodel::blastp_identity_cutoff, basic::options::OptionKeys::blivens::blivens, basic::options::OptionKeys::loodo::bot, basic::options::OptionKeys::willmatch::c2_linker_dist, basic::options::OptionKeys::willmatch::c2_symm_increment, basic::options::OptionKeys::loodo::ca_ratio, basic::options::OptionKeys::loodo::cap, basic::options::OptionKeys::loodo::caphit_rt_file, basic::options::OptionKeys::willmatch::cb_sasa_thresh, basic::options::OptionKeys::smhybrid::centroid_all_val, basic::options::OptionKeys::ufv::centroid_loop_mover, basic::options::OptionKeys::ufv::centroid_sfx, basic::options::OptionKeys::ufv::centroid_sfx_patch, basic::options::OptionKeys::smhybrid::chainbreaks, basic::options::OptionKeys::willmatch::chi1_increment, basic::options::OptionKeys::willmatch::chi2_increment, basic::options::OptionKeys::evolution::childlist, basic::options::OptionKeys::willmatch::chilist, basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::willmatch::clash_dis, basic::options::OptionKeys::cmiles::cmiles, basic::options::OptionKeys::loodo::com_in_grid, basic::options::OptionKeys::ufv::insert::connection_scheme, basic::options::OptionKeys::crossmatch::crossmatch, basic::options::OptionKeys::smhybrid::cst_sub_files, basic::options::OptionKeys::blivens::disulfide_scorer::cys_prob, basic::options::OptionKeys::james::debug, basic::options::OptionKeys::smhybrid::debug, basic::options::OptionKeys::loodo::debug, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::rot_anl::design, basic::options::OptionKeys::smhybrid::design, basic::options::OptionKeys::smhybrid::design_hydrophobic, basic::options::OptionKeys::willmatch::design_interface, basic::options::OptionKeys::smhybrid::design_linker, basic::options::OptionKeys::smhybrid::design_res_files, basic::options::OptionKeys::james::dist_thresholds, basic::options::OptionKeys::loodo::distance_tolerance, basic::options::OptionKeys::blivens::disulfide_scorer::disulfide_scorer, basic::options::OptionKeys::peptide_deriver::do_minimize, basic::options::OptionKeys::ufv::dr_cycles, basic::options::OptionKeys::loodo::dump_all_As, basic::options::OptionKeys::loodo::dump_all_Bs, basic::options::OptionKeys::peptide_deriver::dump_cyclic_poses, basic::options::OptionKeys::rot_anl::dump_pdb, basic::options::OptionKeys::peptide_deriver::dump_peptide_pose, basic::options::OptionKeys::peptide_deriver::dump_prepared_pose, basic::options::OptionKeys::peptide_deriver::dump_report_file, basic::options::OptionKeys::ralford::dump_rotamers::dump_rotamers, basic::options::OptionKeys::tcrmodel::dump_templates, basic::options::OptionKeys::dwkulp::dwkulp, basic::options::OptionKeys::loodo::euler_tolerance, basic::options::OptionKeys::evolution::evolution, basic::options::OptionKeys::willmatch::exclude_ala, basic::options::OptionKeys::willmatch::exclude_res1, basic::options::OptionKeys::willmatch::exclude_res2, basic::options::OptionKeys::willmatch::fa_dun_thresh, basic::options::OptionKeys::smhybrid::fa_refine, basic::options::OptionKeys::willmatch::fixed_res, basic::options::OptionKeys::smhybrid::fixed_res_files, basic::options::OptionKeys::willmatch::forbid_residues, basic::options::OptionKeys::dwkulp::forcePolyAAfragments, basic::options::OptionKeys::smhybrid::frag_res_files, basic::options::OptionKeys::loodo::fragAlength, basic::options::OptionKeys::loodo::fragAnative, basic::options::OptionKeys::loodo::fragBlength, basic::options::OptionKeys::loodo::fragBnative, basic::options::OptionKeys::ufv::fullatom_sfx, basic::options::OptionKeys::ufv::fullatom_sfx_patch, basic::options::OptionKeys::loodo::gridligpath, basic::options::OptionKeys::testing::HCF, basic::options::OptionKeys::willmatch::homodimer, basic::options::OptionKeys::willmatch::identical_match_dis, basic::options::OptionKeys::tcrmodel::ignore_list, basic::options::OptionKeys::tcrmodel::include_ab_templates, basic::options::OptionKeys::loodo::ins_begin, basic::options::OptionKeys::ufv::insert::insert, basic::options::OptionKeys::ufv::insert::insert_pdb, basic::options::OptionKeys::testing::INTEGRATION_TEST, basic::options::OptionKeys::smhybrid::inter_subsub_cst, basic::options::OptionKeys::willmatch::interface_size, basic::options::OptionKeys::murphp::inv_kin_lig_loop_design_filename, utility::options::Option::is_group(), basic::options::OptionKeys::james::james, basic::options::OptionKeys::smhybrid::jumpcut_files, basic::options::OptionKeys::cmiles::jumping::jumping, basic::options::OptionKeys::cmiles::kcluster::kcluster, basic::options::OptionKeys::ufv::keep_junction_torsions, basic::options::OptionKeys::loodo::known, basic::options::OptionKeys::krassk::krassk, basic::options::OptionKeys::ufv::left, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::smhybrid::linker_cst, basic::options::OptionKeys::loodo::loodo, basic::options::OptionKeys::loodo::loud, basic::options::OptionKeys::willmatch::match_overlap_ang, basic::options::OptionKeys::willmatch::match_overlap_dis, basic::options::OptionKeys::willmatch::max_ang_metal, basic::options::OptionKeys::willmatch::max_dis_all, basic::options::OptionKeys::willmatch::max_dis_any, basic::options::OptionKeys::willmatch::max_dis_hb, basic::options::OptionKeys::willmatch::max_dis_hb_colinear, basic::options::OptionKeys::willmatch::max_dis_metal, basic::options::OptionKeys::rot_anl::min, basic::options::OptionKeys::willmatch::min_dis_hb, basic::options::OptionKeys::james::min_seqsep, basic::options::OptionKeys::smhybrid::minbb, basic::options::OptionKeys::tcrmodel::minimize_model, basic::options::OptionKeys::murphp::murphp, basic::options::OptionKeys::james::n_designs, basic::options::OptionKeys::willmatch::native1, basic::options::OptionKeys::willmatch::native2, basic::options::OptionKeys::blivens::disulfide_scorer::nds_prob, basic::options::OptionKeys::phil::nloop, basic::options::OptionKeys::rot_anl::nloop_scmove, basic::options::OptionKeys::ufv::no_neighborhood_design, basic::options::OptionKeys::threadsc::nres, basic::options::OptionKeys::smhybrid::nres_mono, basic::options::OptionKeys::cmiles::kcluster::num_clusters, basic::options::OptionKeys::loodo::num_frags, basic::options::OptionKeys::peptide_deriver::optimize_cyclic_threshold, basic::options::OptionKeys::evolution::padding_score_filter, basic::options::OptionKeys::evolution::padding_stage2_filter, basic::options::OptionKeys::robert::pairdata_input_pdb_list, basic::options::OptionKeys::evolution::parentlist, basic::options::OptionKeys::robert::pcs_cluster_coverage, basic::options::OptionKeys::robert::pcs_cluster_lowscoring, basic::options::OptionKeys::robert::pcs_dump_cluster, basic::options::OptionKeys::robert::pcs_maxsub_filter, basic::options::OptionKeys::robert::pcs_maxsub_rmsd, basic::options::OptionKeys::PDB_diagnostic::PDB_diagnostic, basic::options::OptionKeys::peptide_deriver::pep_lengths, basic::options::OptionKeys::peptide_deriver::peptide_deriver, basic::options::OptionKeys::phil::phil, basic::options::OptionKeys::willmatch::poi, basic::options::OptionKeys::willmatch::poidis, basic::options::OptionKeys::smhybrid::primary_subsubunit, basic::options::OptionKeys::smhybrid::pseudosym, basic::options::OptionKeys::ralford::ralford, basic::options::OptionKeys::smhybrid::rb_mag, basic::options::OptionKeys::PDB_diagnostic::reading_only, basic::options::OptionKeys::james::real, basic::options::OptionKeys::smhybrid::refine, basic::options::OptionKeys::tcrmodel::refine_all_tcr_cdr_loops, basic::options::OptionKeys::tcrmodel::refine_tcr_cdr3_loops, basic::options::OptionKeys::tcrmodel::refine_tcr_cdr3a_loop, basic::options::OptionKeys::tcrmodel::refine_tcr_cdr3b_loop, basic::options::OptionKeys::tcrmodel::relax_model, basic::options::OptionKeys::tcrmodel::remodel_loop_cdr3a, basic::options::OptionKeys::tcrmodel::remodel_loop_cdr3b, basic::options::OptionKeys::tcrmodel::remodel_tcr_cdr3_loops, basic::options::OptionKeys::tcrmodel::remodel_tcr_cdr3a_loop, basic::options::OptionKeys::tcrmodel::remodel_tcr_cdr3b_loop, basic::options::OptionKeys::smhybrid::rep_edge_files, basic::options::OptionKeys::rot_anl::repack, basic::options::OptionKeys::peptide_deriver::report_format, basic::options::OptionKeys::peptide_deriver::report_gzip, basic::options::OptionKeys::cmiles::jumping::resi, basic::options::OptionKeys::willmatch::residues, basic::options::OptionKeys::cmiles::jumping::resj, basic::options::OptionKeys::smhybrid::restrict_design_to_interface, basic::options::OptionKeys::smhybrid::restrict_design_to_subsub_interface, basic::options::OptionKeys::peptide_deriver::restrict_partners_to_chains, basic::options::OptionKeys::peptide_deriver::restrict_receptors_to_chains, basic::options::OptionKeys::ufv::right, basic::options::OptionKeys::evolution::rms_threshold, basic::options::OptionKeys::evolution::rms_topmargin, basic::options::OptionKeys::robert::robert, basic::options::OptionKeys::rot_anl::rot_anl, basic::options::OptionKeys::ralford::dump_rotamers::rotamer_info_prefix, basic::options::OptionKeys::ralford::dump_rotamers::rsd_index, basic::options::OptionKeys::rot_anl::rtmin, basic::options::OptionKeys::smhybrid::scattach_res_files, basic::options::OptionKeys::rot_anl::scmove, basic::options::OptionKeys::blivens::score_type, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::tcrmodel::skip_modeling, basic::options::OptionKeys::PDB_diagnostic::skip_pack_and_min, basic::options::OptionKeys::peptide_deriver::skip_zero_isc, basic::options::OptionKeys::smhybrid::smhybrid, basic::options::OptionKeys::willmatch::splitwork, basic::options::OptionKeys::threadsc::src_chain, basic::options::OptionKeys::threadsc::src_first_resid, basic::options::OptionKeys::ufv::ss, basic::options::OptionKeys::smhybrid::subsubs_attract, basic::options::OptionKeys::smhybrid::switch_concert_sub, basic::options::OptionKeys::smhybrid::symm_def_template, basic::options::OptionKeys::smhybrid::symm_def_template_reduced, basic::options::OptionKeys::smhybrid::symm_file_tag, basic::options::OptionKeys::willmatch::symmetry_c2_dock, basic::options::OptionKeys::willmatch::symmetry_d2, basic::options::OptionKeys::rot_anl::tag, basic::options::OptionKeys::willmatch::taglist, basic::options::OptionKeys::krassk::tail_mode, basic::options::OptionKeys::krassk::tail_mode_name, basic::options::OptionKeys::krassk::tail_output_file_name, basic::options::OptionKeys::evolution::targetdir, basic::options::OptionKeys::tcrmodel::tcr_template_db_path, basic::options::OptionKeys::tcrmodel::tcrmodel, basic::options::OptionKeys::smhybrid::temperature, basic::options::OptionKeys::tcrmodel::template_identity_cutoff, basic::options::OptionKeys::testing::testing, basic::options::OptionKeys::james::thread_unaligned, basic::options::OptionKeys::threadsc::threadsc, basic::options::OptionKeys::james::torsion_thresholds, basic::options::OptionKeys::threadsc::trg_anchor, basic::options::OptionKeys::threadsc::trg_chain, basic::options::OptionKeys::threadsc::trg_first_resid, basic::options::OptionKeys::ufv::ufv, basic::options::OptionKeys::ufv::ufv_loops, basic::options::OptionKeys::tcrmodel::use_alpha_germline_templates, basic::options::OptionKeys::tcrmodel::use_beta_germline_templates, basic::options::OptionKeys::loodo::use_fraglib, basic::options::OptionKeys::loodo::use_fraglibsc, basic::options::OptionKeys::ufv::use_fullmer, basic::options::OptionKeys::tcrmodel::use_user_templates, basic::options::OptionKeys::phil::vall_file, basic::options::OptionKeys::smhybrid::virtual_nterm, basic::options::OptionKeys::smhybrid::virtual_res_files, basic::options::OptionKeys::willmatch::willmatch, basic::options::OptionKeys::willmatch::write_reduced_matchset, and basic::options::OptionKeys::ralford::dump_rotamers::write_rotamers_to_pdbs.

Referenced by add_all_rosetta_options().

