OptionKeys.cc.gen0.hh File Reference

Namespaces
	in
	in::dbms
	in::path
	in::file
	in::rdf
	inout
	inout::dbms
	out
	out::file
	out::path
	rigid
	MM
	qsar
	residues
	PCS
	PCSTS1
	PCSTS2
	PCSTS3
	PCSTS4
	pocket_grid
	fingerprint
	contactMap
	docking
	docking::ligand
	docking::ligand::grid
	docking::symmetry
	pH
	pH::calc_pka
	run
	jd2
	evaluation
	filters
	MonteCarlo
	frags
	frags::scoring
	frags::picking
	frags::nonlocal
	frags::contacts
	frags::ABEGO
	broker
	chunk
	nonlocal
	abinitio
	abinitio::star
	fold_cst
	resample
	loopfcst
	jumps

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::enable_branching ("in:enable_branching")
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")
BooleanOptionKey const	in::dbms::dbms ("in:dbms")
StringVectorOptionKey const	in::dbms::struct_ids ("in:dbms:struct_ids")
IntegerOptionKey const	in::database_protocol ("in:database_protocol")
StringVectorOptionKey const	in::select_structures_from_database ("in:select_structures_from_database")
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")
IntegerVectorOptionKey const	in::file::frag_sizes ("in:file:frag_sizes")
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_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")
IntegerOptionKey const	in::file::fragA_size ("in:file:fragA_size")
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")
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")
BooleanOptionKey const	in::file::silent_optH ("in:file:silent_optH")
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::embedfile ("in:file:embedfile")
StringOptionKey const	in::file::embedparams ("in:file:embedparams")
StringOptionKey const	in::file::membrane_chains ("in:file:membrane_chains")
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")
IntegerVectorOptionKey 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")
StringOptionKey const	out::force_output_name ("out:force_output_name")
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::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")
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::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::silent_decoytime ("out:file:silent_decoytime")
IntegerOptionKey const	out::file::silent_comment_bound ("out:file:silent_comment_bound")
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")
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::movie ("out:path:movie")
PathOptionKey const	out::path::scratch ("out:path:scratch")
BooleanOptionKey const	out::path::mpi_rank_dir ("out:path:mpi_rank_dir")
BooleanOptionKey const	rigid::rigid ("rigid")
RealOptionKey const	rigid::chainbreak_bias ("rigid:chainbreak_bias")
BooleanOptionKey const	rigid::close_loops ("rigid:close_loops")
IntegerOptionKey const	rigid::fragment_cycles ("rigid:fragment_cycles")
BooleanOptionKey const	rigid::log_accepted_moves ("rigid:log_accepted_moves")
RealOptionKey const	rigid::max_ca_ca_dist ("rigid:max_ca_ca_dist")
IntegerOptionKey const	rigid::medium_range_seqsep ("rigid:medium_range_seqsep")
FileOptionKey const	rigid::patch ("rigid:patch")
IntegerOptionKey const	rigid::residues_backbone_move ("rigid:residues_backbone_move")
RealOptionKey const	rigid::rotation ("rigid:rotation")
FileOptionKey const	rigid::sampling_prob ("rigid:sampling_prob")
StringOptionKey const	rigid::score ("rigid:score")
IntegerOptionKey const	rigid::sequence_separation ("rigid:sequence_separation")
IntegerOptionKey const	rigid::short_range_seqsep ("rigid:short_range_seqsep")
IntegerOptionKey const	rigid::small_cycles ("rigid:small_cycles")
IntegerOptionKey const	rigid::stages ("rigid:stages")
RealOptionKey const	rigid::temperature ("rigid:temperature")
RealOptionKey const	rigid::translation ("rigid:translation")
BooleanOptionKey const	MM::MM ("MM")
BooleanOptionKey const	MM::ignore_missing_bondangle_params ("MM:ignore_missing_bondangle_params")
