Rosetta Utilities  2014.35
Namespaces | Functions
OptionKeys.cc.gen0.hh File Reference

Namespaces

 in
 
 in::dbms
 
 in::path
 
 in::file
 
 in::rdf
 
 inout
 
 inout::dbms
 
 out
 
 out::file
 
 out::path
 
 run
 
 jd2
 
 score
 
 score::saxs
 
 packing
 
 packing::ex1
 
 packing::ex2
 
 packing::ex3
 
 packing::ex4
 
 packing::ex1aro
 
 packing::ex2aro
 
 packing::ex1aro_exposed
 
 packing::ex2aro_exposed
 
 packing::exdna
 
 archive
 
 chemical
 
 constraints
 
 corrections
 
 corrections::score
 
 corrections::chemical
 
 evaluation
 
 filters
 
 gpu
 
 jumps
 
 loops
 

Functions

BooleanOptionKey const in::in ("in")
 
StringOptionKey const in::Ntermini ("in:Ntermini")
 
StringOptionKey const in::Ctermini ("in:Ctermini")
 
BooleanOptionKey const in::use_truncated_termini ("in:use_truncated_termini")
 
BooleanOptionKey const in::ignore_unrecognized_res ("in:ignore_unrecognized_res")
 
BooleanOptionKey const in::ignore_waters ("in:ignore_waters")
 
BooleanOptionKey const in::add_orbitals ("in:add_orbitals")
 
BooleanOptionKey const in::show_all_fixes ("in:show_all_fixes")
 
BooleanOptionKey const in::include_sugars ("in:include_sugars")
 
BooleanOptionKey const in::include_lipids ("in:include_lipids")
 
BooleanOptionKey const in::include_surfaces ("in:include_surfaces")
 
BooleanOptionKey const in::membrane ("in:membrane")
 
BooleanOptionKey const in::remember_unrecognized_res ("in:remember_unrecognized_res")
 
BooleanOptionKey const in::remember_unrecognized_water ("in:remember_unrecognized_water")
 
BooleanOptionKey const in::preserve_crystinfo ("in:preserve_crystinfo")
 
BooleanOptionKey const in::detect_oops ("in:detect_oops")
 
BooleanOptionKey const in::detect_disulf ("in:detect_disulf")
 
RealOptionKey const in::detect_disulf_tolerance ("in:detect_disulf_tolerance")
 
BooleanOptionKey const in::auto_setup_metals ("in:auto_setup_metals")
 
RealOptionKey const in::metals_detection_LJ_multiplier ("in:metals_detection_LJ_multiplier")
 
RealOptionKey const in::metals_distance_constraint_multiplier ("in:metals_distance_constraint_multiplier")
 
RealOptionKey const in::metals_angle_constraint_multiplier ("in:metals_angle_constraint_multiplier")
 
FileOptionKey const in::fix_disulf ("in:fix_disulf")
 
BooleanOptionKey const in::missing_density_to_jump ("in:missing_density_to_jump")
 
IntegerVectorOptionKey const in::target_residues ("in:target_residues")
 
IntegerVectorOptionKey const in::replonly_residues ("in:replonly_residues")
 
BooleanOptionKey const in::replonly_loops ("in:replonly_loops")
 
BooleanOptionKey const in::use_database ("in:use_database")
 
StringVectorOptionKey const in::select_structures_from_database ("in:select_structures_from_database")
 
BooleanOptionKey const in::dbms::dbms ("in:dbms")
 
StringVectorOptionKey const in::dbms::struct_ids ("in:dbms:struct_ids")
 
PathVectorOptionKey const in::path::path ("in:path")
 
PathVectorOptionKey const in::path::fragments ("in:path:fragments")
 
PathVectorOptionKey const in::path::pdb ("in:path:pdb")
 
PathVectorOptionKey const in::path::database ("in:path:database")
 
BooleanOptionKey const in::file::file ("in:file")
 
FileVectorOptionKey const in::file::s ("in:file:s")
 
FileVectorOptionKey const in::file::t ("in:file:t")
 
FileVectorOptionKey const in::file::l ("in:file:l")
 
FileVectorOptionKey const in::file::list ("in:file:list")
 
FileVectorOptionKey const in::file::screening_list ("in:file:screening_list")
 
FileOptionKey const in::file::screening_job_file ("in:file:screening_job_file")
 
BooleanOptionKey const in::file::shuffle_screening_jobs ("in:file:shuffle_screening_jobs")
 
FileOptionKey const in::file::native ("in:file:native")
 
FileOptionKey const in::file::torsion_bin_probs ("in:file:torsion_bin_probs")
 
FileOptionKey const in::file::PCS_frag_cst ("in:file:PCS_frag_cst")
 
FileOptionKey const in::file::talos_phi_psi ("in:file:talos_phi_psi")
 
FileOptionKey const in::file::talos_cs ("in:file:talos_cs")
 
FileOptionKey const in::file::ambig_talos_cs_A ("in:file:ambig_talos_cs_A")
 
FileOptionKey const in::file::ambig_talos_cs_B ("in:file:ambig_talos_cs_B")
 
IntegerVectorOptionKey const in::file::native_exclude_res ("in:file:native_exclude_res")
 
StringVectorOptionKey const in::file::tags ("in:file:tags")
 
StringVectorOptionKey const in::file::user_tags ("in:file:user_tags")
 
FileOptionKey const in::file::tagfile ("in:file:tagfile")
 
FileVectorOptionKey const in::file::frag_files ("in:file:frag_files")
 
StringVectorOptionKey const in::file::remap_pdb_atom_names_for ("in:file:remap_pdb_atom_names_for")
 
FileVectorOptionKey const in::file::extra_res ("in:file:extra_res")
 
FileVectorOptionKey const in::file::extra_res_fa ("in:file:extra_res_fa")
 
FileVectorOptionKey const in::file::extra_res_mol ("in:file:extra_res_mol")
 
StringOptionKey const in::file::extra_res_database ("in:file:extra_res_database")
 
StringOptionKey const in::file::extra_res_pq_schema ("in:file:extra_res_pq_schema")
 
StringOptionKey const in::file::extra_res_database_mode ("in:file:extra_res_database_mode")
 
FileOptionKey const in::file::extra_res_database_resname_list ("in:file:extra_res_database_resname_list")
 
FileVectorOptionKey const in::file::extra_res_cen ("in:file:extra_res_cen")
 
PathVectorOptionKey const in::file::extra_res_path ("in:file:extra_res_path")
 
PathVectorOptionKey const in::file::extra_rot_lib_path ("in:file:extra_rot_lib_path")
 
PathVectorOptionKey const in::file::extra_res_batch_path ("in:file:extra_res_batch_path")
 
FileVectorOptionKey const in::file::extra_patch_fa ("in:file:extra_patch_fa")
 
FileVectorOptionKey const in::file::extra_patch_cen ("in:file:extra_patch_cen")
 
StringOptionKey const in::file::frag3 ("in:file:frag3")
 
StringOptionKey const in::file::frag9 ("in:file:frag9")
 
StringOptionKey const in::file::fragA ("in:file:fragA")
 
StringOptionKey const in::file::fragB ("in:file:fragB")
 
StringOptionKey const in::file::surface_vectors ("in:file:surface_vectors")
 
StringOptionKey const in::file::xyz ("in:file:xyz")
 
BooleanOptionKey const in::file::keep_input_scores ("in:file:keep_input_scores")
 
BooleanOptionKey const in::file::lazy_silent ("in:file:lazy_silent")
 
FileVectorOptionKey const in::file::silent ("in:file:silent")
 
BooleanOptionKey const in::file::force_silent_bitflip_on_read ("in:file:force_silent_bitflip_on_read")
 
FileVectorOptionKey const in::file::atom_tree_diff ("in:file:atom_tree_diff")
 
StringOptionKey const in::file::zip ("in:file:zip")
 
FileVectorOptionKey const in::file::boinc_wu_zip ("in:file:boinc_wu_zip")
 
BooleanOptionKey const in::file::fullatom ("in:file:fullatom")
 
BooleanOptionKey const in::file::centroid_input ("in:file:centroid_input")
 
BooleanOptionKey const in::file::centroid ("in:file:centroid")
 
StringOptionKey const in::file::treat_residues_in_these_chains_as_separate_chemical_entities ("in:file:treat_residues_in_these_chains_as_separate_chemical_entities")
 
StringOptionKey const in::file::residue_type_set ("in:file:residue_type_set")
 
FileOptionKey const in::file::pca ("in:file:pca")
 