void add_rosetta_options_2 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::score::fiber_diffraction::a, utility::options::OptionCollection::add(), basic::options::OptionKeys::packing::adducts, basic::options::OptionKeys::score::alignment_sharpness, basic::options::OptionKeys::score::loop_close::allow_complex_loop_graph, basic::options::OptionKeys::archive::archive, basic::options::OptionKeys::score::arg_cation_pi_his_can_be_pi, basic::options::OptionKeys::score::fiber_diffraction::b, basic::options::OptionKeys::score::fiber_diffraction::b_factor, basic::options::OptionKeys::score::fiber_diffraction::b_factor_solv, basic::options::OptionKeys::score::fiber_diffraction::b_factor_solv_K, basic::options::OptionKeys::carbohydrates::carbohydrates, basic::options::OptionKeys::carbohydrates::glycan_sampler::cartmin, basic::options::OptionKeys::carbohydrates::clash_check::cb_clash_distance, basic::options::OptionKeys::packing::cenrot_cutoff, basic::options::OptionKeys::score::fiber_diffraction::centroid_density_mass, basic::options::OptionKeys::carbohydrates::clash_check::check_chains, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::score::fiber_diffraction::chi_iterations, basic::options::OptionKeys::carbohydrates::clash_check::clash_check, basic::options::OptionKeys::score::fiber_diffraction::cn_symmetry, basic::options::OptionKeys::archive::completion_notify_frequency, basic::options::OptionKeys::score::saxs::custom_ff, basic::options::OptionKeys::score::saxs::d_max, basic::options::OptionKeys::score::saxs::d_min, basic::options::OptionKeys::score::saxs::d_step, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::score::rna::disable_orientation_dependent_rna_ch_o_bonds, basic::options::OptionKeys::score::rna::DMS_careful_base_pair_classifier, basic::options::OptionKeys::score::rna::DMS_separate_features, basic::options::OptionKeys::packing::double_lazy_ig, basic::options::OptionKeys::packing::dump_rotamer_sets, basic::options::OptionKeys::packing::dunbrack_prob_buried, basic::options::OptionKeys::packing::dunbrack_prob_buried_semi, basic::options::OptionKeys::packing::dunbrack_prob_nonburied, basic::options::OptionKeys::packing::dunbrack_prob_nonburied_semi, basic::options::OptionKeys::score::elec_context_maxburial, basic::options::OptionKeys::score::envsmooth_zero_negatives, basic::options::OptionKeys::packing::ex1::ex1, basic::options::OptionKeys::packing::ex1aro::ex1aro, basic::options::OptionKeys::packing::ex1aro_exposed::ex1aro_exposed, basic::options::OptionKeys::packing::ex2::ex2, basic::options::OptionKeys::packing::ex2aro::ex2aro, basic::options::OptionKeys::packing::ex2aro_exposed::ex2aro_exposed, basic::options::OptionKeys::packing::ex3::ex3, basic::options::OptionKeys::packing::ex4::ex4, basic::options::OptionKeys::chemical::exclude_patches, basic::options::OptionKeys::packing::exdna::exdna, basic::options::OptionKeys::packing::packer_palette::extra_base_type_file, basic::options::OptionKeys::packing::extrachi_cutoff, basic::options::OptionKeys::score::rna::FA_low_res_rnp_scoring, basic::options::OptionKeys::score::facts_adjbb_elec_scale, basic::options::OptionKeys::score::facts_adjbb_solv_scale, basic::options::OptionKeys::score::facts_adjbs_elec_scale, basic::options::OptionKeys::score::facts_adjbs_solv_scale, basic::options::OptionKeys::score::facts_asp_patch, basic::options::OptionKeys::score::facts_binding_affinity, basic::options::OptionKeys::score::facts_charge_dir, basic::options::OptionKeys::score::facts_die, basic::options::OptionKeys::score::facts_dshift, basic::options::OptionKeys::score::facts_eff_charge_dir, basic::options::OptionKeys::score::facts_eq_type, basic::options::OptionKeys::score::facts_GBpair_cut, basic::options::OptionKeys::score::facts_intbb_elec_scale, basic::options::OptionKeys::score::facts_intbb_solv_scale, basic::options::OptionKeys::score::facts_intbs_elec_scale, basic::options::OptionKeys::score::facts_intbs_solv_scale, basic::options::OptionKeys::score::facts_intrascale_by_level, basic::options::OptionKeys::score::facts_intsc_elec_scale, basic::options::OptionKeys::score::facts_intsc_solv_scale, basic::options::OptionKeys::score::facts_kappa, basic::options::OptionKeys::score::facts_plane_aa, basic::options::OptionKeys::score::facts_plane_to_self, basic::options::OptionKeys::score::facts_saltbridge_correction, basic::options::OptionKeys::score::fiber_diffraction::fiber_diffraction, basic::options::OptionKeys::carbohydrates::glycan_sampler::final_min_glycans, basic::options::OptionKeys::score::saxs::fit_pddf_area, basic::options::OptionKeys::packing::fix_his_tautomer, basic::options::OptionKeys::packing::flip_HNQ, basic::options::OptionKeys::score::loop_close::force_6D_potential_file, basic::options::OptionKeys::score::force_sugar_bb_zero, basic::options::OptionKeys::score::rna::free_2HOprime_bonus, basic::options::OptionKeys::score::rna::free_sugar_bonus, basic::options::OptionKeys::score::rna::free_suite_bonus, basic::options::OptionKeys::carbohydrates::glycam_pdb_format, basic::options::OptionKeys::carbohydrates::clash_check::glycan_branches, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler_kt, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler_movie, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler_refine, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler_rounds, basic::options::OptionKeys::carbohydrates::glycan_sampler::glycan_sampler_test, basic::options::OptionKeys::score::fiber_diffraction::gpu_processor, basic::options::OptionKeys::score::fiber_diffraction::grid_phi, basic::options::OptionKeys::score::fiber_diffraction::grid_r, basic::options::OptionKeys::score::fiber_diffraction::grid_reso, basic::options::OptionKeys::score::fiber_diffraction::grid_z, basic::options::OptionKeys::score::hbond_fade, basic::options::OptionKeys::score::hbond_new_sp3_acc, basic::options::OptionKeys::score::occ_sol_fitted::HOH_amp_scaling, basic::options::OptionKeys::score::ideal_sugars, basic::options::OptionKeys::rings::idealize_rings, basic::options::OptionKeys::carbohydrates::clash_check::ignore_full_res_output, basic::options::OptionKeys::carbohydrates::clash_check::ignore_hydrogens, basic::options::OptionKeys::packing::ignore_ligand_chi, basic::options::OptionKeys::score::ignore_terminal_ss_elements, basic::options::OptionKeys::score::rna::include_neighbor_base_stacks, basic::options::OptionKeys::packing::inneriterations_scaling, basic::options::OptionKeys::multithreading::interaction_graph_threads, utility::options::Option::is_group(), basic::options::OptionKeys::score::just_calc_rmsd, basic::options::OptionKeys::score::fiber_diffraction::layer_lines, basic::options::OptionKeys::packing::lazy_ig, basic::options::OptionKeys::score::ldsrbb_high_scale, basic::options::OptionKeys::score::ldsrbb_low_scale, basic::options::OptionKeys::score::ldsrbb_maxlength, basic::options::OptionKeys::score::ldsrbb_minlength, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::score::length_dep_srbb, basic::options::OptionKeys::packing::ex1::level, basic::options::OptionKeys::packing::ex2::level, basic::options::OptionKeys::packing::ex3::level, basic::options::OptionKeys::packing::ex4::level, basic::options::OptionKeys::packing::ex1aro::level, basic::options::OptionKeys::packing::ex2aro::level, basic::options::OptionKeys::packing::ex1aro_exposed::level, basic::options::OptionKeys::packing::ex2aro_exposed::level, basic::options::OptionKeys::packing::exdna::level, basic::options::OptionKeys::carbohydrates::linkage_conformer_data_file, basic::options::OptionKeys::packing::linmem_ig, basic::options::OptionKeys::rings::lock_rings, basic::options::OptionKeys::score::loop_close::loop_close, basic::options::OptionKeys::score::loop_close::loop_fixed_cost, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::packing::mainchain_h_rebuild_threshold, basic::options::OptionKeys::score::fiber_diffraction::max_bessel_order, basic::options::OptionKeys::score::max_contacting_ss, basic::options::OptionKeys::score::max_motif_per_res, basic::options::OptionKeys::packing::max_rotbump_energy, basic::options::OptionKeys::score::mc_interface_weight, basic::options::OptionKeys::score::mc_optimize_dG, basic::options::OptionKeys::score::mc_total_weight, basic::options::OptionKeys::score::mhc_epitope_setup_file, basic::options::OptionKeys::carbohydrates::glycan_sampler::min_rings, basic::options::OptionKeys::score::saxs::min_score, basic::options::OptionKeys::packing::minpack_disable_bumpcheck, basic::options::OptionKeys::packing::minpack_inner_iteration_scale, basic::options::OptionKeys::packing::minpack_temp_schedule, basic::options::OptionKeys::score::motif_ignore_symmmetry, basic::options::OptionKeys::score::motif_residues, basic::options::OptionKeys::score::ms_dist_exponent, basic::options::OptionKeys::score::ms_dist_midpoint, basic::options::OptionKeys::score::ms_fade_dist, basic::options::OptionKeys::score::ms_fade_outer, basic::options::OptionKeys::score::ms_fit_intercept, basic::options::OptionKeys::score::ms_fit_slope, basic::options::OptionKeys::packing::multi_cool_annealer, basic::options::OptionKeys::multithreading::multithreading, basic::options::OptionKeys::score::occ_sol_fitted::Narg_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Nbb_amp_scaling, basic::options::OptionKeys::packing::packer_palette::NCAA_expanded, basic::options::OptionKeys::packing::ndruns, basic::options::OptionKeys::score::netcharge_setup_file, basic::options::OptionKeys::score::occ_sol_fitted::NH2O_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Nhis_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Nlys_amp_scaling, basic::options::OptionKeys::score::nmer_pssm, basic::options::OptionKeys::score::nmer_pssm_list, basic::options::OptionKeys::score::nmer_pssm_scorecut, basic::options::OptionKeys::score::nmer_ref_energies, basic::options::OptionKeys::score::nmer_ref_energies_list, basic::options::OptionKeys::score::nmer_ref_seq_length, basic::options::OptionKeys::score::nmer_svm, basic::options::OptionKeys::score::nmer_svm_aa_matrix, basic::options::OptionKeys::score::nmer_svm_avg_rank_as_energy, basic::options::OptionKeys::score::nmer_svm_list, basic::options::OptionKeys::score::nmer_svm_pssm_feat, basic::options::OptionKeys::score::nmer_svm_rank, basic::options::OptionKeys::score::nmer_svm_rank_list, basic::options::OptionKeys::score::nmer_svm_scorecut, basic::options::OptionKeys::score::nmer_svm_term_length, basic::options::OptionKeys::packing::no_optH, basic::options::OptionKeys::score::occ_sol_fitted::Ntrp_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Oaro_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::OC3_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::OCbb_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::occ_sol_fitted, basic::options::OptionKeys::score::occ_sol_fitted::Oet2_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Oet3_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::OH_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::OHha_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::Oice_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::ONH2_amp_scaling, basic::options::OptionKeys::score::occ_sol_fitted::OOC_amp_scaling, basic::options::OptionKeys::packing::ex1::operate, basic::options::OptionKeys::packing::ex2::operate, basic::options::OptionKeys::packing::ex3::operate, basic::options::OptionKeys::packing::ex4::operate, basic::options::OptionKeys::score::occ_sol_fitted::OPha_amp_scaling, basic::options::OptionKeys::packing::optH_MCA, basic::options::OptionKeys::score::occ_sol_fitted::OSi_amp_scaling, basic::options::OptionKeys::packing::outeriterations_scaling, basic::options::OptionKeys::score::fiber_diffraction::output_fiber_spectra, basic::options::OptionKeys::carbohydrates::clash_check::output_per_glycan_data, basic::options::OptionKeys::score::fiber_diffraction::p, basic::options::OptionKeys::packing::pack_missing_sidechains, basic::options::OptionKeys::score::rna::pack_phosphate_penalty, basic::options::OptionKeys::packing::packer_palette::packer_palette, basic::options::OptionKeys::packing::packing, basic::options::OptionKeys::carbohydrates::glycan_sampler::population_based_conformer_sampling, basic::options::OptionKeys::packing::precompute_ig, basic::options::OptionKeys::packing::preserve_c_beta, basic::options::OptionKeys::packing::prevent_repacking, basic::options::OptionKeys::score::saxs::print_i_calc, basic::options::OptionKeys::packing::print_pymol_selection, basic::options::OptionKeys::score::protein_dielectric, basic::options::OptionKeys::score::saxs::q_max, basic::options::OptionKeys::score::saxs::q_min, basic::options::OptionKeys::score::saxs::q_step, basic::options::OptionKeys::score::fiber_diffraction::qfht_K1, basic::options::OptionKeys::score::fiber_diffraction::qfht_K2, basic::options::OptionKeys::packing::quasisymmetry, basic::options::OptionKeys::score::fiber_diffraction::radius, basic::options::OptionKeys::score::rama_power, basic::options::OptionKeys::recon::randomize, basic::options::OptionKeys::recon::recon, basic::options::OptionKeys::score::saxs::ref_cen_spectrum, basic::options::OptionKeys::score::saxs::ref_fa_spectrum, basic::options::OptionKeys::score::saxs::ref_pddf, basic::options::OptionKeys::score::saxs::ref_spectrum, basic::options::OptionKeys::packing::repack_only, basic::options::OptionKeys::archive::reread_all_structures, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::score::fiber_diffraction::resolution_cutoff_high, basic::options::OptionKeys::score::fiber_diffraction::resolution_cutoff_low, basic::options::OptionKeys::score::fiber_diffraction::rfactor_refinement, basic::options::OptionKeys::rings::ring_conformer_dbpath, basic::options::OptionKeys::rings::rings, basic::options::OptionKeys::score::rna::rna, basic::options::OptionKeys::score::rna::rna_base_pair_xy_filename, basic::options::OptionKeys::score::rna::rna_bulge_bonus_once_per_loop, basic::options::OptionKeys::score::rna::rna_chem_map_lores_weight, basic::options::OptionKeys::score::rna::rna_chemical_shift_exp_data, basic::options::OptionKeys::score::rna::rna_chemical_shift_H5_prime_mode, basic::options::OptionKeys::score::rna::rna_chemical_shift_include_res, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_beta, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_cut, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_nei, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_par, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_ref, basic::options::OptionKeys::score::rna::rna_chemical_shift_larmord_wt, basic::options::OptionKeys::score::rna::rna_chemical_shift_verbose, basic::options::OptionKeys::score::rna::rna_suite_potential, basic::options::OptionKeys::score::rna_torsion_potential, basic::options::OptionKeys::score::rna::rna_torsion_skip_chainbreak, basic::options::OptionKeys::rings::sample_high_energy_conformers, basic::options::OptionKeys::score::saxs::saxs, basic::options::OptionKeys::packing::sc_branch_rotamers, basic::options::OptionKeys::packing::sequence_symmetric_annealer, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::packing::smart_annealer, basic::options::OptionKeys::packing::smart_annealer_cutoff, basic::options::OptionKeys::packing::smart_annealer_disable_during_quench, basic::options::OptionKeys::packing::smart_annealer_model, basic::options::OptionKeys::packing::smart_annealer_pick_again, basic::options::OptionKeys::carbohydrates::clash_check::soft_clash, basic::options::OptionKeys::packing::soft_rep_design, basic::options::OptionKeys::score::rna::suiteness_bonus, basic::options::OptionKeys::score::rna::syn_G_potential_bonus, basic::options::OptionKeys::multithreading::total_threads, basic::options::OptionKeys::carbohydrates::glycan_sampler::tree_based_min_pack, basic::options::OptionKeys::packing::unboundrot, utility::options::ScalarOption_T_< K, T >::upper(), basic::options::OptionKeys::score::rna::use_2prime_OH_potential, basic::options::OptionKeys::score::loop_close::use_6D_potential, basic::options::OptionKeys::score::loop_close::use_cubic_interp, basic::options::OptionKeys::packing::use_electrostatic_repulsion, basic::options::OptionKeys::carbohydrates::glycan_sampler::use_gaussian_sampling, basic::options::OptionKeys::score::use_gen_kirkwood, basic::options::OptionKeys::packing::use_input_sc, basic::options::OptionKeys::score::use_polarization, basic::options::OptionKeys::score::rna::use_rna_chi_potential, basic::options::OptionKeys::score::voids_penalty_energy_cone_distance_cutoff, basic::options::OptionKeys::score::voids_penalty_energy_cone_dotproduct_cutoff, basic::options::OptionKeys::score::voids_penalty_energy_containing_cones_cutoff, basic::options::OptionKeys::score::voids_penalty_energy_disabled_except_during_packing, basic::options::OptionKeys::score::voids_penalty_energy_voxel_grid_padding, basic::options::OptionKeys::score::voids_penalty_energy_voxel_size, and basic::options::OptionKeys::score::water_dielectric.

Referenced by add_all_rosetta_options().

