Rosetta 3.3
Functions
src/basic/options/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_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 basic::options::OptionKeys::abinitio::abinitio, utility::options::OptionCollection::add(), 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::out::file::alignment, basic::options::OptionKeys::in::file::alignment, basic::options::OptionKeys::in::file::alignment2, basic::options::OptionKeys::out::path::all, basic::options::OptionKeys::frags::allowed_pdb, basic::options::OptionKeys::in::file::ambig_talos_cs_A, basic::options::OptionKeys::in::file::ambig_talos_cs_B, basic::options::OptionKeys::in::matdes_dock::angle, basic::options::OptionKeys::frags::annotate, basic::options::OptionKeys::run::archive, basic::options::OptionKeys::fingerprint::atom_radius_buffer, basic::options::OptionKeys::fingerprint::atom_radius_scale, basic::options::OptionKeys::out::file::atom_tree_diff, basic::options::OptionKeys::in::file::atom_tree_diff, basic::options::OptionKeys::run::batches, basic::options::OptionKeys::run::benchmark, basic::options::OptionKeys::run::benchmark_scale, basic::options::OptionKeys::abinitio::bGDT, basic::options::OptionKeys::in::file::boinc_wu_zip, basic::options::OptionKeys::frags::bounded_protocol, basic::options::OptionKeys::broker::broker, basic::options::OptionKeys::jd2::buffer_silent_output, basic::options::OptionKeys::nonlocal::builder, basic::options::OptionKeys::frags::nonlocal::ca_dist, basic::options::OptionKeys::pH::calc_pka::calc_pka, basic::options::OptionKeys::evaluation::cam_shifts, basic::options::OptionKeys::docking::center_at_interface, basic::options::OptionKeys::pocket_grid::central_relax_pdb_num, basic::options::OptionKeys::in::file::centroid_input, basic::options::OptionKeys::run::chain, basic::options::OptionKeys::run::checkpoint, basic::options::OptionKeys::in::file::checkpoint, basic::options::OptionKeys::run::checkpoint_interval, basic::options::OptionKeys::evaluation::chemical_shifts, basic::options::OptionKeys::out::chname, basic::options::OptionKeys::chunk::chunk, basic::options::OptionKeys::run::clean, basic::options::OptionKeys::abinitio::clear_pose_cache, basic::options::OptionKeys::abinitio::close_loops, basic::options::OptionKeys::evaluation::combine_statistics, basic::options::OptionKeys::evaluation::combined_constraints, basic::options::OptionKeys::evaluation::combined_constraints_column, basic::options::OptionKeys::run::condor, basic::options::OptionKeys::frags::scoring::config, basic::options::OptionKeys::run::constant_seed, basic::options::OptionKeys::evaluation::constraints, basic::options::OptionKeys::evaluation::constraints_column, basic::options::OptionKeys::in::matdes_design::contact_dist, basic::options::OptionKeys::evaluation::contact_map, basic::options::OptionKeys::run::cycles_inner, basic::options::OptionKeys::run::cycles_outer, basic::options::OptionKeys::in::path::database, basic::options::OptionKeys::inout::database_filename, basic::options::OptionKeys::inout::database_mode, basic::options::OptionKeys::jd2::dd_parser, basic::options::OptionKeys::in::file::ddg_predictions_file, basic::options::OptionKeys::abinitio::debug, basic::options::OptionKeys::run::debug, basic::options::OptionKeys::abinitio::debug_structures, basic::options::OptionKeys::run::decoystats, basic::options::OptionKeys::run::delay, basic::options::OptionKeys::run::delete_checkpoints, basic::options::OptionKeys::jd2::delete_old_poses, basic::options::OptionKeys::frags::denied_pdb, basic::options::OptionKeys::frags::describe_fragments, basic::options::OptionKeys::docking::design_chains, basic::options::OptionKeys::out::file::design_contrast, basic::options::OptionKeys::in::detect_disulf, basic::options::OptionKeys::abinitio::detect_disulfide_before_relax, 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::fingerprint::dist_cut_off, basic::options::OptionKeys::docking::dock_lowres_filter, basic::options::OptionKeys::docking::dock_mcm_rot_magnitude, 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::out::file::dont_rewrite_dunbrack_database, basic::options::OptionKeys::run::dry_run, basic::options::OptionKeys::out::dry_run, basic::options::OptionKeys::in::file::dssp, basic::options::OptionKeys::in::matdes_dock::dump_chainA_only, basic::options::OptionKeys::abinitio::dump_frags, basic::options::OptionKeys::in::matdes_dock::dump_pdb, basic::options::OptionKeys::docking::ensemble1, basic::options::OptionKeys::docking::ensemble2, basic::options::OptionKeys::jd2::enzdes_out, basic::options::OptionKeys::evaluation::evaluation, basic::options::OptionKeys::run::evolution, basic::options::OptionKeys::run::exit_if_missing_heavy_atoms, basic::options::OptionKeys::abinitio::exit_when_converged, basic::options::OptionKeys::abinitio::explicit_pdb_debug, basic::options::OptionKeys::in::file::extended_pose, basic::options::OptionKeys::in::file::extra_res_cen, basic::options::OptionKeys::in::file::extra_res_fa, basic::options::OptionKeys::in::file::extra_res_mol, basic::options::OptionKeys::in::file::extra_res_path, 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::in::file::fail_on_bad_hbond, basic::options::OptionKeys::abinitio::fast, basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::abinitio::fastrelax, basic::options::OptionKeys::in::matdes_design::fav_nat_bonus, basic::options::OptionKeys::out::file::file, basic::options::OptionKeys::in::file::file, basic::options::OptionKeys::frags::filter_JC, basic::options::OptionKeys::filters::filters, basic::options::OptionKeys::abinitio::final_clean_relax, basic::options::OptionKeys::run::find_disulf, basic::options::OptionKeys::fingerprint::fingerprint, basic::options::OptionKeys::in::fix_disulf, basic::options::OptionKeys::abinitio::fix_residues_to_native, basic::options::OptionKeys::docking::flexible_bb_docking, basic::options::OptionKeys::docking::flexible_bb_docking_interface_dist, basic::options::OptionKeys::in::file::fold_tree, basic::options::OptionKeys::inout::fold_tree_io, 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::frags::frag_sizes, basic::options::OptionKeys::in::file::frag_sizes, basic::options::OptionKeys::in::file::fragA, basic::options::OptionKeys::in::file::fragA_size, basic::options::OptionKeys::in::file::fragB, basic::options::OptionKeys::in::path::fragments, basic::options::OptionKeys::frags::frags, basic::options::OptionKeys::out::file::fullatom, basic::options::OptionKeys::in::file::fullatom, basic::options::OptionKeys::nonlocal::gap_sampling_extension, basic::options::OptionKeys::evaluation::gdtmm, basic::options::OptionKeys::jd2::generic_job_name, 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::in::matdes_design::grid_nsamp_angle, basic::options::OptionKeys::in::matdes_design::grid_nsamp_radius, basic::options::OptionKeys::in::matdes_design::grid_size_angle, basic::options::OptionKeys::in::matdes_design::grid_size_radius, basic::options::OptionKeys::docking::ligand::harmonic_Calphas, basic::options::OptionKeys::docking::ligand::harmonic_torsions, basic::options::OptionKeys::docking::high_min_patch, basic::options::OptionKeys::docking::high_patch, basic::options::OptionKeys::mysql::host, basic::options::OptionKeys::run::idealize_before_protocol, basic::options::OptionKeys::MM::ignore_missing_bondangle_params, basic::options::OptionKeys::in::ignore_unrecognized_res, basic::options::OptionKeys::docking::ligand::improve_orientation, basic::options::OptionKeys::in::in, basic::options::OptionKeys::abinitio::increase_cycles, basic::options::OptionKeys::inout::inout, basic::options::OptionKeys::run::interactive, basic::options::OptionKeys::run::intermediate_scorefiles, basic::options::OptionKeys::run::intermediate_structures, basic::options::OptionKeys::run::IUPAC, basic::options::OptionKeys::jd2::jd2, basic::options::OptionKeys::abinitio::jdist_rerun, basic::options::OptionKeys::run::jobdist_miscfile_ext, basic::options::OptionKeys::run::jran, basic::options::OptionKeys::evaluation::jscore_evaluator, basic::options::OptionKeys::evaluation::jump_nr, basic::options::OptionKeys::frags::keep_all_protocol, basic::options::OptionKeys::in::file::keep_input_scores, basic::options::OptionKeys::docking::kick_relax, basic::options::OptionKeys::abinitio::kill_hairpins, basic::options::OptionKeys::abinitio::kill_hairpins_frequency, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::in::file::lazy_silent, basic::options::OptionKeys::jd2::lazy_silent_file_reader, basic::options::OptionKeys::out::level, basic::options::OptionKeys::docking::ligand::ligand, basic::options::OptionKeys::in::file::lipofile, basic::options::OptionKeys::in::file::list, basic::options::OptionKeys::chunk::loop2, basic::options::OptionKeys::docking::low_patch, basic::options::OptionKeys::docking::low_res_protocol_only, basic::options::OptionKeys::in::matdes_design::matdes_design, basic::options::OptionKeys::in::matdes_dock::matdes_dock, basic::options::OptionKeys::nonlocal::max_chunk_size, basic::options::OptionKeys::frags::nonlocal::max_ddg_score, basic::options::OptionKeys::run::max_min_iter, basic::options::OptionKeys::docking::ligand::max_poses, basic::options::OptionKeys::docking::max_repeats, basic::options::OptionKeys::run::max_retry_job, basic::options::OptionKeys::frags::nonlocal::max_rmsd_after_relax, basic::options::OptionKeys::run::maxruntime, basic::options::OptionKeys::abinitio::membrane, basic::options::OptionKeys::run::memory_test_cycles, basic::options::OptionKeys::nonlocal::min_chunk_size, basic::options::OptionKeys::frags::nonlocal::min_contacts_per_res, basic::options::OptionKeys::docking::ligand::min_rms, basic::options::OptionKeys::frags::nonlocal::min_seq_sep, basic::options::OptionKeys::run::min_tolerance, basic::options::OptionKeys::run::min_type, basic::options::OptionKeys::docking::symmetry::minimize_backbone, basic::options::OptionKeys::docking::ligand::minimize_backbone, basic::options::OptionKeys::docking::ligand::minimize_ligand, basic::options::OptionKeys::docking::symmetry::minimize_sidechains, basic::options::OptionKeys::MM::MM, basic::options::OptionKeys::nonlocal::mode, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::nonlocal::moves, basic::options::OptionKeys::run::movie, basic::options::OptionKeys::out::path::movie, 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::jd2::mpi_nowait_for_remaining_jobs, basic::options::OptionKeys::out::path::mpi_rank_dir, basic::options::OptionKeys::out::mpi_tracer_to_file, basic::options::OptionKeys::jd2::mpi_work_partition_job_distributor, basic::options::OptionKeys::docking::multibody, basic::options::OptionKeys::abinitio::multifastrelax, basic::options::OptionKeys::run::multiple_processes_writing_to_one_directory, basic::options::OptionKeys::docking::ligand::mutate_same_name3, basic::options::OptionKeys::out::mute, basic::options::OptionKeys::out::mute_debug, basic::options::OptionKeys::out::mute_info, basic::options::OptionKeys::out::mute_warning, basic::options::OptionKeys::mysql::mysql, basic::options::OptionKeys::frags::n_candidates, basic::options::OptionKeys::run::n_cycles, basic::options::OptionKeys::frags::n_frags, basic::options::OptionKeys::in::file::native, basic::options::OptionKeys::in::file::native_exclude_res, basic::options::OptionKeys::run::nblist_autoupdate, basic::options::OptionKeys::run::nblist_autoupdate_narrow, basic::options::OptionKeys::run::nblist_autoupdate_wide, basic::options::OptionKeys::in::matdes_dock::neg_r, basic::options::OptionKeys::in::file::new_chain_order, basic::options::OptionKeys::in::file::no_binary_dunlib, basic::options::OptionKeys::docking::no_filters, basic::options::OptionKeys::jd2::no_output, basic::options::OptionKeys::run::no_prof_info_in_silentout, basic::options::OptionKeys::run::no_scorefile, basic::options::OptionKeys::abinitio::no_write_failures, basic::options::OptionKeys::run::nodelay, basic::options::OptionKeys::nonlocal::nonlocal, basic::options::OptionKeys::frags::nonlocal::nonlocal, basic::options::OptionKeys::out::nooutput, basic::options::OptionKeys::docking::norepack1, basic::options::OptionKeys::docking::norepack2, basic::options::OptionKeys::PCS::normalization_id, basic::options::OptionKeys::run::nproc, basic::options::OptionKeys::frags::nr_large_copies, basic::options::OptionKeys::out::nstruct, basic::options::OptionKeys::jd2::ntrials, basic::options::OptionKeys::in::matdes_design::num_subs_building_block, basic::options::OptionKeys::in::matdes_dock::num_subs_building_block, basic::options