References basic::options::OptionKeys::in::add_orbitals, basic::options::OptionKeys::in::file::alignment, basic::options::OptionKeys::out::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::in::file::atom_tree_diff, basic::options::OptionKeys::out::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::path::bcl, 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::out::path::db, basic::options::OptionKeys::in::dbms::dbms, basic::options::OptionKeys::inout::dbms::dbms, basic::options::OptionKeys::in::file::dc, basic::options::OptionKeys::in::file::ddg_predictions_file, 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::fast_restyping, basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::in::fconfig, basic::options::OptionKeys::in::file::file, basic::options::OptionKeys::out::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::in::file::fullatom, basic::options::OptionKeys::out::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, 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, 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::path::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::path::mpi_rank_dir, 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::in::obey_ssbond, option, 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_database_params, basic::options::OptionKeys::in::file::override_rot_lib_path, basic::options::OptionKeys::out::overwrite, basic::options::OptionKeys::inout::dbms::password, basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::inout::dbms::path, basic::options::OptionKeys::out::path::path, basic::options::OptionKeys::in::file::pca, basic::options::OptionKeys::in::file::PCS_frag_cst, basic::options::OptionKeys::in::path::pdb, basic::options::OptionKeys::out::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::in::file::residue_type_set, basic::options::OptionKeys::out::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::path::score, 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::out::path::scratch, 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, 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::in::file::silent, basic::options::OptionKeys::out::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::in::file::silent_struct_type, basic::options::OptionKeys::out::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::in::file::srlz, basic::options::OptionKeys::out::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::in::tuning_param, basic::options::OptionKeys::out::unmute, basic::options::OptionKeys::inout::dbms::use_compact_residue_schema, basic::options::OptionKeys::in::use_database, basic::options::OptionKeys::out::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.