void add_rosetta_options_3 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::loops::accept_aborted_loops, utility::options::OptionCollection::add(), basic::options::OptionKeys::chemical::add_atom_type_set_parameters, basic::options::OptionKeys::chemical::add_atom_types, basic::options::OptionKeys::chemical::add_mm_atom_type_set_parameters, basic::options::OptionKeys::evaluation::align_rmsd_column, basic::options::OptionKeys::evaluation::align_rmsd_fns, basic::options::OptionKeys::evaluation::align_rmsd_format, basic::options::OptionKeys::evaluation::align_rmsd_target, basic::options::OptionKeys::corrections::chemical::alternate_fullatom_ats, basic::options::OptionKeys::corrections::water::axis_rot_sampling, basic::options::OptionKeys::jumps::bb_moves, basic::options::OptionKeys::corrections::score::bbdep_bond_devs, basic::options::OptionKeys::corrections::score::bbdep_bond_params, basic::options::OptionKeys::corrections::score::bbdep_omega, basic::options::OptionKeys::corrections::beta, basic::options::OptionKeys::corrections::beta_cart, basic::options::OptionKeys::corrections::beta_july15, basic::options::OptionKeys::corrections::beta_july15_cart, basic::options::OptionKeys::corrections::beta_nov16, basic::options::OptionKeys::corrections::beta_nov16_cart, basic::options::OptionKeys::loops::build_all_loops, basic::options::OptionKeys::loops::build_attempts, basic::options::OptionKeys::loops::build_initial, basic::options::OptionKeys::loops::build_specific_loops, basic::options::OptionKeys::evaluation::built_in_rdc, basic::options::OptionKeys::evaluation::Ca_Irms, basic::options::OptionKeys::evaluation::cam_shifts, basic::options::OptionKeys::loops::cen_patch, basic::options::OptionKeys::loops::cen_weights, basic::options::OptionKeys::corrections::score::cenrot, basic::options::OptionKeys::corrections::score::ch_o_bond_potential, basic::options::OptionKeys::jumps::chainbreak_weight_stage1, basic::options::OptionKeys::jumps::chainbreak_weight_stage2, basic::options::OptionKeys::jumps::chainbreak_weight_stage3, basic::options::OptionKeys::jumps::chainbreak_weight_stage4, basic::options::OptionKeys::corrections::chemical::chemical, basic::options::OptionKeys::evaluation::chemical_shifts, basic::options::OptionKeys::evaluation::chirmsd, basic::options::OptionKeys::chemical::clone_atom_types, basic::options::OptionKeys::corrections::water::cluster_cutoff, basic::options::OptionKeys::corrections::water::cluster_radius, basic::options::OptionKeys::constraints::combine, basic::options::OptionKeys::constraints::combine_exclude_region, basic::options::OptionKeys::loops::combine_rate, basic::options::OptionKeys::evaluation::combine_statistics, basic::options::OptionKeys::evaluation::combined_constraints, basic::options::OptionKeys::evaluation::combined_constraints_column, basic::options::OptionKeys::constraints::compute_total_dist_cst, basic::options::OptionKeys::loops::constrain_rigid_segments, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::evaluation::constraints, basic::options::OptionKeys::evaluation::constraints_column, basic::options::OptionKeys::evaluation::contact_map, basic::options::OptionKeys::jumps::contact_score, basic::options::OptionKeys::corrections::correct, basic::options::OptionKeys::corrections::corrections, basic::options::OptionKeys::constraints::cst_fa_file, basic::options::OptionKeys::constraints::cst_fa_weight, basic::options::OptionKeys::constraints::cst_file, basic::options::OptionKeys::constraints::cst_weight, basic::options::OptionKeys::constraints::cull_with_native, basic::options::OptionKeys::loops::debug, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::gpu::device, basic::options::OptionKeys::filters::disable_all_filters, basic::options::OptionKeys::filters::disable_co_filter, basic::options::OptionKeys::filters::disable_rg_filter, basic::options::OptionKeys::filters::disable_sheet_filter, basic::options::OptionKeys::evaluation::DockMetrics, basic::options::OptionKeys::constraints::dump_cst_set, basic::options::OptionKeys::jumps::dump_frags, basic::options::OptionKeys::corrections::score::dun02_file, basic::options::OptionKeys::corrections::score::dun10, basic::options::OptionKeys::corrections::score::dun10_dir, basic::options::OptionKeys::corrections::score::dun_entropy_correction, basic::options::OptionKeys::corrections::score::dun_normsd, basic::options::OptionKeys::corrections::water::dwell_cutoff, basic::options::OptionKeys::enzymes::efficiency, basic::options::OptionKeys::chemical::enlarge_H_lj, basic::options::OptionKeys::enzymes::enzyme, basic::options::OptionKeys::enzymes::enzymes, basic::options::OptionKeys::constraints::epr_distance, basic::options::OptionKeys::jumps::evaluate, basic::options::OptionKeys::constraints::evaluate_max_seq_sep, basic::options::OptionKeys::evaluation::evaluation, basic::options::OptionKeys::constraints::exit_on_bad_read, basic::options::OptionKeys::corrections::chemical::expand_st_chi2sampling, basic::options::OptionKeys::loops::extended, basic::options::OptionKeys::loops::extended_loop_file, basic::options::OptionKeys::jumps::extra_frags_for_ss, basic::options::OptionKeys::evaluation::extra_score, basic::options::OptionKeys::evaluation::extra_score_column, basic::options::OptionKeys::evaluation::extra_score_patch, basic::options::OptionKeys::evaluation::extra_score_select, basic::options::OptionKeys::loops::fa_closure_protocol, basic::options::OptionKeys::corrections::score::fa_dun_canonicals_use_voronoi, basic::options::OptionKeys::corrections::score::fa_dun_correct_achiral_peptoid_libraries, basic::options::OptionKeys::corrections::score::fa_dun_correct_rotamer_well_order, basic::options::OptionKeys::corrections::score::fa_dun_noncanonicals_use_voronoi, basic::options::OptionKeys::corrections::facts_default, basic::options::OptionKeys::loops::fast, basic::options::OptionKeys::jumps::filter_templates, basic::options::OptionKeys::filters::filters, basic::options::OptionKeys::loops::final_clean_fastrelax, basic::options::OptionKeys::jumps::fix_chainbreak, basic::options::OptionKeys::jumps::fix_jumps, basic::options::OptionKeys::loops::fix_natsc, basic::options::OptionKeys::evaluation::Fnat, basic::options::OptionKeys::evaluation::Fnonnat, basic::options::OptionKeys::constraints::force_pdb_info_mapping, basic::options::OptionKeys::constraints::forest_file, basic::options::OptionKeys::loops::frag_files, basic::options::OptionKeys::loops::frag_sizes, basic::options::OptionKeys::evaluation::gdtmm, basic::options::OptionKeys::evaluation::gdttm, basic::options::OptionKeys::corrections::gen_potential, basic::options::OptionKeys::corrections::genpotential::genpotential, basic::options::OptionKeys::gpu::gpu, basic::options::OptionKeys::loops::grow_attempts, basic::options::OptionKeys::corrections::score::hb_cen_soft, basic::options::OptionKeys::corrections::score::hb_exclude_ether_oxygens, basic::options::OptionKeys::corrections::score::hb_fade_energy, basic::options::OptionKeys::corrections::score::hb_sp2_BAH180_rise, basic::options::OptionKeys::corrections::score::hb_sp2_chipen, basic::options::OptionKeys::corrections::score::hb_sp2_outer_width, basic::options::OptionKeys::corrections::score::hbond_energy_shift, basic::options::OptionKeys::corrections::score::hbond_measure_sp3acc_BAH_from_hvy, basic::options::OptionKeys::corrections::hbond_sp2_correction, basic::options::OptionKeys::evaluation::I_sc, basic::options::OptionKeys::corrections::chemical::icoor_05_2009, basic::options::OptionKeys::loops::idealize_after_loop_close, basic::options::OptionKeys::loops::idealize_before_loop_close, basic::options::OptionKeys::chemical::include_patches, basic::options::OptionKeys::corrections::water::include_vrt, basic::options::OptionKeys::jumps::increase_chainbreak, basic::options::OptionKeys::loops::input_pdb, basic::options::OptionKeys::loops::intermedrelax, basic::options::OptionKeys::jumps::invrate_jump_move, basic::options::OptionKeys::evaluation::Irms, utility::options::Option::is_group(), basic::options::OptionKeys::evaluation::jscore_evaluator, basic::options::OptionKeys::jumps::jump_lib, basic::options::OptionKeys::evaluation::jump_nr, basic::options::OptionKeys::jumps::jumps, basic::options::OptionKeys::loops::kic_max_seglen, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::corrections::score::lj_hbond_hdis, basic::options::OptionKeys::corrections::score::lj_hbond_OH_donor_dis, basic::options::OptionKeys::corrections::water::lkb_cluster_radius, basic::options::OptionKeys::corrections::water::lkb_overlap_distance, basic::options::OptionKeys::corrections::water::lkb_rotset_radius, basic::options::OptionKeys::jumps::loop_definition_from_file, basic::options::OptionKeys::loops::loop_file, basic::options::OptionKeys::loops::loops, basic::options::OptionKeys::loops::loopscores, basic::options::OptionKeys::evaluation::Lrmsd, basic::options::OptionKeys::constraints::max_cst_dist, basic::options::OptionKeys::jumps::max_strand_gap_allowed, basic::options::OptionKeys::loops::mm_loop_file, basic::options::OptionKeys::constraints::named, basic::options::OptionKeys::loops::neighbor_dist, basic::options::OptionKeys::corrections::newdna, basic::options::OptionKeys::jumps::njumps, basic::options::OptionKeys::corrections::score::no_autogen_cart_improper, basic::options::OptionKeys::jumps::no_chainbreak_in_relax, basic::options::OptionKeys::constraints::no_cst_in_relax, basic::options::OptionKeys::chemical::no_hbonds_to_ether_oxygens, basic::options::OptionKeys::corrections::score::no_his_DE_pairE, basic::options::OptionKeys::corrections::score::no_his_his_pairE, basic::options::OptionKeys::constraints::no_linearize_bounded, basic::options::OptionKeys::jumps::no_sample_ss_jumps, basic::options::OptionKeys::jumps::no_shear, basic::options::OptionKeys::jumps::no_wobble, basic::options::OptionKeys::constraints::normalize_mixture_func, basic::options::OptionKeys::corrections::water::ordered_pt_wat_penalty, basic::options::OptionKeys::corrections::water::ordered_wat_penalty, basic::options::OptionKeys::loops::output_pdb, basic::options::OptionKeys::jumps::overlap_chainbreak, basic::options::OptionKeys::chemical::override_rsd_type_limit, basic::options::OptionKeys::corrections::score::p_aa_pp, basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift, basic::options::OptionKeys::jumps::pairing_file, basic::options::OptionKeys::evaluation::pales, basic::options::OptionKeys::corrections::chemical::parse_charge, basic::options::OptionKeys::chemical::patch_selectors, basic::options::OptionKeys::constraints::penalize_mixture_func, basic::options::OptionKeys::constraints::pocket_constraint_weight, basic::options::OptionKeys::constraints::pocket_zero_derivatives, basic::options::OptionKeys::corrections::water::pointwat_wat_bonus, basic::options::OptionKeys::corrections::water::pointwat_wat_bonus_width, basic::options::OptionKeys::corrections::water::pointwater_params, basic::options::OptionKeys::evaluation::pool, basic::options::OptionKeys::evaluation::predicted_burial_fn, basic::options::OptionKeys::corrections::score::rama_map, basic::options::OptionKeys::corrections::score::rama_map_average_L_flat, basic::options::OptionKeys::corrections::score::rama_map_average_L_flat_stringent, basic::options::OptionKeys::corrections::score::rama_map_sym_average_L_flat, basic::options::OptionKeys::corrections::score::rama_map_sym_average_L_flat_stringent, basic::options::OptionKeys::corrections::score::rama_map_sym_gly_flat, basic::options::OptionKeys::corrections::score::rama_map_sym_gly_flat_stringent, basic::options::OptionKeys::corrections::score::rama_map_sym_pro_flat, basic::options::OptionKeys::corrections::score::rama_map_sym_pro_flat_stringent, basic::options::OptionKeys::corrections::score::rama_not_squared, basic::options::OptionKeys::corrections::score::rama_pp_map, basic::options::OptionKeys::corrections::score::rama_prepro_nobidentate, basic::options::OptionKeys::corrections::score::rama_prepro_steep, basic::options::OptionKeys::jumps::ramp_chainbreaks, basic::options::OptionKeys::loops::random_grow_loops_by, basic::options::OptionKeys::loops::random_order, basic::options::OptionKeys::jumps::random_sheets, basic::options::OptionKeys::evaluation::rdc, basic::options::OptionKeys::evaluation::rdc_column, basic::options::OptionKeys::evaluation::rdc_target, basic::options::OptionKeys::chemical::reassign_atom_types, basic::options::OptionKeys::chemical::reassign_icoor, basic::options::OptionKeys::loops::refine, basic::options::OptionKeys::loops::refine_only, basic::options::OptionKeys::loops::relax, basic::options::OptionKeys::loops::relax_with_foldtree, basic::options::OptionKeys::loops::remodel, basic::options::OptionKeys::loops::remove_extended_loops, basic::options::OptionKeys::jumps::residue_pair_jump_file, basic::options::OptionKeys::corrections::restore_talaris_behavior, basic::options::OptionKeys::evaluation::rms_type, basic::options::OptionKeys::evaluation::rmsd, basic::options::OptionKeys::evaluation::rmsd_column, basic::options::OptionKeys::evaluation::rmsd_select, basic::options::OptionKeys::evaluation::rmsd_target, basic::options::OptionKeys::corrections::score::score, basic::options::OptionKeys::corrections::score::score12prime, basic::options::OptionKeys::evaluation::score_exclude_res, basic::options::OptionKeys::evaluation::score_sscore_maxloop, basic::options::OptionKeys::evaluation::score_sscore_short_helix, basic::options::OptionKeys::evaluation::score_with_rmsd, basic::options::OptionKeys::loops::select_best_loop_from, basic::options::OptionKeys::jumps::sep_switch_accelerate, basic::options::OptionKeys::chemical::set_atom_properties, basic::options::OptionKeys::chemical::set_atomic_charge, basic::options::OptionKeys::chemical::set_patch_atomic_charge, basic::options::OptionKeys::filters::set_pddf_filter, basic::options::OptionKeys::filters::set_saxs_filter, basic::options::OptionKeys::corrections::genpotential::set_special_torsion_params, basic::options::OptionKeys::corrections::genpotential::set_torsion_params, basic::options::OptionKeys::corrections::shapovalov_lib::shap_dun10_dir, basic::options::OptionKeys::corrections::shapovalov_lib::shap_dun10_enable, basic::options::OptionKeys::corrections::shapovalov_lib::shap_dun10_smooth_level, basic::options::OptionKeys::corrections::shapovalov_lib::shap_dun10_use_minus_log_P_ignore_P, basic::options::OptionKeys::corrections::shapovalov_lib::shap_p_aa_pp, basic::options::OptionKeys::corrections::shapovalov_lib::shap_p_aa_pp_enable, basic::options::OptionKeys::corrections::shapovalov_lib::shap_p_aa_pp_smooth_level, basic::options::OptionKeys::corrections::shapovalov_lib::shap_rama_enable, basic::options::OptionKeys::corrections::shapovalov_lib::shap_rama_map, basic::options::OptionKeys::corrections::shapovalov_lib::shap_rama_nogridshift, basic::options::OptionKeys::corrections::shapovalov_lib::shap_rama_smooth_level, basic::options::OptionKeys::corrections::shapovalov_lib::shapovalov_lib, basic::options::OptionKeys::corrections::shapovalov_lib_fixes_enable, basic::options::OptionKeys::jumps::sheets, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::loops::skip_initial_loop_build, basic::options::OptionKeys::constraints::skip_redundant, basic::options::OptionKeys::constraints::skip_redundant_width, basic::options::OptionKeys::constraints::sog_cst_param, basic::options::OptionKeys::constraints::sog_upper_bound, basic::options::OptionKeys::evaluation::sparta_dir, basic::options::OptionKeys::enzymes::species, basic::options::OptionKeys::loops::strict_loops, basic::options::OptionKeys::evaluation::structural_similarity, basic::options::OptionKeys::loops::superimpose_native, basic::options::OptionKeys::evaluation::symmetric_rmsd, basic::options::OptionKeys::gpu::threads, basic::options::OptionKeys::loops::timer, basic::options::OptionKeys::jumps::topology_file, basic::options::OptionKeys::chemical::unset_acceptor_ether_oxygens, basic::options::OptionKeys::corrections::score::use_bicubic_interpolation, basic::options::OptionKeys::loops::vall_file, basic::options::OptionKeys::loops::vicinity_degree, basic::options::OptionKeys::loops::vicinity_sampling, basic::options::OptionKeys::constraints::viol, basic::options::OptionKeys::constraints::viol_level, basic::options::OptionKeys::constraints::viol_type, basic::options::OptionKeys::corrections::water::wat_axis_sampling, basic::options::OptionKeys::corrections::water::wat_rot_params, basic::options::OptionKeys::corrections::water::wat_rot_sampling, basic::options::OptionKeys::corrections::water::water, basic::options::OptionKeys::corrections::water::water_bump_check, basic::options::OptionKeys::corrections::water::watlim_scale, and basic::options::OptionKeys::evaluation::window_size.

Referenced by add_all_rosetta_options().

void add_rosetta_options_4 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::abinitio::abinitio, utility::options::OptionCollection::add(), basic::options::OptionKeys::mp::dock::allow_flips, basic::options::OptionKeys::loops::allow_lig_move, basic::options::OptionKeys::loops::allow_omega_move, basic::options::OptionKeys::loops::allow_takeoff_torsion_move, basic::options::OptionKeys::loops::alternative_closure_protocol, basic::options::OptionKeys::loops::always_remodel_full_loop, basic::options::OptionKeys::mp::lipid_acc::angle_cutoff, basic::options::OptionKeys::mp::quickrelax::angle_max, basic::options::OptionKeys::optimization::armijo_min_stepsize, basic::options::OptionKeys::mp::assembly::assembly, basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff, basic::options::OptionKeys::loops::backrub_trials, basic::options::OptionKeys::orbitals::bb_stats, basic::options::OptionKeys::mp::benchmark::benchmark, basic::options::OptionKeys::loops::ccd::ccd, basic::options::OptionKeys::loops::ccd_closure, basic::options::OptionKeys::mp::setup::center, basic::options::OptionKeys::mp::center_delta, basic::options::OptionKeys::membrane::center_mag, basic::options::OptionKeys::membrane::center_max_delta, basic::options::OptionKeys::membrane::center_search, basic::options::OptionKeys::mp::center_search_cycles, basic::options::OptionKeys::mp::center_start, basic::options::OptionKeys::loops::chain_break_tol, basic::options::OptionKeys::mp::chain_normal_angle_max, basic::options::OptionKeys::rigid::chainbreak_bias, basic::options::OptionKeys::loops::chainbreak_max_accept, basic::options::OptionKeys::intf::chains, basic::options::OptionKeys::loops::ccd::check_rama_scores, basic::options::OptionKeys::mistakes::chemical::chemical, basic::options::OptionKeys::abinitio::clear_pose_cache, basic::options::OptionKeys::rigid::close_loops, basic::options::OptionKeys::mp::lipids::composition, basic::options::OptionKeys::pose_metrics::contact_cutoffE, basic::options::OptionKeys::loops::coord_cst, basic::options::OptionKeys::abinitio::debug, basic::options::OptionKeys::membrane::debug, basic::options::OptionKeys::optimization::debug_inaccurate_G, basic::options::OptionKeys::loops::debug_loop_closure, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::optimization::default_max_cycles, basic::options::OptionKeys::loops::derive_torsion_string_from_native_pose, basic::options::OptionKeys::symmetry::detect_bonds, basic::options::OptionKeys::mp::lipid_acc::dist_cutoff, basic::options::OptionKeys::mp::dock::dock, test.T009_Exceptions::e, basic::options::OptionKeys::mp::visualize::embedding, basic::options::OptionKeys::sasa::exclude_polar_atoms_by_charge_in_hsasa, basic::options::OptionKeys::sasa::explicit_hydrogen_radii_set, basic::options::OptionKeys::abinitio::explicit_pdb_debug, basic::options::OptionKeys::loops::extend_length, basic::options::OptionKeys::loops::extended_beta, basic::options::OptionKeys::membrane::Fa_Membed_update, basic::options::OptionKeys::abinitio::fastrelax, basic::options::OptionKeys::abinitio::final_clean_relax, basic::options::OptionKeys::loops::final_score_filter, basic::options::OptionKeys::loops::fix_ca_bond_angles, basic::options::OptionKeys::membrane::fixed_membrane, basic::options::OptionKeys::mp::dock::flexible_bb, basic::options::OptionKeys::mp::dock::flexible_sc, basic::options::OptionKeys::rigid::fragment_cycles, basic::options::OptionKeys::loops::gapspan, basic::options::OptionKeys::orbitals::Haro, basic::options::OptionKeys::mp::lipids::has_pore, basic::options::OptionKeys::mp::scoring::hbond, basic::options::OptionKeys::mp::Hbond_depth_correction, basic::options::OptionKeys::mp::benchmark::ideal_helix::helix_end, basic::options::OptionKeys::mp::benchmark::ideal_helix::helix_start, basic::options::OptionKeys::orbitals::Hpol, basic::options::OptionKeys::mp::benchmark::ideal_helix::ideal_helix, basic::options::OptionKeys::sasa::implicit_hydrogen_radii_set, basic::options::OptionKeys::sasa::include_hydrogens_explicitly, basic::options::OptionKeys::sasa::include_only_C_S_in_hsasa, basic::options::OptionKeys::sasa::include_probe_radius_in_atom_radii, basic::options::OptionKeys::symmetry::initialize_rigid_body_dofs, basic::options::OptionKeys::pose_metrics::inter_group_neighbors_cutoff, basic::options::OptionKeys::pose_metrics::interface_cutoff, basic::options::OptionKeys::intf::intf, utility::options::Option::is_group(), basic::options::OptionKeys::loops::keep_natro, basic::options::OptionKeys::loops::kic_bump_overlap_factor, basic::options::OptionKeys::loops::kic_leave_centroid_after_initial_closure, basic::options::OptionKeys::loops::kic_min_after_repack, basic::options::OptionKeys::loops::kic_num_rotamer_trials, basic::options::OptionKeys::loops::kic_omega_sampling, basic::options::OptionKeys::loops::kic_rama2b, basic::options::OptionKeys::loops::kic_recover_last, basic::options::OptionKeys::loops::kic_use_linear_chainbreak, basic::options::OptionKeys::loops::kic_with_cartmin, basic::options::OptionKeys::abinitio::kill_hairpins, basic::options::OptionKeys::abinitio::kill_hairpins_frequency, basic::options::OptionKeys::loops::kinematic_wrapper_cycles, basic::options::OptionKeys::optimization::lbfgs_M, basic::options::OptionKeys::loops::legacy_kic, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::mp::lipid_acc::lipid_acc, basic::options::OptionKeys::mp::lipids::lipids, basic::options::OptionKeys::mp::setup::lipsfile, basic::options::OptionKeys::rigid::log_accepted_moves, basic::options::OptionKeys::loops::loop_combine_rate, basic::options::OptionKeys::loops::loop_model, basic::options::OptionKeys::abinitio::loophash_filter_acceptance_rate, basic::options::OptionKeys::loops::looprlx_cycle_ratio, basic::options::OptionKeys::loops::loops_subset, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::mp::dock::lowres, basic::options::OptionKeys::rigid::max_ca_ca_dist, basic::options::OptionKeys::loops::ccd::max_cycles, basic::options::OptionKeys::loops::max_inner_cycles, basic::options::OptionKeys::loops::max_kic_build_attempts, basic::options::OptionKeys::loops::max_kic_perturber_samples, basic::options::OptionKeys::loops::ccd::max_rama_score_increase, basic::options::OptionKeys::loops::ccd::max_torsion_delta, basic::options::OptionKeys::loops::ccd::max_torsion_delta_per_move, basic::options::OptionKeys::membrane::Membed_init, basic::options::OptionKeys::membrane::membrane, basic::options::OptionKeys::abinitio::membrane, basic::options::OptionKeys::membrane::membrane_center, basic::options::OptionKeys::mp::membrane_core, basic::options::OptionKeys::membrane::membrane_normal, basic::options::OptionKeys::mp::setup::membrane_rsd, basic::options::OptionKeys::membrane::Menv_penalties, basic::options::OptionKeys::sasa::method, basic::options::OptionKeys::membrane::Mhbond_depth, basic::options::OptionKeys::pose_metrics::min_sequence_separation, basic::options::OptionKeys::loops::minimize_max_iter, basic::options::OptionKeys::mistakes::mistakes, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::mp::mp, basic::options::OptionKeys::abinitio::multifastrelax, basic::options::OptionKeys::mp::mutate_relax::mutant_file, basic::options::OptionKeys::mp::mutate_relax::mutate_relax, basic::options::OptionKeys::mp::mutate_relax::mutation, basic::options::OptionKeys::pose_metrics::neighbor_by_distance_cutoff, basic::options::OptionKeys::mp::mutate_relax::nmodels, basic::options::OptionKeys::mp::quickrelax::nmoves, basic::options::OptionKeys::loops::no_combine_if_fail, basic::options::OptionKeys::membrane::no_interpolate_Mpair, basic::options::OptionKeys::mp::no_interpolate_Mpair, basic::options::OptionKeys::loops::no_looprebuild, basic::options::OptionKeys::loops::no_randomize_loop, basic::options::OptionKeys::mp::non_helix, basic::options::OptionKeys::loops::non_ideal_loop_closing, basic::options::OptionKeys::optimization::nonideal, basic::options::OptionKeys::loops::nonpivot_torsion_sampling, basic::options::OptionKeys::mp::setup::normal, basic::options::OptionKeys::mp::normal_angle_delta, basic::options::OptionKeys::mp::normal_angle_start, basic::options::OptionKeys::membrane::normal_cycles, basic::options::OptionKeys::membrane::normal_delta_angle, basic::options::OptionKeys::membrane::normal_mag, basic::options::OptionKeys::membrane::normal_max_angle, basic::options::OptionKeys::membrane::normal_search, basic::options::OptionKeys::mp::normal_search_cycles, basic::options::OptionKeys::mp::normal_start, basic::options::OptionKeys::membrane::normal_start_angle, basic::options::OptionKeys::mp::output::normalize_to_thk, basic::options::OptionKeys::loops::num_desired_loops, basic::options::OptionKeys::mp::viewer::num_points, basic::options::OptionKeys::optimization::old_sym_min, basic::options::OptionKeys::optimization::optimization, basic::options::OptionKeys::mp::setup::optimize1, basic::options::OptionKeys::mp::setup::optimize2, basic::options::OptionKeys::mp::transform::optimize_embedding, basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move, basic::options::OptionKeys::orbitals::orbitals, basic::options::OptionKeys::mp::benchmark::tilt_angle::output, basic::options::OptionKeys::mp::output::output, basic::options::OptionKeys::mp::output::output_mem_to_pdb, basic::options::OptionKeys::rigid::patch, basic::options::OptionKeys::loops::perturb_outer_cycles, basic::options::OptionKeys::symmetry::perturb_rigid_body_dofs, basic::options::OptionKeys::mp::visualize::plane_radius, basic::options::OptionKeys::sasa::polar_charge_cutoff, basic::options::OptionKeys::pose_metrics::pose_metrics, basic::options::OptionKeys::mp::pose_normal_angle_max, basic::options::OptionKeys::mp::assembly::poses, basic::options::OptionKeys::mp::setup::position_from_topo, basic::options::OptionKeys::mistakes::chemical::pre_talaris2013_geometries, basic::options::OptionKeys::sasa::probe_radius, basic::options::OptionKeys::mp::quickrelax::quickrelax, basic::options::OptionKeys::loops::ccd::rama_2b, basic::options::OptionKeys::loops::ramp_fa_rep, basic::options::OptionKeys::loops::ramp_rama, basic::options::OptionKeys::loops::random_loop, basic::options::OptionKeys::loops::refine_design_iterations, basic::options::OptionKeys::loops::refine_final_temp, basic::options::OptionKeys::loops::refine_init_temp, basic::options::OptionKeys::loops::refine_outer_cycles, basic::options::OptionKeys::abinitio::relax, basic::options::OptionKeys::mp::mutate_relax::relax, basic::options::OptionKeys::loops::remodel_final_temp, basic::options::OptionKeys::loops::remodel_init_temp, basic::options::OptionKeys::loops::remodel_kic_attempts, basic::options::OptionKeys::mp::quickrelax::repack_again, basic::options::OptionKeys::mp::mutate_relax::repack_mutation_only, basic::options::OptionKeys::loops::repack_period, basic::options::OptionKeys::mp::mutate_relax::repack_radius, basic::options::OptionKeys::rigid::residues_backbone_move, basic::options::OptionKeys::mp::restore_lazaridis_imm_behavior, basic::options::OptionKeys::mistakes::restore_pre_talaris_2013_behavior, basic::options::OptionKeys::loops::restrict_kic_sampling_to_torsion_string, basic::options::OptionKeys::symmetry::reweight_symm_interactions, basic::options::OptionKeys::rigid::rigid, basic::options::OptionKeys::loops::rmsd_tol, basic::options::OptionKeys::rigid::rotation, basic::options::OptionKeys::loops::sample_omega_at_pre_prolines, basic::options::OptionKeys::rigid::sampling_prob, basic::options::OptionKeys::sasa::sasa, basic::options::OptionKeys::pose_metrics::sasa_calculator_probe_radius, basic::options::OptionKeys::orbitals::sc_stats, basic::options::OptionKeys::optimization::scale_d, basic::options::OptionKeys::optimization::scale_normalmode_dampen, basic::options::OptionKeys::optimization::scale_rb, basic::options::OptionKeys::optimization::scale_rbangle, basic::options::OptionKeys::optimization::scale_theta, basic::options::OptionKeys::optimization::scmin_cartesian, basic::options::OptionKeys::optimization::scmin_nonideal, basic::options::OptionKeys::rigid::score, basic::options::OptionKeys::loops::score_filter_cutoff, basic::options::OptionKeys::loops::scored_frag_cycles, basic::options::OptionKeys::mp::scoring::scoring, basic::options::OptionKeys::mp::secstruct, basic::options::OptionKeys::pose_metrics::semiex_water_burial_cutoff, basic::options::OptionKeys::rigid::sequence_separation, basic::options::OptionKeys::mp::setup::setup, basic::options::OptionKeys::mp::lipid_acc::shell_radius, basic::options::OptionKeys::pose_metrics::shobuns::sho_cutoff, basic::options::OptionKeys::pose_metrics::shobuns::shobuns, basic::options::OptionKeys::loops::short_frag_cycles, basic::options::OptionKeys::loops::shorten_long_terminal_loop, basic::options::OptionKeys::loops::skip_1mers, basic::options::OptionKeys::loops::skip_3mers, basic::options::OptionKeys::loops::skip_9mers, basic::options::OptionKeys::loops::skip_ccd_moves, basic::options::OptionKeys::mp::lipid_acc::slice_width, basic::options::OptionKeys::mp::dock::slide_threshold, basic::options::OptionKeys::rigid::small_cycles, basic::options::OptionKeys::abinitio::smooth_cycles_only, basic::options::OptionKeys::membrane::smooth_move_frac, basic::options::OptionKeys::mp::visualize::spacing, basic::options::OptionKeys::mp::setup::spanfiles, basic::options::OptionKeys::mp::spanning, basic::options::OptionKeys::mp::setup::spans_from_structure, basic::options::OptionKeys::loops::spread, basic::options::OptionKeys::rigid::stages, basic::options::OptionKeys::loops::stealfrags, basic::options::OptionKeys::loops::stealfrags_times, basic::options::OptionKeys::mp::steepness, basic::options::OptionKeys::symmetry::symmetric_rmsd, basic::options::OptionKeys::symmetry::symmetry, basic::options::OptionKeys::symmetry::symmetry_definition, basic::options::OptionKeys::loops::taboo_in_fa, basic::options::OptionKeys::loops::taboo_sampling, basic::options::OptionKeys::MonteCarlo::temp_final, basic::options::OptionKeys::MonteCarlo::temp_initial, basic::options::OptionKeys::rigid::temperature, basic::options::OptionKeys::mp::lipids::temperature, basic::options::OptionKeys::loops::ccd::temperature, basic::options::OptionKeys::mp::termini, basic::options::OptionKeys::pose_metrics::shobuns::tgt_amino, basic::options::OptionKeys::pose_metrics::shobuns::tgt_atom, basic::options::OptionKeys::pose_metrics::shobuns::tgt_res, basic::options::OptionKeys::mp::thickness, basic::options::OptionKeys::membrane::thickness, basic::options::OptionKeys::mp::viewer::thickness, basic::options::OptionKeys::mp::visualize::thickness, basic::options::OptionKeys::mp::benchmark::tilt_angle::tilt_angle, basic::options::OptionKeys::mp::lipid_acc::tm_alpha, basic::options::OptionKeys::mp::assembly::TM_pose_number, basic::options::OptionKeys::mp::TMprojection, basic::options::OptionKeys::loops::ccd::tolerance, basic::options::OptionKeys::mp::transform::transform, basic::options::OptionKeys::mp::setup::transform_into_membrane, basic::options::OptionKeys::rigid::translation, basic::options::OptionKeys::abinitio::use_loophash_filter, basic::options::OptionKeys::membrane::view, basic::options::OptionKeys::mp::viewer::viewer, basic::options::OptionKeys::mp::visualize::visualize, basic::options::OptionKeys::mp::dock::weights_cen, basic::options::OptionKeys::mp::dock::weights_fa, basic::options::OptionKeys::mp::visualize::width, basic::options::OptionKeys::mp::wt_non_helix, basic::options::OptionKeys::mp::wt_secstruct, basic::options::OptionKeys::mp::wt_spanning, basic::options::OptionKeys::mp::wt_termini, and basic::options::OptionKeys::mp::wt_TMprojection.