::OptionKeys::in::matdes_dock::num_subs_total, basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::in::file::obey_ENDMDL, basic::options::OptionKeys::docking::ligand::old_estat, basic::options::OptionKeys::docking::ligand::option_file, basic::options::OptionKeys::run::other_pose_scorefile, basic::options::OptionKeys::run::other_pose_to_scorefile, basic::options::OptionKeys::out::out, basic::options::OptionKeys::out::output, basic::options::OptionKeys::frags::nonlocal::output_frags_pdbs, basic::options::OptionKeys::run::output_hbond_info, basic::options::OptionKeys::frags::nonlocal::output_idealized, basic::options::OptionKeys::out::file::output_orbitals, basic::options::OptionKeys::out::output_tag, basic::options::OptionKeys::out::file::output_torsions, basic::options::OptionKeys::out::file::output_virtual, basic::options::OptionKeys::out::overwrite, basic::options::OptionKeys::frags::p_value_selection, basic::options::OptionKeys::docking::pack_patch, basic::options::OptionKeys::fingerprint::packing_weight, basic::options::OptionKeys::evaluation::pales, basic::options::OptionKeys::docking::partners, basic::options::OptionKeys::mysql::password, basic::options::OptionKeys::residues::patch_selectors, basic::options::OptionKeys::out::path::path, basic::options::OptionKeys::in::path::path, basic::options::OptionKeys::in::file::pca, basic::options::OptionKeys::PCS::PCS, basic::options::OptionKeys::in::file::PCS_frag_cst, basic::options::OptionKeys::out::path::pdb, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::in::path::pdb, basic::options::OptionKeys::chunk::pdb2, basic::options::OptionKeys::out::pdb_gz, basic::options::OptionKeys::out::file::pdb_parents, basic::options::OptionKeys::in::matdes_dock::pdbID, basic::options::OptionKeys::out::file::per_chain_renumbering, basic::options::OptionKeys::abinitio::perturb, basic::options::OptionKeys::pH::pH, basic::options::OptionKeys::pH::pH_mode, basic::options::OptionKeys::frags::picking::picking, basic::options::OptionKeys::pH::calc_pka::pka_for_chainno, basic::options::OptionKeys::pH::calc_pka::pka_for_resno, basic::options::OptionKeys::pocket_grid::pocket_buried_dist, basic::options::OptionKeys::pocket_grid::pocket_buried_score, basic::options::OptionKeys::pocket_grid::pocket_dump_pdbs, basic::options::OptionKeys::pocket_grid::pocket_dump_rama, 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_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_probe_radius, basic::options::OptionKeys::pocket_grid::pocket_psp, basic::options::OptionKeys::pocket_grid::pocket_restrict_size, basic::options::OptionKeys::pocket_grid::pocket_side, basic::options::OptionKeys::pocket_grid::pocket_sps, basic::options::OptionKeys::pocket_grid::pocket_surface_dist, basic::options::OptionKeys::pocket_grid::pocket_surface_score, basic::options::OptionKeys::evaluation::pool, basic::options::OptionKeys::mysql::port, basic::options::OptionKeys::jd2::pose_input_stream, basic::options::OptionKeys::frags::scoring::predicted_secondary, basic::options::OptionKeys::out::prefix, basic::options::OptionKeys::in::matdes_dock::prefix, basic::options::OptionKeys::run::preserve_header, basic::options::OptionKeys::run::proc_id, basic::options::OptionKeys::abinitio::process_store, basic::options::OptionKeys::run::profile, basic::options::OptionKeys::frags::scoring::profile_score, basic::options::OptionKeys::run::protein, basic::options::OptionKeys::run::protocol, basic::options::OptionKeys::docking::ligand::protocol, basic::options::OptionKeys::in::file::psipred_ss2, basic::options::OptionKeys::in::file::pssm, basic::options::OptionKeys::qsar::qsar, basic::options::OptionKeys::frags::picking::query_pos, basic::options::OptionKeys::frags::picking::quota_config_file, basic::options::OptionKeys::frags::quota_protocol, basic::options::OptionKeys::in::matdes_dock::radial_disp, basic::options::OptionKeys::in::file::rama2b_map, basic::options::OptionKeys::frags::rama_B, basic::options::OptionKeys::frags::rama_C, basic::options::OptionKeys::frags::rama_norm, basic::options::OptionKeys::nonlocal::ramp_chainbreaks, basic::options::OptionKeys::nonlocal::ramp_constraints, basic::options::OptionKeys::nonlocal::ramp_constraints_cycles, basic::options::OptionKeys::docking::ligand::random_conformer, basic::options::OptionKeys::run::random_delay, basic::options::OptionKeys::docking::randomize1, basic::options::OptionKeys::docking::randomize2, basic::options::OptionKeys::nonlocal::randomize_missing, basic::options::OptionKeys::run::randomize_missing_coords, basic::options::OptionKeys::out::file::raw, basic::options::OptionKeys::evaluation::rdc, basic::options::OptionKeys::in::file::rdc, basic::options::OptionKeys::evaluation::rdc_column, basic::options::OptionKeys::evaluation::rdc_select, basic::options::OptionKeys::evaluation::rdc_target, basic::options::OptionKeys::nonlocal::rdc_weight, basic::options::OptionKeys::in::rdf::rdf, basic::options::OptionKeys::run::rebuild_disulf, basic::options::OptionKeys::run::regions, basic::options::OptionKeys::run::reinitialize_mover_for_each_job, basic::options::OptionKeys::run::reinitialize_mover_for_new_input, basic::options::OptionKeys::abinitio::relax, basic::options::OptionKeys::abinitio::relax_failures, 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::abinitio::relax_with_jumps, basic::options::OptionKeys::in::remember_unrecognized_res, basic::options::OptionKeys::in::remember_unrecognized_water, basic::options::OptionKeys::run::remove_ss_length_screen, basic::options::OptionKeys::out::file::renumber_pdb, basic::options::OptionKeys::run::repack_rate, basic::options::OptionKeys::in::file::repair_sidechains, basic::options::OptionKeys::run::repeat, basic::options::OptionKeys::in::replonly_loops, basic::options::OptionKeys::in::replonly_residues, basic::options::OptionKeys::abinitio::rerun, basic::options::OptionKeys::docking::ligand::rescore, 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::residues::residues, basic::options::OptionKeys::abinitio::return_full_atom, basic::options::OptionKeys::in::matdes_design::revert_ids, basic::options::OptionKeys::in::matdes_design::revert_pos, basic::options::OptionKeys::abinitio::rg_reweight, basic::options::OptionKeys::evaluation::rmsd, basic::options::OptionKeys::evaluation::rmsd_column, basic::options::OptionKeys::abinitio::rmsd_residues, basic::options::OptionKeys::evaluation::rmsd_select, basic::options::OptionKeys::evaluation::rmsd_target, basic::options::OptionKeys::run::rng, basic::options::OptionKeys::run::rng_seed_device, basic::options::OptionKeys::evaluation::rpf, basic::options::OptionKeys::abinitio::rsd_wt_helix, basic::options::OptionKeys::abinitio::rsd_wt_loop, basic::options::OptionKeys::abinitio::rsd_wt_strand, basic::options::OptionKeys::run::run, basic::options::OptionKeys::run::run_level, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::docking::sc_min, basic::options::OptionKeys::out::path::score, basic::options::OptionKeys::evaluation::score_exclude_res, basic::options::OptionKeys::run::score_only, basic::options::OptionKeys::out::file::score_only, 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::out::scorecut, basic::options::OptionKeys::out::file::scorefile, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::path::scratch, basic::options::OptionKeys::nonlocal::search, basic::options::OptionKeys::run::seed_offset, basic::options::OptionKeys::frags::picking::selecting_rule, basic::options::OptionKeys::in::rdf::sep_bb_ss, basic::options::OptionKeys::in::file::seq, basic::options::OptionKeys::frags::seqsim_E, basic::options::OptionKeys::frags::seqsim_H, basic::options::OptionKeys::frags::seqsim_L, basic::options::OptionKeys::run::series, basic::options::OptionKeys::filters::set_pddf_filter, basic::options::OptionKeys::filters::set_saxs_filter, basic::options::OptionKeys::broker::setup, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::docking::ligand::shear_moves, basic::options::OptionKeys::out::show_accessed_options, basic::options::OptionKeys::run::shuffle, basic::options::OptionKeys::out::shuffle_nstruct, basic::options::OptionKeys::frags::sigmoid_cs_A, basic::options::OptionKeys::frags::sigmoid_cs_B, basic::options::OptionKeys::run::silent, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::out::file::silent_comment_bound, basic::options::OptionKeys::out::file::silent_decoytime, basic::options::OptionKeys::in::file::silent_energy_cut, basic::options::OptionKeys::out::silent_gz, basic::options::OptionKeys::run::silent_input, basic::options::OptionKeys::in::file::silent_list, basic::options::OptionKeys::in::file::silent_optH, 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::out::file::silent_struct_type, basic::options::OptionKeys::in::file::silent_struct_type, basic::options::OptionKeys::frags::nonlocal::single_chain, basic::options::OptionKeys::abinitio::skip_convergence_check, basic::options::OptionKeys::run::skip_set_reasonable_fold_tree, basic::options::OptionKeys::abinitio::smooth_cycles_only, basic::options::OptionKeys::docking::ligand::soft_rep, basic::options::OptionKeys::in::file::spanfile, basic::options::OptionKeys::evaluation::sparta_dir, basic::options::OptionKeys::docking::spin, basic::options::OptionKeys::frags::ss_pred, 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::docking::ligand::start_from, basic::options::OptionKeys::abinitio::start_native, basic::options::OptionKeys::run::status, basic::options::OptionKeys::abinitio::steal_3mers, basic::options::OptionKeys::abinitio::steal_9mers, basic::options::OptionKeys::abinitio::strand_dist_cutoff, basic::options::OptionKeys::abinitio::stretch_strand_dist_cutoff, basic::options::OptionKeys::evaluation::structural_similarity, basic::options::OptionKeys::in::file::sucker_params, basic::options::OptionKeys::out::suffix, basic::options::OptionKeys::run::suppress_checkpoints, basic::options::OptionKeys::evaluation::symmetric_rmsd, basic::options::OptionKeys::docking::symmetry::symmetry, 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::MonteCarlo::temp_final, basic::options::OptionKeys::MonteCarlo::temp_initial, basic::options::OptionKeys::abinitio::temperature, basic::options::OptionKeys::in::file::template_pdb, basic::options::OptionKeys::in::file::template_silent, basic::options::OptionKeys::in::termini, basic::options::OptionKeys::run::test_cycles, basic::options::OptionKeys::docking::ligand::tether_ligand, basic::options::OptionKeys::run::timer, basic::options::OptionKeys::in::file::torsion_bin_probs, basic::options::OptionKeys::run::trajectory, basic::options::OptionKeys::run::trust_missing_coords, basic::options::OptionKeys::docking::uniform_trans, basic::options::OptionKeys::out::unmute, basic::options::OptionKeys::out::unmute_debug, basic::options::OptionKeys::out::unmute_error, basic::options::OptionKeys::out::unmute_info, basic::options::OptionKeys::out::unmute_warning, basic::options::OptionKeys::docking::ligand::use_ambig_constraints, basic::options::OptionKeys::out::use_database, basic::options::OptionKeys::in::use_database, basic::options::OptionKeys::abinitio::use_filters, basic::options::OptionKeys::docking::use_legacy_protocol, basic::options::OptionKeys::in::use_stupid_foldtree_format, basic::options::OptionKeys::run::use_time_as_seed, basic::options::OptionKeys::mysql::user, basic::options::OptionKeys::out::user_tag, basic::options::OptionKeys::in::file::user_tags, basic::options::OptionKeys::in::file::vall, basic::options::OptionKeys::pH::value_pH, basic::options::OptionKeys::run::verbose, basic::options::OptionKeys::run::verbosity, basic::options::OptionKeys::run::version, basic::options::OptionKeys::docking::view, basic::options::OptionKeys::out::file::weight_silent_scores, basic::options::OptionKeys::qsar::weights, basic::options::OptionKeys::run::wide_nblist_extension, basic::options::OptionKeys::frags::write_ca_coordinates, basic::options::OptionKeys::PCS::write_extra, basic::options::OptionKeys::run::write_failures, basic::options::OptionKeys::frags::write_rama_tables, 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::smhybrid::abinitio_cycles, basic::options::OptionKeys::smhybrid::abinitio_design, basic::options::OptionKeys::abrelax::abrelax, 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::enzdes::additional_packing_ligand_rb_confs, basic::options::OptionKeys::packing::adducts, basic::options::OptionKeys::phil::align_file, basic::options::OptionKeys::enzdes::arg_sweep_interface, basic::options::OptionKeys::holes::atom_scores, 