RealOptionKey const in::file::silent_energy_cut ("in:file:silent_energy_cut")
 
FileVectorOptionKey const in::file::silent_list ("in:file:silent_list")
 
BooleanOptionKey const in::file::silent_renumber ("in:file:silent_renumber")
 
StringOptionKey const in::file::silent_struct_type ("in:file:silent_struct_type")
 
BooleanOptionKey const in::file::silent_read_through_errors ("in:file:silent_read_through_errors")
 
StringOptionKey const in::file::silent_score_prefix ("in:file:silent_score_prefix")
 
IntegerOptionKey const in::file::silent_select_random ("in:file:silent_select_random")
 
IntegerOptionKey const in::file::silent_select_range_start ("in:file:silent_select_range_start")
 
IntegerOptionKey const in::file::silent_select_range_mul ("in:file:silent_select_range_mul")
 
IntegerOptionKey const in::file::silent_select_range_len ("in:file:silent_select_range_len")
 
BooleanOptionKey const in::file::skip_failed_simulations ("in:file:skip_failed_simulations")
 
StringVectorOptionKey const in::file::silent_scores_wanted ("in:file:silent_scores_wanted")
 
FileVectorOptionKey const in::file::fasta ("in:file:fasta")
 
FileVectorOptionKey const in::file::pssm ("in:file:pssm")
 
StringVectorOptionKey const in::file::seq ("in:file:seq")
 
FileOptionKey const in::file::checkpoint ("in:file:checkpoint")
 
FileOptionKey const in::file::binary_chk ("in:file:binary_chk")
 
FileVectorOptionKey const in::file::alignment ("in:file:alignment")
 
FileVectorOptionKey const in::file::alignment2 ("in:file:alignment2")
 
FileOptionKey const in::file::rama2b_map ("in:file:rama2b_map")
 
FileOptionKey const in::file::psipred_ss2 ("in:file:psipred_ss2")
 
FileOptionKey const in::file::dssp ("in:file:dssp")
 
BooleanOptionKey const in::file::fail_on_bad_hbond ("in:file:fail_on_bad_hbond")
 
FileOptionKey const in::file::movemap ("in:file:movemap")
 
BooleanOptionKey const in::file::repair_sidechains ("in:file:repair_sidechains")
 
BooleanOptionKey const in::file::no_binary_dunlib ("in:file:no_binary_dunlib")
 
IntegerOptionKey const in::file::extended_pose ("in:file:extended_pose")
 
FileVectorOptionKey const in::file::template_pdb ("in:file:template_pdb")
 
FileOptionKey const in::file::template_silent ("in:file:template_silent")
 
FileVectorOptionKey const in::file::rdc ("in:file:rdc")
 
FileVectorOptionKey const in::file::csa ("in:file:csa")
 
FileVectorOptionKey const in::file::dc ("in:file:dc")
 
FileVectorOptionKey const in::file::burial ("in:file:burial")
 
FileVectorOptionKey const in::file::vall ("in:file:vall")
 
BooleanOptionKey const in::file::rescore ("in:file:rescore")
 
StringOptionKey const in::file::spanfile ("in:file:spanfile")
 
StringOptionKey const in::file::lipofile ("in:file:lipofile")
 
StringOptionKey const in::file::HDX ("in:file:HDX")
 
RealOptionKey const in::file::d2h_sa_reweight ("in:file:d2h_sa_reweight")
 
FileOptionKey const in::file::sucker_params ("in:file:sucker_params")
 
FileOptionKey const in::file::fold_tree ("in:file:fold_tree")
 
BooleanOptionKey const in::file::obey_ENDMDL ("in:file:obey_ENDMDL")
 
BooleanOptionKey const in::file::new_chain_order ("in:file:new_chain_order")
 
FileOptionKey const in::file::ddg_predictions_file ("in:file:ddg_predictions_file")
 
ResidueChainVectorOptionKey const in::file::input_res ("in:file:input_res")
 
IntegerVectorOptionKey const in::file::minimize_res ("in:file:minimize_res")
 
StringOptionKey const in::file::md_schfile ("in:file:md_schfile")
 
BooleanOptionKey const in::file::read_pdb_link_records ("in:file:read_pdb_link_records")
 
FileOptionKey const in::file::native_contacts ("in:file:native_contacts")
 
BooleanOptionKey const in::rdf::rdf ("in:rdf")
 
BooleanOptionKey const in::rdf::sep_bb_ss ("in:rdf:sep_bb_ss")
 
BooleanOptionKey const inout::inout ("inout")
 
BooleanOptionKey const inout::fold_tree_io ("inout:fold_tree_io")
 
BooleanOptionKey const inout::dump_connect_info ("inout:dump_connect_info")
 
RealOptionKey const inout::connect_info_cutoff ("inout:connect_info_cutoff")
 
BooleanOptionKey const inout::dbms::dbms ("inout:dbms")
 
StringOptionKey const inout::dbms::mode ("inout:dbms:mode")
 
StringOptionKey const inout::dbms::database_name ("inout:dbms:database_name")
 
StringOptionKey const inout::dbms::pq_schema ("inout:dbms:pq_schema")
 
StringOptionKey const inout::dbms::host ("inout:dbms:host")
 
StringOptionKey const inout::dbms::user ("inout:dbms:user")
 
StringOptionKey const inout::dbms::password ("inout:dbms:password")
 
IntegerOptionKey const inout::dbms::port ("inout:dbms:port")
 
BooleanOptionKey const inout::dbms::readonly ("inout:dbms:readonly")
 
BooleanOptionKey const inout::dbms::separate_db_per_mpi_process ("inout:dbms:separate_db_per_mpi_process")
 
IntegerOptionKey const inout::dbms::database_partition ("inout:dbms:database_partition")
 
BooleanOptionKey const inout::dbms::use_compact_residue_schema ("inout:dbms:use_compact_residue_schema")
 
BooleanOptionKey const inout::dbms::retry_failed_reads ("inout:dbms:retry_failed_reads")
 
BooleanOptionKey const out::out ("out")
 
BooleanOptionKey const out::overwrite ("out:overwrite")
 
IntegerOptionKey const out::nstruct ("out:nstruct")
 
IntegerOptionKey const out::shuffle_nstruct ("out:shuffle_nstruct")
 
StringOptionKey const out::prefix ("out:prefix")
 
StringOptionKey const out::suffix ("out:suffix")
 
BooleanOptionKey const out::no_nstruct_label ("out:no_nstruct_label")
 
BooleanOptionKey const out::pdb_gz ("out:pdb_gz")
 
BooleanOptionKey const out::pdb ("out:pdb")
 
BooleanOptionKey const out::silent_gz ("out:silent_gz")
 
BooleanOptionKey const out::membrane_pdb ("out:membrane_pdb")
 
RealOptionKey const out::membrane_pdb_thickness ("out:membrane_pdb_thickness")
 
BooleanOptionKey const out::use_database ("out:use_database")
 
IntegerOptionKey const out::database_protocol_id ("out:database_protocol_id")
 
StringVectorOptionKey const out::database_filter ("out:database_filter")
 
IntegerVectorOptionKey const out::resume_batch ("out:resume_batch")
 
BooleanOptionKey const out::nooutput ("out:nooutput")
 
BooleanOptionKey const out::output ("out:output")
 
RealOptionKey const out::scorecut ("out:scorecut")
 
BooleanOptionKey const out::show_accessed_options ("out:show_accessed_options")
 
BooleanOptionKey const out::show_unused_options ("out:show_unused_options")
 
FileOptionKey const out::sf ("out:sf")
 
StringVectorOptionKey const out::mute ("out:mute")
 
StringVectorOptionKey const out::unmute ("out:unmute")
 
IntegerOptionKey const out::level ("out:level")
 
StringVectorOptionKey const out::levels ("out:levels")
 
IntegerOptionKey const out::std_IO_exit_error_code ("out:std_IO_exit_error_code")
 
BooleanOptionKey const out::chname ("out:chname")
 
BooleanOptionKey const out::chtimestamp ("out:chtimestamp")
 
BooleanOptionKey const out::dry_run ("out:dry_run")
 
StringOptionKey const out::mpi_tracer_to_file ("out:mpi_tracer_to_file")
 
StringOptionKey const out::user_tag ("out:user_tag")
 
StringOptionKey const out::output_tag ("out:output_tag")
 
BooleanOptionKey const out::file::file ("out:file")
 
StringOptionKey const out::file::o ("out:file:o")
 
FileOptionKey const out::file::design_contrast ("out:file:design_contrast")
 