BooleanOptionKey const	qsar::qsar ("qsar")
StringOptionKey const	qsar::weights ("qsar:weights")
StringOptionKey const	qsar::grid_dir ("qsar:grid_dir")
IntegerOptionKey const	qsar::max_grid_cache_size ("qsar:max_grid_cache_size")
BooleanOptionKey const	residues::residues ("residues")
StringVectorOptionKey const	residues::patch_selectors ("residues:patch_selectors")
BooleanOptionKey const	PCS::PCS ("PCS")
FileOptionKey const	PCS::write_extra ("PCS:write_extra")
IntegerOptionKey const	PCS::normalization_id ("PCS:normalization_id")
BooleanOptionKey const	PCSTS1::PCSTS1 ("PCSTS1")
FileOptionKey const	PCSTS1::write_extra ("PCSTS1:write_extra")
IntegerOptionKey const	PCSTS1::normalization_id ("PCSTS1:normalization_id")
BooleanOptionKey const	PCSTS2::PCSTS2 ("PCSTS2")
FileOptionKey const	PCSTS2::write_extra ("PCSTS2:write_extra")
IntegerOptionKey const	PCSTS2::normalization_id ("PCSTS2:normalization_id")
BooleanOptionKey const	PCSTS3::PCSTS3 ("PCSTS3")
FileOptionKey const	PCSTS3::write_extra ("PCSTS3:write_extra")
IntegerOptionKey const	PCSTS3::normalization_id ("PCSTS3:normalization_id")
BooleanOptionKey const	PCSTS4::PCSTS4 ("PCSTS4")
FileOptionKey const	PCSTS4::write_extra ("PCSTS4:write_extra")
IntegerOptionKey const	PCSTS4::normalization_id ("PCSTS4:normalization_id")
BooleanOptionKey const	pocket_grid::pocket_grid ("pocket_grid")
RealOptionKey const	pocket_grid::pocket_grid_size ("pocket_grid:pocket_grid_size")
RealOptionKey const	pocket_grid::pocket_grid_size_x ("pocket_grid:pocket_grid_size_x")
RealOptionKey const	pocket_grid::pocket_grid_size_y ("pocket_grid:pocket_grid_size_y")
RealOptionKey const	pocket_grid::pocket_grid_size_z ("pocket_grid:pocket_grid_size_z")
RealOptionKey const	pocket_grid::pocket_grid_spacing ("pocket_grid:pocket_grid_spacing")
RealOptionKey const	pocket_grid::pocket_max_spacing ("pocket_grid:pocket_max_spacing")
RealOptionKey const	pocket_grid::pocket_min_size ("pocket_grid:pocket_min_size")
RealOptionKey const	pocket_grid::pocket_max_size ("pocket_grid:pocket_max_size")
RealOptionKey const	pocket_grid::pocket_probe_radius ("pocket_grid:pocket_probe_radius")
StringOptionKey const	pocket_grid::central_relax_pdb_num ("pocket_grid:central_relax_pdb_num")
IntegerOptionKey const	pocket_grid::pocket_ntrials ("pocket_grid:pocket_ntrials")
IntegerOptionKey const	pocket_grid::pocket_num_angles ("pocket_grid:pocket_num_angles")
BooleanOptionKey const	pocket_grid::pocket_side ("pocket_grid:pocket_side")
BooleanOptionKey const	pocket_grid::pocket_dump_pdbs ("pocket_grid:pocket_dump_pdbs")
BooleanOptionKey const	pocket_grid::pocket_dump_exemplars ("pocket_grid:pocket_dump_exemplars")
BooleanOptionKey const	pocket_grid::pocket_filter_by_exemplar ("pocket_grid:pocket_filter_by_exemplar")
BooleanOptionKey const	pocket_grid::pocket_dump_rama ("pocket_grid:pocket_dump_rama")
BooleanOptionKey const	pocket_grid::pocket_restrict_size ("pocket_grid:pocket_restrict_size")
BooleanOptionKey const	pocket_grid::pocket_ignore_buried ("pocket_grid:pocket_ignore_buried")
BooleanOptionKey const	pocket_grid::pocket_only_buried ("pocket_grid:pocket_only_buried")
BooleanOptionKey const	pocket_grid::pocket_psp ("pocket_grid:pocket_psp")
BooleanOptionKey const	pocket_grid::pocket_sps ("pocket_grid:pocket_sps")
BooleanOptionKey const	pocket_grid::pocket_search13 ("pocket_grid:pocket_search13")
RealOptionKey const	pocket_grid::pocket_surface_score ("pocket_grid:pocket_surface_score")
RealOptionKey const	pocket_grid::pocket_surface_dist ("pocket_grid:pocket_surface_dist")
RealOptionKey const	pocket_grid::pocket_buried_score ("pocket_grid:pocket_buried_score")
RealOptionKey const	pocket_grid::pocket_buried_dist ("pocket_grid:pocket_buried_dist")
RealOptionKey const	pocket_grid::pocket_exemplar_vdw_pen ("pocket_grid:pocket_exemplar_vdw_pen")