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::batch_relax::batch_relax, basic::options::OptionKeys::batch_relax::batch_size, basic::options::OptionKeys::enzdes::bb_bump_cutoff, basic::options::OptionKeys::enzdes::bb_min, basic::options::OptionKeys::enzdes::bb_min_allowed_dev, basic::options::OptionKeys::relax::bb_move, basic::options::OptionKeys::jumps::bb_moves, basic::options::OptionKeys::score::bonded_params, basic::options::OptionKeys::relax::cartesian, basic::options::OptionKeys::holes::cav_shrink, basic::options::OptionKeys::packstat::cavity_burial_probe_radius, basic::options::OptionKeys::smhybrid::centroid_all_val, basic::options::OptionKeys::corrections::score::ch_o_bond_potential, basic::options::OptionKeys::relax::chainbreak_weight, 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::smhybrid::chainbreaks, basic::options::OptionKeys::enzdes::change_lig, basic::options::OptionKeys::templates::change_movemap, basic::options::OptionKeys::enzdes::checkpoint, basic::options::OptionKeys::corrections::chemical::chemical, basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::enzdes::chi_min, basic::options::OptionKeys::relax::chi_move, basic::options::OptionKeys::evolution::childlist, basic::options::OptionKeys::crossmatch::clash_dis, basic::options::OptionKeys::relax::classic, basic::options::OptionKeys::abinitio::close_chbrk, basic::options::OptionKeys::abinitio::close_loops_by_idealizing, basic::options::OptionKeys::cluster::cluster, basic::options::OptionKeys::packstat::cluster_min_volume, basic::options::OptionKeys::enzdes::compare_native, basic::options::OptionKeys::templates::config, 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::fold_cst::constraint_skip_rate, basic::options::OptionKeys::jumps::contact_score, basic::options::OptionKeys::mc::convergence_check_frequency, basic::options::OptionKeys::loopfcst::coord_cst_all_atom, basic::options::OptionKeys::relax::coord_cst_stdev, basic::options::OptionKeys::loopfcst::coord_cst_weight, basic::options::OptionKeys::loopfcst::coord_cst_weight_array, basic::options::OptionKeys::relax::coord_cst_width, basic::options::OptionKeys::corrections::correct, basic::options::OptionKeys::corrections::corrections, basic::options::OptionKeys::crossmatch::crossmatch, basic::options::OptionKeys::templates::cst::cst, 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::smhybrid::cst_sub_files, basic::options::OptionKeys::enzdes::cstfile, basic::options::OptionKeys::score::custom_atom_pair, basic::options::OptionKeys::score::saxs::custom_ff, basic::options::OptionKeys::enzdes::cut1, basic::options::OptionKeys::enzdes::cut2, basic::options::OptionKeys::enzdes::cut3, basic::options::OptionKeys::enzdes::cut4, basic::options::OptionKeys::relax::cycle_ratio, basic::options::OptionKeys::score::saxs::d_max, basic::options::OptionKeys::score::saxs::d_min, basic::options::OptionKeys::score::saxs::d_step, basic::options::OptionKeys::holes::dalphaball, basic::options::OptionKeys::lh::db_path, basic::options::OptionKeys::lh::db_prefix, basic::options::OptionKeys::smhybrid::debug, basic::options::OptionKeys::relax::default_repeats, basic::options::OptionKeys::smhybrid::design, basic::options::OptionKeys::smhybrid::design_hydrophobic, basic::options::OptionKeys::smhybrid::design_linker, basic::options::OptionKeys::enzdes::design_min_cycles, basic::options::OptionKeys::smhybrid::design_res_files, basic::options::OptionKeys::enzdes::detect_design_interface, basic::options::OptionKeys::score::disable_orientation_dependent_rna_ch_o_bonds, basic::options::OptionKeys::score::disulf_matching_probe, basic::options::OptionKeys::enzdes::dock_trials, basic::options::OptionKeys::packing::double_lazy_ig, basic::options::OptionKeys::packing::double_lazy_ig_mem_limit, basic::options::OptionKeys::loopfcst::dump_coord_cst_weight_array, basic::options::OptionKeys::enzdes::dump_final_repack_without_ligand_pdb, basic::options::OptionKeys::jumps::dump_frags, basic::options::OptionKeys::enzdes::dump_inverse_rotamers, basic::options::OptionKeys::enzdes::dump_loop_samples, basic::options::OptionKeys::packing::dump_rotamer_sets, basic::options::OptionKeys::corrections::score::dun02_file, basic::options::OptionKeys::corrections::score::dun08, basic::options::OptionKeys::corrections::score::dun08_dir, basic::options::OptionKeys::corrections::score::dun10, basic::options::OptionKeys::corrections::score::dun10_dir, basic::options::OptionKeys::packing::dunbrack_prob_buried, basic::options::OptionKeys::packing::dunbrack_prob_nonburied, basic::options::OptionKeys::packing::dunbrack_prob_nonburied_semirotameric, basic::options::OptionKeys::score::empty, basic::options::OptionKeys::abinitio::end_bias, basic::options::OptionKeys::relax::energycut, 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::score::etable_lr, basic::options::OptionKeys::jumps::evaluate, basic::options::OptionKeys::evolution::evolution, 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::enzdes::ex_catalytic_rot, basic::options::OptionKeys::score::exact_occ_include_Hbond_contribution, 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::lh::exclude_homo, basic::options::OptionKeys::chemical::exclude_patches, basic::options::OptionKeys::cluster::exclude_res, basic::options::OptionKeys::packing::exdna::exdna, basic::options::OptionKeys::packing::explicit_h2o, basic::options::OptionKeys::cluster::export_only_low, basic::options::OptionKeys::jumps::extra_frags_for_ss, basic::options::OptionKeys::wum::extra_scorefxn, basic::options::OptionKeys::wum::extra_scorefxn_ref_structure, basic::options::OptionKeys::wum::extra_scorefxn_relax, basic::options::OptionKeys::packing::extrachi_cutoff, 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::smhybrid::fa_refine, basic::options::OptionKeys::abrelax::fail_unclosed, basic::options::OptionKeys::relax::fast, basic::options::OptionKeys::enzdes::favor_native_res, basic::options::OptionKeys::smhybrid::filter, 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::abrelax::filters, basic::options::OptionKeys::enzdes::final_repack_without_ligand, basic::options::OptionKeys::score::find_neighbors_3dgrid, basic::options::OptionKeys::score::saxs::fit_pddf_area, basic::options::OptionKeys::templates::fix_aligned_residues, basic::options::OptionKeys::enzdes::fix_catalytic_aa, basic::options::OptionKeys::jumps::fix_chainbreak, basic::options::OptionKeys::templates::fix_frag_file, basic::options::OptionKeys::packing::fix_his_tautomer, basic::options::OptionKeys::jumps::fix_jumps, basic::options::OptionKeys::templates::fix_margin, basic::options::OptionKeys::smhybrid::fixed_res_files, basic::options::OptionKeys::enzdes::flexbb_outstructs, basic::options::OptionKeys::enzdes::flexbb_protocol, basic::options::OptionKeys::packing::flip_HNQ, basic::options::OptionKeys::smhybrid::floating_scs_rep, basic::options::OptionKeys::smhybrid::flxbb, basic::options::OptionKeys::fold_cst::fold_cst, basic::options::OptionKeys::fold_cst::force_minimize, basic::options::OptionKeys::templates::force_native_topology, basic::options::OptionKeys::smhybrid::frag_res_files, basic::options::OptionKeys::templates::fragsteal::fragsteal, basic::options::OptionKeys::cluster::gdtmm, basic::options::OptionKeys::holes::h_mode, basic::options::OptionKeys::corrections::score::hack_elec_co_only, basic::options::OptionKeys::score::hackelec_die, basic::options::OptionKeys::score::hackelec_max_dis, basic::options::OptionKeys::score::hackelec_r_option, basic::options::OptionKeys::score::hb_sp2_amp, basic::options::OptionKeys::score::hb_sp2_chipen, basic::options::OptionKeys::score::hb_sp2_peak_heigh_above_trough, basic::options::OptionKeys::corrections::score::hbond_His_Phil_fix, basic::options::OptionKeys::score::hbond_params, basic::options::OptionKeys::abinitio::HD_EX_Info, basic::options::OptionKeys::abinitio::HD_fa_penalty, basic::options::OptionKeys::abinitio::HD_penalty, basic::options::OptionKeys::mc::heat_convergence_check, basic::options::OptionKeys::corrections::score::helix_hb_06_2009, basic::options::OptionKeys::templates::helix_pairings, basic::options::OptionKeys::mc::hierarchical_pool, basic::options::OptionKeys::holes::holes, basic::options::OptionKeys::cluster::hotspot_hash, basic::options::OptionKeys::corrections::chemical::icoor_05_2009, basic::options::OptionKeys::cluster::idealize_final_structures, basic::options::OptionKeys::crossmatch::identical_match_dis, basic::options::OptionKeys::fold_cst::ignore_sequence_seperation, basic::options::OptionKeys::enzdes::include_catres_in_interface_detection, basic::options::OptionKeys::abinitio::include_stage5, basic::options::OptionKeys::packstat::include_water, basic::options::OptionKeys::jumps::increase_chainbreak, basic::options::OptionKeys::packing::inneriterations_scaling, basic::options::OptionKeys::score::input_etables, basic::options::OptionKeys::cluster::input_score_filter, basic::options::OptionKeys::smhybrid::inter_subsub_cst, basic::options::OptionKeys::crossmatch::interface_size, basic::options::OptionKeys::smhybrid::inversion_subs, basic::options::OptionKeys::jumps::invrate_jump_move, basic::options::OptionKeys::jumps::jump_lib, basic::options::OptionKeys::relax::jump_move, basic::options::OptionKeys::smhybrid::jumpcut_files, basic::options::OptionKeys::jumps::jumps, basic::options::OptionKeys::resample::jumps, 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::cluster::K_threshold, basic::options::OptionKeys::fold_cst::keep_skipped_csts, basic::options::OptionKeys::enzdes::kic_loop_sampling, basic::options::OptionKeys::mc::known_structures, basic::options::OptionKeys::packing::lazy_ig, basic::options::OptionKeys::packing::exdna::level, basic::options::OptionKeys::packing::ex2aro_exposed::level, basic::options::OptionKeys::packing::ex1aro_exposed::level, basic::options::OptionKeys::packing::ex2aro::level, basic::options::OptionKeys::packing::ex1aro::level, basic::options::OptionKeys::packing::ex4::level, basic::options::OptionKeys::packing::ex3::level, basic::options::OptionKeys::packing::ex2::level, basic::options::OptionKeys::packing::ex1::level, basic::options::OptionKeys::lh::lh, basic::options::OptionKeys::enzdes::lig_packer_weight, basic::options::OptionKeys::relax::limit_aroma_chi2, basic::options::OptionKeys::cluster::limit_cluster_size, basic::options::OptionKeys::cluster::limit_clusters, basic::options::OptionKeys::cluster::limit_dist_matrix, basic::options::OptionKeys::cluster::limit_total_structures, basic::options::OptionKeys::relax::linear_chainbreak_weight, basic::options::OptionKeys::smhybrid::linker_cst, basic::options::OptionKeys::packing::linmem_ig, basic::options::OptionKeys::cluster::lite, basic::options::OptionKeys::corrections::score::lj_hbond_hdis, basic::options::OptionKeys::corrections::score::lj_hbond_OH_donor_dis, basic::options::OptionKeys::abinitio::log_frags, basic::options::OptionKeys::enzdes::loop_bb_min_allowed_dev, basic::options::OptionKeys::jumps::loop_definition_from_file, basic::options::OptionKeys::enzdes::loop_generator_trials, basic::options::OptionKeys::loopfcst::loopfcst, basic::options::OptionKeys::cluster::loops, basic::options::OptionKeys::lh::loopsizes, basic::options::OptionKeys::enzdes::make_consensus_mutations, basic::options::OptionKeys::cluster::make_ensemble_cst, basic::options::OptionKeys::holes::make_pdb, basic::options::OptionKeys::holes::make_voids, basic::options::OptionKeys::templates::max_align_pos, basic::options::OptionKeys::enzdes::max_bb_deviation, basic::options::OptionKeys::enzdes::max_bb_deviation_from_startstruct, basic::options::OptionKeys::packstat::max_cav_ball_radius, basic::options::OptionKeys::cluster::max_cluster_seeds, basic::options::OptionKeys::crossmatch::max_dis_all, basic::options::OptionKeys::crossmatch::max_dis_any, basic::options::OptionKeys::crossmatch::max_dis_metal, basic::options::OptionKeys::mc::max_rmsd_against_known_structures, basic::options::OptionKeys::packing::max_rotbump_energy, basic::options::OptionKeys::templates::max_shrink, basic::options::OptionKeys::jumps::max_strand_gap_allowed, basic::options::OptionKeys::cluster::max_total_cluster, basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::enzdes::mc_kt_high, basic::options::OptionKeys::enzdes::mc_kt_low, basic::options::OptionKeys::relax::membrane, basic::options::OptionKeys::wum::memory_limit, basic::options::OptionKeys::templates::min_align_pos, basic::options::OptionKeys::enzdes::min_all_jumps, basic::options::OptionKeys::enzdes::min_cacb_deviation, basic::options::OptionKeys::packstat::min_cav_ball_radius, basic::options::OptionKeys::packstat::min_cluster_overlap, basic::options::OptionKeys::templates::min_frag_size, basic::options::OptionKeys::resample::min_max_start_seq_sep, basic::options::OptionKeys::templates::min_nr_large_frags, basic::options::OptionKeys::templates::min_nr_small_frags, basic::options::OptionKeys::templates::min_padding, basic::options::OptionKeys::score::saxs::min_score, basic::options::OptionKeys::packstat::min_surface_accessibility, basic::options::OptionKeys::relax::min_tolerance, basic::options::OptionKeys::relax::min_type, basic::options::OptionKeys::smhybrid::minbb, basic::options::OptionKeys::relax::mini, basic::options::OptionKeys::holes::minimize, basic::options::OptionKeys::enzdes::minimize_all_ligand_torsions, basic::options::OptionKeys::relax::minimize_bond_angles, basic::options::OptionKeys::relax::minimize_bond_lengths, basic::options::OptionKeys::enzdes::minimize_ligand_torsions, basic::options::OptionKeys::relax::minimize_mainchain_bond_angles, basic::options::OptionKeys::relax::minimize_mainchain_bond_lengths, basic::options::OptionKeys::relax::minirelax_repeats, basic::options::OptionKeys::relax::minirelax_sdev, 