StringOptionKey const out::file::residue_type_set ("out:file:residue_type_set")
 
StringOptionKey const out::file::atom_tree_diff ("out:file:atom_tree_diff")
 
IntegerOptionKey const out::file::atom_tree_diff_bb ("out:file:atom_tree_diff_bb")
 
IntegerOptionKey const out::file::atom_tree_diff_sc ("out:file:atom_tree_diff_sc")
 
IntegerOptionKey const out::file::atom_tree_diff_bl ("out:file:atom_tree_diff_bl")
 
StringOptionKey const out::file::alignment ("out:file:alignment")
 
StringOptionKey const out::file::score_only ("out:file:score_only")
 
StringOptionKey const out::file::scorefile ("out:file:scorefile")
 
StringOptionKey const out::file::scorefile_format ("out:file:scorefile_format")
 
StringOptionKey const out::file::silent ("out:file:silent")
 
StringOptionKey const out::file::silent_struct_type ("out:file:silent_struct_type")
 
BooleanOptionKey const out::file::silent_print_all_score_headers ("out:file:silent_print_all_score_headers")
 
BooleanOptionKey const out::file::raw ("out:file:raw")
 
BooleanOptionKey const out::file::weight_silent_scores ("out:file:weight_silent_scores")
 
BooleanOptionKey const out::file::silent_preserve_H ("out:file:silent_preserve_H")
 
BooleanOptionKey const out::file::fullatom ("out:file:fullatom")
 
BooleanOptionKey const out::file::suppress_zero_occ_pdb_output ("out:file:suppress_zero_occ_pdb_output")
 
BooleanOptionKey const out::file::output_virtual ("out:file:output_virtual")
 
BooleanOptionKey const out::file::no_output_cen ("out:file:no_output_cen")
 
BooleanOptionKey const out::file::output_orbitals ("out:file:output_orbitals")
 
BooleanOptionKey const out::file::renumber_pdb ("out:file:renumber_pdb")
 
BooleanOptionKey const out::file::pdb_parents ("out:file:pdb_parents")
 
BooleanOptionKey const out::file::per_chain_renumbering ("out:file:per_chain_renumbering")
 
BooleanOptionKey const out::file::output_torsions ("out:file:output_torsions")
 
BooleanOptionKey const out::file::use_occurrence_data ("out:file:use_occurrence_data")
 
BooleanOptionKey const out::file::pdb_comments ("out:file:pdb_comments")
 
BooleanOptionKey const out::file::force_nonideal_structure ("out:file:force_nonideal_structure")
 
BooleanOptionKey const out::file::write_pdb_link_records ("out:file:write_pdb_link_records")
 
BooleanOptionKey const out::file::dont_rewrite_dunbrack_database ("out:file:dont_rewrite_dunbrack_database")
 
StringOptionKey const out::file::frag_prefix ("out:file:frag_prefix")
 
BooleanOptionKey const out::file::no_extra_sdf_data ("out:file:no_extra_sdf_data")
 
PathOptionKey const out::path::all ("out:path:all")
 
PathOptionKey const out::path::path ("out:path")
 
PathOptionKey const out::path::pdb ("out:path:pdb")
 
PathOptionKey const out::path::score ("out:path:score")
 
PathOptionKey const out::path::scratch ("out:path:scratch")
 
BooleanOptionKey const out::path::mpi_rank_dir ("out:path:mpi_rank_dir")
 
BooleanOptionKey const run::run ("run")
 
FileVectorOptionKey const run::batches ("run:batches")
 
BooleanOptionKey const run::no_prof_info_in_silentout ("run:no_prof_info_in_silentout")
 
BooleanOptionKey const run::archive ("run:archive")
 
IntegerOptionKey const run::n_replica ("run:n_replica")
 
BooleanOptionKey const run::shuffle ("run:shuffle")
 
IntegerOptionKey const run::n_cycles ("run:n_cycles")
 
IntegerOptionKey const run::repeat ("run:repeat")
 
IntegerOptionKey const run::max_min_iter ("run:max_min_iter")
 
IntegerOptionKey const run::maxruntime ("run:maxruntime")
 
BooleanOptionKey const run::write_failures ("run:write_failures")
 
BooleanOptionKey const run::benchmark ("run:benchmark")
 
BooleanOptionKey const run::test_cycles ("run:test_cycles")
 
BooleanOptionKey const run::memory_test_cycles ("run:memory_test_cycles")
 
BooleanOptionKey const run::dry_run ("run:dry_run")
 
BooleanOptionKey const run::debug ("run:debug")
 
BooleanOptionKey const run::profile ("run:profile")
 
IntegerOptionKey const run::max_retry_job ("run:max_retry_job")
 
BooleanOptionKey const run::version ("run:version")
 
BooleanOptionKey const run::nodelay ("run:nodelay")
 
IntegerOptionKey const run::delay ("run:delay")
 
IntegerOptionKey const run::random_delay ("run:random_delay")
 
BooleanOptionKey const run::timer ("run:timer")
 
StringOptionKey const run::chain ("run:chain")
 
BooleanOptionKey const run::score_only ("run:score_only")
 
BooleanOptionKey const run::decoystats ("run:decoystats")
 
BooleanOptionKey const run::output_hbond_info ("run:output_hbond_info")
 
RealOptionKey const run::wide_nblist_extension ("run:wide_nblist_extension")
 
BooleanOptionKey const run::constant_seed ("run:constant_seed")
 
IntegerOptionKey const run::jran ("run:jran")
 
BooleanOptionKey const run::use_time_as_seed ("run:use_time_as_seed")
 
StringOptionKey const run::rng_seed_device ("run:rng_seed_device")
 
IntegerOptionKey const run::seed_offset ("run:seed_offset")
 
StringOptionKey const run::rng ("run:rng")
 
BooleanOptionKey const run::rebuild_disulf ("run:rebuild_disulf")
 
BooleanOptionKey const run::preserve_header ("run:preserve_header")
 
BooleanOptionKey const run::suppress_checkpoints ("run:suppress_checkpoints")
 
BooleanOptionKey const run::checkpoint ("run:checkpoint")
 
BooleanOptionKey const run::delete_checkpoints ("run:delete_checkpoints")
 
IntegerOptionKey const run::checkpoint_interval ("run:checkpoint_interval")
 
StringOptionKey const run::protocol ("run:protocol")
 
BooleanOptionKey const run::remove_ss_length_screen ("run:remove_ss_length_screen")
 
StringOptionKey const run::min_type ("run:min_type")
 
RealOptionKey const run::min_tolerance ("run:min_tolerance")
 
BooleanOptionKey const run::nblist_autoupdate ("run:nblist_autoupdate")
 
RealOptionKey const run::nblist_autoupdate_narrow ("run:nblist_autoupdate_narrow")
 
RealOptionKey const run::nblist_autoupdate_wide ("run:nblist_autoupdate_wide")
 
BooleanOptionKey const run::skip_set_reasonable_fold_tree ("run:skip_set_reasonable_fold_tree")
 
BooleanOptionKey const run::randomize_missing_coords ("run:randomize_missing_coords")
 
BooleanOptionKey const run::ignore_zero_occupancy ("run:ignore_zero_occupancy")
 
IntegerOptionKey const run::cycles_outer ("run:cycles_outer")
 
IntegerOptionKey const run::cycles_inner ("run:cycles_inner")
 
IntegerOptionKey const run::repack_rate ("run:repack_rate")
 
BooleanOptionKey const run::reinitialize_mover_for_each_job ("run:reinitialize_mover_for_each_job")
 
BooleanOptionKey const run::reinitialize_mover_for_new_input ("run:reinitialize_mover_for_new_input")
 
BooleanOptionKey const run::multiple_processes_writing_to_one_directory ("run:multiple_processes_writing_to_one_directory")
 
StringOptionKey const run::jobdist_miscfile_ext ("run:jobdist_miscfile_ext")
 
BooleanOptionKey const run::no_scorefile ("run:no_scorefile")
 
BooleanOptionKey const run::other_pose_to_scorefile ("run:other_pose_to_scorefile")
 
FileOptionKey const run::other_pose_scorefile ("run:other_pose_scorefile")
 
BooleanOptionKey const run::intermediate_scorefiles ("run:intermediate_scorefiles")
 
BooleanOptionKey const run::intermediate_structures ("run:intermediate_structures")
 
BooleanOptionKey const run::idealize_before_protocol ("run:idealize_before_protocol")
 
BooleanOptionKey const run::interactive ("run:interactive")
 