Referenced by add_all_rosetta_options().

void add_rosetta_options_5 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::abrelax::abrelax, basic::options::OptionKeys::antibody::design::adapt_graft, utility::options::OptionCollection::add(), basic::options::OptionKeys::antibody::design::add_backrub_pivots, basic::options::OptionKeys::antibody::design::add_graft_log_to_pdb, basic::options::OptionKeys::bunsat_calc2::AHD_cutoff, basic::options::OptionKeys::AnchoredDesign::akash::akash, basic::options::OptionKeys::antibody::all_atom_mode_kink_constraint, basic::options::OptionKeys::AnchoredDesign::allow_anchor_repack, basic::options::OptionKeys::antibody::allow_omega_mismatches_for_north_clusters, basic::options::OptionKeys::AnchoredDesign::anchor, basic::options::OptionKeys::AnchoredDesign::testing::anchor_noise_constraints_mode, basic::options::OptionKeys::AnchoredDesign::testing::anchor_via_constraints, basic::options::OptionKeys::AnchoredDesign::AnchoredDesign, basic::options::OptionKeys::antibody::antibody, basic::options::OptionKeys::antibody::design::antibody_database, basic::options::OptionKeys::abinitio::apply_end_bias, basic::options::OptionKeys::assembly::assembly, basic::options::OptionKeys::antibody::design::atom_pair_cst_weight, basic::options::OptionKeys::antibody::auto_generate_h3_kink_constraint, basic::options::OptionKeys::antibody::auto_generate_kink_constraint, basic::options::OptionKeys::backrub::backrub, basic::options::OptionKeys::canonical_sampling::probabilities::backrub, basic::options::OptionKeys::antibody::design::base_cdr_instructions, basic::options::OptionKeys::batch_relax::batch_relax, basic::options::OptionKeys::batch_relax::batch_size, basic::options::OptionKeys::bbg::bbg, basic::options::OptionKeys::antibody::bfactor_cutoff, basic::options::OptionKeys::abinitio::bGDT, basic::options::OptionKeys::antibody::blastp, basic::options::OptionKeys::boinc::boinc, basic::options::OptionKeys::broker::broker, basic::options::OptionKeys::bunsat_calc2::bunsat_calc2, basic::options::OptionKeys::antibody::camelid, basic::options::OptionKeys::antibody::camelid_constraints, basic::options::OptionKeys::canonical_sampling::canonical_sampling, basic::options::OptionKeys::antibody::cdr_definition, basic::options::OptionKeys::antibody::design::cdr_instructions, basic::options::OptionKeys::antibody::design::cdr_set_cache_limit, basic::options::OptionKeys::antibody::centroid_refine, basic::options::OptionKeys::AnchoredDesign::chainbreak_weight, basic::options::OptionKeys::antibody::check_cdr_chainbreaks, basic::options::OptionKeys::antibody::check_cdr_pep_bond_geom, basic::options::OptionKeys::abinitio::close_chbrk, basic::options::OptionKeys::abinitio::close_loops, basic::options::OptionKeys::abinitio::close_loops_by_idealizing, basic::options::OptionKeys::antibody::cluster_csts_stats_cutoff, basic::options::OptionKeys::task_operations::cons_design_data_source, basic::options::OptionKeys::antibody::design::conservative_framework_design, basic::options::OptionKeys::antibody::constrain_cter, basic::options::OptionKeys::antibody::constrain_vlvh_qq, basic::options::OptionKeys::boinc::cpu_frac, basic::options::OptionKeys::boinc::cpu_run_time, basic::options::OptionKeys::boinc::cpu_run_timeout, basic::options::OptionKeys::abinitio::cyclic_peptide, basic::options::OptionKeys::AnchoredDesign::debug, basic::options::OptionKeys::abinitio::debug_structures, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::AnchoredDesign::testing::delete_interface_native_sidechains, basic::options::OptionKeys::boinc::description_file, basic::options::OptionKeys::antibody::design::design, basic::options::OptionKeys::antibody::design::design_antigen, basic::options::OptionKeys::antibody::design::design_framework, basic::options::OptionKeys::antibody::design::design_H3_stem, basic::options::OptionKeys::antibody::design::design_proline, basic::options::OptionKeys::antibody::design::design_protocol, basic::options::OptionKeys::abinitio::detect_disulfide_before_relax, basic::options::OptionKeys::antibody::design::dihedral_cst_weight, basic::options::OptionKeys::antibody::design::disallow_aa, basic::options::OptionKeys::bunsat_calc2::dist_cutoff, basic::options::OptionKeys::antibody::design::do_dock, basic::options::OptionKeys::antibody::design::dock_cycle_rounds, basic::options::OptionKeys::abinitio::dump_frags, basic::options::OptionKeys::AnchoredDesign::akash::dyepos, basic::options::OptionKeys::antibody::design::enable_adapt_graft_cartesian, basic::options::OptionKeys::abinitio::end_bias, basic::options::OptionKeys::antibody::design::epitope, basic::options::OptionKeys::antibody::exclude_homologs, basic::options::OptionKeys::antibody::exclude_homologs_cdr_cutoff, basic::options::OptionKeys::antibody::exclude_homologs_fr_cutoff, basic::options::OptionKeys::antibody::exclude_pdbs, basic::options::OptionKeys::antibody::extend_h3_before_modeling, basic::options::OptionKeys::bbg::factorA, basic::options::OptionKeys::bbg::factorB, basic::options::OptionKeys::abrelax::fail_unclosed, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves_ntrials, basic::options::OptionKeys::AnchoredDesign::filters::filters, basic::options::OptionKeys::abinitio::fix_residues_to_native, basic::options::OptionKeys::bbg::fix_short_segment, basic::options::OptionKeys::antibody::design::force_mutate_framework_for_cluster, basic::options::OptionKeys::antibody::force_use_of_cluster_csts_with_outliers, basic::options::OptionKeys::boinc::frame_rate, basic::options::OptionKeys::antibody::frh_template, basic::options::OptionKeys::antibody::frl_template, basic::options::OptionKeys::boinc::fullscreen, basic::options::OptionKeys::antibody::general_dihedral_cst_phi_sd, basic::options::OptionKeys::antibody::general_dihedral_cst_psi_sd, basic::options::OptionKeys::bunsat_calc2::generous_hbonds, basic::options::OptionKeys::antibody::design::global_atom_pair_cst_scoring, basic::options::OptionKeys::antibody::design::global_dihedral_cst_scoring, basic::options::OptionKeys::antibody::design::graft_design_cdrs, basic::options::OptionKeys::antibody::graft_h1, basic::options::OptionKeys::antibody::graft_h2, basic::options::OptionKeys::antibody::graft_h3, basic::options::OptionKeys::antibody::graft_l1, basic::options::OptionKeys::antibody::graft_l2, basic::options::OptionKeys::antibody::graft_l3, basic::options::OptionKeys::antibody::grafting_database, basic::options::OptionKeys::boinc::graphics, basic::options::OptionKeys::antibody::h1_template, basic::options::OptionKeys::antibody::h2_template, basic::options::OptionKeys::antibody::h3_filter, basic::options::OptionKeys::antibody::h3_filter_tolerance, basic::options::OptionKeys::antibody::h3_loop_csts_hr, basic::options::OptionKeys::antibody::h3_loop_csts_lr, basic::options::OptionKeys::antibody::h3_no_stem_graft, basic::options::OptionKeys::antibody::h3_template, basic::options::OptionKeys::antibody::design::high_mem_mode, basic::options::OptionKeys::bunsat_calc2::hxl_dist_cutoff, basic::options::OptionKeys::antibody::design::idealize_graft_cdrs, basic::options::OptionKeys::bbg::ignore_improper_res, basic::options::OptionKeys::abinitio::include_stage5, basic::options::OptionKeys::abinitio::increase_cycles, basic::options::OptionKeys::abinitio::star::initial_dist_cutoff, basic::options::OptionKeys::backrub::initial_pack, basic::options::OptionKeys::antibody::design::inner_cycle_rounds, basic::options::OptionKeys::antibody::design::inner_kt, basic::options::OptionKeys::antibody::input_ab_scheme, basic::options::OptionKeys::antibody::input_fv, basic::options::OptionKeys::antibody::design::interface_dis, utility::options::Option::is_group(), basic::options::OptionKeys::abinitio::jdist_rerun, basic::options::OptionKeys::antibody::json_cdr, basic::options::OptionKeys::antibody::l1_template, basic::options::OptionKeys::antibody::l2_template, basic::options::OptionKeys::antibody::l3_template, basic::options::OptionKeys::broker::large_frag_mover_stage1_weight, basic::options::OptionKeys::bunsat_calc2::layered_sasa, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::antibody::light_chain, basic::options::OptionKeys::antibody::light_heavy_template, basic::options::OptionKeys::canonical_sampling::probabilities::localbb, basic::options::OptionKeys::abinitio::log_frags, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::backrub::max_atoms, basic::options::OptionKeys::boinc::max_cpu, basic::options::OptionKeys::boinc::max_fps, basic::options::OptionKeys::boinc::max_nstruct, basic::options::OptionKeys::backrub::mc_kt, basic::options::OptionKeys::bunsat_calc2::metal_dist_cutoff, basic::options::OptionKeys::backrub::min_atoms, basic::options::OptionKeys::abinitio::star::min_unaligned_len, basic::options::OptionKeys::backrub::minimize_movemap, basic::options::OptionKeys::antibody::design::mintype, basic::options::OptionKeys::backrub::mm_bend_weight, basic::options::OptionKeys::antibody::model_h3, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_bcast, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_sync_pools, basic::options::OptionKeys::antibody::design::mutate_framework_for_cluster, basic::options::OptionKeys::antibody::n_multi_templates, basic::options::OptionKeys::antibody::design::neighbor_dis, basic::options::OptionKeys::AnchoredDesign::no_frags, basic::options::OptionKeys::canonical_sampling::probabilities::no_jd2_output, basic::options::OptionKeys::antibody::design::no_profile_probabilities, basic::options::OptionKeys::abinitio::no_write_failures, basic::options::OptionKeys::boinc::noshmem, basic::options::OptionKeys::backrub::ntrials, basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, basic::options::OptionKeys::antibody::numbering_scheme, basic::options::OptionKeys::antibody::ocd_cutoff, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::OptionKeys::abinitio::only_stage1, basic::options::OptionKeys::abinitio::optimize_cutpoints_margin, basic::options::OptionKeys::abinitio::optimize_cutpoints_using_kic, basic::options::OptionKeys::antibody::design::outer_cycle_rounds, basic::options::OptionKeys::antibody::design::outer_kt, basic::options::OptionKeys::antibody::output_ab_scheme, basic::options::OptionKeys::abinitio::override_vdw_all_stages, basic::options::OptionKeys::antibody::packonly_after_graft, basic::options::OptionKeys::antibody::design::paper_ab_db, basic::options::OptionKeys::antibody::design::paper_ab_db_path, basic::options::OptionKeys::antibody::design::paratope, basic::options::OptionKeys::assembly::pdb1, basic::options::OptionKeys::assembly::pdb2, basic::options::OptionKeys::abinitio::perturb, basic::options::OptionKeys::AnchoredDesign::perturb_CCD_off, basic::options::OptionKeys::AnchoredDesign::perturb_cycles, basic::options::OptionKeys::AnchoredDesign::perturb_KIC_off, basic::options::OptionKeys::AnchoredDesign::perturb_show, basic::options::OptionKeys::AnchoredDesign::perturb_temp, basic::options::OptionKeys::backrub::pivot_atoms, basic::options::OptionKeys::backrub::pivot_residues, basic::options::OptionKeys::antibody::prefix, basic::options::OptionKeys::antibody::preprocessing_script_version, basic::options::OptionKeys::antibody::design::primary_cdrs, basic::options::OptionKeys::canonical_sampling::probabilities::probabilities, basic::options::OptionKeys::abinitio::process_store, basic::options::OptionKeys::antibody::design::random_start, basic::options::OptionKeys::AnchoredDesign::testing::randomize_input_sequence, basic::options::OptionKeys::broker::rb_mover_stage1_weight, basic::options::OptionKeys::abinitio::recover_low_in_stages, basic::options::OptionKeys::AnchoredDesign::refine_CCD_off, basic::options::OptionKeys::AnchoredDesign::refine_cycles, basic::options::OptionKeys::antibody::refine_h3, basic::options::OptionKeys::AnchoredDesign::refine_KIC_off, basic::options::OptionKeys::AnchoredDesign::refine_only, basic::options::OptionKeys::AnchoredDesign::refine_repack_cycles, basic::options::OptionKeys::AnchoredDesign::refine_temp, basic::options::OptionKeys::abinitio::relax_failures, basic::options::OptionKeys::abinitio::relax_with_jumps, basic::options::OptionKeys::antibody::design::remove_antigen, basic::options::OptionKeys::abinitio::rerun, basic::options::OptionKeys::abinitio::return_full_atom, basic::options::OptionKeys::abinitio::rg_reweight, basic::options::OptionKeys::AnchoredDesign::rmsd, basic::options::OptionKeys::AnchoredDesign::testing::RMSD_only_this, basic::options::OptionKeys::abinitio::rmsd_residues, basic::options::OptionKeys::abinitio::rsd_wt_helix, basic::options::OptionKeys::abinitio::rsd_wt_loop, basic::options::OptionKeys::abinitio::rsd_wt_strand, basic::options::OptionKeys::antibody::rt_min, basic::options::OptionKeys::antibody::design::run_interface_analyzer, basic::options::OptionKeys::antibody::design::run_relax, basic::options::OptionKeys::antibody::run_snugdock, basic::options::OptionKeys::antibody::design::sample_zero_probs_at, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::bunsat_calc2::sasa_burial_cutoff, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::antibody::sc_min, basic::options::OptionKeys::backrub::sc_prob, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform, basic::options::OptionKeys::backrub::sc_prob_uniform, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot, basic::options::OptionKeys::backrub::sc_prob_withinrot, basic::options::OptionKeys::AnchoredDesign::filters::score, basic::options::OptionKeys::boinc::score_cut_fl, basic::options::OptionKeys::boinc::score_cut_pct, basic::options::OptionKeys::boinc::score_cut_smart_throttle, basic::options::OptionKeys::antibody::design::seq_design_cdrs, basic::options::OptionKeys::antibody::design::seq_design_profile_samples, basic::options::OptionKeys::antibody::design::seq_design_stats_cutoff, basic::options::OptionKeys::broker::setup, basic::options::OptionKeys::AnchoredDesign::show_extended, basic::options::OptionKeys::abinitio::skip_convergence_check, basic::options::OptionKeys::abinitio::skip_stages, basic::options::OptionKeys::backrub::sm_prob, basic::options::OptionKeys::broker::small_frag_mover_stage1_weight, basic::options::OptionKeys::antibody::snug_loops, basic::options::OptionKeys::antibody::snugfit, basic::options::OptionKeys::abinitio::stage1_patch, basic::options::OptionKeys::abinitio::stage2_patch, basic::options::OptionKeys::abinitio::stage3a_patch, basic::options::OptionKeys::abinitio::stage3b_patch, basic::options::OptionKeys::abinitio::stage4_patch, basic::options::OptionKeys::abinitio::stage5_patch, basic::options::OptionKeys::abinitio::star::star, basic::options::OptionKeys::abinitio::start_native, basic::options::OptionKeys::abinitio::steal_3mers, basic::options::OptionKeys::abinitio::steal_9mers, basic::options::OptionKeys::antibody::stem_optimize, basic::options::OptionKeys::antibody::stem_optimize_size, basic::options::OptionKeys::bunsat_calc2::sulph_dist_cutoff, basic::options::OptionKeys::AnchoredDesign::testing::super_secret_fixed_interface_mode, basic::options::OptionKeys::abinitio::symmetry_residue, basic::options::OptionKeys::task_operations::task_operations, basic::options::OptionKeys::abinitio::temperature, basic::options::OptionKeys::AnchoredDesign::testing::testing, basic::options::OptionKeys::antibody::design::top_designs, basic::options::OptionKeys::backrub::trajectory, basic::options::OptionKeys::backrub::trajectory_gz, basic::options::OptionKeys::backrub::trajectory_stride, basic::options::OptionKeys::AnchoredDesign::unbound_mode, basic::options::OptionKeys::antibody::design::use_epitope_constraints, basic::options::OptionKeys::abinitio::use_filters, basic::options::OptionKeys::antibody::design::use_H3_graft_outliers, basic::options::OptionKeys::canonical_sampling::probabilities::use_hierarchical_clustering, basic::options::OptionKeys::antibody::use_mean_cluster_cst_data, basic::options::OptionKeys::antibody::design::use_only_H3_kinked, basic::options::OptionKeys::antibody::design::use_outliers, basic::options::OptionKeys::AnchoredDesign::vary_cutpoints, basic::options::OptionKeys::AnchoredDesign::testing::VDW_weight, basic::options::OptionKeys::abinitio::vdw_weight_stage1, basic::options::OptionKeys::antibody::design::view, basic::options::OptionKeys::boinc::watchdog, and basic::options::OptionKeys::boinc::watchdog_time.