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::rescore::msms_analysis, basic::options::OptionKeys::packing::multi_cool_annealer, basic::options::OptionKeys::wum::n_masters, basic::options::OptionKeys::wum::n_slaves_per_master, basic::options::OptionKeys::packing::ndruns, basic::options::OptionKeys::jumps::njumps, basic::options::OptionKeys::phil::nloop, basic::options::OptionKeys::enzdes::no_catres_min_in_loopgen, basic::options::OptionKeys::jumps::no_chainbreak_in_relax, basic::options::OptionKeys::templates::no_culling, basic::options::OptionKeys::corrections::score::no_his_his_pairE, basic::options::OptionKeys::score::no_lk_polar_desolvation, basic::options::OptionKeys::fold_cst::no_minimize, basic::options::OptionKeys::packing::no_optH, basic::options::OptionKeys::enzdes::no_packstat_calculation, basic::options::OptionKeys::templates::no_pick_fragments, basic::options::OptionKeys::fold_cst::no_recover_low_at_constraint_switch, basic::options::OptionKeys::jumps::no_sample_ss_jumps, basic::options::OptionKeys::jumps::no_shear, basic::options::OptionKeys::score::no_smooth_etables, basic::options::OptionKeys::enzdes::no_unconstrained_repack, basic::options::OptionKeys::jumps::no_wobble, basic::options::OptionKeys::templates::nr_large_copies, basic::options::OptionKeys::templates::nr_small_copies, basic::options::OptionKeys::smhybrid::nres_mono, basic::options::OptionKeys::lh::num_partitions, basic::options::OptionKeys::score::NV_lbound, basic::options::OptionKeys::score::NV_table, basic::options::OptionKeys::score::NV_ubound, basic::options::OptionKeys::abinitio::only_stage1, basic::options::OptionKeys::packing::ex4::operate, basic::options::OptionKeys::packing::ex3::operate, basic::options::OptionKeys::packing::ex2::operate, basic::options::OptionKeys::packing::ex1::operate, basic::options::OptionKeys::packing::optH_MCA, basic::options::OptionKeys::score::optH_patch, basic::options::OptionKeys::score::optH_weights, basic::options::OptionKeys::abinitio::optimize_cutpoints_margin, basic::options::OptionKeys::abinitio::optimize_cutpoints_using_kic, basic::options::OptionKeys::packing::outeriterations_scaling, basic::options::OptionKeys::score::output_etables, basic::options::OptionKeys::score::output_residue_energies, basic::options::OptionKeys::cluster::output_score_filter, basic::options::OptionKeys::jumps::overlap_chainbreak, basic::options::OptionKeys::relax::overlap_chainbreak_weight, basic::options::OptionKeys::abinitio::override_vdw_all_stages, basic::options::OptionKeys::packstat::oversample, basic::options::OptionKeys::corrections::score::p_aa_pp, basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift, basic::options::OptionKeys::packing::pack_missing_sidechains, basic::options::OptionKeys::packing::packing, basic::options::OptionKeys::packstat::packstat, basic::options::OptionKeys::packstat::packstat_pdb, basic::options::OptionKeys::evolution::padding_score_filter, basic::options::OptionKeys::evolution::padding_stage2_filter, basic::options::OptionKeys::jumps::pairing_file, basic::options::OptionKeys::templates::pairings, basic::options::OptionKeys::holes::params, basic::options::OptionKeys::evolution::parentlist, basic::options::OptionKeys::corrections::chemical::parse_charge, basic::options::OptionKeys::enzdes::parser_read_cloud_pdb, basic::options::OptionKeys::score::patch, basic::options::OptionKeys::corrections::score::PB_potential_file, basic::options::OptionKeys::corrections::score::PB_score_residue_range, basic::options::OptionKeys::phil::phil, basic::options::OptionKeys::templates::pick_multiple_sizes, basic::options::OptionKeys::cluster::population_weight, basic::options::OptionKeys::rescore::pose_metrics, basic::options::OptionKeys::templates::prefix, basic::options::OptionKeys::packing::preserve_c_beta, basic::options::OptionKeys::packing::prevent_repacking, basic::options::OptionKeys::smhybrid::primary_subsubunit, basic::options::OptionKeys::score::saxs::print_i_calc, basic::options::OptionKeys::packing::print_pymol_selection, basic::options::OptionKeys::enzdes::process_ligrot_separately, basic::options::OptionKeys::smhybrid::pseudosym, basic::options::OptionKeys::score::saxs::q_max, basic::options::OptionKeys::score::saxs::q_min, basic::options::OptionKeys::score::saxs::q_step, basic::options::OptionKeys::relax::quick, basic::options::OptionKeys::cluster::radius, basic::options::OptionKeys::corrections::score::rama_map, basic::options::OptionKeys::corrections::score::rama_not_squared, 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::score::ramaneighbors, basic::options::OptionKeys::jumps::ramp_chainbreaks, basic::options::OptionKeys::relax::ramp_constraints, basic::options::OptionKeys::fold_cst::ramp_coord_cst, basic::options::OptionKeys::jumps::random_sheets, basic::options::OptionKeys::packstat::raw_stats, basic::options::OptionKeys::smhybrid::rb_mag, basic::options::OptionKeys::mc::read_structures_into_pool, basic::options::OptionKeys::abinitio::recover_low_in_stages, basic::options::OptionKeys::score::saxs::ref_cen_spectrum, basic::options::OptionKeys::score::saxs::ref_fa_spectrum, basic::options::OptionKeys::score::ref_offsets, basic::options::OptionKeys::score::saxs::ref_pddf, basic::options::OptionKeys::score::saxs::ref_spectrum, basic::options::OptionKeys::smhybrid::refine, basic::options::OptionKeys::lh::refstruct, basic::options::OptionKeys::relax::relax, 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::cluster::remove_highest_energy_member, basic::options::OptionKeys::cluster::remove_singletons, basic::options::OptionKeys::smhybrid::rep_edge_files, basic::options::OptionKeys::packing::repack_only, 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::resample::resample, basic::options::OptionKeys::rescore::rescore, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::jumps::residue_pair_jump_file, basic::options::OptionKeys::packstat::residue_scores, basic::options::OptionKeys::holes::residue_scores, basic::options::OptionKeys::smhybrid::restrict_design_to_interface, basic::options::OptionKeys::smhybrid::restrict_design_to_subsub_interface, basic::options::OptionKeys::score::rms_target, basic::options::OptionKeys::evolution::rms_threshold, basic::options::OptionKeys::evolution::rms_topmargin, basic::options::OptionKeys::enzdes::rot_magnitude, basic::options::OptionKeys::enzdes::run_ligand_motifs, basic::options::OptionKeys::score::saxs::saxs, basic::options::OptionKeys::relax::sc_cst_maxdist, basic::options::OptionKeys::enzdes::sc_sc_bump_cutoff, basic::options::OptionKeys::smhybrid::scattach_res_files, basic::options::OptionKeys::corrections::score::score, basic::options::OptionKeys::score::score, basic::options::OptionKeys::corrections::score::score12prime, basic::options::OptionKeys::relax::script, basic::options::OptionKeys::relax::script_max_accept, basic::options::OptionKeys::enzdes::secmatch_Ecutoff, basic::options::OptionKeys::score::secondary_seqdep_refene_fname, basic::options::OptionKeys::abinitio::SEP_score_scalling, basic::options::OptionKeys::jumps::sep_switch_accelerate, basic::options::OptionKeys::fold_cst::seq_sep_stages, basic::options::OptionKeys::score::seqdep_refene_fname, basic::options::OptionKeys::relax::sequence, basic::options::OptionKeys::relax::sequence_file, basic::options::OptionKeys::abinitio::sheet_edge_pred, basic::options::OptionKeys::jumps::sheets, basic::options::OptionKeys::templates::shrink_pos_step, basic::options::OptionKeys::templates::shrink_step, basic::options::OptionKeys::score::sidechain_buried, basic::options::OptionKeys::score::sidechain_exposed, basic::options::OptionKeys::resample::silent, basic::options::OptionKeys::enzdes::single_loop_ensemble_size, basic::options::OptionKeys::rescore::skip, basic::options::OptionKeys::score::saxs::skip_hydrogens, basic::options::OptionKeys::fold_cst::skip_on_noviolation_in_stage1, basic::options::OptionKeys::abinitio::skip_stages, basic::options::OptionKeys::smhybrid::smhybrid, basic::options::OptionKeys::packing::soft_rep_design, basic::options::OptionKeys::packing::solvate, basic::options::OptionKeys::cluster::sort_groups_by_energy, basic::options::OptionKeys::smhybrid::ss, basic::options::OptionKeys::resample::stage1, basic::options::OptionKeys::fold_cst::stage1_ramp_cst_cycle_factor, basic::options::OptionKeys::relax::stage1_ramp_cycles, basic::options::OptionKeys::relax::stage1_ramp_inner_cycles, basic::options::OptionKeys::resample::stage2, basic::options::OptionKeys::fold_cst::stage2_constraint_threshold, basic::options::OptionKeys::relax::stage2_cycles, basic::options::OptionKeys::relax::stage2_repack_period, basic::options::OptionKeys::relax::stage3_cycles, basic::options::OptionKeys::enzdes::start_from_random_rb_conf, basic::options::OptionKeys::templates::strand_constraint, basic::options::OptionKeys::smhybrid::subsubs_attract, basic::options::OptionKeys::relax::superimpose_to_file, basic::options::OptionKeys::relax::superimpose_to_native, basic::options::OptionKeys::packstat::surface_accessibility, basic::options::OptionKeys::smhybrid::switch_concert_sub, basic::options::OptionKeys::score::symE_bonus, basic::options::OptionKeys::score::symE_units, 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::abinitio::symmetry_residue, basic::options::OptionKeys::resample::tag, basic::options::OptionKeys::evolution::targetdir, basic::options::OptionKeys::smhybrid::temperature, basic::options::OptionKeys::cluster::template_scores, basic::options::OptionKeys::templates::templates, basic::options::OptionKeys::cluster::thinout_factor, basic::options::OptionKeys::relax::thorough, basic::options::OptionKeys::packstat::threads, basic::options::OptionKeys::templates::fragsteal::topN, basic::options::OptionKeys::templates::cst::topN, basic::options::OptionKeys::jumps::topology_file, basic::options::OptionKeys::templates::topology_rank_cutoff, basic::options::OptionKeys::enzdes::trans_magnitude, basic::options::OptionKeys::wum::trim_proportion, basic::options::OptionKeys::packing::unboundrot, basic::options::OptionKeys::packing::use_electrostatic_repulsion, basic::options::OptionKeys::loopfcst::use_general_protocol, basic::options::OptionKeys::corrections::score::use_incorrect_hbond_deriv, basic::options::OptionKeys::packing::use_input_sc, basic::options::OptionKeys::phil::vall_file, basic::options::OptionKeys::templates::vary_frag_size, basic::options::OptionKeys::abinitio::vdw_weight_stage1, basic::options::OptionKeys::rescore::verbose, basic::options::OptionKeys::fold_cst::violation_skip_basis, basic::options::OptionKeys::fold_cst::violation_skip_ignore, basic::options::OptionKeys::smhybrid::virtual_nterm, basic::options::OptionKeys::smhybrid::virtual_res_files, basic::options::OptionKeys::holes::water, basic::options::OptionKeys::score::weights, basic::options::OptionKeys::templates::fragsteal::wExtern, basic::options::OptionKeys::templates::cst::wExtern, basic::options::OptionKeys::relax::wobblemoves, basic::options::OptionKeys::crossmatch::write_reduced_matchset, basic::options::OptionKeys::templates::fragsteal::wTopol, basic::options::OptionKeys::templates::cst::wTopol, and basic::options::OptionKeys::wum::wum.

Referenced by add_all_rosetta_options().