BooleanOptionKey const run::condor ("run:condor")
 
IntegerOptionKey const run::nproc ("run:nproc")
 
IntegerOptionKey const run::proc_id ("run:proc_id")
 
BooleanOptionKey const run::exit_if_missing_heavy_atoms ("run:exit_if_missing_heavy_atoms")
 
RealOptionKey const run::show_simulation_in_pymol ("run:show_simulation_in_pymol")
 
BooleanOptionKey const run::update_pymol_on_energy_changes_only ("run:update_pymol_on_energy_changes_only")
 
BooleanOptionKey const run::update_pymol_on_conformation_changes_only ("run:update_pymol_on_conformation_changes_only")
 
BooleanOptionKey const run::keep_pymol_simulation_history ("run:keep_pymol_simulation_history")
 
BooleanOptionKey const jd2::jd2 ("jd2")
 
BooleanOptionKey const jd2::pose_input_stream ("jd2:pose_input_stream")
 
BooleanOptionKey const jd2::lazy_silent_file_reader ("jd2:lazy_silent_file_reader")
 
BooleanOptionKey const jd2::mpi_nowait_for_remaining_jobs ("jd2:mpi_nowait_for_remaining_jobs")
 
RealOptionKey const jd2::mpi_timeout_factor ("jd2:mpi_timeout_factor")
 
BooleanOptionKey const jd2::mpi_work_partition_job_distributor ("jd2:mpi_work_partition_job_distributor")
 
BooleanOptionKey const jd2::mpi_file_buf_job_distributor ("jd2:mpi_file_buf_job_distributor")
 
BooleanOptionKey const jd2::mpi_filebuf_jobdistributor ("jd2:mpi_filebuf_jobdistributor")
 
BooleanOptionKey const jd2::mpi_fast_nonblocking_output ("jd2:mpi_fast_nonblocking_output")
 
BooleanOptionKey const jd2::dd_parser ("jd2:dd_parser")
 
IntegerOptionKey const jd2::ntrials ("jd2:ntrials")
 
StringOptionKey const jd2::generic_job_name ("jd2:generic_job_name")
 
BooleanOptionKey const jd2::no_output ("jd2:no_output")
 
BooleanOptionKey const jd2::enzdes_out ("jd2:enzdes_out")
 
IntegerOptionKey const jd2::buffer_silent_output ("jd2:buffer_silent_output")
 
RealOptionKey const jd2::buffer_flush_frequency ("jd2:buffer_flush_frequency")
 
BooleanOptionKey const jd2::delete_old_poses ("jd2:delete_old_poses")
 
FileVectorOptionKey const jd2::resource_definition_files ("jd2:resource_definition_files")
 
FileOptionKey const jd2::checkpoint_file ("jd2:checkpoint_file")
 
BooleanOptionKey const score::score_pose_cutpoint_variants ("score:score_pose_cutpoint_variants")
 
BooleanOptionKey const score::score ("score")
 
StringOptionKey const score::weights ("score:weights")
 
StringVectorOptionKey const score::set_weights ("score:set_weights")
 
StringOptionKey const score::pack_weights ("score:pack_weights")
 
StringOptionKey const score::soft_wts ("score:soft_wts")
 
BooleanOptionKey const score::docking_interface_score ("score:docking_interface_score")
 
RealOptionKey const score::min_score_score ("score:min_score_score")
 
StringOptionKey const score::custom_atom_pair ("score:custom_atom_pair")
 
FileVectorOptionKey const score::patch ("score:patch")
 
BooleanOptionKey const score::empty ("score:empty")
 
RealOptionKey const score::fa_max_dis ("score:fa_max_dis")
 
BooleanOptionKey const score::fa_Hatr ("score:fa_Hatr")
 
BooleanOptionKey const score::no_smooth_etables ("score:no_smooth_etables")
 
BooleanOptionKey const score::no_lk_polar_desolvation ("score:no_lk_polar_desolvation")
 
StringOptionKey const score::input_etables ("score:input_etables")
 
StringOptionKey const score::output_etables ("score:output_etables")
 
BooleanOptionKey const score::analytic_etable_evaluation ("score:analytic_etable_evaluation")
 
RealOptionKey const score::rms_target ("score:rms_target")
 
BooleanOptionKey const score::ramaneighbors ("score:ramaneighbors")
 
StringOptionKey const score::optH_weights ("score:optH_weights")
 
StringOptionKey const score::optH_patch ("score:optH_patch")
 
StringOptionKey const score::hbond_params ("score:hbond_params")
 
BooleanOptionKey const score::hbond_bb_per_residue_energy ("score:hbond_bb_per_residue_energy")
 
BooleanOptionKey const score::hbond_disable_bbsc_exclusion_rule ("score:hbond_disable_bbsc_exclusion_rule")
 
IntegerOptionKey const score::symE_units ("score:symE_units")
 
RealOptionKey const score::symE_bonus ("score:symE_bonus")
 
RealOptionKey const score::NV_lbound ("score:NV_lbound")
 
RealOptionKey const score::NV_ubound ("score:NV_ubound")
 
StringOptionKey const score::NV_table ("score:NV_table")
 
BooleanOptionKey const score::disable_orientation_dependent_rna_ch_o_bonds ("score:disable_orientation_dependent_rna_ch_o_bonds")
 
StringOptionKey const score::rna_torsion_potential ("score:rna_torsion_potential")
 
StringOptionKey const score::rna_suite_potential ("score:rna_suite_potential")
 
BooleanOptionKey const score::rna_torsion_skip_chainbreak ("score:rna_torsion_skip_chainbreak")
 
StringOptionKey const score::rna_chemical_shift_exp_data ("score:rna_chemical_shift_exp_data")
 
StringOptionKey const score::rna_chemical_shift_H5_prime_mode ("score:rna_chemical_shift_H5_prime_mode")
 
IntegerVectorOptionKey const score::rna_chemical_shift_include_res ("score:rna_chemical_shift_include_res")
 
BooleanOptionKey const score::DMS_separate_features ("score:DMS_separate_features")
 
BooleanOptionKey const score::DMS_careful_base_pair_classifier ("score:DMS_careful_base_pair_classifier")
 
RealOptionKey const score::rna_chem_map_lores_weight ("score:rna_chem_map_lores_weight")
 
BooleanOptionKey const score::use_2prime_OH_potential ("score:use_2prime_OH_potential")
 
BooleanOptionKey const score::include_neighbor_base_stacks ("score:include_neighbor_base_stacks")
 
BooleanOptionKey const score::find_neighbors_3dgrid ("score:find_neighbors_3dgrid")
 
BooleanOptionKey const score::find_neighbors_stripehash ("score:find_neighbors_stripehash")
 
StringOptionKey const score::seqdep_refene_fname ("score:seqdep_refene_fname")
 
StringOptionKey const score::secondary_seqdep_refene_fname ("score:secondary_seqdep_refene_fname")
 
BooleanOptionKey const score::exact_occ_pairwise ("score:exact_occ_pairwise")
 
BooleanOptionKey const score::exact_occ_skip_Hbonders ("score:exact_occ_skip_Hbonders")
 
BooleanOptionKey const score::exact_occ_include_Hbond_contribution ("score:exact_occ_include_Hbond_contribution")
 
BooleanOptionKey const score::exact_occ_pairwise_by_res ("score:exact_occ_pairwise_by_res")
 
BooleanOptionKey const score::exact_occ_split_between_res ("score:exact_occ_split_between_res")
 
BooleanOptionKey const score::exact_occ_self_res_no_occ ("score:exact_occ_self_res_no_occ")
 
RealOptionKey const score::exact_occ_radius_scaling ("score:exact_occ_radius_scaling")
 
StringVectorOptionKey const score::ref_offsets ("score:ref_offsets")
 
RealOptionKey const score::ref_offset ("score:ref_offset")
 
BooleanOptionKey const score::output_residue_energies ("score:output_residue_energies")
 
StringOptionKey const score::fa_custom_pair_distance_file ("score:fa_custom_pair_distance_file")
 
RealOptionKey const score::disulf_matching_probe ("score:disulf_matching_probe")
 
RealVectorOptionKey const score::bonded_params ("score:bonded_params")
 
StringOptionKey const score::bonded_params_dir ("score:bonded_params_dir")
 
StringOptionKey const score::extra_improper_file ("score:extra_improper_file")
 
RealOptionKey const score::pro_close_planar_constraint ("score:pro_close_planar_constraint")
 