BooleanOptionKey const	pocket_grid::pocket_debug_output ("pocket_grid:pocket_debug_output")
BooleanOptionKey const	pocket_grid::print_grid ("pocket_grid:print_grid")
BooleanOptionKey const	pocket_grid::extend_eggshell ("pocket_grid:extend_eggshell")
RealOptionKey const	pocket_grid::extend_eggshell_dist ("pocket_grid:extend_eggshell_dist")
RealOptionKey const	pocket_grid::extra_eggshell_dist ("pocket_grid:extra_eggshell_dist")
RealOptionKey const	pocket_grid::eggshell_dist ("pocket_grid:eggshell_dist")
BooleanOptionKey const	pocket_grid::reduce_rays ("pocket_grid:reduce_rays")
BooleanOptionKey const	pocket_grid::pocket_static_grid ("pocket_grid:pocket_static_grid")
BooleanOptionKey const	fingerprint::fingerprint ("fingerprint")
BooleanOptionKey const	fingerprint::print_eggshell ("fingerprint:print_eggshell")
RealOptionKey const	fingerprint::atom_radius_scale ("fingerprint:atom_radius_scale")
RealOptionKey const	fingerprint::atom_radius_buffer ("fingerprint:atom_radius_buffer")
RealOptionKey const	fingerprint::packing_weight ("fingerprint:packing_weight")
RealOptionKey const	fingerprint::dist_cut_off ("fingerprint:dist_cut_off")
BooleanOptionKey const	fingerprint::include_hydrogens ("fingerprint:include_hydrogens")
BooleanOptionKey const	fingerprint::use_DARC_gpu ("fingerprint:use_DARC_gpu")
BooleanOptionKey const	fingerprint::square_score ("fingerprint:square_score")
IntegerOptionKey const	fingerprint::set_origin ("fingerprint:set_origin")
IntegerOptionKey const	fingerprint::origin_res_num ("fingerprint:origin_res_num")
BooleanOptionKey const	contactMap::contactMap ("contactMap")
StringOptionKey const	contactMap::prefix ("contactMap:prefix")
RealOptionKey const	contactMap::distance_cutoff ("contactMap:distance_cutoff")
RealOptionKey const	contactMap::energy_cutoff ("contactMap:energy_cutoff")
StringOptionKey const	contactMap::region_def ("contactMap:region_def")
BooleanOptionKey const	contactMap::row_format ("contactMap:row_format")
BooleanOptionKey const	contactMap::distance_matrix ("contactMap:distance_matrix")
BooleanOptionKey const	docking::kick_relax ("docking:kick_relax")
BooleanOptionKey const	docking::docking ("docking")
BooleanOptionKey const	docking::view ("docking:view")
BooleanOptionKey const	docking::no_filters ("docking:no_filters")
StringVectorOptionKey const	docking::design_chains ("docking:design_chains")
FileOptionKey const	docking::recover_sidechains ("docking:recover_sidechains")
StringOptionKey const	docking::partners ("docking:partners")
BooleanOptionKey const	docking::docking_local_refine ("docking:docking_local_refine")
BooleanOptionKey const	docking::low_res_protocol_only ("docking:low_res_protocol_only")
BooleanOptionKey const	docking::randomize1 ("docking:randomize1")
BooleanOptionKey const	docking::randomize2 ("docking:randomize2")
BooleanOptionKey const	docking::use_ellipsoidal_randomization ("docking:use_ellipsoidal_randomization")
BooleanOptionKey const	docking::spin ("docking:spin")
RealVectorOptionKey const	docking::dock_pert ("docking:dock_pert")
RealOptionKey const	docking::uniform_trans ("docking:uniform_trans")
BooleanOptionKey const	docking::center_at_interface ("docking:center_at_interface")
IntegerOptionKey const	docking::dock_mcm_first_cycles ("docking:dock_mcm_first_cycles")
IntegerOptionKey const	docking::dock_mcm_second_cycles ("docking:dock_mcm_second_cycles")
IntegerOptionKey const	docking::docking_centroid_outer_cycles ("docking:docking_centroid_outer_cycles")
IntegerOptionKey const	docking::docking_centroid_inner_cycles ("docking:docking_centroid_inner_cycles")
BooleanOptionKey const	docking::dock_min ("docking:dock_min")
StringOptionKey const	docking::flexible_bb_docking ("docking:flexible_bb_docking")
RealOptionKey const	docking::flexible_bb_docking_interface_dist ("docking:flexible_bb_docking_interface_dist")