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

References basic::options::OptionKeys::loops::accept_aborted_loops, utility::options::OptionCollection::add(), basic::options::OptionKeys::AnchoredDesign::akash::akash, basic::options::OptionKeys::cm::aligner, basic::options::OptionKeys::AnchoredDesign::allow_anchor_repack, basic::options::OptionKeys::loops::allow_lig_move, basic::options::OptionKeys::cm::aln_format, basic::options::OptionKeys::cm::aln_length_filter, basic::options::OptionKeys::cm::aln_length_filter_quantile, basic::options::OptionKeys::loops::alternative_closure_protocol, basic::options::OptionKeys::AnchoredDesign::anchor, basic::options::OptionKeys::AnchoredDesign::testing::anchor_noise_constraints_mode, basic::options::OptionKeys::ms::anchor_offset, basic::options::OptionKeys::AnchoredDesign::testing::anchor_via_constraints, basic::options::OptionKeys::AnchoredDesign::AnchoredDesign, basic::options::OptionKeys::ddg::apply_rot_cst_to_mutation_region_only, basic::options::OptionKeys::assembly::assembly, basic::options::OptionKeys::james::atom_names, basic::options::OptionKeys::pose_metrics::atomic_burial_cutoff, basic::options::OptionKeys::ddg::avg_rot_cst_enrg, basic::options::OptionKeys::james::awesome_mode, basic::options::OptionKeys::loops::backrub_trials, basic::options::OptionKeys::dna::design::base_contacts_only, basic::options::OptionKeys::dna::design::bb_moves, basic::options::OptionKeys::dna::design::binding, basic::options::OptionKeys::blivens::blivens, basic::options::OptionKeys::fldsgn::blueprint, basic::options::OptionKeys::flxbb::blueprint, basic::options::OptionKeys::boinc::boinc, basic::options::OptionKeys::ms::Boltz_temp, basic::options::OptionKeys::dna::design::Boltz_temp, basic::options::OptionKeys::motifs::BPData, 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::flxbb::layer::burial, basic::options::OptionKeys::constraints::CA_tether, basic::options::OptionKeys::ddg::cap_rot_cst_enrg, basic::options::OptionKeys::casp::casp, basic::options::OptionKeys::loops::ccd_closure, basic::options::OptionKeys::loops::cen_patch, basic::options::OptionKeys::loops::cen_weights, basic::options::OptionKeys::membrane::center_mag, basic::options::OptionKeys::membrane::center_max_delta, basic::options::OptionKeys::membrane::center_search, basic::options::OptionKeys::lh::centroid_only, basic::options::OptionKeys::fldsgn::centroid_sfx, basic::options::OptionKeys::fldsgn::centroid_sfx_patch, basic::options::OptionKeys::loops::chain_break_tol, basic::options::OptionKeys::fast_loops::chainbreak_max, basic::options::OptionKeys::loops::chainbreak_max_accept, basic::options::OptionKeys::AnchoredDesign::chainbreak_weight, basic::options::OptionKeys::ms::checkpoint::checkpoint, basic::options::OptionKeys::dna::design::checkpoint, basic::options::OptionKeys::motifs::clear_bprots, basic::options::OptionKeys::motifs::close_enough, basic::options::OptionKeys::cm::cm, basic::options::OptionKeys::constraints::combine, basic::options::OptionKeys::constraints::combine_exclude_region, basic::options::OptionKeys::loops::combine_rate, basic::options::OptionKeys::constraints::compute_total_dist_cst, basic::options::OptionKeys::loops::constrain_rigid_segments, basic::options::OptionKeys::motifs::constraint_max, basic::options::OptionKeys::ddg::constraint_weight, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::flxbb::constraints_NtoC, basic::options::OptionKeys::flxbb::constraints_sheet, basic::options::OptionKeys::pose_metrics::contact_cutoffE, basic::options::OptionKeys::loops::coord_cst, basic::options::OptionKeys::boinc::cpu_frac, basic::options::OptionKeys::boinc::cpu_run_time, basic::options::OptionKeys::boinc::cpu_run_timeout, basic::options::OptionKeys::lh::create_db, basic::options::OptionKeys::lh::createdb_rms_cutoff, 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::assembly::cterm_seq, basic::options::OptionKeys::constraints::cull_with_native, basic::options::OptionKeys::blivens::disulfide_scorer::cys_prob, basic::options::OptionKeys::motifs::data_file, basic::options::OptionKeys::ddg::ddg, basic::options::OptionKeys::AnchoredDesign::debug, basic::options::OptionKeys::loops::debug, basic::options::OptionKeys::membrane::debug, basic::options::OptionKeys::james::debug, basic::options::OptionKeys::loops::debug_loop_closure, basic::options::OptionKeys::ddg::debug_output, basic::options::OptionKeys::casp::decoy, basic::options::OptionKeys::AnchoredDesign::testing::delete_interface_native_sidechains, basic::options::OptionKeys::DenovoProteinDesign::DenovoProteinDesign, basic::options::OptionKeys::boinc::description_file, basic::options::OptionKeys::dna::design::design, basic::options::OptionKeys::dna::specificity::design_DNA, basic::options::OptionKeys::dna::design::designable_second_shell, basic::options::OptionKeys::james::dist_thresholds, basic::options::OptionKeys::blivens::disulfide_scorer::disulfide_scorer, basic::options::OptionKeys::dna::dna, basic::options::OptionKeys::dna::design::dna_defs, basic::options::OptionKeys::dna::design::dna_defs_file, basic::options::OptionKeys::ddg::downweight_by_sasa, basic::options::OptionKeys::fldsgn::dr_cycles, basic::options::OptionKeys::dna::design::reversion::dscore_cutoff, basic::options::OptionKeys::dna::design::reversion::dspec_cutoff, basic::options::OptionKeys::motifs::dtest, basic::options::OptionKeys::constraints::dump_cst_set, basic::options::OptionKeys::motifs::dump_motifs, basic::options::OptionKeys::dna::specificity::dump_pdbs, basic::options::OptionKeys::ddg::dump_pdbs, basic::options::OptionKeys::AnchoredDesign::akash::dyepos, basic::options::OptionKeys::ddg::ens_variation, basic::options::OptionKeys::constraints::epr_distance, basic::options::OptionKeys::cm::ev_map, basic::options::OptionKeys::constraints::evaluate_max_seq_sep, basic::options::OptionKeys::flxbb::exclude_Ala, basic::options::OptionKeys::dna::specificity::exclude_bb_sc_hbonds, basic::options::OptionKeys::flxbb::exclude_Met, basic::options::OptionKeys::ddg::exclude_solvent_exposed_res, basic::options::OptionKeys::constraints::exit_on_bad_read, basic::options::OptionKeys::motifs::expand_motifs, basic::options::OptionKeys::lh::expire_after_rounds, basic::options::OptionKeys::loops::extend_length, basic::options::OptionKeys::loops::extended, basic::options::OptionKeys::loops::extended_beta, basic::options::OptionKeys::loops::extended_loop_file, basic::options::OptionKeys::loops::fa_closure_protocol, basic::options::OptionKeys::loops::fa_input, basic::options::OptionKeys::membrane::Fa_Membed_update, basic::options::OptionKeys::loops::fast, basic::options::OptionKeys::dna::specificity::fast, basic::options::OptionKeys::fast_loops::fast_loops, basic::options::OptionKeys::fast_loops::fast_relax_sequence_file, basic::options::OptionKeys::loops::fastrelax, 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::AnchoredDesign::filters::filters, basic::options::OptionKeys::loops::final_clean_fastrelax, basic::options::OptionKeys::loops::final_score_filter, basic::options::OptionKeys::loops::fix_natsc, basic::options::OptionKeys::membrane::fixed_membrane, basic::options::OptionKeys::fldsgn::fldsgn, basic::options::OptionKeys::motifs::flex_sugar, basic::options::OptionKeys::dna::design::flush, basic::options::OptionKeys::flxbb::flxbb, basic::options::OptionKeys::constraints::forest_file, basic::options::OptionKeys::cm::fr_temperature, basic::options::OptionKeys::ms::fraction_by_recombination, basic::options::OptionKeys::SSrbrelax::frag_files, basic::options::OptionKeys::loops::frag_files, basic::options::OptionKeys::dna::specificity::frag_files, basic::options::OptionKeys::SSrbrelax::frag_sizes, basic::options::OptionKeys::loops::frag_sizes, basic::options::OptionKeys::fast_loops::fragsample_patch, basic::options::OptionKeys::fast_loops::fragsample_score, basic::options::OptionKeys::boinc::frame_rate, basic::options::OptionKeys::fldsgn::fullatom_sfx, basic::options::OptionKeys::fldsgn::fullatom_sfx_patch, basic::options::OptionKeys::boinc::fullscreen, basic::options::OptionKeys::loops::gapspan, basic::options::OptionKeys::ms::generations, basic::options::OptionKeys::fast_loops::give_up, basic::options::OptionKeys::ddg::global, basic::options::OptionKeys::boinc::graphics, basic::options::OptionKeys::lh::grid_angle_multiplier, basic::options::OptionKeys::lh::grid_space_multiplier, basic::options::OptionKeys::loops::grow_attempts, basic::options::OptionKeys::ms::checkpoint::gz, basic::options::OptionKeys::ddg::harmonic_ca_tether, basic::options::OptionKeys::cm::hh_map, basic::options::OptionKeys::lh::homo_file, basic::options::OptionKeys::loops::idealize_after_loop_close, basic::options::OptionKeys::loops::idealize_before_loop_close, basic::options::OptionKeys::dna::design::specificity::include_dna_potentials, basic::options::OptionKeys::constraints::increase_constraints, basic::options::OptionKeys::ddg::initial_repack, basic::options::OptionKeys::LoopModel::input_pdb, basic::options::OptionKeys::SSrbrelax::input_pdb, basic::options::OptionKeys::loops::input_pdb, basic::options::OptionKeys::pose_metrics::inter_group_neighbors_cutoff, basic::options::OptionKeys::pose_metrics::interface_cutoff, basic::options::OptionKeys::ddg::interface_ddg, basic::options::OptionKeys::loops::intermedrelax, basic::options::OptionKeys::ms::checkpoint::interval, basic::options::OptionKeys::murphp::inv_kin_lig_loop_design_filename, basic::options::OptionKeys::dna::design::iterations, basic::options::OptionKeys::ddg::iterations, basic::options::OptionKeys::james::james, basic::options::OptionKeys::lh::jobname, basic::options::OptionKeys::loops::keep_natro, basic::options::OptionKeys::loops::kic_max_seglen, basic::options::OptionKeys::loops::kic_min_after_repack, basic::options::OptionKeys::loops::kic_recover_last, basic::options::OptionKeys::loops::kinematic_wrapper_cycles, basic::options::OptionKeys::krassk::krassk, basic::options::OptionKeys::ddg::last_accepted_pose_dir, basic::options::OptionKeys::flxbb::layer::layer, basic::options::OptionKeys::krassk::left_tail, basic::options::OptionKeys::lh::library_expiry_time, basic::options::OptionKeys::motifs::ligand_motif_sphere, basic::options::OptionKeys::cm::ligand_pdb, basic::options::OptionKeys::assembly::linkers_pdb1, basic::options::OptionKeys::assembly::linkers_pdb2, basic::options::OptionKeys::motifs::list_dnaconformers, basic::options::OptionKeys::motifs::list_motifs, basic::options::OptionKeys::ddg::local_opt_only, basic::options::OptionKeys::cm::loop_close_level, basic::options::OptionKeys::loops::loop_combine_rate, basic::options::OptionKeys::loops::loop_farlx, basic::options::OptionKeys::LoopModel::loop_file, basic::options::OptionKeys::loops::loop_file, basic::options::OptionKeys::loops::loop_model, basic::options::OptionKeys::cm::loop_mover, basic::options::OptionKeys::cm::loop_rebuild_filter, basic::options::OptionKeys::LoopModel::LoopModel, basic::options::OptionKeys::loops::looprlx_cycle_ratio, basic::options::OptionKeys::loops::loops, basic::options::OptionKeys::loops::loops_subset, basic::options::OptionKeys::loops::loopscores, basic::options::OptionKeys::ddg::lowest_x_decoys, basic::options::OptionKeys::lh::max_bbrms, basic::options::OptionKeys::boinc::max_cpu, basic::options::OptionKeys::constraints::max_cst_dist, basic::options::OptionKeys::motifs::max_depth, basic::options::OptionKeys::lh::max_emperor_lib_round, basic::options::OptionKeys::lh::max_emperor_lib_size, basic::options::OptionKeys::boinc::max_fps, basic::options::OptionKeys::cm::max_gap_extend, basic::options::OptionKeys::cm::max_gap_open, 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::lh::max_lib_size, basic::options::OptionKeys::cm::max_loop_rebuild, basic::options::OptionKeys::lh::max_loophash_per_structure, basic::options::OptionKeys::boinc::max_nstruct, basic::options::OptionKeys::lh::max_rms, basic::options::OptionKeys::ddg::mean, basic::options::OptionKeys::membrane::Membed_init, basic::options::OptionKeys::membrane::membrane, basic::options::OptionKeys::membrane::membrane_center, basic::options::OptionKeys::membrane::membrane_normal, basic::options::OptionKeys::membrane::Menv_penalties, basic::options::OptionKeys::dna::specificity::methylate, basic::options::OptionKeys::membrane::Mhbond_depth, basic::options::OptionKeys::ddg::min, basic::options::OptionKeys::lh::min_bbrms, basic::options::OptionKeys::fast_loops::min_breakout_fast_loops, basic::options::OptionKeys::fast_loops::min_breakout_good_loops, basic::options::OptionKeys::ddg::min_cst, basic::options::OptionKeys::ddg::min_cst_weights, basic::options::OptionKeys::fast_loops::min_fast_loops, basic::options::OptionKeys::cm::min_gap_extend, basic::options::OptionKeys::cm::min_gap_open, basic::options::OptionKeys::fast_loops::min_good_loops, basic::options::OptionKeys::cm::min_loop_size, basic::options::OptionKeys::lh::min_rms, basic::options::OptionKeys::james::min_seqsep, basic::options::OptionKeys::pose_metrics::min_sequence_separation, basic::options::OptionKeys::james::min_tol, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::james::min_type, basic::options::OptionKeys::ddg::min_with_cst, basic::options::OptionKeys::ddg::minimization_patch, basic::options::OptionKeys::ddg::minimization_scorefunction, basic::options::OptionKeys::dna::design::minimize, basic::options::OptionKeys::motifs::minimize, basic::options::OptionKeys::motifs::minimize_dna, basic::options::OptionKeys::rna::minimize_rounds, basic::options::OptionKeys::dna::specificity::minimize_tolerance, basic::options::OptionKeys::loops::mm_loop_file, basic::options::OptionKeys::dna::specificity::mode, basic::options::OptionKeys::dna::design::more_stats, basic::options::OptionKeys::dna::specificity::motif_begin, basic::options::OptionKeys::motifs::motif_build_defs, basic::options::OptionKeys::motifs::motif_build_position_chain, basic::options::OptionKeys::motifs::motif_build_positions, basic::options::OptionKeys::motifs::motif_filename, basic::options::OptionKeys::dna::specificity::motif_size, basic::options::OptionKeys::motifs::motifs, basic::options::OptionKeys::flxbb::movemap_from_blueprint, basic::options::OptionKeys::dna::specificity::moving_jump, 