BooleanOptionKey const score::linear_bonded_potential ("score:linear_bonded_potential")
 
RealOptionKey const score::free_suite_bonus ("score:free_suite_bonus")
 
RealOptionKey const score::free_sugar_bonus ("score:free_sugar_bonus")
 
RealOptionKey const score::free_2HOprime_bonus ("score:free_2HOprime_bonus")
 
RealOptionKey const score::syn_G_potential_bonus ("score:syn_G_potential_bonus")
 
RealOptionKey const score::pack_phosphate_penalty ("score:pack_phosphate_penalty")
 
RealOptionKey const score::free_side_chain_bonus ("score:free_side_chain_bonus")
 
IntegerVectorOptionKey const score::rg_local_span ("score:rg_local_span")
 
BooleanOptionKey const score::unmodifypot ("score:unmodifypot")
 
RealOptionKey const score::conc ("score:conc")
 
RealOptionKey const score::loop_fixed_cost ("score:loop_fixed_cost")
 
IntegerVectorOptionKey const score::sidechain_buried ("score:sidechain_buried")
 
IntegerVectorOptionKey const score::sidechain_exposed ("score:sidechain_exposed")
 
RealOptionKey const score::elec_min_dis ("score:elec_min_dis")
 
RealOptionKey const score::elec_max_dis ("score:elec_max_dis")
 
RealOptionKey const score::elec_die ("score:elec_die")
 
BooleanOptionKey const score::elec_r_option ("score:elec_r_option")
 
RealOptionKey const score::intrares_elec_correction_scale ("score:intrares_elec_correction_scale")
 
BooleanOptionKey const score::smooth_fa_elec ("score:smooth_fa_elec")
 
RealOptionKey const score::facts_GBpair_cut ("score:facts_GBpair_cut")
 
RealOptionKey const score::facts_kappa ("score:facts_kappa")
 
IntegerOptionKey const score::facts_asp_patch ("score:facts_asp_patch")
 
BooleanOptionKey const score::facts_plane_to_self ("score:facts_plane_to_self")
 
RealOptionKey const score::facts_saltbridge_correction ("score:facts_saltbridge_correction")
 
RealVectorOptionKey const score::facts_dshift ("score:facts_dshift")
 
RealOptionKey const score::facts_die ("score:facts_die")
 
BooleanOptionKey const score::facts_binding_affinity ("score:facts_binding_affinity")
 
BooleanOptionKey const score::facts_intrascale_by_level ("score:facts_intrascale_by_level")
 
RealVectorOptionKey const score::facts_intbb_elec_scale ("score:facts_intbb_elec_scale")
 
RealVectorOptionKey const score::facts_intbb_solv_scale ("score:facts_intbb_solv_scale")
 
RealVectorOptionKey const score::facts_adjbb_elec_scale ("score:facts_adjbb_elec_scale")
 
RealVectorOptionKey const score::facts_adjbb_solv_scale ("score:facts_adjbb_solv_scale")
 
RealVectorOptionKey const score::facts_intbs_elec_scale ("score:facts_intbs_elec_scale")
 
RealVectorOptionKey const score::facts_intbs_solv_scale ("score:facts_intbs_solv_scale")
 
RealVectorOptionKey const score::facts_adjbs_elec_scale ("score:facts_adjbs_elec_scale")
 
RealVectorOptionKey const score::facts_adjbs_solv_scale ("score:facts_adjbs_solv_scale")
 
RealVectorOptionKey const score::facts_intsc_elec_scale ("score:facts_intsc_elec_scale")
 
RealVectorOptionKey const score::facts_intsc_solv_scale ("score:facts_intsc_solv_scale")
 
StringOptionKey const score::facts_charge_dir ("score:facts_charge_dir")
 
StringOptionKey const score::facts_eff_charge_dir ("score:facts_eff_charge_dir")
 
StringVectorOptionKey const score::facts_plane_aa ("score:facts_plane_aa")
 
StringOptionKey const score::facts_eq_type ("score:facts_eq_type")
 
BooleanOptionKey const score::length_dep_srbb ("score:length_dep_srbb")
 
RealOptionKey const score::ldsrbb_low_scale ("score:ldsrbb_low_scale")
 
RealOptionKey const score::ldsrbb_high_scale ("score:ldsrbb_high_scale")
 
IntegerOptionKey const score::ldsrbb_minlength ("score:ldsrbb_minlength")
 
IntegerOptionKey const score::ldsrbb_maxlength ("score:ldsrbb_maxlength")
 
StringOptionKey const score::nmer_ref_energies ("score:nmer_ref_energies")
 
StringOptionKey const score::nmer_ref_energies_list ("score:nmer_ref_energies_list")
 
StringOptionKey const score::nmer_pssm ("score:nmer_pssm")
 
StringOptionKey const score::nmer_pssm_list ("score:nmer_pssm_list")
 
RealOptionKey const score::nmer_pssm_scorecut ("score:nmer_pssm_scorecut")
 
StringOptionKey const score::nmer_svm ("score:nmer_svm")
 
StringOptionKey const score::nmer_svm_list ("score:nmer_svm_list")
 
RealOptionKey const score::nmer_svm_scorecut ("score:nmer_svm_scorecut")
 
StringOptionKey const score::nmer_svm_aa_matrix ("score:nmer_svm_aa_matrix")
 
IntegerOptionKey const score::nmer_svm_term_length ("score:nmer_svm_term_length")
 
BooleanOptionKey const score::nmer_svm_pssm_feat ("score:nmer_svm_pssm_feat")
 
IntegerOptionKey const score::nmer_ref_seq_length ("score:nmer_ref_seq_length")
 
BooleanOptionKey const score::just_calc_rmsd ("score:just_calc_rmsd")
 
BooleanOptionKey const score::saxs::saxs ("score:saxs")
 
RealOptionKey const score::saxs::min_score ("score:saxs:min_score")
 
StringOptionKey const score::saxs::custom_ff ("score:saxs:custom_ff")
 
StringOptionKey const score::saxs::print_i_calc ("score:saxs:print_i_calc")
 
FileOptionKey const score::saxs::ref_fa_spectrum ("score:saxs:ref_fa_spectrum")
 
FileOptionKey const score::saxs::ref_cen_spectrum ("score:saxs:ref_cen_spectrum")
 
FileOptionKey const score::saxs::ref_spectrum ("score:saxs:ref_spectrum")
 
FileOptionKey const score::saxs::ref_pddf ("score:saxs:ref_pddf")
 
RealOptionKey const score::saxs::d_min ("score:saxs:d_min")
 
RealOptionKey const score::saxs::d_max ("score:saxs:d_max")
 
RealOptionKey const score::saxs::d_step ("score:saxs:d_step")
 
RealOptionKey const score::saxs::q_min ("score:saxs:q_min")
 
RealOptionKey const score::saxs::q_max ("score:saxs:q_max")
 
RealOptionKey const score::saxs::q_step ("score:saxs:q_step")
 
BooleanOptionKey const score::saxs::fit_pddf_area ("score:saxs:fit_pddf_area")
 
BooleanOptionKey const packing::packing ("packing")
 
BooleanOptionKey const packing::repack_only ("packing:repack_only")
 
BooleanOptionKey const packing::prevent_repacking ("packing:prevent_repacking")
 
RealOptionKey const packing::cenrot_cutoff ("packing:cenrot_cutoff")
 
BooleanOptionKey const packing::ignore_ligand_chi ("packing:ignore_ligand_chi")
 
IntegerOptionKey const packing::ndruns ("packing:ndruns")
 
BooleanOptionKey const packing::soft_rep_design ("packing:soft_rep_design")
 
BooleanOptionKey const packing::use_electrostatic_repulsion ("packing:use_electrostatic_repulsion")
 
BooleanOptionKey const packing::dump_rotamer_sets ("packing:dump_rotamer_sets")
 
RealOptionKey const packing::dunbrack_prob_buried ("packing:dunbrack_prob_buried")
 
RealOptionKey const packing::dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied")
 
BooleanOptionKey const packing::no_optH ("packing:no_optH")
 
BooleanOptionKey const packing::optH_MCA ("packing:optH_MCA")
 
BooleanOptionKey const packing::pack_missing_sidechains ("packing:pack_missing_sidechains")
 
BooleanOptionKey const packing::preserve_c_beta ("packing:preserve_c_beta")
 
BooleanOptionKey const packing::flip_HNQ ("packing:flip_HNQ")
 
IntegerVectorOptionKey const packing::fix_his_tautomer ("packing:fix_his_tautomer")
 