Referenced by add_all_rosetta_options().

void add_rosetta_options_6 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::cyclization::add_constraints, basic::options::OptionKeys::cm::hybridize::add_non_init_chunks, basic::options::OptionKeys::cm::aligner, basic::options::OptionKeys::cm::aln_format, basic::options::OptionKeys::cm::aln_length_filter, basic::options::OptionKeys::cm::aln_length_filter_quantile, basic::options::OptionKeys::constel::amphetamine, basic::options::OptionKeys::constel::aromatic, basic::options::OptionKeys::cloud::auth, basic::options::OptionKeys::cm::hybridize::auto_frag_insertion_weight, basic::options::OptionKeys::cluster::auto_tune, basic::options::OptionKeys::coupled_moves::backbone_mover, basic::options::OptionKeys::coupled_moves::bias_sampling, basic::options::OptionKeys::cm::hybridize::big_frag_insertion_weight, basic::options::OptionKeys::cloud::block, basic::options::OptionKeys::coupled_moves::boltzmann_kt, basic::options::OptionKeys::coupled_moves::bump_check, basic::options::OptionKeys::casp::casp, basic::options::OptionKeys::constel::chain_interface, basic::options::OptionKeys::cyclization::chains_to_cyclize, basic::options::OptionKeys::cluster::energy_based_clustering::chains_to_ignore, basic::options::OptionKeys::cyclic_peptide::checkpoint_file, basic::options::OptionKeys::cyclic_peptide::checkpoint_job_identifier, basic::options::OptionKeys::chemically_conjugated_docking::chemically_conjugated_docking, basic::options::OptionKeys::chunk::chunk, basic::options::OptionKeys::cloud::clean, basic::options::OptionKeys::cloud::cloud, basic::options::OptionKeys::cluster::cluster, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_by, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_cyclic_permutations, basic::options::OptionKeys::cluster::energy_based_clustering::cluster_radius, basic::options::OptionKeys::cm::cm, basic::options::OptionKeys::constel::cnl_exclude, basic::options::OptionKeys::constel::cnl_stripped, basic::options::OptionKeys::canonical_sampling::probabilities::conrot, basic::options::OptionKeys::constel::constel, basic::options::OptionKeys::contactMap::contactMap, basic::options::OptionKeys::cyclic_peptide::count_sc_hbonds, basic::options::OptionKeys::coupled_moves::coupled_moves, basic::options::OptionKeys::cp::cp, basic::options::OptionKeys::cryst::cryst, basic::options::OptionKeys::cryst::crystal_refine, basic::options::OptionKeys::csa::csa, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::cm::sanitize::cst_weight_coord, basic::options::OptionKeys::cm::sanitize::cst_weight_pair, basic::options::OptionKeys::cp::cutoff, basic::options::OptionKeys::cutoutdomain::cutoutdomain, basic::options::OptionKeys::cluster::energy_based_clustering::cyclic, basic::options::OptionKeys::cyclic_peptide::cyclic_peptide, basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_permutation_offset, basic::options::OptionKeys::cyclic_peptide::cyclic_permutations, basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry, basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry_mirroring, basic::options::OptionKeys::cluster::energy_based_clustering::cyclic_symmetry_threshold, basic::options::OptionKeys::cyclization::cyclization, basic::options::OptionKeys::cyclic_peptide::cyclization_type, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::cyclic_peptide::default_rama_sampling_table, basic::options::OptionKeys::contactMap::distance_cutoff, basic::options::OptionKeys::contactMap::distance_matrix, basic::options::OptionKeys::cluster::energy_based_clustering::disulfide_positions, basic::options::OptionKeys::cyclic_peptide::do_not_count_adjacent_res_hbonds, basic::options::OptionKeys::chemically_conjugated_docking::dont_minimize_omega, basic::options::OptionKeys::canonical_sampling::sampling::dump_loops_only, basic::options::OptionKeys::chemically_conjugated_docking::E2_residue, basic::options::OptionKeys::chemically_conjugated_docking::E2pdb, basic::options::OptionKeys::cp::easy_vip_acceptance, basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::cluster::energy_based_clustering::energy_based_clustering, basic::options::OptionKeys::cm::ev_map, basic::options::OptionKeys::cp::exclude_file, basic::options::OptionKeys::coupled_moves::exclude_nonclashing_positions, basic::options::OptionKeys::cluster::exclude_res, basic::options::OptionKeys::cyclic_peptide::exclude_residues_from_rms, basic::options::OptionKeys::cluster::export_only_low, basic::options::OptionKeys::chemically_conjugated_docking::extra_bodies, basic::options::OptionKeys::cluster::energy_based_clustering::extra_rms_atoms, basic::options::OptionKeys::cyclic_peptide::fast_relax_rounds, basic::options::OptionKeys::coupled_moves::fix_backbone, basic::options::OptionKeys::cm::hybridize::frag_1mer_insertion_weight, basic::options::OptionKeys::cm::hybridize::frag_weight_aligned, basic::options::OptionKeys::cluster::gdtmm, basic::options::OptionKeys::cyclic_peptide::genkic_closure_attempts, basic::options::OptionKeys::cyclic_peptide::genkic_min_solution_count, basic::options::OptionKeys::chemically_conjugated_docking::GTPase_residue, basic::options::OptionKeys::chemically_conjugated_docking::GTPasepdb, basic::options::OptionKeys::cyclic_peptide::hbond_energy_cutoff, basic::options::OptionKeys::cm::hh_map, basic::options::OptionKeys::cyclic_peptide::high_hbond_weight_multiplier, basic::options::OptionKeys::constel::histamine, basic::options::OptionKeys::cluster::energy_based_clustering::homooligomer_swap, basic::options::OptionKeys::cloud::host, basic::options::OptionKeys::cluster::hotspot_hash, basic::options::OptionKeys::cm::hybridize::hybridize, basic::options::OptionKeys::cluster::idealize_final_structures, basic::options::OptionKeys::cm::hybridize::include_loop_ss_chunks, basic::options::OptionKeys::constel::indole_coo, basic::options::OptionKeys::coupled_moves::initial_repack, basic::options::OptionKeys::cluster::input_score_filter, basic::options::OptionKeys::cryst::interaction_shell, basic::options::OptionKeys::canonical_sampling::sampling::interval_data_dump, basic::options::OptionKeys::canonical_sampling::sampling::interval_pose_dump, utility::options::Option::is_group(), basic::options::OptionKeys::cluster::K_deque_level, basic::options::OptionKeys::cluster::K_deque_size, basic::options::OptionKeys::cluster::K_level, basic::options::OptionKeys::cluster::K_n_cluster, basic::options::OptionKeys::cluster::K_n_sub, basic::options::OptionKeys::cluster::K_not_fit_xyz, basic::options::OptionKeys::cluster::K_radius, basic::options::OptionKeys::cluster::K_redundant, basic::options::OptionKeys::cluster::K_save_headers, basic::options::OptionKeys::cluster::K_style, basic::options::OptionKeys::cloud::key, basic::options::OptionKeys::coupled_moves::kic_loop_size, basic::options::OptionKeys::coupled_moves::kic_perturber, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::coupled_moves::ligand_mode, basic::options::OptionKeys::coupled_moves::ligand_prob, basic::options::OptionKeys::coupled_moves::ligand_weight, basic::options::OptionKeys::cluster::limit_cluster_size, basic::options::OptionKeys::cluster::limit_cluster_size_percent, basic::options::OptionKeys::cluster::limit_clusters, basic::options::OptionKeys::cluster::energy_based_clustering::limit_clusters, basic::options::OptionKeys::cluster::limit_dist_matrix, basic::options::OptionKeys::cluster::energy_based_clustering::limit_structures_per_cluster, basic::options::OptionKeys::cluster::limit_total_structures, basic::options::OptionKeys::cm::hybridize::linmin_only, basic::options::OptionKeys::cluster::lite, basic::options::OptionKeys::cp::local_relax, basic::options::OptionKeys::chunk::loop2, basic::options::OptionKeys::cm::loop_close_level, basic::options::OptionKeys::cm::loop_mover, basic::options::OptionKeys::cm::loop_rebuild_filter, basic::options::OptionKeys::cluster::loops, basic::options::OptionKeys::cluster::make_ensemble_cst, basic::options::OptionKeys::constel::max_atom_sasa, basic::options::OptionKeys::cp::max_failures, basic::options::OptionKeys::canonical_sampling::sampling::max_files_per_dir, basic::options::OptionKeys::cm::max_gap_extend, basic::options::OptionKeys::cm::max_gap_open, basic::options::OptionKeys::cm::max_loop_rebuild, basic::options::OptionKeys::cm::hybridize::max_registry_shift, basic::options::OptionKeys::cluster::max_rms_matrix, basic::options::OptionKeys::cluster::max_total_cluster, basic::options::OptionKeys::coupled_moves::mc_kt, basic::options::OptionKeys::canonical_sampling::sampling::mc_kt, basic::options::OptionKeys::cyclic_peptide::min_final_hbonds, basic::options::OptionKeys::cm::min_gap_extend, basic::options::OptionKeys::cm::min_gap_open, basic::options::OptionKeys::cyclic_peptide::min_genkic_hbonds, basic::options::OptionKeys::cm::min_loop_size, basic::options::OptionKeys::coupled_moves::min_pack, basic::options::OptionKeys::cp::minimizer_score_fxn, basic::options::OptionKeys::coupled_moves::mm_bend_weight, basic::options::OptionKeys::cryst::mtzfile, basic::options::OptionKeys::cluster::energy_based_clustering::mutate_to_ala, basic::options::OptionKeys::chemically_conjugated_docking::n_tail_res, basic::options::OptionKeys::cp::ncycles, basic::options::OptionKeys::canonical_sampling::out::new_structures, basic::options::OptionKeys::cm::nn, basic::options::OptionKeys::canonical_sampling::sampling::no_detailed_balance, basic::options::OptionKeys::cm::hybridize::no_global_frame, basic::options::OptionKeys::cm::nremain_reset, basic::options::OptionKeys::coupled_moves::ntrials, basic::options::OptionKeys::canonical_sampling::sampling::ntrials, basic::options::OptionKeys::cm::sanitize::num_fragments, basic::options::OptionKeys::casp::num_iterations, basic::options::OptionKeys::cyclization::num_min_rebuild, basic::options::OptionKeys::coupled_moves::number_ligands, basic::options::OptionKeys::casp::opt_radius, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::cp::output, basic::options::OptionKeys::coupled_moves::output_fasta, basic::options::OptionKeys::canonical_sampling::sampling::output_only_cluster_transitions, basic::options::OptionKeys::coupled_moves::output_prefix, basic::options::OptionKeys::cluster::output_score_filter, basic::options::OptionKeys::coupled_moves::output_stats, basic::options::OptionKeys::cp::pack_sfxn, basic::options::OptionKeys::constel::pair_all_res, basic::options::OptionKeys::constel::pair_target_mutations, basic::options::OptionKeys::constel::pair_target_resnum, basic::options::OptionKeys::partial_thread::partial_thread, basic::options::OptionKeys::chunk::pdb2, basic::options::OptionKeys::chemically_conjugated_docking::pdz, basic::options::OptionKeys::cluster::energy_based_clustering::perform_ABOXYZ_bin_analysis, basic::options::OptionKeys::cluster::population_weight, basic::options::OptionKeys::cloud::port, basic::options::OptionKeys::contactMap::prefix, basic::options::OptionKeys::cluster::energy_based_clustering::prerelax, basic::options::OptionKeys::cp::print_intermediate_pdbs, basic::options::OptionKeys::cp::print_reports, basic::options::OptionKeys::constel::prox_ct_max, basic::options::OptionKeys::constel::prox_nres, basic::options::OptionKeys::constel::prox_tt_max, basic::options::OptionKeys::chemically_conjugated_docking::publication, basic::options::OptionKeys::cm::quota_per_silent, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::cyclic_peptide::rama_cutoff, basic::options::OptionKeys::cyclic_peptide::rama_sampling_table_by_res, basic::options::OptionKeys::cyclic_peptide::rand_checkpoint_file, basic::options::OptionKeys::cluster::random_limit_cluster_size_percent, basic::options::OptionKeys::cm::hybridize::realign_domains, basic::options::OptionKeys::cm::hybridize::realign_domains_stage2, basic::options::OptionKeys::cluster::energy_based_clustering::rebuild_all_in_dihedral_mode, basic::options::OptionKeys::cm::recover_side_chains, basic::options::OptionKeys::cryst::refinable_lattice, basic::options::OptionKeys::casp::refine_res, basic::options::OptionKeys::cm::refsimilarity_cut, basic::options::OptionKeys::contactMap::region_def, basic::options::OptionKeys::cm::hybridize::relax, basic::options::OptionKeys::cp::relax_mover, basic::options::OptionKeys::cluster::energy_based_clustering::relax_rounds, basic::options::OptionKeys::cp::relax_sfxn, basic::options::OptionKeys::cluster::remove_highest_energy_member, basic::options::OptionKeys::cluster::remove_singletons, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::coupled_moves::repack_neighborhood, basic::options::OptionKeys::cyclic_peptide::require_disulfides, basic::options::OptionKeys::cluster::energy_based_clustering::residues_to_ignore, basic::options::OptionKeys::cluster::rna_P, basic::options::OptionKeys::contactMap::row_format, basic::options::OptionKeys::canonical_sampling::sampling::sampling, basic::options::OptionKeys::cm::sanitize::sanitize, basic::options::OptionKeys::chemically_conjugated_docking::SASAfilter, basic::options::OptionKeys::canonical_sampling::sampling::save_loops_only, basic::options::OptionKeys::coupled_moves::save_sequences, basic::options::OptionKeys::coupled_moves::save_structures, basic::options::OptionKeys::casp::sc_min, basic::options::OptionKeys::cluster::score_diff_cut, basic::options::OptionKeys::chemically_conjugated_docking::scorefilter, basic::options::OptionKeys::cm::seeds, basic::options::OptionKeys::cm::seq_score, basic::options::OptionKeys::cyclic_peptide::sequence_file, basic::options::OptionKeys::casp::sequential, basic::options::OptionKeys::cluster::energy_based_clustering::silent_output, basic::options::OptionKeys::cm::similarity_cut, basic::options::OptionKeys::cm::similarity_limit, basic::options::OptionKeys::cluster::skip_align, basic::options::OptionKeys::cp::skip_relax, basic::options::OptionKeys::partial_thread::skip_repack, basic::options::OptionKeys::cm::hybridize::skip_stage2, basic::options::OptionKeys::cm::hybridize::small_frag_insertion_weight, basic::options::OptionKeys::cluster::sort_groups_by_energy, basic::options::OptionKeys::cluster::sort_groups_by_size, basic::options::OptionKeys::cm::hybridize::stage1_1_cycles, basic::options::OptionKeys::cm::hybridize::stage1_2_cycles, basic::options::OptionKeys::cm::hybridize::stage1_3_cycles, basic::options::OptionKeys::cm::hybridize::stage1_4_cenrot_score, basic::options::OptionKeys::cm::hybridize::stage1_4_cycles, basic::options::OptionKeys::cm::hybridize::stage1_increase_cycles, basic::options::OptionKeys::cm::hybridize::stage1_probability, basic::options::OptionKeys::cm::hybridize::stage2_increase_cycles, basic::options::OptionKeys::cm::hybridize::stage2_temperature, basic::options::OptionKeys::cm::hybridize::stage2min_increase_cycles, basic::options::OptionKeys::cutoutdomain::start, basic::options::OptionKeys::cm::start_models_only, basic::options::OptionKeys::cm::hybridize::starting_template, basic::options::OptionKeys::cm::steal_extra_residues, basic::options::OptionKeys::constel::target_chain, basic::options::OptionKeys::constel::target_cnl, basic::options::OptionKeys::cluster::template_scores, basic::options::OptionKeys::cluster::thinout_factor, basic::options::OptionKeys::cyclic_peptide::total_energy_cutoff, basic::options::OptionKeys::coupled_moves::trajectory, basic::options::OptionKeys::coupled_moves::trajectory_file, basic::options::OptionKeys::coupled_moves::trajectory_gz, basic::options::OptionKeys::coupled_moves::trajectory_stride, basic::options::OptionKeys::canonical_sampling::sampling::transition_threshold, basic::options::OptionKeys::constel::triple_all_res, basic::options::OptionKeys::constel::triple_target_resnum, basic::options::OptionKeys::constel::tryptamine, basic::options::OptionKeys::chemically_conjugated_docking::two_ubiquitins, basic::options::OptionKeys::chemically_conjugated_docking::UBQ2_lys, basic::options::OptionKeys::chemically_conjugated_docking::UBQ2_pdb, basic::options::OptionKeys::chemically_conjugated_docking::UBQpdb, basic::options::OptionKeys::coupled_moves::uniform_backrub, basic::options::OptionKeys::cluster::energy_based_clustering::use_CB, basic::options::OptionKeys::cyclic_peptide::use_chainbreak_energy, basic::options::OptionKeys::cyclic_peptide::use_rama_filter, basic::options::OptionKeys::cp::use_unrelaxed_starting_points, basic::options::OptionKeys::csa::useZ, basic::options::OptionKeys::cp::vipReportFile, basic::options::OptionKeys::coupled_moves::walking_perturber_magnitude, and basic::options::OptionKeys::cluster::write_centers.