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_split_size, basic::options::OptionKeys::lh::mpi_master_save_score_only, basic::options::OptionKeys::lh::mpi_metropolis_temp, basic::options::OptionKeys::lh::mpi_outbound_wu_buffer_size, basic::options::OptionKeys::lh::mpi_resume, basic::options::OptionKeys::lh::mpi_save_state_interval, basic::options::OptionKeys::ms::ms, basic::options::OptionKeys::murphp::murphp, basic::options::OptionKeys::ddg::mut, basic::options::OptionKeys::ddg::mut_file, basic::options::OptionKeys::ddg::mut_only, basic::options::OptionKeys::ms::mutate_rate, basic::options::OptionKeys::james::n_clusters, basic::options::OptionKeys::james::n_designs, basic::options::OptionKeys::dna::specificity::n_inner, basic::options::OptionKeys::dna::specificity::n_outer, basic::options::OptionKeys::loops::n_rebuild_tries, basic::options::OptionKeys::constraints::named, basic::options::OptionKeys::flxbb::ncycle, basic::options::OptionKeys::blivens::disulfide_scorer::nds_prob, basic::options::OptionKeys::pose_metrics::neighbor_by_distance_cutoff, basic::options::OptionKeys::loops::neighbor_dist, basic::options::OptionKeys::dna::specificity::nloop, basic::options::OptionKeys::cm::nn, basic::options::OptionKeys::ddg::no_bb_movement, basic::options::OptionKeys::loops::no_combine_if_fail, basic::options::OptionKeys::ddg::no_constraints, basic::options::OptionKeys::constraints::no_cst_in_relax, basic::options::OptionKeys::AnchoredDesign::no_frags, basic::options::OptionKeys::membrane::no_interpolate_Mpair, basic::options::OptionKeys::constraints::no_linearize_bounded, basic::options::OptionKeys::loops::no_looprebuild, basic::options::OptionKeys::loops::no_randomize_loop, basic::options::OptionKeys::loops::non_ideal_loop_closing, basic::options::OptionKeys::loops::nonpivot_torsion_sampling, basic::options::OptionKeys::dna::design::nopack, basic::options::OptionKeys::dna::design::nopdb, 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::membrane::normal_start_angle, basic::options::OptionKeys::constraints::normalize_mixture_func, basic::options::OptionKeys::boinc::noshmem, basic::options::OptionKeys::fast_loops::nr_scored_fragments, basic::options::OptionKeys::fast_loops::nr_scored_sampling_passes, basic::options::OptionKeys::dna::specificity::nstep_water, basic::options::OptionKeys::assembly::nterm_seq, basic::options::OptionKeys::loops::num_desired_loops, basic::options::OptionKeys::casp::num_iterations, basic::options::OptionKeys::ms::num_packs, basic::options::OptionKeys::motifs::num_repacks, basic::options::OptionKeys::ms::numresults, basic::options::OptionKeys::lh::objective_function, basic::options::OptionKeys::AnchoredDesign::filters::omega, basic::options::OptionKeys::dna::specificity::only_repack, basic::options::OptionKeys::ddg::opt_input_structure, basic::options::OptionKeys::ddg::opt_radius, basic::options::OptionKeys::casp::opt_radius, basic::options::OptionKeys::loops::optimize_only_kic_region_sidechains_after_move, basic::options::OptionKeys::ddg::out, basic::options::OptionKeys::ddg::out_pdb_prefix, basic::options::OptionKeys::loops::outer_cycles, basic::options::OptionKeys::ddg::output_dir, basic::options::OptionKeys::motifs::output_file, basic::options::OptionKeys::dna::design::output_initial_pdb, basic::options::OptionKeys::loops::output_pdb, 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::fast_loops::overwrite_filter_scorefxn, basic::options::OptionKeys::ddg::pack_until_converge, basic::options::OptionKeys::robert::pairdata_input_pdb_list, basic::options::OptionKeys::dna::specificity::params, basic::options::OptionKeys::fast_loops::patch_filter_scorefxn, 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::assembly::pdb1, basic::options::OptionKeys::assembly::pdb2, basic::options::OptionKeys::dna::design::pdb_each_iteration, basic::options::OptionKeys::dna::specificity::pdb_pos, basic::options::OptionKeys::constraints::penalize_mixture_func, 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::constraints::pocket_constraint_weight, basic::options::OptionKeys::constraints::pocket_zero_derivatives, basic::options::OptionKeys::ms::pop_from_ss, basic::options::OptionKeys::ms::pop_size, basic::options::OptionKeys::flxbb::layer::pore_radius, basic::options::OptionKeys::pose_metrics::pose_metrics, basic::options::OptionKeys::dna::specificity::post_minimize, basic::options::OptionKeys::dna::specificity::pre_minimize, basic::options::OptionKeys::dna::specificity::pre_pack, basic::options::OptionKeys::ms::checkpoint::prefix, basic::options::OptionKeys::dna::design::preminimize_interface, basic::options::OptionKeys::dna::design::prepack_interface, basic::options::OptionKeys::assembly::preserve_sidechains_pdb1, basic::options::OptionKeys::assembly::preserve_sidechains_pdb2, basic::options::OptionKeys::ddg::print_per_res_diff, basic::options::OptionKeys::dna::design::probe_specificity, basic::options::OptionKeys::dna::design::protein_scan, basic::options::OptionKeys::motifs::quick_and_dirty, basic::options::OptionKeys::motifs::r1, basic::options::OptionKeys::motifs::r2, basic::options::OptionKeys::ddg::radius, basic::options::OptionKeys::ddg::ramp_repulsive, basic::options::OptionKeys::loops::random_grow_loops_by, basic::options::OptionKeys::loops::random_loop, basic::options::OptionKeys::loops::random_order, basic::options::OptionKeys::dna::specificity::randomize_motif, basic::options::OptionKeys::SSrbrelax::rb_file, basic::options::OptionKeys::ddg::rb_file, basic::options::OptionKeys::SSrbrelax::rb_param_file, basic::options::OptionKeys::ddg::rb_restrict_to_mutsite_nbrs, basic::options::OptionKeys::james::real, basic::options::OptionKeys::cm::recover_side_chains, 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::loops::refine, basic::options::OptionKeys::AnchoredDesign::refine_CCD_off, basic::options::OptionKeys::AnchoredDesign::refine_cycles, basic::options::OptionKeys::loops::refine_design_iterations, basic::options::OptionKeys::loops::refine_final_temp, basic::options::OptionKeys::loops::refine_init_temp, basic::options::OptionKeys::AnchoredDesign::refine_KIC_off, basic::options::OptionKeys::AnchoredDesign::refine_only, basic::options::OptionKeys::loops::refine_only, basic::options::OptionKeys::AnchoredDesign::refine_repack_cycles, basic::options::OptionKeys::casp::refine_res, basic::options::OptionKeys::AnchoredDesign::refine_temp, basic::options::OptionKeys::loops::relax, basic::options::OptionKeys::loops::relax_with_foldtree, basic::options::OptionKeys::loops::remodel, basic::options::OptionKeys::loops::remodel_final_temp, basic::options::OptionKeys::loops::remodel_init_temp, basic::options::OptionKeys::loops::remodel_kic_attempts, basic::options::OptionKeys::loops::remove_extended_loops, basic::options::OptionKeys::ms::checkpoint::rename, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::loops::repack_never, basic::options::OptionKeys::dna::design::repack_only, basic::options::OptionKeys::loops::repack_period, basic::options::OptionKeys::ms::restrict_to_canonical, basic::options::OptionKeys::dna::design::reversion::reversion, basic::options::OptionKeys::dna::design::reversion_scan, basic::options::OptionKeys::krassk::right_tail, basic::options::OptionKeys::lh::rms_limit, basic::options::OptionKeys::AnchoredDesign::rmsd, basic::options::OptionKeys::AnchoredDesign::testing::RMSD_only_this, basic::options::OptionKeys::loops::rmsd_tol, basic::options::OptionKeys::rna::rna, basic::options::OptionKeys::robert::robert, basic::options::OptionKeys::ddg::rot_cst_enrg_cutoff, basic::options::OptionKeys::motifs::rotlevel, basic::options::OptionKeys::casp::rots, basic::options::OptionKeys::motifs::rots2add, basic::options::OptionKeys::lh::rounds, basic::options::OptionKeys::fldsgn::run_flxbb, basic::options::OptionKeys::motifs::run_motifs, basic::options::OptionKeys::dna::specificity::run_test, basic::options::OptionKeys::lh::sandbox, basic::options::OptionKeys::AnchoredDesign::filters::sasa, basic::options::OptionKeys::pose_metrics::sasa_calculator_probe_radius, basic::options::OptionKeys::casp::sc_min, basic::options::OptionKeys::ddg::sc_min_only, basic::options::OptionKeys::AnchoredDesign::filters::score, basic::options::OptionKeys::loops::score_filter_cutoff, basic::options::OptionKeys::dna::specificity::score_function, basic::options::OptionKeys::blivens::score_type, basic::options::OptionKeys::loops::scored_frag_cycles, basic::options::OptionKeys::loops::select_best_loop_from, basic::options::OptionKeys::cm::seq_score, basic::options::OptionKeys::casp::sequential, basic::options::OptionKeys::ms::share_data, basic::options::OptionKeys::james::shift_sog_func, basic::options::OptionKeys::loops::short_frag_cycles, basic::options::OptionKeys::loops::shorten_long_terminal_loop, basic::options::OptionKeys::loops::shortrelax, basic::options::OptionKeys::AnchoredDesign::show_extended, basic::options::OptionKeys::ddg::single_res_scoring, basic::options::OptionKeys::lh::skim_size, 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::constraints::skip_redundant, basic::options::OptionKeys::constraints::skip_redundant_width, basic::options::OptionKeys::membrane::smooth_move_frac, basic::options::OptionKeys::dna::specificity::soft_rep, basic::options::OptionKeys::constraints::sog_cst_param, basic::options::OptionKeys::james::sog_cutoff, basic::options::OptionKeys::dna::design::sparse_pdb_output, basic::options::OptionKeys::motifs::special_rotweight, basic::options::OptionKeys::dna::design::specificity::specificity, basic::options::OptionKeys::dna::specificity::specificity, basic::options::OptionKeys::loops::spread, basic::options::OptionKeys::SSrbrelax::SSrbrelax, basic::options::OptionKeys::cm::start_models_only, basic::options::OptionKeys::loops::stealfrags, basic::options::OptionKeys::loops::stealfrags_times, basic::options::OptionKeys::loops::strict_loops, basic::options::OptionKeys::loops::superimpose_native, basic::options::OptionKeys::ddg::suppress_checkpointing, basic::options::OptionKeys::flxbb::layer::surface, basic::options::OptionKeys::krassk::tail_mode, basic::options::OptionKeys::krassk::tail_mode_name, basic::options::OptionKeys::krassk::tail_output_file_name, basic::options::OptionKeys::motifs::target_dna_defs, basic::options::OptionKeys::ddg::temperature, basic::options::OptionKeys::cm::template_ids, basic::options::OptionKeys::AnchoredDesign::testing::testing, basic::options::OptionKeys::dna::specificity::tf, basic::options::OptionKeys::james::thread_unaligned, basic::options::OptionKeys::loops::timer, basic::options::OptionKeys::james::torsion_thresholds, basic::options::OptionKeys::AnchoredDesign::unbound_mode, basic::options::OptionKeys::ddg::use_bound_cst, basic::options::OptionKeys::ddg::use_rotamer_constraints_to_native, basic::options::OptionKeys::loops::vall_file, basic::options::OptionKeys::AnchoredDesign::vary_cutpoints, basic::options::OptionKeys::fast_loops::vdw_delta, basic::options::OptionKeys::AnchoredDesign::testing::VDW_weight, basic::options::OptionKeys::ms::verbose, basic::options::OptionKeys::loops::vicinity_degree, basic::options::OptionKeys::loops::vicinity_sampling, basic::options::OptionKeys::fldsgn::view, basic::options::OptionKeys::flxbb::view, basic::options::OptionKeys::membrane::view, basic::options::OptionKeys::constraints::viol, basic::options::OptionKeys::constraints::viol_level, basic::options::OptionKeys::constraints::viol_type, basic::options::OptionKeys::boinc::watchdog, basic::options::OptionKeys::boinc::watchdog_time, basic::options::OptionKeys::dna::specificity::Wdna_bp, basic::options::OptionKeys::dna::specificity::Wdna_bs, basic::options::OptionKeys::ddg::weight_file, basic::options::OptionKeys::casp::weight_file, basic::options::OptionKeys::dna::specificity::weights_tag, basic::options::OptionKeys::dna::specificity::weights_tag_list, basic::options::OptionKeys::dna::specificity::Whack_elec, basic::options::OptionKeys::fast_loops::window_accept_ratio, basic::options::OptionKeys::lh::write_centroid_structs, basic::options::OptionKeys::ddg::wt, basic::options::OptionKeys::casp::wt, basic::options::OptionKeys::ddg::wt_only, basic::options::OptionKeys::motifs::z1, basic::options::OptionKeys::motifs::z2, and basic::options::OptionKeys::dna::design::z_cutoff.

Referenced by add_all_rosetta_options().