StringOptionKey const	docking::ensemble1 ("docking:ensemble1")
StringOptionKey const	docking::ensemble2 ("docking:ensemble2")
RealOptionKey const	docking::dock_mcm_trans_magnitude ("docking:dock_mcm_trans_magnitude")
RealOptionKey const	docking::dock_mcm_rot_magnitude ("docking:dock_mcm_rot_magnitude")
RealOptionKey const	docking::minimization_threshold ("docking:minimization_threshold")
RealOptionKey const	docking::temperature ("docking:temperature")
IntegerOptionKey const	docking::repack_period ("docking:repack_period")
BooleanOptionKey const	docking::extra_rottrial ("docking:extra_rottrial")
BooleanOptionKey const	docking::dock_rtmin ("docking:dock_rtmin")
BooleanOptionKey const	docking::sc_min ("docking:sc_min")
BooleanOptionKey const	docking::norepack1 ("docking:norepack1")
BooleanOptionKey const	docking::norepack2 ("docking:norepack2")
IntegerVectorOptionKey const	docking::bb_min_res ("docking:bb_min_res")
IntegerVectorOptionKey const	docking::sc_min_res ("docking:sc_min_res")
BooleanOptionKey const	docking::dock_ppk ("docking:dock_ppk")
IntegerOptionKey const	docking::max_repeats ("docking:max_repeats")
RealVectorOptionKey const	docking::dock_lowres_filter ("docking:dock_lowres_filter")
IntegerVectorOptionKey const	docking::multibody ("docking:multibody")
BooleanOptionKey const	docking::ignore_default_docking_task ("docking:ignore_default_docking_task")
StringOptionKey const	docking::low_patch ("docking:low_patch")
StringOptionKey const	docking::high_patch ("docking:high_patch")
StringOptionKey const	docking::high_min_patch ("docking:high_min_patch")
StringOptionKey const	docking::pack_patch ("docking:pack_patch")
BooleanOptionKey const	docking::use_legacy_protocol ("docking:use_legacy_protocol")
RealOptionKey const	docking::docklowres_trans_magnitude ("docking:docklowres_trans_magnitude")
RealOptionKey const	docking::docklowres_rot_magnitude ("docking:docklowres_rot_magnitude")
BooleanOptionKey const	docking::ligand::ligand ("docking:ligand")
StringOptionKey const	docking::ligand::protocol ("docking:ligand:protocol")
BooleanOptionKey const	docking::ligand::soft_rep ("docking:ligand:soft_rep")
BooleanOptionKey const	docking::ligand::tweak_sxfn ("docking:ligand:tweak_sxfn")
BooleanOptionKey const	docking::ligand::old_estat ("docking:ligand:old_estat")
BooleanOptionKey const	docking::ligand::random_conformer ("docking:ligand:random_conformer")
IntegerOptionKey const	docking::ligand::improve_orientation ("docking:ligand:improve_orientation")
BooleanOptionKey const	docking::ligand::mutate_same_name3 ("docking:ligand:mutate_same_name3")
RealOptionKey const	docking::ligand::subset_to_keep ("docking:ligand:subset_to_keep")
RealOptionKey const	docking::ligand::min_rms ("docking:ligand:min_rms")
IntegerOptionKey const	docking::ligand::max_poses ("docking:ligand:max_poses")
BooleanOptionKey const	docking::ligand::minimize_ligand ("docking:ligand:minimize_ligand")
RealOptionKey const	docking::ligand::harmonic_torsions ("docking:ligand:harmonic_torsions")
BooleanOptionKey const	docking::ligand::use_ambig_constraints ("docking:ligand:use_ambig_constraints")
IntegerOptionKey const	docking::ligand::shear_moves ("docking:ligand:shear_moves")
BooleanOptionKey const	docking::ligand::minimize_backbone ("docking:ligand:minimize_backbone")
RealOptionKey const	docking::ligand::harmonic_Calphas ("docking:ligand:harmonic_Calphas")
RealOptionKey const	docking::ligand::tether_ligand ("docking:ligand:tether_ligand")
RealVectorOptionKey const	docking::ligand::start_from ("docking:ligand:start_from")
StringOptionKey const	docking::ligand::option_file ("docking:ligand:option_file")
BooleanOptionKey const	docking::ligand::rescore ("docking:ligand:rescore")
BooleanOptionKey const	docking::ligand::grid::grid ("docking:ligand:grid")