Referenced by add_all_rosetta_options().

void add_rosetta_options_7 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::cyclic_peptide::allowed_residues_by_position, basic::options::OptionKeys::cyclic_peptide::angle_length_relax_rounds, basic::options::OptionKeys::cyclic_peptide::angle_relax_rounds, basic::options::OptionKeys::dna::design::base_contacts_only, basic::options::OptionKeys::docking::bb_min_res, basic::options::OptionKeys::ddg::bbnbrs, basic::options::OptionKeys::dna::design::binding, basic::options::OptionKeys::dna::design::Boltz_temp, basic::options::OptionKeys::cyclic_peptide::bondangle_perturbation_magnitude, basic::options::OptionKeys::cyclic_peptide::bondlength_perturbation_magnitude, basic::options::OptionKeys::DisulfideInsertion::c_cyd_seqpos, basic::options::OptionKeys::ddg::cartesian, basic::options::OptionKeys::cyclic_peptide::cartesian_relax_rounds, basic::options::OptionKeys::docking::center_at_interface, basic::options::OptionKeys::dna::design::checkpoint, basic::options::OptionKeys::cyclic_peptide::compute_ensemble_sasa_metrics, basic::options::OptionKeys::cyclic_peptide::compute_pnear_to_this_fract, basic::options::OptionKeys::cyclic_peptide::compute_rmsd_to_lowest, basic::options::OptionKeys::DisulfideInsertion::constraint_weight, basic::options::OptionKeys::ddg::constraint_weight, basic::options::OptionKeys::DenovoProteinDesign::create_from_secondary_structure, basic::options::OptionKeys::DenovoProteinDesign::create_from_template_pdb, basic::options::OptionKeys::ddg::cst_dist_cutoff, basic::options::OptionKeys::cyclic_peptide::D_alpha_comp_file, basic::options::OptionKeys::cyclic_peptide::D_beta_comp_file, basic::options::OptionKeys::dc::dc, basic::options::OptionKeys::ddg::ddg, basic::options::OptionKeys::ddg::debug_output, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::DenovoProteinDesign::DenovoProteinDesign, basic::options::OptionKeys::dna::design::design, basic::options::OptionKeys::docking::design_chains, basic::options::OptionKeys::dna::specificity::design_DNA, basic::options::OptionKeys::cyclic_peptide::design_peptide, basic::options::OptionKeys::dna::design::designable_second_shell, basic::options::OptionKeys::cyclic_peptide::disulf_cutoff_postrelax, basic::options::OptionKeys::cyclic_peptide::disulf_cutoff_prerelax, basic::options::OptionKeys::DisulfideInsertion::DisulfideInsertion, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::dna::specificity::dna_backbone_torsion_sdevs, basic::options::OptionKeys::dna::specificity::dna_chi_torsion_sdev, basic::options::OptionKeys::dna::design::dna_defs, basic::options::OptionKeys::dna::design::dna_defs_file, basic::options::OptionKeys::dna::specificity::dna_sugar_torsion_sdev, basic::options::OptionKeys::docking::dock_lowres_filter, basic::options::OptionKeys::docking::dock_mcm_first_cycles, basic::options::OptionKeys::docking::dock_mcm_rot_magnitude, basic::options::OptionKeys::docking::dock_mcm_second_cycles, basic::options::OptionKeys::docking::dock_mcm_trans_magnitude, basic::options::OptionKeys::docking::dock_min, basic::options::OptionKeys::docking::dock_pert, basic::options::OptionKeys::docking::dock_ppk, basic::options::OptionKeys::docking::dock_rtmin, basic::options::OptionKeys::docking::docking, basic::options::OptionKeys::docking::docking_centroid_inner_cycles, basic::options::OptionKeys::docking::docking_centroid_outer_cycles, basic::options::OptionKeys::docking::docking_local_refine, basic::options::OptionKeys::docking::docking_low_res_score, basic::options::OptionKeys::docking::docklowres_rot_magnitude, basic::options::OptionKeys::docking::docklowres_trans_magnitude, basic::options::OptionKeys::dna::design::reversion::dscore_cutoff, basic::options::OptionKeys::dna::design::reversion::dspec_cutoff, basic::options::OptionKeys::dna::specificity::dump_pdbs, basic::options::OptionKeys::ddg::dump_pdbs, basic::options::OptionKeys::docking::enable_pymol_viewer, basic::options::OptionKeys::ddg::ens_variation, basic::options::OptionKeys::docking::ensemble1, basic::options::OptionKeys::docking::ensemble2, basic::options::OptionKeys::dna::specificity::exclude_dna_dna, basic::options::OptionKeys::docking::extra_rottrial, basic::options::OptionKeys::ddg::extract_element_nbrs, basic::options::OptionKeys::dna::specificity::fast, basic::options::OptionKeys::ddg::fd_mode, basic::options::OptionKeys::cyclic_peptide::filter_oversaturated_hbond_acceptors, basic::options::OptionKeys::ddg::flex_bb, basic::options::OptionKeys::docking::flexible_bb_docking, basic::options::OptionKeys::docking::flexible_bb_docking_interface_dist, basic::options::OptionKeys::ddg::force_iterations, basic::options::OptionKeys::dna::specificity::frag_files, basic::options::OptionKeys::ddg::frag_nbrs, basic::options::OptionKeys::ddg::harmonic_ca_tether, basic::options::OptionKeys::cyclic_peptide::hbond_acceptor_energy_cutoff, basic::options::OptionKeys::docking::high_min_patch, basic::options::OptionKeys::docking::high_patch, basic::options::OptionKeys::DenovoProteinDesign::hydrophobic_polar_pattern, basic::options::OptionKeys::docking::ignore_default_docking_task, basic::options::OptionKeys::dna::design::specificity::include_dna_potentials, basic::options::OptionKeys::ddg::initial_repack, basic::options::OptionKeys::ddg::interface_ddg, utility::options::Option::is_group(), basic::options::OptionKeys::ddg::iterations, basic::options::OptionKeys::ddg::json, basic::options::OptionKeys::docking::kick_relax, basic::options::OptionKeys::cyclic_peptide::L_alpha_comp_file, basic::options::OptionKeys::cyclic_peptide::L_beta_comp_file, basic::options::OptionKeys::cyclic_peptide::lariat_sidechain_index, basic::options::OptionKeys::ddg::last_accepted_pose_dir, basic::options::OptionKeys::ddg::legacy, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::docking::ligand::ligand, basic::options::OptionKeys::cyclic_peptide::link_all_cys_with_TBMB, basic::options::OptionKeys::dna::specificity::lk_ball_bridge_angle_widthscale, basic::options::OptionKeys::dna::specificity::lk_ball_for_bb, basic::options::OptionKeys::dna::specificity::lk_ball_overlap_gap, basic::options::OptionKeys::dna::specificity::lk_ball_overlap_width_A2, basic::options::OptionKeys::dna::specificity::lk_ball_ramp_width_A2, basic::options::OptionKeys::dna::specificity::lk_ball_water_fade, basic::options::OptionKeys::dna::specificity::lk_ball_waters_donor, basic::options::OptionKeys::dna::specificity::lk_ball_waters_ring, basic::options::OptionKeys::dna::specificity::lk_ball_waters_sp2, basic::options::OptionKeys::dna::specificity::lk_ball_waters_sp3, basic::options::OptionKeys::dna::specificity::lk_ball_wtd_prefactors, basic::options::OptionKeys::dna::specificity::lk_ball_wtd_tag, basic::options::OptionKeys::ddg::local_opt_only, basic::options::OptionKeys::docking::low_patch, basic::options::OptionKeys::docking::low_res_protocol_only, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::ddg::lowest_x_decoys, basic::options::OptionKeys::DisulfideInsertion::max_dslf_dist_multiplier, basic::options::OptionKeys::DisulfideInsertion::max_dslf_energy, basic::options::OptionKeys::DisulfideInsertion::max_dslf_pot, basic::options::OptionKeys::docking::max_repeats, basic::options::OptionKeys::ddg::mean, basic::options::OptionKeys::dna::specificity::methylate, basic::options::OptionKeys::ddg::min, basic::options::OptionKeys::ddg::min_cst, basic::options::OptionKeys::ddg::min_cst_weights, basic::options::OptionKeys::DisulfideInsertion::min_dslf_dist_multiplier, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::ddg::min_with_cst, basic::options::OptionKeys::ddg::minimization_patch, basic::options::OptionKeys::ddg::minimization_scorefunction, basic::options::OptionKeys::docking::minimization_threshold, basic::options::OptionKeys::dna::design::minimize, basic::options::OptionKeys::dna::specificity::minimize_tolerance, basic::options::OptionKeys::dna::specificity::mode, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::dna::specificity::motif_size, basic::options::OptionKeys::dna::specificity::moving_jump, basic::options::OptionKeys::cyclic_peptide::MPI_auto_2level_distribution, basic::options::OptionKeys::cyclic_peptide::MPI_batchsize_by_level, basic::options::OptionKeys::cyclic_peptide::MPI_choose_highest, basic::options::OptionKeys::cyclic_peptide::MPI_output_fraction, basic::options::OptionKeys::cyclic_peptide::MPI_pnear_kbt, basic::options::OptionKeys::cyclic_peptide::MPI_pnear_lambda, basic::options::OptionKeys::cyclic_peptide::MPI_processes_by_level, basic::options::OptionKeys::cyclic_peptide::MPI_sort_by, basic::options::OptionKeys::cyclic_peptide::MPI_stop_after_time, basic::options::OptionKeys::docking::multibody, basic::options::OptionKeys::ddg::mut_file, basic::options::OptionKeys::ddg::mut_only, basic::options::OptionKeys::ddg::n_converged, basic::options::OptionKeys::DisulfideInsertion::n_cyd_seqpos, basic::options::OptionKeys::dna::specificity::n_inner, basic::options::OptionKeys::cyclic_peptide::n_methyl_positions, basic::options::OptionKeys::dna::specificity::n_outer, basic::options::OptionKeys::ddg::nfrags, basic::options::OptionKeys::dna::specificity::nloop, basic::options::OptionKeys::ddg::no_bb_movement, basic::options::OptionKeys::ddg::no_constraints, basic::options::OptionKeys::docking::no_filters, basic::options::OptionKeys::dna::design::nopdb, basic::options::OptionKeys::docking::norepack1, basic::options::OptionKeys::docking::norepack2, basic::options::OptionKeys::dna::specificity::nstep_water, basic::options::OptionKeys::ddg::ntrials, basic::options::OptionKeys::cyclic_peptide::octahedral_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::octahedral_metal_positions, basic::options::OptionKeys::cyclic_peptide::octahedral_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::dna::specificity::only_repack, basic::options::OptionKeys::ddg::opt_input_structure, basic::options::OptionKeys::ddg::opt_radius, basic::options::OptionKeys::DenovoProteinDesign::optimize_loops, basic::options::OptionKeys::ddg::optimize_proline, basic::options::OptionKeys::ddg::optimize_wt, basic::options::OptionKeys::ddg::out, basic::options::OptionKeys::ddg::out_pdb_prefix, basic::options::OptionKeys::ddg::output_dir, basic::options::OptionKeys::ddg::output_silent, basic::options::OptionKeys::dna::design::specificity::output_structures, basic::options::OptionKeys::dna::design::output_unbound_pdb, basic::options::OptionKeys::docking::pack_patch, basic::options::OptionKeys::ddg::pack_until_converge, basic::options::OptionKeys::dna::specificity::params, basic::options::OptionKeys::docking::partners, basic::options::OptionKeys::dna::specificity::pdb_pos, basic::options::OptionKeys::DisulfideInsertion::peptide_chain, basic::options::OptionKeys::dna::specificity::post_minimize, basic::options::OptionKeys::dna::specificity::pre_minimize, basic::options::OptionKeys::dna::specificity::pre_pack, basic::options::OptionKeys::ddg::print_per_res_diff, basic::options::OptionKeys::dna::design::probe_specificity, basic::options::OptionKeys::cyclic_peptide::prohibit_D_at_negative_phi, basic::options::OptionKeys::cyclic_peptide::prohibit_L_at_positive_phi, basic::options::OptionKeys::dna::design::protein_scan, basic::options::OptionKeys::docking::ligand::protocol, basic::options::OptionKeys::ddg::ramp_repulsive, basic::options::OptionKeys::docking::randomize1, basic::options::OptionKeys::docking::randomize2, basic::options::OptionKeys::dna::specificity::randomize_motif, basic::options::OptionKeys::docking::recover_sidechains, basic::options::OptionKeys::DenovoProteinDesign::redesign_complete, basic::options::OptionKeys::DenovoProteinDesign::redesign_core, basic::options::OptionKeys::DenovoProteinDesign::redesign_loops, basic::options::OptionKeys::DenovoProteinDesign::redesign_surface, basic::options::OptionKeys::dna::design::repack_only, basic::options::OptionKeys::docking::repack_period, basic::options::OptionKeys::cyclic_peptide::require_symmetry_angle_threshold, basic::options::OptionKeys::cyclic_peptide::require_symmetry_mirroring, basic::options::OptionKeys::cyclic_peptide::require_symmetry_perturbation, basic::options::OptionKeys::cyclic_peptide::require_symmetry_repeats, basic::options::OptionKeys::dna::design::reversion::reversion, basic::options::OptionKeys::dna::design::reversion_scan, basic::options::OptionKeys::ddg::rna_all_prot_sc_min_only, basic::options::OptionKeys::cyclic_peptide::sample_cis_pro_frequency, basic::options::OptionKeys::docking::sc_min, basic::options::OptionKeys::ddg::sc_min_only, basic::options::OptionKeys::docking::sc_min_res, basic::options::OptionKeys::ddg::score_cutoff, basic::options::OptionKeys::dna::specificity::score_function, basic::options::OptionKeys::DisulfideInsertion::scorefxn, basic::options::OptionKeys::DenovoProteinDesign::secondary_structure_file, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::cyclic_peptide::sidechain_isopeptide_indices, basic::options::OptionKeys::dna::specificity::soft_rep, basic::options::OptionKeys::dna::design::sparse_pdb_output, basic::options::OptionKeys::dna::specificity::specificity, basic::options::OptionKeys::dna::design::specificity::specificity, basic::options::OptionKeys::docking::spin, basic::options::OptionKeys::cyclic_peptide::square_planar_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::square_planar_metal_positions, basic::options::OptionKeys::cyclic_peptide::square_planar_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_positions, basic::options::OptionKeys::cyclic_peptide::square_pyramidal_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::ddg::suppress_checkpointing, basic::options::OptionKeys::docking::SymDock_fa_rep_max, basic::options::OptionKeys::docking::SymDock_fa_sol_max, basic::options::OptionKeys::docking::SymDock_lowres_filter, basic::options::OptionKeys::docking::SymDock_reduce_motif_dock_weights, basic::options::OptionKeys::cyclic_peptide::TBMB_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::TBMB_positions, basic::options::OptionKeys::cyclic_peptide::TBMB_sidechain_distance_filter_multiplier, basic::options::OptionKeys::ddg::temperature, basic::options::OptionKeys::docking::temperature, basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_positions, basic::options::OptionKeys::cyclic_peptide::tetrahedral_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::threads_per_worker, basic::options::OptionKeys::docking::tilt, basic::options::OptionKeys::docking::tilt1_center, basic::options::OptionKeys::docking::tilt2_center, basic::options::OptionKeys::cyclic_peptide::TMA_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::TMA_positions, basic::options::OptionKeys::cyclic_peptide::TMA_sidechain_distance_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_positions, basic::options::OptionKeys::cyclic_peptide::trigonal_planar_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_constraints_energy_filter_multiplier, basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_positions, basic::options::OptionKeys::cyclic_peptide::trigonal_pyramidal_metal_sidechain_distance_filter_multiplier, basic::options::OptionKeys::docking::uniform_trans, basic::options::OptionKeys::cyclic_peptide::use_classic_rama_for_sampling, basic::options::OptionKeys::docking::use_ellipsoidal_randomization, basic::options::OptionKeys::docking::use_legacy_protocol, basic::options::OptionKeys::cyclic_peptide::use_octahedral_metal_filters, basic::options::OptionKeys::ddg::use_rotamer_constraints_to_native, basic::options::OptionKeys::cyclic_peptide::use_square_planar_metal_filters, basic::options::OptionKeys::cyclic_peptide::use_square_pyramidal_metal_filters, basic::options::OptionKeys::cyclic_peptide::use_TBMB_filters, basic::options::OptionKeys::DenovoProteinDesign::use_template_sequence, basic::options::OptionKeys::DenovoProteinDesign::use_template_topology, basic::options::OptionKeys::cyclic_peptide::use_tetrahedral_metal_filters, basic::options::OptionKeys::cyclic_peptide::use_TMA_filters, basic::options::OptionKeys::cyclic_peptide::use_trigonal_planar_metal_filters, basic::options::OptionKeys::cyclic_peptide::use_trigonal_pyramidal_metal_filters, basic::options::OptionKeys::cyclic_peptide::user_set_alpha_dihedral_perturbation, basic::options::OptionKeys::cyclic_peptide::user_set_alpha_dihedrals, basic::options::OptionKeys::dc::useZ, basic::options::OptionKeys::docking::view, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::ddg::weight_file, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, basic::options::OptionKeys::dna::specificity::Wfa_elec, basic::options::OptionKeys::ddg::wt_only, and basic::options::OptionKeys::dna::design::z_cutoff.