BooleanOptionKey const packing::print_pymol_selection ("packing:print_pymol_selection")
 
IntegerOptionKey const packing::extrachi_cutoff ("packing:extrachi_cutoff")
 
FileVectorOptionKey const packing::resfile ("packing:resfile")
 
RealOptionKey const packing::outeriterations_scaling ("packing:outeriterations_scaling")
 
RealOptionKey const packing::inneriterations_scaling ("packing:inneriterations_scaling")
 
StringVectorOptionKey const packing::adducts ("packing:adducts")
 
BooleanOptionKey const packing::use_input_sc ("packing:use_input_sc")
 
FileVectorOptionKey const packing::unboundrot ("packing:unboundrot")
 
RealOptionKey const packing::max_rotbump_energy ("packing:max_rotbump_energy")
 
BooleanOptionKey const packing::lazy_ig ("packing:lazy_ig")
 
BooleanOptionKey const packing::double_lazy_ig ("packing:double_lazy_ig")
 
IntegerOptionKey const packing::linmem_ig ("packing:linmem_ig")
 
IntegerOptionKey const packing::multi_cool_annealer ("packing:multi_cool_annealer")
 
RealVectorOptionKey const packing::minpack_temp_schedule ("packing:minpack_temp_schedule")
 
IntegerOptionKey const packing::minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale")
 
BooleanOptionKey const packing::minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck")
 
BooleanOptionKey const packing::ex1::ex1 ("packing:ex1")
 
IntegerOptionKey const packing::ex1::level ("packing:ex1:level")
 
BooleanOptionKey const packing::ex1::operate ("packing:ex1:operate")
 
BooleanOptionKey const packing::ex2::ex2 ("packing:ex2")
 
IntegerOptionKey const packing::ex2::level ("packing:ex2:level")
 
BooleanOptionKey const packing::ex2::operate ("packing:ex2:operate")
 
BooleanOptionKey const packing::ex3::ex3 ("packing:ex3")
 
IntegerOptionKey const packing::ex3::level ("packing:ex3:level")
 
BooleanOptionKey const packing::ex3::operate ("packing:ex3:operate")
 
BooleanOptionKey const packing::ex4::ex4 ("packing:ex4")
 
IntegerOptionKey const packing::ex4::level ("packing:ex4:level")
 
BooleanOptionKey const packing::ex4::operate ("packing:ex4:operate")
 
BooleanOptionKey const packing::ex1aro::ex1aro ("packing:ex1aro")
 
IntegerOptionKey const packing::ex1aro::level ("packing:ex1aro:level")
 
BooleanOptionKey const packing::ex2aro::ex2aro ("packing:ex2aro")
 
IntegerOptionKey const packing::ex2aro::level ("packing:ex2aro:level")
 
BooleanOptionKey const packing::ex1aro_exposed::ex1aro_exposed ("packing:ex1aro_exposed")
 
IntegerOptionKey const packing::ex1aro_exposed::level ("packing:ex1aro_exposed:level")
 
BooleanOptionKey const packing::ex2aro_exposed::ex2aro_exposed ("packing:ex2aro_exposed")
 
IntegerOptionKey const packing::ex2aro_exposed::level ("packing:ex2aro_exposed:level")
 
BooleanOptionKey const packing::exdna::exdna ("packing:exdna")
 
IntegerOptionKey const packing::exdna::level ("packing:exdna:level")
 
BooleanOptionKey const archive::archive ("archive")
 
BooleanOptionKey const archive::reread_all_structures ("archive:reread_all_structures")
 
IntegerOptionKey const archive::completion_notify_frequency ("archive:completion_notify_frequency")
 
BooleanOptionKey const chemical::chemical ("chemical")
 
StringVectorOptionKey const chemical::exclude_patches ("chemical:exclude_patches")
 
StringVectorOptionKey const chemical::include_patches ("chemical:include_patches")
 
BooleanOptionKey const chemical::enlarge_H_lj ("chemical:enlarge_H_lj")
 
StringVectorOptionKey const chemical::add_atom_type_set_parameters ("chemical:add_atom_type_set_parameters")
 
StringVectorOptionKey const chemical::set_atom_properties ("chemical:set_atom_properties")
 
StringVectorOptionKey const chemical::patch_selectors ("chemical:patch_selectors")
 
BooleanOptionKey const chemical::override_rsd_type_limit ("chemical:override_rsd_type_limit")
 
BooleanOptionKey const constraints::constraints ("constraints")
 
BooleanOptionKey const constraints::exit_on_bad_read ("constraints:exit_on_bad_read")
 
StringVectorOptionKey const constraints::cst_file ("constraints:cst_file")
 
RealOptionKey const constraints::cst_weight ("constraints:cst_weight")
 
RealOptionKey const constraints::max_cst_dist ("constraints:max_cst_dist")
 
StringVectorOptionKey const constraints::cst_fa_file ("constraints:cst_fa_file")
 
RealOptionKey const constraints::cst_fa_weight ("constraints:cst_fa_weight")
 
BooleanOptionKey const constraints::normalize_mixture_func ("constraints:normalize_mixture_func")
 
BooleanOptionKey const constraints::penalize_mixture_func ("constraints:penalize_mixture_func")
 
FileOptionKey const constraints::forest_file ("constraints:forest_file")
 
BooleanOptionKey const constraints::compute_total_dist_cst ("constraints:compute_total_dist_cst")
 
IntegerOptionKey const constraints::cull_with_native ("constraints:cull_with_native")
 
FileOptionKey const constraints::dump_cst_set ("constraints:dump_cst_set")
 
IntegerVectorOptionKey const constraints::evaluate_max_seq_sep ("constraints:evaluate_max_seq_sep")
 
BooleanOptionKey const constraints::named ("constraints:named")
 
BooleanOptionKey const constraints::no_cst_in_relax ("constraints:no_cst_in_relax")
 
BooleanOptionKey const constraints::no_linearize_bounded ("constraints:no_linearize_bounded")
 
RealOptionKey const constraints::pocket_constraint_weight ("constraints:pocket_constraint_weight")
 
BooleanOptionKey const constraints::pocket_zero_derivatives ("constraints:pocket_zero_derivatives")
 
BooleanOptionKey const constraints::viol ("constraints:viol")
 
IntegerOptionKey const constraints::viol_level ("constraints:viol_level")
 
StringOptionKey const constraints::viol_type ("constraints:viol_type")
 
RealOptionKey const constraints::sog_cst_param ("constraints:sog_cst_param")
 
RealOptionKey const constraints::sog_upper_bound ("constraints:sog_upper_bound")
 
BooleanOptionKey const constraints::epr_distance ("constraints:epr_distance")
 
IntegerOptionKey const constraints::combine ("constraints:combine")
 
FileOptionKey const constraints::combine_exclude_region ("constraints:combine_exclude_region")
 
BooleanOptionKey const constraints::skip_redundant ("constraints:skip_redundant")
 
IntegerOptionKey const constraints::skip_redundant_width ("constraints:skip_redundant_width")
 
BooleanOptionKey const corrections::corrections ("corrections")
 
BooleanOptionKey const corrections::beta ("corrections:beta")
 
BooleanOptionKey const corrections::correct ("corrections:correct")
 
BooleanOptionKey const corrections::hbond_sp2_correction ("corrections:hbond_sp2_correction")
 
BooleanOptionKey const corrections::facts_default ("corrections:facts_default")
 
BooleanOptionKey const corrections::score::score ("corrections:score")
 
BooleanOptionKey const corrections::score::bbdep_omega ("corrections:score:bbdep_omega")
 
BooleanOptionKey const corrections::score::bbdep_bond_params ("corrections:score:bbdep_bond_params")
 
BooleanOptionKey const corrections::score::bbdep_bond_devs ("corrections:score:bbdep_bond_devs")
 
BooleanOptionKey const corrections::score::no_his_his_pairE ("corrections:score:no_his_his_pairE")
 
BooleanOptionKey const corrections::score::no_his_DE_pairE ("corrections:score:no_his_DE_pairE")
 
StringOptionKey const corrections::score::p_aa_pp ("corrections:score:p_aa_pp")
 
BooleanOptionKey const corrections::score::p_aa_pp_nogridshift ("corrections:score:p_aa_pp_nogridshift")
 
BooleanOptionKey const corrections::score::rama_not_squared ("corrections:score:rama_not_squared")
 
FileOptionKey const corrections::score::rama_map ("corrections:score:rama_map")
 
BooleanOptionKey const corrections::score::cenrot ("corrections:score:cenrot")
 