FileOptionKey const	docking::ligand::grid::grid_kin ("docking:ligand:grid:grid_kin")
FileOptionKey const	docking::ligand::grid::grid_map ("docking:ligand:grid:grid_map")
BooleanOptionKey const	docking::symmetry::symmetry ("docking:symmetry")
BooleanOptionKey const	docking::symmetry::minimize_backbone ("docking:symmetry:minimize_backbone")
BooleanOptionKey const	docking::symmetry::minimize_sidechains ("docking:symmetry:minimize_sidechains")
BooleanOptionKey const	pH::pH ("pH")
BooleanOptionKey const	pH::pH_mode ("pH:pH_mode")
BooleanOptionKey const	pH::keep_input_protonation_state ("pH:keep_input_protonation_state")
RealOptionKey const	pH::value_pH ("pH:value_pH")
BooleanOptionKey const	pH::calc_pka::calc_pka ("pH:calc_pka")
BooleanOptionKey const	pH::calc_pka::pka_all ("pH:calc_pka:pka_all")
RealVectorOptionKey const	pH::calc_pka::pka_for_resnos ("pH:calc_pka:pka_for_resnos")
StringOptionKey const	pH::calc_pka::pka_for_chainno ("pH:calc_pka:pka_for_chainno")
BooleanOptionKey const	pH::calc_pka::pH_neighbor_pack ("pH:calc_pka:pH_neighbor_pack")
RealOptionKey const	pH::calc_pka::pka_rad ("pH:calc_pka:pka_rad")
BooleanOptionKey const	pH::calc_pka::pH_prepack ("pH:calc_pka:pH_prepack")
BooleanOptionKey const	pH::calc_pka::pH_relax ("pH:calc_pka:pH_relax")
BooleanOptionKey const	pH::calc_pka::rotamer_prot_stats ("pH:calc_pka:rotamer_prot_stats")
FileVectorOptionKey const	pH::pH_unbound ("pH:pH_unbound")
BooleanOptionKey const	pH::output_raw_scores ("pH:output_raw_scores")
BooleanOptionKey const	pH::pre_process ("pH:pre_process")
StringOptionKey const	pH::cognate_partners ("pH:cognate_partners")
FileOptionKey const	pH::cognate_pdb ("pH:cognate_pdb")
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::clean ("run:clean")
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")
IntegerOptionKey const	run::verbosity ("run:verbosity")
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::series ("run:series")
StringOptionKey const	run::protein ("run:protein")
StringOptionKey const	run::chain ("run:chain")
BooleanOptionKey const	run::score_only ("run:score_only")
BooleanOptionKey const	run::silent_input ("run:silent_input")
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::status ("run:status")
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")
IntegerOptionKey const	run::run_level ("run:run_level")
StringOptionKey const	run::verbose ("run:verbose")
BooleanOptionKey const	run::silent ("run:silent")
BooleanOptionKey const	run::regions ("run:regions")
BooleanOptionKey const	run::find_disulf ("run:find_disulf")
BooleanOptionKey const	run::rebuild_disulf ("run:rebuild_disulf")
BooleanOptionKey const	run::movie ("run:movie")
BooleanOptionKey const	run::trajectory ("run:trajectory")
BooleanOptionKey const	run::IUPAC ("run:IUPAC")
BooleanOptionKey const	run::preserve_header ("run:preserve_header")
BooleanOptionKey const	run::evolution ("run:evolution")
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::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	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_select ("evaluation:rdc_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")
BooleanOptionKey const	evaluation::rpf ("evaluation:rpf")
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	MonteCarlo::MonteCarlo ("MonteCarlo")
RealOptionKey const	MonteCarlo::temp_initial ("MonteCarlo:temp_initial")
RealOptionKey const	MonteCarlo::temp_final ("MonteCarlo:temp_final")
BooleanOptionKey const	frags::frags ("frags")
IntegerOptionKey const	frags::j ("frags:j")
BooleanOptionKey const	frags::filter_JC ("frags:filter_JC")
BooleanOptionKey const	frags::bounded_protocol ("frags:bounded_protocol")
BooleanOptionKey const	frags::keep_all_protocol ("frags:keep_all_protocol")
BooleanOptionKey const	frags::quota_protocol ("frags:quota_protocol")