Referenced by add_all_rosetta_options().

void add_rosetta_options_8 ( utility::options::OptionCollection option)
inline

References utility::options::OptionCollection::add(), basic::options::OptionKeys::fold_from_loops::add_relax_cycles, basic::options::OptionKeys::enzdes::additional_packing_ligand_rb_confs, basic::options::OptionKeys::flexpack::annealer::annealer, basic::options::OptionKeys::enzdes::arg_sweep_cutoff, basic::options::OptionKeys::enzdes::arg_sweep_interface, basic::options::OptionKeys::edensity::atom_mask, basic::options::OptionKeys::edensity::atom_mask_min, basic::options::OptionKeys::flexPepDocking::backrub_peptide, basic::options::OptionKeys::enzdes::bb_bump_cutoff, basic::options::OptionKeys::enzdes::bb_min, basic::options::OptionKeys::enzdes::bb_min_allowed_dev, basic::options::OptionKeys::flxbb::blueprint, basic::options::OptionKeys::flexPepDocking::boost_fa_atr, basic::options::OptionKeys::FloppyTail::C_root, basic::options::OptionKeys::fold_from_loops::ca_csts_dev, basic::options::OptionKeys::edensity::ca_mask, basic::options::OptionKeys::fold_from_loops::ca_rmsd_cutoff, basic::options::OptionKeys::FloppyTail::cen_weights, basic::options::OptionKeys::edensity::centroid_density_mass, basic::options::OptionKeys::fast_loops::chainbreak_max, basic::options::OptionKeys::enzdes::change_lig, basic::options::OptionKeys::enzdes::checkpoint, basic::options::OptionKeys::fold_from_loops::checkpoint, basic::options::OptionKeys::enzdes::chi_min, basic::options::OptionKeys::FloppyTail::COM_root, basic::options::OptionKeys::enzdes::compare_native, basic::options::OptionKeys::fold_cst::constraint_skip_rate, basic::options::OptionKeys::flxbb::constraints_NtoC, basic::options::OptionKeys::flxbb::constraints_sheet, basic::options::OptionKeys::flxbb::constraints_sheet_include_cacb_pseudotorsion, basic::options::OptionKeys::epr_deer::coords_files, basic::options::OptionKeys::edensity::cryoem_scatterers, basic::options::OptionKeys::enzdes::cst_design, basic::options::OptionKeys::enzdes::cst_dock, basic::options::OptionKeys::enzdes::cst_min, basic::options::OptionKeys::enzdes::cst_opt, basic::options::OptionKeys::enzdes::cst_predock, basic::options::OptionKeys::enzdes::cstfile, basic::options::OptionKeys::enzdes::cut1, basic::options::OptionKeys::enzdes::cut2, basic::options::OptionKeys::enzdes::cut3, basic::options::OptionKeys::enzdes::cut4, basic::options::OptionKeys::DomainAssembly::da_eval_pose_map, basic::options::OptionKeys::DomainAssembly::da_linker_file, basic::options::OptionKeys::DomainAssembly::da_linker_file_rna, basic::options::OptionKeys::DomainAssembly::da_nruns, basic::options::OptionKeys::DomainAssembly::da_require_buried, basic::options::OptionKeys::DomainAssembly::da_setup, basic::options::OptionKeys::DomainAssembly::da_setup_option_file, basic::options::OptionKeys::DomainAssembly::da_setup_output_pdb, basic::options::OptionKeys::DomainAssembly::da_start_pdb, basic::options::OptionKeys::DomainAssembly::da_start_pdb_num, basic::options::OptionKeys::edensity::debug, basic::options::OptionKeys::FloppyTail::debug, basic::options::OptionKeys::edensity::debug_derivatives, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::enzdes::design_min_cycles, basic::options::OptionKeys::flexPepDocking::design_peptide, basic::options::OptionKeys::enzdes::detect_design_interface, basic::options::OptionKeys::enzdes::dock_trials, basic::options::OptionKeys::DomainAssembly::DomainAssembly, basic::options::OptionKeys::enzdes::dump_final_repack_without_ligand_pdb, basic::options::OptionKeys::enzdes::dump_inverse_rotamers, basic::options::OptionKeys::enzdes::dump_loop_samples, basic::options::OptionKeys::dump_trajectory::dump_trajectory, basic::options::OptionKeys::flexPepDocking::dumpPDB_abinitio, basic::options::OptionKeys::flexPepDocking::dumpPDB_hires, basic::options::OptionKeys::flexPepDocking::dumpPDB_lowres, basic::options::OptionKeys::edensity::edensity, basic::options::OptionKeys::enzdes::enz_debug, basic::options::OptionKeys::enzdes::enz_loops_file, basic::options::OptionKeys::enzdes::enz_repack, basic::options::OptionKeys::enzdes::enz_score, basic::options::OptionKeys::enzdes::enzdes, basic::options::OptionKeys::epr_deer::epr_deer, basic::options::OptionKeys::enzdes::ex_catalytic_rot, basic::options::OptionKeys::flexPepDocking::extend_peptide, basic::options::OptionKeys::fast_loops::fast_loops, basic::options::OptionKeys::fast_loops::fast_relax_sequence_file, basic::options::OptionKeys::edensity::fastdens_params, basic::options::OptionKeys::edensity::fastdens_wt, basic::options::OptionKeys::enzdes::favor_native_res, basic::options::OptionKeys::fast_loops::filter_cst_file, basic::options::OptionKeys::fast_loops::filter_cst_weight, basic::options::OptionKeys::flxbb::filter_trial, basic::options::OptionKeys::flxbb::filter_type, basic::options::OptionKeys::enzdes::final_repack_without_ligand, basic::options::OptionKeys::enzdes::fix_catalytic_aa, basic::options::OptionKeys::flexpack::annealer::fixbb_substitutions_scale, basic::options::OptionKeys::enzdes::flexbb_protocol, basic::options::OptionKeys::FloppyTail::flexible_chain, basic::options::OptionKeys::FloppyTail::flexible_start_resnum, basic::options::OptionKeys::FloppyTail::flexible_stop_resnum, basic::options::OptionKeys::flexpack::flexpack, basic::options::OptionKeys::flexPepDocking::flexpep_noprepack1, basic::options::OptionKeys::flexPepDocking::flexpep_noprepack2, basic::options::OptionKeys::flexPepDocking::flexpep_prepack, basic::options::OptionKeys::flexPepDocking::flexpep_score_only, basic::options::OptionKeys::flexPepDocking::flexPepDocking, basic::options::OptionKeys::flexPepDocking::flexPepDockingMinimizeOnly, basic::options::OptionKeys::FloppyTail::FloppyTail, basic::options::OptionKeys::flxbb::flxbb, basic::options::OptionKeys::fold_and_dock::fold_and_dock, basic::options::OptionKeys::fold_cst::fold_cst, basic::options::OptionKeys::fold_from_loops::fold_from_loops, basic::options::OptionKeys::edensity::force_apix, basic::options::OptionKeys::FloppyTail::force_linear_fold_tree, basic::options::OptionKeys::fold_cst::force_minimize, basic::options::OptionKeys::flexPepDocking::frag3_weight, basic::options::OptionKeys::flexPepDocking::frag5, basic::options::OptionKeys::flexPepDocking::frag5_weight, basic::options::OptionKeys::flexPepDocking::frag9_weight, basic::options::OptionKeys::fast_loops::fragsample_patch, basic::options::OptionKeys::fast_loops::fragsample_score, basic::options::OptionKeys::fast_loops::give_up, basic::options::OptionKeys::docking::ligand::grid::grid, basic::options::OptionKeys::docking::ligand::grid::grid_kin, basic::options::OptionKeys::docking::ligand::grid::grid_map, basic::options::OptionKeys::edensity::grid_spacing, basic::options::OptionKeys::dump_trajectory::gz, basic::options::OptionKeys::docking::ligand::harmonic_Calphas, basic::options::OptionKeys::docking::ligand::harmonic_torsions, basic::options::OptionKeys::flexPepDocking::hb_filter, basic::options::OptionKeys::flexPepDocking::hotspot_filter, basic::options::OptionKeys::fold_cst::ignore_sequence_seperation, basic::options::OptionKeys::docking::ligand::improve_orientation, basic::options::OptionKeys::enzdes::include_catres_in_interface_detection, basic::options::OptionKeys::flexpack::annealer::inner_iteration_scale, basic::options::OptionKeys::epr_deer::input_files, utility::options::Option::is_group(), basic::options::OptionKeys::fold_cst::keep_skipped_csts, basic::options::OptionKeys::enzdes::kic_loop_sampling, basic::options::OptionKeys::flxbb::layer::layer, basic::options::OptionKeys::edensity::legacy_fastdens_score, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::enzdes::lig_packer_weight, basic::options::OptionKeys::docking::ligand::ligand_ensemble, basic::options::OptionKeys::enzdes::loop_bb_min_allowed_dev, basic::options::OptionKeys::enzdes::loop_generator_trials, basic::options::OptionKeys::fold_from_loops::loop_mov_cterm, basic::options::OptionKeys::fold_from_loops::loop_mov_nterm, utility::options::ScalarOption_T_< K, T >::lower(), basic::options::OptionKeys::flexPepDocking::lowres_abinitio, basic::options::OptionKeys::flexPepDocking::lowres_preoptimize, basic::options::OptionKeys::enzdes::make_consensus_mutations, basic::options::OptionKeys::edensity::mapfile, basic::options::OptionKeys::edensity::mapreso, basic::options::OptionKeys::enzdes::max_bb_deviation, basic::options::OptionKeys::enzdes::max_bb_deviation_from_startstruct, basic::options::OptionKeys::docking::ligand::max_poses, basic::options::OptionKeys::enzdes::mc_kt_high, basic::options::OptionKeys::enzdes::mc_kt_low, basic::options::OptionKeys::flexPepDocking::mcm_cycles, basic::options::OptionKeys::edensity::membrane_axis, basic::options::OptionKeys::enzdes::min_all_jumps, basic::options::OptionKeys::fast_loops::min_breakout_fast_loops, basic::options::OptionKeys::fast_loops::min_breakout_good_loops, basic::options::OptionKeys::enzdes::min_cacb_deviation, basic::options::OptionKeys::fast_loops::min_fast_loops, basic::options::OptionKeys::fast_loops::min_good_loops, basic::options::OptionKeys::flexPepDocking::min_receptor_bb, basic::options::OptionKeys::docking::ligand::min_rms, basic::options::OptionKeys::enzdes::minimize_all_ligand_torsions, basic::options::OptionKeys::docking::ligand::minimize_backbone, basic::options::OptionKeys::docking::ligand::minimize_ligand, basic::options::OptionKeys::enzdes::minimize_ligand_torsions, basic::options::OptionKeys::fold_and_dock::move_anchor_frequency, basic::options::OptionKeys::fold_and_dock::move_anchor_points, basic::options::OptionKeys::flxbb::movemap_from_blueprint, basic::options::OptionKeys::docking::ligand::mutate_same_name3, basic::options::OptionKeys::edensity::n_kbins, basic::options::OptionKeys::fold_from_loops::native_ca_cst, basic::options::OptionKeys::flxbb::ncycle, basic::options::OptionKeys::enzdes::no_catres_min_in_loopgen, basic::options::OptionKeys::fold_cst::no_minimize, basic::options::OptionKeys::enzdes::no_packstat_calculation, basic::options::OptionKeys::fold_cst::no_recover_low_at_constraint_switch, basic::options::OptionKeys::enzdes::no_unconstrained_repack, basic::options::OptionKeys::fast_loops::nr_scored_fragments, basic::options::OptionKeys::fast_loops::nr_scored_sampling_passes, basic::options::OptionKeys::docking::ligand::old_estat, basic::options::OptionKeys::docking::ligand::option_file, basic::options::OptionKeys::flexpack::annealer::outer_iteration_scale, basic::options::OptionKeys::fast_loops::overwrite_filter_scorefxn, basic::options::OptionKeys::FloppyTail::pair_off, basic::options::OptionKeys::flexPepDocking::params_file, basic::options::OptionKeys::enzdes::parser_read_cloud_pdb, basic::options::OptionKeys::fast_loops::patch_filter_scorefxn, basic::options::OptionKeys::flexPepDocking::pep_fold_only, basic::options::OptionKeys::flexPepDocking::pep_refine, basic::options::OptionKeys::flexPepDocking::peptide_anchor, basic::options::OptionKeys::flexPepDocking::peptide_chain, basic::options::OptionKeys::flexPepDocking::peptide_loop_model, basic::options::OptionKeys::FloppyTail::perturb_cycles, basic::options::OptionKeys::FloppyTail::perturb_show, basic::options::OptionKeys::FloppyTail::perturb_temp, basic::options::OptionKeys::flexPepDocking::place_peptide_on_binding_site, basic::options::OptionKeys::dump_trajectory::prefix, basic::options::OptionKeys::epr_deer::print_data, basic::options::OptionKeys::enzdes::process_ligrot_separately, basic::options::OptionKeys::flexPepDocking::pSer2Asp_centroid, basic::options::OptionKeys::flexPepDocking::pSer2Glu_centroid, basic::options::OptionKeys::FloppyTail::publication, basic::options::OptionKeys::flexpack::annealer::pure_movebb_substitutions_scale, basic::options::OptionKeys::fold_cst::ramp_coord_cst, basic::options::OptionKeys::flexPepDocking::ramp_fa_rep, basic::options::OptionKeys::flexPepDocking::ramp_rama, basic::options::OptionKeys::docking::ligand::random_conformer, basic::options::OptionKeys::flexPepDocking::random_phi_psi_preturbation, basic::options::OptionKeys::flexPepDocking::random_rot_start, basic::options::OptionKeys::flexPepDocking::random_trans_start, basic::options::OptionKeys::fold_and_dock::rb_rot_magnitude, basic::options::OptionKeys::fold_and_dock::rb_trans_magnitude, basic::options::OptionKeys::flexPepDocking::rbMCM, basic::options::OptionKeys::edensity::realign, basic::options::OptionKeys::flexPepDocking::recalculate_foldtree, basic::options::OptionKeys::flexPepDocking::receptor_chain, basic::options::OptionKeys::flexPepDocking::ref_startstruct, basic::options::OptionKeys::FloppyTail::refine_cycles, basic::options::OptionKeys::FloppyTail::refine_repack_cycles, basic::options::OptionKeys::FloppyTail::refine_temp, basic::options::OptionKeys::enzdes::remodel_aggressiveness, basic::options::OptionKeys::enzdes::remodel_protocol, basic::options::OptionKeys::enzdes::remodel_secmatch, basic::options::OptionKeys::enzdes::remodel_trials, basic::options::OptionKeys::edensity::render_density, basic::options::OptionKeys::flexPepDocking::rep_ramp_cycles, basic::options::OptionKeys::fold_cst::reramp_cst_cycles, basic::options::OptionKeys::fold_cst::reramp_iterations, basic::options::OptionKeys::fold_cst::reramp_start_cstweight, basic::options::OptionKeys::fold_from_loops::res_design_bs, basic::options::OptionKeys::DomainAssembly::residues_repack_only, basic::options::OptionKeys::fold_and_dock::rigid_body_cycles, basic::options::OptionKeys::fold_and_dock::rigid_body_disable_mc, basic::options::OptionKeys::fold_and_dock::rigid_body_frequency, basic::options::OptionKeys::fold_and_dock::rot_mag_smooth, basic::options::OptionKeys::enzdes::rot_magnitude, basic::options::OptionKeys::fold_and_dock::rotate_anchor_to_x, basic::options::OptionKeys::flexpack::annealer::rotsub_movebb_substitutions_scale, basic::options::OptionKeys::DomainAssembly::run_centroid, basic::options::OptionKeys::DomainAssembly::run_centroid_abinitio, basic::options::OptionKeys::DomainAssembly::run_fullatom, basic::options::OptionKeys::enzdes::run_ligand_motifs, basic::options::OptionKeys::flexPepDocking::sample_pcs, basic::options::OptionKeys::enzdes::sc_sc_bump_cutoff, basic::options::OptionKeys::edensity::sc_scaling, basic::options::OptionKeys::flexPepDocking::score_filter, basic::options::OptionKeys::edensity::score_sliding_window_context, basic::options::OptionKeys::edensity::score_symm_complex, basic::options::OptionKeys::enzdes::secmatch_Ecutoff, basic::options::OptionKeys::fold_cst::seq_sep_stages, basic::options::OptionKeys::fold_and_dock::set_anchor_at_closest_point, basic::options::OptionKeys::docking::ligand::shear_moves, basic::options::OptionKeys::FloppyTail::shear_on, basic::options::OptionKeys::FloppyTail::short_tail::short_tail, basic::options::OptionKeys::FloppyTail::short_tail::short_tail_fraction, basic::options::OptionKeys::FloppyTail::short_tail::short_tail_off, utility::options::ScalarOption_T_< K, T >::shortd(), basic::options::OptionKeys::enzdes::single_loop_ensemble_size, basic::options::OptionKeys::fold_cst::skip_on_noviolation_in_stage1, basic::options::OptionKeys::fold_and_dock::slide_contact_frequency, basic::options::OptionKeys::flexPepDocking::SlideIntoContact, basic::options::OptionKeys::edensity::sliding_window, basic::options::OptionKeys::edensity::sliding_window_wt, basic::options::OptionKeys::flexPepDocking::smove_angle_range, basic::options::OptionKeys::docking::ligand::soft_rep, basic::options::OptionKeys::fold_cst::stage1_ramp_cst_cycle_factor, basic::options::OptionKeys::fold_cst::stage2_constraint_threshold, basic::options::OptionKeys::docking::ligand::start_from, basic::options::OptionKeys::enzdes::start_from_random_rb_conf, basic::options::OptionKeys::dump_trajectory::stride, basic::options::OptionKeys::docking::ligand::subset_to_keep, basic::options::OptionKeys::fold_from_loops::swap_loops, basic::options::OptionKeys::docking::ligand::tether_ligand, basic::options::OptionKeys::flexPepDocking::torsionsMCM, basic::options::OptionKeys::fold_and_dock::trans_mag_smooth, basic::options::OptionKeys::enzdes::trans_magnitude, basic::options::OptionKeys::docking::ligand::tweak_sxfn, basic::options::OptionKeys::edensity::unmask_bb, basic::options::OptionKeys::docking::ligand::use_ambig_constraints, basic::options::OptionKeys::flexPepDocking::use_cen_score, basic::options::OptionKeys::fast_loops::vdw_delta, basic::options::OptionKeys::flxbb::view, basic::options::OptionKeys::fold_cst::violation_skip_basis, basic::options::OptionKeys::fold_cst::violation_skip_ignore, basic::options::OptionKeys::edensity::whole_structure_allatom_wt, basic::options::OptionKeys::edensity::whole_structure_ca_wt, and basic::options::OptionKeys::fast_loops::window_accept_ratio.