BooleanOptionKey const corrections::score::dun10 ("corrections:score:dun10")
 
StringOptionKey const corrections::score::dun10_dir ("corrections:score:dun10_dir")
 
StringOptionKey const corrections::score::dun02_file ("corrections:score:dun02_file")
 
StringOptionKey const corrections::score::ch_o_bond_potential ("corrections:score:ch_o_bond_potential")
 
RealOptionKey const corrections::score::lj_hbond_hdis ("corrections:score:lj_hbond_hdis")
 
RealOptionKey const corrections::score::lj_hbond_OH_donor_dis ("corrections:score:lj_hbond_OH_donor_dis")
 
BooleanOptionKey const corrections::score::score12prime ("corrections:score:score12prime")
 
BooleanOptionKey const corrections::score::talaris2014 ("corrections:score:talaris2014")
 
RealOptionKey const corrections::score::hbond_energy_shift ("corrections:score:hbond_energy_shift")
 
RealOptionKey const corrections::score::hb_sp2_BAH180_rise ("corrections:score:hb_sp2_BAH180_rise")
 
RealOptionKey const corrections::score::hb_sp2_outer_width ("corrections:score:hb_sp2_outer_width")
 
BooleanOptionKey const corrections::score::hb_sp2_chipen ("corrections:score:hb_sp2_chipen")
 
BooleanOptionKey const corrections::score::hbond_measure_sp3acc_BAH_from_hvy ("corrections:score:hbond_measure_sp3acc_BAH_from_hvy")
 
BooleanOptionKey const corrections::score::hb_fade_energy ("corrections:score:hb_fade_energy")
 
BooleanOptionKey const corrections::score::use_bicubic_interpolation ("corrections:score:use_bicubic_interpolation")
 
BooleanOptionKey const corrections::score::dun_normsd ("corrections:score:dun_normsd")
 
BooleanOptionKey const corrections::score::dun_entropy_correction ("corrections:score:dun_entropy_correction")
 
BooleanOptionKey const corrections::chemical::chemical ("corrections:chemical")
 
BooleanOptionKey const corrections::chemical::icoor_05_2009 ("corrections:chemical:icoor_05_2009")
 
BooleanOptionKey const corrections::chemical::parse_charge ("corrections:chemical:parse_charge")
 
BooleanOptionKey const corrections::chemical::expand_st_chi2sampling ("corrections:chemical:expand_st_chi2sampling")
 
BooleanOptionKey const evaluation::evaluation ("evaluation")
 
FileVectorOptionKey const evaluation::rmsd_target ("evaluation:rmsd_target")
 
StringVectorOptionKey const evaluation::rmsd_column ("evaluation:rmsd_column")
 
FileVectorOptionKey const evaluation::rmsd_select ("evaluation:rmsd_select")
 
FileVectorOptionKey const evaluation::align_rmsd_target ("evaluation:align_rmsd_target")
 
FileVectorOptionKey const evaluation::structural_similarity ("evaluation:structural_similarity")
 
BooleanOptionKey const evaluation::contact_map ("evaluation:contact_map")
 
StringVectorOptionKey const evaluation::jscore_evaluator ("evaluation:jscore_evaluator")
 
StringVectorOptionKey const evaluation::align_rmsd_column ("evaluation:align_rmsd_column")
 
FileVectorOptionKey const evaluation::align_rmsd_fns ("evaluation:align_rmsd_fns")
 
StringOptionKey const evaluation::align_rmsd_format ("evaluation:align_rmsd_format")
 
StringOptionKey const evaluation::predicted_burial_fn ("evaluation:predicted_burial_fn")
 
FileOptionKey const evaluation::pool ("evaluation:pool")
 
FileVectorOptionKey const evaluation::rmsd ("evaluation:rmsd")
 
FileVectorOptionKey const evaluation::chirmsd ("evaluation:chirmsd")
 
BooleanOptionKey const evaluation::gdtmm ("evaluation:gdtmm")
 
BooleanOptionKey const evaluation::gdttm ("evaluation:gdttm")
 
BooleanOptionKey const evaluation::score_with_rmsd ("evaluation:score_with_rmsd")
 
FileVectorOptionKey const evaluation::constraints ("evaluation:constraints")
 
FileVectorOptionKey const evaluation::constraints_column ("evaluation:constraints_column")
 
FileVectorOptionKey const evaluation::combined_constraints ("evaluation:combined_constraints")
 
FileVectorOptionKey const evaluation::combined_constraints_column ("evaluation:combined_constraints_column")
 
IntegerOptionKey const evaluation::combine_statistics ("evaluation:combine_statistics")
 
StringVectorOptionKey const evaluation::chemical_shifts ("evaluation:chemical_shifts")
 
StringOptionKey const evaluation::sparta_dir ("evaluation:sparta_dir")
 
StringVectorOptionKey const evaluation::cam_shifts ("evaluation:cam_shifts")
 
StringVectorOptionKey const evaluation::pales ("evaluation:pales")
 
FileVectorOptionKey const evaluation::extra_score ("evaluation:extra_score")
 
FileVectorOptionKey const evaluation::extra_score_patch ("evaluation:extra_score_patch")
 
StringVectorOptionKey const evaluation::extra_score_column ("evaluation:extra_score_column")
 
FileVectorOptionKey const evaluation::extra_score_select ("evaluation:extra_score_select")
 
FileVectorOptionKey const evaluation::rdc_target ("evaluation:rdc_target")
 
BooleanOptionKey const evaluation::symmetric_rmsd ("evaluation:symmetric_rmsd")
 
StringVectorOptionKey const evaluation::rdc_column ("evaluation:rdc_column")
 
StringVectorOptionKey const evaluation::rdc ("evaluation:rdc")
 
StringOptionKey const evaluation::built_in_rdc ("evaluation:built_in_rdc")
 
BooleanOptionKey const evaluation::jump_nr ("evaluation:jump_nr")
 
IntegerVectorOptionKey const evaluation::score_exclude_res ("evaluation:score_exclude_res")
 
IntegerOptionKey const evaluation::score_sscore_short_helix ("evaluation:score_sscore_short_helix")
 
IntegerOptionKey const evaluation::score_sscore_maxloop ("evaluation:score_sscore_maxloop")
 
IntegerOptionKey const evaluation::window_size ("evaluation:window_size")
 
StringOptionKey const evaluation::I_sc ("evaluation:I_sc")
 
BooleanOptionKey const evaluation::Irms ("evaluation:Irms")
 
BooleanOptionKey const evaluation::Ca_Irms ("evaluation:Ca_Irms")
 
BooleanOptionKey const evaluation::Fnat ("evaluation:Fnat")
 
BooleanOptionKey const evaluation::Lrmsd ("evaluation:Lrmsd")
 
BooleanOptionKey const evaluation::Fnonnat ("evaluation:Fnonnat")
 
BooleanOptionKey const evaluation::DockMetrics ("evaluation:DockMetrics")
 
BooleanOptionKey const filters::filters ("filters")
 
BooleanOptionKey const filters::disable_all_filters ("filters:disable_all_filters")
 
BooleanOptionKey const filters::disable_rg_filter ("filters:disable_rg_filter")
 
BooleanOptionKey const filters::disable_co_filter ("filters:disable_co_filter")
 
BooleanOptionKey const filters::disable_sheet_filter ("filters:disable_sheet_filter")
 
RealOptionKey const filters::set_pddf_filter ("filters:set_pddf_filter")
 
RealOptionKey const filters::set_saxs_filter ("filters:set_saxs_filter")
 
BooleanOptionKey const gpu::gpu ("gpu")
 
IntegerOptionKey const gpu::device ("gpu:device")
 
IntegerOptionKey const gpu::threads ("gpu:threads")
 
BooleanOptionKey const jumps::jumps ("jumps")
 
BooleanOptionKey const jumps::evaluate ("jumps:evaluate")
 
FileOptionKey const jumps::extra_frags_for_ss ("jumps:extra_frags_for_ss")
 
BooleanOptionKey const jumps::fix_chainbreak ("jumps:fix_chainbreak")
 
FileOptionKey const jumps::fix_jumps ("jumps:fix_jumps")
 
FileOptionKey const jumps::jump_lib ("jumps:jump_lib")
 
FileOptionKey const jumps::loop_definition_from_file ("jumps:loop_definition_from_file")
 
BooleanOptionKey const jumps::no_chainbreak_in_relax ("jumps:no_chainbreak_in_relax")
 
FileOptionKey const jumps::pairing_file ("jumps:pairing_file")
 