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

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, 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::pepspec::add_buffer_res, basic::options::OptionKeys::fold_from_loops::add_cst_loop, basic::options::OptionKeys::fold_from_loops::add_relax_cycles, basic::options::OptionKeys::hotspot::allow_gly, basic::options::OptionKeys::hotspot::allow_proline, basic::options::OptionKeys::remodel::RemodelLoopMover::allowed_closure_attempts, basic::options::OptionKeys::pepspec::anchor_type, basic::options::OptionKeys::matdes::dock::angle, basic::options::OptionKeys::hotspot::angle, basic::options::OptionKeys::hotspot::angle_res, basic::options::OptionKeys::flexpack::annealer::annealer, basic::options::OptionKeys::antibody::antibody, basic::options::OptionKeys::optE::approximate_decoy_entropy, basic::options::OptionKeys::archive::archive, basic::options::OptionKeys::optimization::armijo_min_stepsize, basic::options::OptionKeys::edensity::atom_mask, basic::options::OptionKeys::orbitals::atomic_cutoff, basic::options::OptionKeys::ufv::insert::attached_pdb, basic::options::OptionKeys::remodel::autopilot, basic::options::OptionKeys::canonical_sampling::probabilities::backrub, basic::options::OptionKeys::remodel::backrub, basic::options::OptionKeys::backrub::backrub, basic::options::OptionKeys::flexPepDocking::backrub_peptide, basic::options::OptionKeys::orbitals::bb_smooth, basic::options::OptionKeys::orbitals::bb_stats, basic::options::OptionKeys::bbg::bbg, basic::options::OptionKeys::hotspot::benchmark, basic::options::OptionKeys::pepspec::binding_score, basic::options::OptionKeys::remodel::blueprint, basic::options::OptionKeys::flexPepDocking::boost_fa_atr, basic::options::OptionKeys::patterson::Bsol, basic::options::OptionKeys::remodel::build_disulf, basic::options::OptionKeys::match::bump_tolerance, basic::options::OptionKeys::remodel::RemodelLoopMover::bypass_closure, basic::options::OptionKeys::remodel::bypass_fragments, 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::pepspec::calc_sasa, basic::options::OptionKeys::antibody::camelid, basic::options::OptionKeys::antibody::camelid_constraints, basic::options::OptionKeys::canonical_sampling::canonical_sampling, basic::options::OptionKeys::pepspec::cen_wts, basic::options::OptionKeys::edensity::centroid_density_mass, basic::options::OptionKeys::ufv::centroid_loop_mover, basic::options::OptionKeys::ufv::centroid_sfx, basic::options::OptionKeys::ufv::centroid_sfx_patch, basic::options::OptionKeys::pepspec::cg_res_type, basic::options::OptionKeys::fold_from_loops::checkpoint, basic::options::OptionKeys::remodel::checkpoint, basic::options::OptionKeys::chrisk::chrisk, basic::options::OptionKeys::pepspec::clash_cutoff, basic::options::OptionKeys::fold_from_loops::clear_csts, basic::options::OptionKeys::hotspot::cluster, basic::options::OptionKeys::remodel::cluster_on_entire_pose, basic::options::OptionKeys::remodel::cluster_radius, basic::options::OptionKeys::remodel::collect_clustered_top, basic::options::OptionKeys::hotspot::colonyE, basic::options::OptionKeys::archive::completion_notify_frequency, basic::options::OptionKeys::optE::component_weights, basic::options::OptionKeys::ufv::insert::connection_scheme, basic::options::OptionKeys::canonical_sampling::probabilities::conrot, basic::options::OptionKeys::match::consolidate_matches, basic::options::OptionKeys::optE::constant_logic_taskops_file, basic::options::OptionKeys::optE::constrain_weights, basic::options::OptionKeys::matdes::design::contact_dist, basic::options::OptionKeys::optE::rescore::context_round, basic::options::OptionKeys::rdc::correct_NH_length, basic::options::OptionKeys::DenovoProteinDesign::create_from_secondary_structure, basic::options::OptionKeys::DenovoProteinDesign::create_from_template_pdb, basic::options::OptionKeys::RBSegmentRelax::cst_pdb, basic::options::OptionKeys::RBSegmentRelax::cst_seqwidth, basic::options::OptionKeys::RBSegmentRelax::cst_width, basic::options::OptionKeys::RBSegmentRelax::cst_wt, basic::options::OptionKeys::remodel::cstfile, 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_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::optE::data_in, basic::options::OptionKeys::optE::data_out, basic::options::OptionKeys::patterson::debug, basic::options::OptionKeys::edensity::debug, basic::options::OptionKeys::edensity::debug_derivatives, basic::options::OptionKeys::RBSegmentRelax::default_movement_params, basic::options::OptionKeys::match::define_match_by_single_downstream_positioning, basic::options::OptionKeys::hotspot::density, basic::options::OptionKeys::matdes::design::design, basic::options::OptionKeys::rot_anl::design, basic::options::OptionKeys::remodel::design::design, basic::options::OptionKeys::optE::design_first, basic::options::OptionKeys::remodel::design::design_neighbors, basic::options::OptionKeys::flexPepDocking::design_peptide, basic::options::OptionKeys::optE::design_with_minpack, basic::options::OptionKeys::optimization::dfpmin_max_cycles, basic::options::OptionKeys::rot_anl::diff_to_min, basic::options::OptionKeys::DenovoProteinDesign::disallow_native_aa, basic::options::OptionKeys::orbitals::dist, basic::options::OptionKeys::remodel::disulf_landing_range, basic::options::OptionKeys::pepspec::diversify_lvl, basic::options::OptionKeys::pepspec::diversify_pep_seqs, basic::options::OptionKeys::matdes::dock::dock, basic::options::OptionKeys::DomainAssembly::DomainAssembly, basic::options::OptionKeys::remodel::domainFusion::domainFusion, basic::options::OptionKeys::optE::dont_use_reference_energies, basic::options::OptionKeys::patterson::dont_use_symm_in_pcalc, basic::options::OptionKeys::ufv::dr_cycles, basic::options::OptionKeys::remodel::dr_cycles, basic::options::OptionKeys::pepspec::dump_cg_bb, basic::options::OptionKeys::matdes::dock::dump_chainA_only, basic::options::OptionKeys::canonical_sampling::sampling::dump_loops_only, basic::options::OptionKeys::matdes::dock::dump_pdb, basic::options::OptionKeys::rot_anl::dump_pdb, basic::options::OptionKeys::rdc::dump_weight_trajectory, basic::options::OptionKeys::dwkulp::dwkulp, basic::options::OptionKeys::match::dynamic_grid_refinement, basic::options::OptionKeys::edensity::edensity, basic::options::OptionKeys::remodel::enable_ligand_aa, 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::optE::exclude_badrep_ddGs, basic::options::OptionKeys::flexPepDocking::extend_peptide, basic::options::OptionKeys::bbg::factorA, basic::options::OptionKeys::bbg::factorB, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves, basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves_ntrials, basic::options::OptionKeys::matdes::design::fav_nat_bonus, basic::options::OptionKeys::match::filter_colliding_upstream_residues, basic::options::OptionKeys::match::filter_upstream_downstream_collisions, basic::options::OptionKeys::remodel::design::find_neighbors, basic::options::OptionKeys::optE::fit_reference_energies_to_aa_profile_recovery, basic::options::OptionKeys::orbitals::fiveA, basic::options::OptionKeys::optE::fix, basic::options::OptionKeys::rdc::fix_normAzz, basic::options::OptionKeys::bbg::fix_short_segment, basic::options::OptionKeys::flexpack::annealer::fixbb_substitutions_scale, basic::options::OptionKeys::optE::fixed, 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::fold_and_dock::fold_and_dock, basic::options::OptionKeys::fold_from_loops::fold_from_loops, basic::options::OptionKeys::remodel::RemodelLoopMover::force_cutting_N, basic::options::OptionKeys::dwkulp::forcePolyAAfragments, 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::pepspec::frag_file, basic::options::OptionKeys::optE::free, basic::options::OptionKeys::patterson::Fsol, basic::options::OptionKeys::ufv::fullatom_sfx, basic::options::OptionKeys::ufv::fullatom_sfx_patch, basic::options::OptionKeys::hotspot::fxnal_group, basic::options::OptionKeys::pepspec::gen_pep_bb_sequential, basic::options::OptionKeys::remodel::generic_aa, basic::options::OptionKeys::match::geom_csts_downstream_output, basic::options::OptionKeys::match::geometric_constraint_file, 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::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::edensity::grid_spacing, basic::options::OptionKeys::match::grouper_downstream_rmsd, basic::options::OptionKeys::antibody::h1_template, basic::options::OptionKeys::antibody::h2_template, basic::options::OptionKeys::antibody::h3_template, basic::options::OptionKeys::orbitals::Haro, basic::options::OptionKeys::hotspot::hashfile, basic::options::OptionKeys::chrisk::hb_elec, basic::options::OptionKeys::flexPepDocking::hb_filter, basic::options::OptionKeys::remodel::hb_lrbb, basic::options::OptionKeys::remodel::hb_srbb, basic::options::OptionKeys::RBSegmentRelax::helical_movement_params, basic::options::OptionKeys::remodel::help, basic::options::OptionKeys::canonical_sampling::probabilities::hierarchical_max_cache_size, basic::options::OptionKeys::pepspec::homol_csts, basic::options::OptionKeys::hotspot::hotspot, basic::options::OptionKeys::flexPepDocking::hotspot_filter, basic::options::OptionKeys::orbitals::Hpol, basic::options::OptionKeys::DenovoProteinDesign::hydrophobic_polar_pattern, basic::options::OptionKeys::bbg::ignore_improper_res, basic::options::OptionKeys::remodel::RemodelLoopMover::independent_cycles, basic::options::OptionKeys::symmetry::initialize_rigid_body_dofs, basic::options::OptionKeys::flexpack::annealer::inner_iteration_scale, basic::options::OptionKeys::antibody::input_fv, basic::options::OptionKeys::RBSegmentRelax::input_pdb, basic::options::OptionKeys::pepspec::input_seq, basic::options::OptionKeys::ufv::insert::insert, basic::options::OptionKeys::ufv::insert::insert_pdb, basic::options::OptionKeys::remodel::domainFusion::insert_segment_from_pdb, basic::options::OptionKeys::pepspec::interface_cutoff, basic::options::OptionKeys::canonical_sampling::sampling::interval_data_dump, basic::options::OptionKeys::canonical_sampling::sampling::interval_pose_dump, basic::options::OptionKeys::optE::inv_kT_nataa, basic::options::OptionKeys::optE::inv_kT_natrot, basic::options::OptionKeys::optE::inv_kT_natstruct, basic::options::OptionKeys::rdc::iterate_reset, basic::options::OptionKeys::rdc::iterate_tol, basic::options::OptionKeys::rdc::iterate_weights, basic::options::OptionKeys::remodel::keep_jumps_in_minimizer, basic::options::OptionKeys::ufv::keep_junction_torsions, basic::options::OptionKeys::antibody::l1_template, basic::options::OptionKeys::antibody::l2_template, basic::options::OptionKeys::antibody::l3_template, basic::options::OptionKeys::optimization::lbfgs_M, basic::options::OptionKeys::optimization::lbfgs_max_cycles, basic::options::OptionKeys::ufv::left, basic::options::OptionKeys::hotspot::length, basic::options::OptionKeys::match::lig_name, basic::options::OptionKeys::match::ligand_rotamer_index, basic::options::OptionKeys::canonical_sampling::probabilities::localbb, basic::options::OptionKeys::remodel::RemodelLoopMover::lockdown_cycles, basic::options::OptionKeys::fold_from_loops::loop_mov_cterm, basic::options::OptionKeys::fold_from_loops::loop_mov_nterm, basic::options::OptionKeys::flexPepDocking::lowres_abinitio, basic::options::OptionKeys::flexPepDocking::lowres_preoptimize, basic::options::OptionKeys::edensity::mapfile, basic::options::OptionKeys::edensity::mapreso, basic::options::OptionKeys::match::match, basic::options::OptionKeys::match::match_grouper, basic::options::OptionKeys::remodel::match_rt_limit, basic::options::OptionKeys::matdes::matdes, basic::options::OptionKeys::backrub::max_atoms, basic::options::OptionKeys::remodel::max_disulf_allowed, basic::options::OptionKeys::canonical_sampling::sampling::max_files_per_dir, basic::options::OptionKeys::remodel::RemodelLoopMover::max_linear_chainbreak, basic::options::OptionKeys::optE::max_rms_from_native, basic::options::OptionKeys::canonical_sampling::sampling::mc_kt, basic::options::OptionKeys::flexPepDocking::mcm_cycles, basic::options::OptionKeys::optE::rescore::measure_sequence_recovery, basic::options::OptionKeys::edensity::membrane_axis, basic::options::OptionKeys::rot_anl::min, basic::options::OptionKeys::backrub::min_atoms, basic::options::OptionKeys::optE::min_decoy_rms_to_native, basic::options::OptionKeys::flexPepDocking::min_receptor_bb, basic::options::OptionKeys::patterson::model_B, basic::options::OptionKeys::antibody::model_h3, basic::options::OptionKeys::fold_and_dock::move_anchor_points, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_bcast, basic::options::OptionKeys::canonical_sampling::probabilities::MPI_sync_pools, basic::options::OptionKeys::optE::mpi_weight_minimization, 