BooleanOptionKey const	frags::nonlocal_pairs ("frags:nonlocal_pairs")
BooleanOptionKey const	frags::fragment_contacts ("frags:fragment_contacts")
BooleanOptionKey const	frags::p_value_selection ("frags:p_value_selection")
IntegerOptionKey const	frags::n_frags ("frags:n_frags")
FileOptionKey const	frags::allowed_pdb ("frags:allowed_pdb")
StringVectorOptionKey const	frags::ss_pred ("frags:ss_pred")
FileOptionKey const	frags::spine_x ("frags:spine_x")
FileOptionKey const	frags::depth ("frags:depth")
FileOptionKey const	frags::denied_pdb ("frags:denied_pdb")
IntegerVectorOptionKey const	frags::frag_sizes ("frags:frag_sizes")
BooleanOptionKey const	frags::write_ca_coordinates ("frags:write_ca_coordinates")
BooleanOptionKey const	frags::write_scores ("frags:write_scores")
BooleanOptionKey const	frags::annotate ("frags:annotate")
IntegerOptionKey const	frags::nr_large_copies ("frags:nr_large_copies")
IntegerOptionKey const	frags::n_candidates ("frags:n_candidates")
BooleanOptionKey const	frags::write_rama_tables ("frags:write_rama_tables")
RealOptionKey const	frags::rama_C ("frags:rama_C")
RealOptionKey const	frags::rama_B ("frags:rama_B")
RealOptionKey const	frags::sigmoid_cs_A ("frags:sigmoid_cs_A")
RealOptionKey const	frags::sigmoid_cs_B ("frags:sigmoid_cs_B")
RealOptionKey const	frags::seqsim_H ("frags:seqsim_H")
RealOptionKey const	frags::seqsim_E ("frags:seqsim_E")
RealOptionKey const	frags::seqsim_L ("frags:seqsim_L")
RealOptionKey const	frags::rama_norm ("frags:rama_norm")
StringOptionKey const	frags::describe_fragments ("frags:describe_fragments")
RealOptionKey const	frags::picking_old_max_score ("frags:picking_old_max_score")
BooleanOptionKey const	frags::write_sequence_only ("frags:write_sequence_only")
BooleanOptionKey const	frags::output_silent ("frags:output_silent")
BooleanOptionKey const	frags::score_output_silent ("frags:score_output_silent")
BooleanOptionKey const	frags::scoring::scoring ("frags:scoring")
FileOptionKey const	frags::scoring::config ("frags:scoring:config")
StringOptionKey const	frags::scoring::profile_score ("frags:scoring:profile_score")
FileVectorOptionKey const	frags::scoring::predicted_secondary ("frags:scoring:predicted_secondary")
BooleanOptionKey const	frags::picking::picking ("frags:picking")
StringOptionKey const	frags::picking::selecting_rule ("frags:picking:selecting_rule")
StringOptionKey const	frags::picking::selecting_scorefxn ("frags:picking:selecting_scorefxn")
FileOptionKey const	frags::picking::quota_config_file ("frags:picking:quota_config_file")
IntegerVectorOptionKey const	frags::picking::query_pos ("frags:picking:query_pos")
BooleanOptionKey const	frags::nonlocal::nonlocal ("frags:nonlocal")
BooleanOptionKey const	frags::nonlocal::relax_input ("frags:nonlocal:relax_input")
BooleanOptionKey const	frags::nonlocal::relax_input_with_coordinate_constraints ("frags:nonlocal:relax_input_with_coordinate_constraints")
IntegerOptionKey const	frags::nonlocal::relax_frags_repeats ("frags:nonlocal:relax_frags_repeats")
BooleanOptionKey const	frags::nonlocal::single_chain ("frags:nonlocal:single_chain")
RealOptionKey const	frags::nonlocal::min_contacts_per_res ("frags:nonlocal:min_contacts_per_res")
RealOptionKey const	frags::nonlocal::max_ddg_score ("frags:nonlocal:max_ddg_score")
RealOptionKey const	frags::nonlocal::max_rmsd_after_relax ("frags:nonlocal:max_rmsd_after_relax")
BooleanOptionKey const	frags::nonlocal::output_frags_pdbs ("frags:nonlocal:output_frags_pdbs")
BooleanOptionKey const	frags::nonlocal::output_idealized ("frags:nonlocal:output_idealized")
BooleanOptionKey const	frags::nonlocal::output_silent ("frags:nonlocal:output_silent")
BooleanOptionKey const	frags::contacts::contacts ("frags:contacts")
IntegerOptionKey const	frags::contacts::min_seq_sep ("frags:contacts:min_seq_sep")
RealVectorOptionKey const	frags::contacts::dist_cutoffs ("frags:contacts:dist_cutoffs")