Referenced by add_all_rosetta_options().

void add_rosetta_options_9 ( utility::options::OptionCollection option)
inline

References basic::options::OptionKeys::frags::ABEGO::ABEGO, basic::options::OptionKeys::match::active_site_definition_by_gridlig, basic::options::OptionKeys::match::active_site_definition_by_residue, utility::options::OptionCollection::add(), basic::options::OptionKeys::fold_from_loops::add_cst_loop, basic::options::OptionKeys::lh::additional_objective_functions, basic::options::OptionKeys::hotspot::allow_gly, basic::options::OptionKeys::hotspot::allow_proline, basic::options::OptionKeys::frags::allowed_pdb, basic::options::OptionKeys::matdes::angle, basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::hotspot::angle_res, basic::options::OptionKeys::frags::annotate, basic::options::OptionKeys::holes::atom_scores, basic::options::OptionKeys::hotspot::batch_size, basic::options::OptionKeys::hotspot::benchmark, basic::options::OptionKeys::lh::fragpdb::bin, basic::options::OptionKeys::frags::bounded_protocol, basic::options::OptionKeys::lh::bss, basic::options::OptionKeys::match::build_round1_hits_twice, basic::options::OptionKeys::match::bump_tolerance, basic::options::OptionKeys::frags::contacts::centroid_distance_scale_factor, basic::options::OptionKeys::helical_bundle_predict::centroid_max_temperature, basic::options::OptionKeys::helical_bundle_predict::centroid_min_temperature, basic::options::OptionKeys::lh::centroid_only, basic::options::OptionKeys::fold_from_loops::clear_csts, basic::options::OptionKeys::hotspot::cluster, basic::options::OptionKeys::hotspot::colonyE, basic::options::OptionKeys::frags::scoring::config, basic::options::OptionKeys::match::consolidate_matches, basic::options::OptionKeys::matdes::design::contact_dist, basic::options::OptionKeys::frags::contacts::contacts, basic::options::OptionKeys::loopfcst::coord_cst_all_atom, basic::options::OptionKeys::loopfcst::coord_cst_weight, basic::options::OptionKeys::loopfcst::coord_cst_weight_array, basic::options::OptionKeys::lh::create_db, basic::options::OptionKeys::lh::createdb_rms_cutoff, basic::options::OptionKeys::holes::dalphaball, basic::options::OptionKeys::lh::db_path, basic::options::OptionKeys::holes::debug, utility::options::ScalarOption_T_< K, T >::def(), basic::options::OptionKeys::match::define_match_by_single_downstream_positioning, basic::options::OptionKeys::frags::denied_pdb, basic::options::OptionKeys::hotspot::density, basic::options::OptionKeys::frags::depth, basic::options::OptionKeys::frags::describe_fragments, basic::options::OptionKeys::matdes::design::design, basic::options::OptionKeys::frags::contacts::dist_cutoffs, basic::options::OptionKeys::helical_bundle_predict::do_final_fullatom_refinement, basic::options::OptionKeys::make_mainchain_potential::do_minimization, basic::options::OptionKeys::matdes::dock::dock, basic::options::OptionKeys::matdes::dock::dump_chainA_only, basic::options::OptionKeys::loopfcst::dump_coord_cst_weight_array, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::match::dynamic_grid_refinement, basic::options::OptionKeys::lh::edensity_weight_for_sampling, basic::options::OptionKeys::match::enumerate_ligand_rotamers, basic::options::OptionKeys::hotspot::envhb, basic::options::OptionKeys::match::euclid_bin_size, basic::options::OptionKeys::match::euler_bin_size, basic::options::OptionKeys::lh::exclude_homo, basic::options::OptionKeys::indexed_structure_store::exclude_homo, basic::options::OptionKeys::lh::expire_after_rounds, basic::options::OptionKeys::helical_bundle_predict::fast_relax_rounds, basic::options::OptionKeys::matdes::design::fav_nat_bonus, basic::options::OptionKeys::lh::filter_by_phipsi, basic::options::OptionKeys::match::filter_colliding_upstream_residues, basic::options::OptionKeys::frags::filter_JC, basic::options::OptionKeys::lh::filter_up_to_maxlib, basic::options::OptionKeys::match::filter_upstream_downstream_collisions, basic::options::OptionKeys::helical_bundle_predict::find_disulfides, basic::options::OptionKeys::frags::frag_sizes, basic::options::OptionKeys::frags::fragment_contacts, basic::options::OptionKeys::indexed_structure_store::fragment_store, basic::options::OptionKeys::indexed_structure_store::fragment_threshold_distance, basic::options::OptionKeys::lh::fragpdb::fragpdb, basic::options::OptionKeys::frags::frags, basic::options::OptionKeys::hotspot::fxnal_group, basic::options::OptionKeys::match::geom_csts_downstream_output, basic::options::OptionKeys::match::geometric_constraint_file, basic::options::OptionKeys::lh::grid_angle_multiplier, basic::options::OptionKeys::match::grid_boundary, basic::options::OptionKeys::matdes::design::grid_nsamp_angle, basic::options::OptionKeys::matdes::design::grid_nsamp_radius, basic::options::OptionKeys::matdes::design::grid_size_angle, basic::options::OptionKeys::matdes::design::grid_size_radius, basic::options::OptionKeys::lh::grid_space_multiplier, basic::options::OptionKeys::match::grouper_downstream_rmsd, basic::options::OptionKeys::holes::h_mode, basic::options::OptionKeys::hotspot::hashfile, basic::options::OptionKeys::helical_bundle_predict::helical_bundle_predict, basic::options::OptionKeys::helical_bundle_predict::helix_assignment_file, basic::options::OptionKeys::holes::holes, basic::options::OptionKeys::lh::homo_file, basic::options::OptionKeys::hotspot::hotspot, basic::options::OptionKeys::helical_bundle_predict::ignore_native_residues_in_rmsd, basic::options::OptionKeys::helical_bundle_predict::ignore_prediction_residues_in_rmsd, basic::options::OptionKeys::indexed_structure_store::indexed_structure_store, basic::options::OptionKeys::lh::fragpdb::indexoffset, basic::options::OptionKeys::LoopModel::input_pdb, utility::options::Option::is_group(), basic::options::OptionKeys::frags::j, basic::options::OptionKeys::lh::jobname, basic::options::OptionKeys::make_rot_lib::k_medoids, basic::options::OptionKeys::frags::keep_all_protocol, utility::options::ScalarOption_T_< K, T >::legal(), basic::options::OptionKeys::hotspot::length, basic::options::OptionKeys::lh::lh, basic::options::OptionKeys::lh::library_expiry_time, basic::options::OptionKeys::match::lig_name, basic::options::OptionKeys::match::ligand_rotamer_index, basic::options::OptionKeys::lh::loop_string, basic::options::OptionKeys::loopfcst::loopfcst, basic::options::OptionKeys::LoopModel::LoopModel, basic::options::OptionKeys::lh::loopresdef, basic::options::OptionKeys::lh::loopsizes, basic::options::OptionKeys::make_mainchain_potential::mainchain_potential_points_per_dimension, basic::options::OptionKeys::make_mainchain_potential::mainchain_torsions_covered, basic::options::OptionKeys::make_mainchain_potential::make_mainchain_potential, basic::options::OptionKeys::holes::make_pdb, basic::options::OptionKeys::make_mainchain_potential::make_pre_proline_potential, basic::options::OptionKeys::make_rot_lib::make_rot_lib, basic::options::OptionKeys::holes::make_voids, basic::options::OptionKeys::match::match, basic::options::OptionKeys::match::match_grouper, basic::options::OptionKeys::matdes::matdes, basic::options::OptionKeys::lh::max_bbrms, basic::options::OptionKeys::frags::nonlocal::max_ddg_score, basic::options::OptionKeys::lh::max_emperor_lib_round, basic::options::OptionKeys::lh::max_emperor_lib_size, basic::options::OptionKeys::lh::max_lib_size, basic::options::OptionKeys::lh::max_loophash_per_structure, basic::options::OptionKeys::lh::max_radius, basic::options::OptionKeys::lh::max_ref_lib_size, basic::options::OptionKeys::lh::max_rms, basic::options::OptionKeys::frags::nonlocal::max_rmsd_after_relax, basic::options::OptionKeys::lh::max_sample_per_structure, basic::options::OptionKeys::lh::max_struct, basic::options::OptionKeys::lh::max_struct_per_radius, basic::options::OptionKeys::lh::min_bbrms, basic::options::OptionKeys::frags::nonlocal::min_contacts_per_res, basic::options::OptionKeys::lh::min_rms, basic::options::OptionKeys::frags::contacts::min_seq_sep, basic::options::OptionKeys::holes::minimize, basic::options::OptionKeys::lh::minimize_after_nmsearch, basic::options::OptionKeys::lh::mpi_batch_relax_absolute_max, basic::options::OptionKeys::lh::mpi_batch_relax_chunks, basic::options::OptionKeys::lh::mpi_feedback, basic::options::OptionKeys::lh::mpi_loophash_scan_type, basic::options::OptionKeys::lh::mpi_loophash_split_size, basic::options::OptionKeys::lh::mpi_master_cpu_weight, basic::options::OptionKeys::lh::mpi_master_save_score_only, basic::options::OptionKeys::lh::mpi_master_schfile, basic::options::OptionKeys::lh::mpi_metropolis_temp, basic::options::OptionKeys::lh::mpi_outbound_wu_buffer_size, basic::options::OptionKeys::lh::mpi_packmin_init, basic::options::OptionKeys::lh::mpi_read_structure_for_emperor, basic::options::OptionKeys::lh::mpi_resume, basic::options::OptionKeys::lh::mpi_save_state_interval, basic::options::OptionKeys::lh::multi_objective_functions, basic::options::OptionKeys::frags::n_candidates, basic::options::OptionKeys::frags::n_frags, basic::options::OptionKeys::matdes::dock::neg_r, basic::options::OptionKeys::frags::contacts::neighbors, basic::options::OptionKeys::lh::NMdist, basic::options::OptionKeys::frags::nonlocal::nonlocal, basic::options::OptionKeys::frags::nonlocal_pairs, basic::options::OptionKeys::frags::nr_large_copies, basic::options::OptionKeys::lh::num_partitions, basic::options::OptionKeys::helical_bundle_predict::num_simulated_annealing_rounds_centroid, basic::options::OptionKeys::helical_bundle_predict::num_steps_per_simulated_annealing_round_centroid, basic::options::OptionKeys::matdes::num_subs_building_block, basic::options::OptionKeys::matdes::num_subs_total, basic::options::OptionKeys::lh::objective_cut_increment, basic::options::OptionKeys::lh::objective_dominate_cut, basic::options::OptionKeys::lh::objective_function, basic::options::OptionKeys::match::only_enumerate_non_match_redundant_ligand_rotamers, basic::options::OptionKeys::make_rot_lib::options_file, basic::options::OptionKeys::match::orientation_atoms, basic::options::OptionKeys::lh::fragpdb::out_path, basic::options::OptionKeys::frags::contacts::output_all, basic::options::OptionKeys::fold_from_loops::output_centroid, basic::options::OptionKeys::make_mainchain_potential::output_filename, basic::options::OptionKeys::match::output_format, basic::options::OptionKeys::frags::nonlocal::output_frags_pdbs, basic::options::OptionKeys::frags::nonlocal::output_idealized, basic::options::OptionKeys::frags::output_index, basic::options::OptionKeys::make_rot_lib::output_logging, basic::options::OptionKeys::match::output_matches_per_group, basic::options::OptionKeys::match::output_matchres_only, basic::options::OptionKeys::frags::output_silent, basic::options::OptionKeys::frags::nonlocal::output_silent, basic::options::OptionKeys::frags::p_value_selection, basic::options::OptionKeys::holes::params, basic::options::OptionKeys::lh::parent_selection_kT, basic::options::OptionKeys::make_rot_lib::patch_name_for_residue, basic::options::OptionKeys::matdes::pdbID, basic::options::OptionKeys::lh::symfragrm::pdblist, basic::options::OptionKeys::lh::pert_init_loop, basic::options::OptionKeys::frags::ABEGO::phi_psi_range_A, basic::options::OptionKeys::frags::picking::picking, basic::options::OptionKeys::frags::picking_old_max_score, basic::options::OptionKeys::make_rot_lib::polymeric_context, basic::options::OptionKeys::matdes::prefix, basic::options::OptionKeys::lh::prob_terminus_ramapert, basic::options::OptionKeys::frags::scoring::profile_score, basic::options::OptionKeys::frags::picking::query_pos, basic::options::OptionKeys::frags::picking::quota_config_file, basic::options::OptionKeys::frags::quota_protocol, basic::options::OptionKeys::matdes::radial_disp, basic::options::OptionKeys::lh::radius_size, basic::options::OptionKeys::frags::rama_B, basic::options::OptionKeys::frags::rama_C, basic::options::OptionKeys::frags::rama_norm, basic::options::OptionKeys::lh::refstruct, basic::options::OptionKeys::frags::nonlocal::relax_frags_repeats, basic::options::OptionKeys::frags::nonlocal::relax_input, basic::options::OptionKeys::frags::nonlocal::relax_input_with_coordinate_constraints, basic::options::OptionKeys::match::required_active_site_atom_names, basic::options::OptionKeys::hotspot::rescore, basic::options::OptionKeys::hotspot::residue, basic::options::OptionKeys::make_mainchain_potential::residue_name, basic::options::OptionKeys::holes::residue_scores, basic::options::OptionKeys::hotspot::rms_hotspot, basic::options::OptionKeys::hotspot::rms_hotspot_res, basic::options::OptionKeys::lh::rms_limit, basic::options::OptionKeys::hotspot::rms_target, basic::options::OptionKeys::lh::rounds, basic::options::OptionKeys::lh::sample_weight_file, basic::options::OptionKeys::lh::sandbox, basic::options::OptionKeys::hotspot::sc_only, basic::options::OptionKeys::match::scaffold_active_site_residues, basic::options::OptionKeys::match::scaffold_active_site_residues_for_geomcsts, basic::options::OptionKeys::frags::score_output_silent, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::lh::seg_string, basic::options::OptionKeys::frags::picking::selecting_rule, basic::options::OptionKeys::frags::picking::selecting_scorefxn, basic::options::OptionKeys::frags::seqsim_E, basic::options::OptionKeys::frags::seqsim_H, basic::options::OptionKeys::frags::seqsim_L, basic::options::OptionKeys::helical_bundle_predict::sequence_file, basic::options::OptionKeys::frags::sigmoid_cs_A, basic::options::OptionKeys::frags::sigmoid_cs_B, basic::options::OptionKeys::lh::sim_replace_obj, basic::options::OptionKeys::lh::similarity_measure, basic::options::OptionKeys::lh::similarity_method, basic::options::OptionKeys::lh::similarity_reference, basic::options::OptionKeys::lh::similarity_tolerance, basic::options::OptionKeys::frags::nonlocal::single_chain, basic::options::OptionKeys::lh::skim_size, basic::options::OptionKeys::frags::spine_x, basic::options::OptionKeys::frags::ss_pred, basic::options::OptionKeys::indexed_structure_store::store_name, basic::options::OptionKeys::lh::symfragrm::symfragrm, basic::options::OptionKeys::make_mainchain_potential::symmetrize_output, basic::options::OptionKeys::matdes::tag, basic::options::OptionKeys::hotspot::target, basic::options::OptionKeys::hotspot::target_dist, basic::options::OptionKeys::hotspot::target_res, basic::options::OptionKeys::make_rot_lib::three_fold_symmetry_90_210_330, basic::options::OptionKeys::hotspot::threshold, basic::options::OptionKeys::make_rot_lib::two_fold_symmetry_0_180, basic::options::OptionKeys::make_rot_lib::two_fold_symmetry_135_315, basic::options::OptionKeys::frags::contacts::type, basic::options::OptionKeys::lh::ulr_mulfactor, basic::options::OptionKeys::match::updown_collision_tolerance, basic::options::OptionKeys::match::updown_residue_collision_score_cutoff, basic::options::OptionKeys::match::updown_residue_collision_Wfa_atr, basic::options::OptionKeys::match::updown_residue_collision_Wfa_rep, basic::options::OptionKeys::match::updown_residue_collision_Wfa_sol, basic::options::OptionKeys::match::upstream_residue_collision_score_cutoff, basic::options::OptionKeys::match::upstream_residue_collision_tolerance, basic::options::OptionKeys::match::upstream_residue_collision_Wfa_atr, basic::options::OptionKeys::match::upstream_residue_collision_Wfa_rep, basic::options::OptionKeys::match::upstream_residue_collision_Wfa_sol, basic::options::OptionKeys::loopfcst::use_general_protocol, basic::options::OptionKeys::make_rot_lib::use_terminal_residues, basic::options::OptionKeys::holes::water, basic::options::OptionKeys::hotspot::weighted_density, basic::options::OptionKeys::lh::write_all_fa_structs, basic::options::OptionKeys::frags::write_ca_coordinates, basic::options::OptionKeys::lh::write_centroid_structs, basic::options::OptionKeys::make_mainchain_potential::write_potentials_for_individual_scoreterms, basic::options::OptionKeys::frags::write_rama_tables, basic::options::OptionKeys::frags::write_scores, and basic::options::OptionKeys::frags::write_sequence_only.

Referenced by add_all_rosetta_options().