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::fold_from_loops::native_ca_cst, basic::options::OptionKeys::pepspec::native_pep_anchor, basic::options::OptionKeys::pepspec::native_pep_chain, basic::options::OptionKeys::orbitals::nbr_distance_squared, basic::options::OptionKeys::matdes::dock::neg_r, basic::options::OptionKeys::canonical_sampling::out::new_structures, basic::options::OptionKeys::rot_anl::nloop_scmove, basic::options::OptionKeys::pepspec::no_cen, basic::options::OptionKeys::pepspec::no_cen_rottrials, basic::options::OptionKeys::pepspec::no_design, basic::options::OptionKeys::remodel::design::no_design, basic::options::OptionKeys::optE::no_design, basic::options::OptionKeys::canonical_sampling::sampling::no_detailed_balance, basic::options::OptionKeys::patterson::no_ecalc, basic::options::OptionKeys::edensity::no_edens_in_minimizer, basic::options::OptionKeys::optE::no_hb_env_dependence, basic::options::OptionKeys::optE::no_hb_env_dependence_DNA, basic::options::OptionKeys::canonical_sampling::probabilities::no_jd2_output, basic::options::OptionKeys::remodel::no_jumps, basic::options::OptionKeys::ufv::no_neighborhood_design, basic::options::OptionKeys::orbitals::no_pos_bonus, basic::options::OptionKeys::pepspec::no_prepack_prot, basic::options::OptionKeys::optE::normalize_decoy_score_spread, basic::options::OptionKeys::RBSegmentRelax::nrbmoves, basic::options::OptionKeys::RBSegmentRelax::nrboutercycles, basic::options::OptionKeys::threadsc::nres, basic::options::OptionKeys::patterson::nshells, basic::options::OptionKeys::canonical_sampling::sampling::ntrials, basic::options::OptionKeys::remodel::num_frag_moves, basic::options::OptionKeys::matdes::design::num_subs_building_block, basic::options::OptionKeys::matdes::dock::num_subs_building_block, basic::options::OptionKeys::matdes::dock::num_subs_total, basic::options::OptionKeys::remodel::num_trajectory, basic::options::OptionKeys::optE::number_of_swarm_cycles, basic::options::OptionKeys::optE::number_of_swarm_particles, basic::options::OptionKeys::match::only_enumerate_non_match_redundant_ligand_rotamers, basic::options::OptionKeys::optE::optE, basic::options::OptionKeys::optE::optE_no_protein_hack_elec, basic::options::OptionKeys::optE::optE_soft_rep, basic::options::OptionKeys::optimization::optimization, 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::DenovoProteinDesign::optimize_loops, basic::options::OptionKeys::optE::optimize_nat_aa, basic::options::OptionKeys::optE::optimize_nat_rot, basic::options::OptionKeys::optE::optimize_pssm, basic::options::OptionKeys::optE::optimize_starting_free_weights, basic::options::OptionKeys::orbitals::orb_orb_stats, basic::options::OptionKeys::orbitals::orbital, basic::options::OptionKeys::orbitals::orbitals, basic::options::OptionKeys::match::orientation_atoms, basic::options::OptionKeys::canonical_sampling::out::out, basic::options::OptionKeys::flexpack::annealer::outer_iteration_scale, basic::options::OptionKeys::optE::rescore::outlog, basic::options::OptionKeys::fold_from_loops::output_centroid, basic::options::OptionKeys::match::output_format, basic::options::OptionKeys::remodel::output_fragfiles, basic::options::OptionKeys::match::output_matches_per_group, basic::options::OptionKeys::match::output_matchres_only, basic::options::OptionKeys::canonical_sampling::sampling::output_only_cluster_transitions, basic::options::OptionKeys::optE::output_top_n_new_decoys, basic::options::OptionKeys::pepspec::p_homol_csts, basic::options::OptionKeys::flexPepDocking::params_file, basic::options::OptionKeys::optE::parse_tagfile, basic::options::OptionKeys::parser::parser, basic::options::OptionKeys::parser::patchdock, basic::options::OptionKeys::parser::patchdock_random_entry, basic::options::OptionKeys::patterson::patterson, basic::options::OptionKeys::pepspec::pdb_list, basic::options::OptionKeys::matdes::dock::pdbID, basic::options::OptionKeys::pepspec::pep_anchor, basic::options::OptionKeys::pepspec::pep_chain, basic::options::OptionKeys::flexPepDocking::pep_fold_only, basic::options::OptionKeys::flexPepDocking::pep_refine, basic::options::OptionKeys::pepspec::pepspec, basic::options::OptionKeys::flexPepDocking::peptide_anchor, basic::options::OptionKeys::flexPepDocking::peptide_chain, basic::options::OptionKeys::flexPepDocking::peptide_loop_model, basic::options::OptionKeys::symmetry::perturb_rigid_body_dofs, basic::options::OptionKeys::pepspec::phipsi_analysis, basic::options::OptionKeys::backrub::pivot_atoms, basic::options::OptionKeys::backrub::pivot_residues, basic::options::OptionKeys::matdes::dock::prefix, basic::options::OptionKeys::rot_anl::premin, 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::rdc::print_rdc_values, basic::options::OptionKeys::canonical_sampling::probabilities::probabilities, basic::options::OptionKeys::parser::protocol, basic::options::OptionKeys::flexpack::annealer::pure_movebb_substitutions_scale, basic::options::OptionKeys::remodel::quick_and_dirty, basic::options::OptionKeys::matdes::dock::radial_disp, basic::options::OptionKeys::patterson::radius_cutoffs, basic::options::OptionKeys::flexPepDocking::ramp_fa_rep, basic::options::OptionKeys::optE::ramp_nativeness, basic::options::OptionKeys::flexPepDocking::ramp_rama, 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::remodel::randomize_equivalent_fragments, basic::options::OptionKeys::remodel::RemodelLoopMover::randomize_loops, basic::options::OptionKeys::optE::randomly_perturb_starting_free_weights, basic::options::OptionKeys::remodel::rank_by_bsasa, basic::options::OptionKeys::RBSegmentRelax::rb_file, basic::options::OptionKeys::fold_and_dock::rb_rot_magnitude, basic::options::OptionKeys::RBSegmentRelax::rb_scorefxn, basic::options::OptionKeys::fold_and_dock::rb_trans_magnitude, basic::options::OptionKeys::flexPepDocking::rbMCM, basic::options::OptionKeys::RBSegmentRelax::RBSegmentRelax, basic::options::OptionKeys::rdc::rdc, basic::options::OptionKeys::remodel::read_fragfile, basic::options::OptionKeys::edensity::realign, basic::options::OptionKeys::flexPepDocking::receptor_chain, basic::options::OptionKeys::optE::recover_nat_rot, basic::options::OptionKeys::rdc::reduced_couplings, basic::options::OptionKeys::pepspec::ref_pdb_list, basic::options::OptionKeys::flexPepDocking::ref_startstruct, basic::options::OptionKeys::remodel::remodel, basic::options::OptionKeys::remodel::RemodelLoopMover::RemodelLoopMover, basic::options::OptionKeys::pepspec::remove_input_bb, basic::options::OptionKeys::edensity::render_sigma, basic::options::OptionKeys::flexPepDocking::rep_ramp_cycles, basic::options::OptionKeys::rot_anl::repack, 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::match::required_active_site_atom_names, basic::options::OptionKeys::archive::reread_all_structures, basic::options::OptionKeys::fold_from_loops::res_design_bs, basic::options::OptionKeys::hotspot::rescore, basic::options::OptionKeys::optE::rescore::rescore, basic::options::OptionKeys::hotspot::residue, basic::options::OptionKeys::patterson::resolution_cutoffs, basic::options::OptionKeys::matdes::design::revert_ids, basic::options::OptionKeys::matdes::design::revert_pos, basic::options::OptionKeys::remodel::rg, basic::options::OptionKeys::ufv::right, 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::hotspot::rms_hotspot, basic::options::OptionKeys::hotspot::rms_hotspot_res, basic::options::OptionKeys::hotspot::rms_target, basic::options::OptionKeys::patterson::rmsd, basic::options::OptionKeys::pepspec::rmsd_analysis, basic::options::OptionKeys::rot_anl::rmsd_tol, basic::options::OptionKeys::rot_anl::rot_anl, basic::options::OptionKeys::fold_and_dock::rot_mag_smooth, basic::options::OptionKeys::fold_and_dock::rotate_anchor_to_x, basic::options::OptionKeys::flexpack::annealer::rotsub_movebb_substitutions_scale, basic::options::OptionKeys::remodel::rsigma, basic::options::OptionKeys::rot_anl::rtmin, basic::options::OptionKeys::remodel::run_confirmation, basic::options::OptionKeys::pepspec::run_sequential, basic::options::OptionKeys::canonical_sampling::sampling::sampling, basic::options::OptionKeys::pepspec::save_all_pdbs, basic::options::OptionKeys::canonical_sampling::sampling::save_loops_only, basic::options::OptionKeys::pepspec::save_low_pdbs, basic::options::OptionKeys::remodel::save_top, basic::options::OptionKeys::canonical_sampling::probabilities::sc, basic::options::OptionKeys::orbitals::sc_bb, basic::options::OptionKeys::hotspot::sc_only, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform, basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot, basic::options::OptionKeys::patterson::sc_scaling, basic::options::OptionKeys::edensity::sc_scaling, basic::options::OptionKeys::orbitals::sc_stats, basic::options::OptionKeys::match::scaffold_active_site_residues, basic::options::OptionKeys::match::scaffold_active_site_residues_for_geomcsts, basic::options::OptionKeys::rot_anl::scmove, basic::options::OptionKeys::flexPepDocking::score_filter, basic::options::OptionKeys::edensity::score_symm_complex, basic::options::OptionKeys::rot_anl::score_tol, basic::options::OptionKeys::parser::script_vars, basic::options::OptionKeys::DenovoProteinDesign::secondary_structure_file, basic::options::OptionKeys::rdc::segment_file, basic::options::OptionKeys::rdc::segment_scoring_mode, basic::options::OptionKeys::rdc::select_residues_file, basic::options::OptionKeys::pepspec::seq_align, basic::options::OptionKeys::fold_and_dock::set_anchor_at_closest_point, basic::options::OptionKeys::remodel::design::silent, basic::options::OptionKeys::remodel::RemodelLoopMover::simultaneous_cycles, basic::options::OptionKeys::RBSegmentRelax::skip_fragment_moves, basic::options::OptionKeys::remodel::design::skip_partial, basic::options::OptionKeys::RBSegmentRelax::skip_rb_moves, basic::options::OptionKeys::RBSegmentRelax::skip_seqshift_moves, basic::options::OptionKeys::fold_and_dock::slide_contact_frequency, basic::options::OptionKeys::edensity::sliding_window, basic::options::OptionKeys::edensity::sliding_window_wt, basic::options::OptionKeys::flexPepDocking::smove_angle_range, basic::options::OptionKeys::antibody::snug_loops, basic::options::OptionKeys::antibody::snugfit, basic::options::OptionKeys::pepspec::soft_wts, basic::options::OptionKeys::optE::sqrt_pssm, basic::options::OptionKeys::threadsc::src_chain, basic::options::OptionKeys::threadsc::src_first_resid, basic::options::OptionKeys::ufv::ss, basic::options::OptionKeys::remodel::ss_pair, basic::options::OptionKeys::pepspec::ss_type, basic::options::OptionKeys::optE::starting_refEs, basic::options::OptionKeys::RBSegmentRelax::strand_movement_params, basic::options::OptionKeys::fold_from_loops::swap_loops, basic::options::OptionKeys::remodel::swap_refine_confirm_protocols, basic::options::OptionKeys::symmetry::symmetric_rmsd, basic::options::OptionKeys::symmetry::symmetry, basic::options::OptionKeys::symmetry::symmetry_definition, basic::options::OptionKeys::rot_anl::tag, basic::options::OptionKeys::hotspot::target, basic::options::OptionKeys::hotspot::target_dist, basic::options::OptionKeys::hotspot::target_res, basic::options::OptionKeys::orbitals::ten, basic::options::OptionKeys::rdc::tensor_weight, basic::options::OptionKeys::threadsc::threadsc, basic::options::OptionKeys::orbitals::threeA, basic::options::OptionKeys::hotspot::threshold, basic::options::OptionKeys::flexPepDocking::torsionsMCM, basic::options::OptionKeys::rdc::total_weight, basic::options::OptionKeys::fold_and_dock::trans_mag_smooth, basic::options::OptionKeys::canonical_sampling::sampling::transition_threshold, basic::options::OptionKeys::threadsc::trg_anchor, basic::options::OptionKeys::threadsc::trg_chain, basic::options::OptionKeys::threadsc::trg_first_resid, basic::options::OptionKeys::remodel::two_chain_tree, basic::options::OptionKeys::ufv::ufv, basic::options::OptionKeys::ufv::ufv_loops, 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::pepspec::upweight_interface, basic::options::OptionKeys::remodel::use_blueprint_sequence, basic::options::OptionKeys::remodel::use_ccd_refine, basic::options::OptionKeys::flexPepDocking::use_cen_score, basic::options::OptionKeys::remodel::use_clusters, basic::options::OptionKeys::remodel::use_dssp_assignment, basic::options::OptionKeys::ufv::use_fullmer, basic::options::OptionKeys::canonical_sampling::probabilities::use_hierarchical_clustering, basic::options::OptionKeys::pepspec::use_input_bb, basic::options::OptionKeys::patterson::use_on_repack, basic::options::OptionKeys::remodel::use_pose_relax, basic::options::OptionKeys::remodel::use_same_length_fragments, basic::options::OptionKeys::patterson::use_spline_interpolation, basic::options::OptionKeys::DenovoProteinDesign::use_template_sequence, basic::options::OptionKeys::DenovoProteinDesign::use_template_topology, basic::options::OptionKeys::orbitals::verbose, basic::options::OptionKeys::parser::view, basic::options::OptionKeys::patterson::weight, basic::options::OptionKeys::hotspot::weighted_density, basic::options::OptionKeys::rdc::weights, basic::options::OptionKeys::optE::rescore::weights, basic::options::OptionKeys::optE::weights, basic::options::OptionKeys::edensity::whole_structure_allatom_wt, basic::options::OptionKeys::edensity::whole_structure_ca_wt, and basic::options::OptionKeys::optE::wrap_dof_optimization.

Referenced by add_all_rosetta_options().

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