RealOptionKey const	frags::contacts::centroid_distance_scale_factor ("frags:contacts:centroid_distance_scale_factor")
StringVectorOptionKey const	frags::contacts::type ("frags:contacts:type")
IntegerOptionKey const	frags::contacts::neighbors ("frags:contacts:neighbors")
BooleanOptionKey const	frags::contacts::output_all ("frags:contacts:output_all")
BooleanOptionKey const	frags::ABEGO::ABEGO ("frags:ABEGO")
RealOptionKey const	frags::ABEGO::phi_psi_range_A ("frags:ABEGO:phi_psi_range_A")
BooleanOptionKey const	broker::broker ("broker")
FileVectorOptionKey const	broker::setup ("broker:setup")
BooleanOptionKey const	chunk::chunk ("chunk")
FileOptionKey const	chunk::pdb2 ("chunk:pdb2")
FileOptionKey const	chunk::loop2 ("chunk:loop2")
BooleanOptionKey const	nonlocal::nonlocal ("nonlocal")
StringOptionKey const	nonlocal::builder ("nonlocal:builder")
FileOptionKey const	nonlocal::chunks ("nonlocal:chunks")
IntegerOptionKey const	nonlocal::max_chunk_size ("nonlocal:max_chunk_size")
BooleanOptionKey const	nonlocal::randomize_missing ("nonlocal:randomize_missing")
RealOptionKey const	nonlocal::rdc_weight ("nonlocal:rdc_weight")
BooleanOptionKey const	abinitio::star::star ("abinitio:star")
RealOptionKey const	abinitio::star::initial_dist_cutoff ("abinitio:star:initial_dist_cutoff")
IntegerOptionKey const	abinitio::star::min_unaligned_len ("abinitio:star:min_unaligned_len")
IntegerOptionKey const	abinitio::star::short_loop_len ("abinitio:star:short_loop_len")
RealOptionKey const	abinitio::prob_perturb_weights ("abinitio:prob_perturb_weights")
BooleanOptionKey const	abinitio::abinitio ("abinitio")
BooleanOptionKey const	abinitio::membrane ("abinitio:membrane")
FileOptionKey const	abinitio::kill_hairpins ("abinitio:kill_hairpins")
RealOptionKey const	abinitio::kill_hairpins_frequency ("abinitio:kill_hairpins_frequency")
BooleanOptionKey const	abinitio::smooth_cycles_only ("abinitio:smooth_cycles_only")
BooleanOptionKey const	abinitio::relax ("abinitio:relax")
BooleanOptionKey const	abinitio::final_clean_relax ("abinitio:final_clean_relax")
BooleanOptionKey const	abinitio::fastrelax ("abinitio:fastrelax")
BooleanOptionKey const	abinitio::multifastrelax ("abinitio:multifastrelax")
BooleanOptionKey const	abinitio::debug ("abinitio:debug")
BooleanOptionKey const	abinitio::clear_pose_cache ("abinitio:clear_pose_cache")
BooleanOptionKey const	abinitio::explicit_pdb_debug ("abinitio:explicit_pdb_debug")
BooleanOptionKey const	abinitio::use_filters ("abinitio:use_filters")
RealOptionKey const	abinitio::increase_cycles ("abinitio:increase_cycles")
IntegerOptionKey const	abinitio::number_3mer_frags ("abinitio:number_3mer_frags")
IntegerOptionKey const	abinitio::number_9mer_frags ("abinitio:number_9mer_frags")
RealOptionKey const	abinitio::temperature ("abinitio:temperature")
RealOptionKey const	abinitio::rg_reweight ("abinitio:rg_reweight")
RealOptionKey const	abinitio::strand_dist_cutoff ("abinitio:strand_dist_cutoff")
BooleanOptionKey const	abinitio::stretch_strand_dist_cutoff ("abinitio:stretch_strand_dist_cutoff")
RealOptionKey const	abinitio::rsd_wt_helix ("abinitio:rsd_wt_helix")
RealOptionKey const	abinitio::rsd_wt_strand ("abinitio:rsd_wt_strand")
RealOptionKey const	abinitio::rsd_wt_loop ("abinitio:rsd_wt_loop")
BooleanOptionKey const	abinitio::fast ("abinitio:fast")
BooleanOptionKey const	abinitio::skip_convergence_check ("abinitio:skip_convergence_check")
FileVectorOptionKey const	abinitio::stage1_patch ("abinitio:stage1_patch")
FileVectorOptionKey const	abinitio::stage2_patch ("abinitio:stage2_patch")
FileVectorOptionKey const	abinitio::stage3a_patch ("abinitio:stage3a_patch")
FileVectorOptionKey const	abinitio::stage3b_patch ("abinitio:stage3b_patch")
FileVectorOptionKey const	abinitio::stage4_patch ("abinitio:stage4_patch")