IntegerVectorOptionKey const jumps::random_sheets ("jumps:random_sheets")
 
FileOptionKey const jumps::residue_pair_jump_file ("jumps:residue_pair_jump_file")
 
IntegerVectorOptionKey const jumps::sheets ("jumps:sheets")
 
FileOptionKey const jumps::topology_file ("jumps:topology_file")
 
BooleanOptionKey const jumps::bb_moves ("jumps:bb_moves")
 
BooleanOptionKey const jumps::no_wobble ("jumps:no_wobble")
 
BooleanOptionKey const jumps::no_shear ("jumps:no_shear")
 
BooleanOptionKey const jumps::no_sample_ss_jumps ("jumps:no_sample_ss_jumps")
 
IntegerOptionKey const jumps::invrate_jump_move ("jumps:invrate_jump_move")
 
RealOptionKey const jumps::chainbreak_weight_stage1 ("jumps:chainbreak_weight_stage1")
 
RealOptionKey const jumps::chainbreak_weight_stage2 ("jumps:chainbreak_weight_stage2")
 
RealOptionKey const jumps::chainbreak_weight_stage3 ("jumps:chainbreak_weight_stage3")
 
RealOptionKey const jumps::chainbreak_weight_stage4 ("jumps:chainbreak_weight_stage4")
 
BooleanOptionKey const jumps::ramp_chainbreaks ("jumps:ramp_chainbreaks")
 
RealOptionKey const jumps::increase_chainbreak ("jumps:increase_chainbreak")
 
BooleanOptionKey const jumps::overlap_chainbreak ("jumps:overlap_chainbreak")
 
RealOptionKey const jumps::sep_switch_accelerate ("jumps:sep_switch_accelerate")
 
BooleanOptionKey const jumps::dump_frags ("jumps:dump_frags")
 
IntegerOptionKey const jumps::njumps ("jumps:njumps")
 
IntegerOptionKey const jumps::max_strand_gap_allowed ("jumps:max_strand_gap_allowed")
 
RealOptionKey const jumps::contact_score ("jumps:contact_score")
 
BooleanOptionKey const jumps::filter_templates ("jumps:filter_templates")
 
BooleanOptionKey const loops::loops ("loops")
 
StringOptionKey const loops::cen_weights ("loops:cen_weights")
 
StringOptionKey const loops::cen_patch ("loops:cen_patch")
 
FileOptionKey const loops::input_pdb ("loops:input_pdb")
 
StringVectorOptionKey const loops::loop_file ("loops:loop_file")
 
FileOptionKey const loops::extended_loop_file ("loops:extended_loop_file")
 
FileOptionKey const loops::mm_loop_file ("loops:mm_loop_file")
 
BooleanOptionKey const loops::fix_natsc ("loops:fix_natsc")
 
BooleanOptionKey const loops::refine_only ("loops:refine_only")
 
BooleanOptionKey const loops::fast ("loops:fast")
 
FileOptionKey const loops::vall_file ("loops:vall_file")
 
IntegerVectorOptionKey const loops::frag_sizes ("loops:frag_sizes")
 
FileVectorOptionKey const loops::frag_files ("loops:frag_files")
 
FileOptionKey const loops::output_pdb ("loops:output_pdb")
 
BooleanOptionKey const loops::debug ("loops:debug")
 
BooleanOptionKey const loops::build_initial ("loops:build_initial")
 
BooleanOptionKey const loops::extended ("loops:extended")
 
BooleanOptionKey const loops::remove_extended_loops ("loops:remove_extended_loops")
 
BooleanOptionKey const loops::idealize_after_loop_close ("loops:idealize_after_loop_close")
 
BooleanOptionKey const loops::idealize_before_loop_close ("loops:idealize_before_loop_close")
 
IntegerOptionKey const loops::select_best_loop_from ("loops:select_best_loop_from")
 
IntegerOptionKey const loops::build_attempts ("loops:build_attempts")
 
IntegerOptionKey const loops::grow_attempts ("loops:grow_attempts")
 
RealOptionKey const loops::random_grow_loops_by ("loops:random_grow_loops_by")
 
BooleanOptionKey const loops::accept_aborted_loops ("loops:accept_aborted_loops")
 
BooleanOptionKey const loops::strict_loops ("loops:strict_loops")
 
BooleanOptionKey const loops::superimpose_native ("loops:superimpose_native")
 
IntegerVectorOptionKey const loops::build_specific_loops ("loops:build_specific_loops")
 
BooleanOptionKey const loops::random_order ("loops:random_order")
 
BooleanOptionKey const loops::build_all_loops ("loops:build_all_loops")
 
BooleanOptionKey const loops::fa_closure_protocol ("loops:fa_closure_protocol")
 
RealOptionKey const loops::combine_rate ("loops:combine_rate")
 
StringOptionKey const loops::remodel ("loops:remodel")
 
StringOptionKey const loops::intermedrelax ("loops:intermedrelax")
 
StringOptionKey const loops::refine ("loops:refine")
 
StringOptionKey const loops::relax ("loops:relax")
 
BooleanOptionKey const loops::final_clean_fastrelax ("loops:final_clean_fastrelax")
 
BooleanOptionKey const loops::relax_with_foldtree ("loops:relax_with_foldtree")
 
RealOptionKey const loops::constrain_rigid_segments ("loops:constrain_rigid_segments")
 
StringOptionKey const loops::loopscores ("loops:loopscores")
 
BooleanOptionKey const loops::timer ("loops:timer")
 
BooleanOptionKey const loops::vicinity_sampling ("loops:vicinity_sampling")
 
RealOptionKey const loops::vicinity_degree ("loops:vicinity_degree")
 
RealOptionKey const loops::neighbor_dist ("loops:neighbor_dist")
 
IntegerOptionKey const loops::kic_max_seglen ("loops:kic_max_seglen")
 
BooleanOptionKey const loops::kic_recover_last ("loops:kic_recover_last")
 
BooleanOptionKey const loops::kic_min_after_repack ("loops:kic_min_after_repack")
 
BooleanOptionKey const loops::optimize_only_kic_region_sidechains_after_move ("loops:optimize_only_kic_region_sidechains_after_move")
 
IntegerOptionKey const loops::max_kic_build_attempts ("loops:max_kic_build_attempts")
 
IntegerOptionKey const loops::remodel_kic_attempts ("loops:remodel_kic_attempts")
 
IntegerOptionKey const loops::max_kic_perturber_samples ("loops:max_kic_perturber_samples")
 
BooleanOptionKey const loops::nonpivot_torsion_sampling ("loops:nonpivot_torsion_sampling")
 
BooleanOptionKey const loops::fix_ca_bond_angles ("loops:fix_ca_bond_angles")
 
BooleanOptionKey const loops::kic_use_linear_chainbreak ("loops:kic_use_linear_chainbreak")
 
BooleanOptionKey const loops::sample_omega_at_pre_prolines ("loops:sample_omega_at_pre_prolines")
 
BooleanOptionKey const loops::allow_omega_move ("loops:allow_omega_move")
 
BooleanOptionKey const loops::kic_with_cartmin ("loops:kic_with_cartmin")
 
BooleanOptionKey const loops::allow_takeoff_torsion_move ("loops:allow_takeoff_torsion_move")
 
IntegerOptionKey const loops::extend_length ("loops:extend_length")
 
IntegerOptionKey const loops::outer_cycles ("loops:outer_cycles")
 
IntegerOptionKey const loops::max_inner_cycles ("loops:max_inner_cycles")
 
IntegerOptionKey const loops::repack_period ("loops:repack_period")
 
RealOptionKey const loops::remodel_init_temp ("loops:remodel_init_temp")
 
RealOptionKey const loops::remodel_final_temp ("loops:remodel_final_temp")
 
RealOptionKey const loops::refine_init_temp ("loops:refine_init_temp")
 
RealOptionKey const loops::refine_final_temp ("loops:refine_final_temp")
 
IntegerOptionKey const loops::gapspan ("loops:gapspan")
 
IntegerOptionKey const loops::spread ("loops:spread")
 
IntegerOptionKey const loops::kinematic_wrapper_cycles ("loops:kinematic_wrapper_cycles")
 
IntegerOptionKey const loops::kic_num_rotamer_trials ("loops:kic_num_rotamer_trials")
 
BooleanOptionKey const loops::kic_omega_sampling ("loops:kic_omega_sampling")
 
RealOptionKey const loops::kic_bump_overlap_factor ("loops:kic_bump_overlap_factor")