FileVectorOptionKey const	abinitio::stage5_patch ("abinitio:stage5_patch")
BooleanOptionKey const	abinitio::exit_when_converged ("abinitio:exit_when_converged")
BooleanOptionKey const	abinitio::steal_3mers ("abinitio:steal_3mers")
BooleanOptionKey const	abinitio::steal_9mers ("abinitio:steal_9mers")
BooleanOptionKey const	abinitio::no_write_failures ("abinitio:no_write_failures")
BooleanOptionKey const	abinitio::relax_failures ("abinitio:relax_failures")
BooleanOptionKey const	abinitio::relax_with_jumps ("abinitio:relax_with_jumps")
BooleanOptionKey const	abinitio::process_store ("abinitio:process_store")
IntegerVectorOptionKey const	abinitio::fix_residues_to_native ("abinitio:fix_residues_to_native")
BooleanOptionKey const	abinitio::return_full_atom ("abinitio:return_full_atom")
BooleanOptionKey const	abinitio::detect_disulfide_before_relax ("abinitio:detect_disulfide_before_relax")
BooleanOptionKey const	abinitio::close_loops ("abinitio:close_loops")
BooleanOptionKey const	abinitio::bGDT ("abinitio:bGDT")
BooleanOptionKey const	abinitio::dump_frags ("abinitio:dump_frags")
BooleanOptionKey const	abinitio::jdist_rerun ("abinitio:jdist_rerun")
RealOptionKey const	abinitio::perturb ("abinitio:perturb")
BooleanOptionKey const	abinitio::rerun ("abinitio:rerun")
IntegerVectorOptionKey const	abinitio::rmsd_residues ("abinitio:rmsd_residues")
BooleanOptionKey const	abinitio::start_native ("abinitio:start_native")
BooleanOptionKey const	abinitio::debug_structures ("abinitio:debug_structures")
FileOptionKey const	abinitio::log_frags ("abinitio:log_frags")
BooleanOptionKey const	abinitio::only_stage1 ("abinitio:only_stage1")
RealOptionKey const	abinitio::end_bias ("abinitio:end_bias")
IntegerOptionKey const	abinitio::symmetry_residue ("abinitio:symmetry_residue")
RealOptionKey const	abinitio::vdw_weight_stage1 ("abinitio:vdw_weight_stage1")
BooleanOptionKey const	abinitio::override_vdw_all_stages ("abinitio:override_vdw_all_stages")
IntegerVectorOptionKey const	abinitio::recover_low_in_stages ("abinitio:recover_low_in_stages")
IntegerVectorOptionKey const	abinitio::skip_stages ("abinitio:skip_stages")
BooleanOptionKey const	abinitio::close_chbrk ("abinitio:close_chbrk")
BooleanOptionKey const	abinitio::include_stage5 ("abinitio:include_stage5")
BooleanOptionKey const	abinitio::close_loops_by_idealizing ("abinitio:close_loops_by_idealizing")
BooleanOptionKey const	abinitio::optimize_cutpoints_using_kic ("abinitio:optimize_cutpoints_using_kic")
IntegerOptionKey const	abinitio::optimize_cutpoints_margin ("abinitio:optimize_cutpoints_margin")
FileOptionKey const	abinitio::HD_EX_Info ("abinitio:HD_EX_Info")
RealOptionKey const	abinitio::HD_penalty ("abinitio:HD_penalty")
RealOptionKey const	abinitio::HD_fa_penalty ("abinitio:HD_fa_penalty")
FileOptionKey const	abinitio::sheet_edge_pred ("abinitio:sheet_edge_pred")
RealOptionKey const	abinitio::SEP_score_scalling ("abinitio:SEP_score_scalling")
BooleanOptionKey const	fold_cst::fold_cst ("fold_cst")
RealOptionKey const	fold_cst::constraint_skip_rate ("fold_cst:constraint_skip_rate")
IntegerOptionKey const	fold_cst::violation_skip_basis ("fold_cst:violation_skip_basis")
IntegerOptionKey const	fold_cst::violation_skip_ignore ("fold_cst:violation_skip_ignore")
BooleanOptionKey const	fold_cst::keep_skipped_csts ("fold_cst:keep_skipped_csts")
BooleanOptionKey const	fold_cst::no_minimize ("fold_cst:no_minimize")
BooleanOptionKey const	fold_cst::force_minimize ("fold_cst:force_minimize")
RealVectorOptionKey const	fold_cst::seq_sep_stages ("fold_cst:seq_sep_stages")
IntegerOptionKey const	fold_cst::reramp_cst_cycles ("fold_cst:reramp_cst_cycles")
RealOptionKey const	fold_cst::reramp_start_cstweight ("fold_cst:reramp_start_cstweight")
IntegerOptionKey const	fold_cst::reramp_iterations ("fold_cst:reramp_iterations")
BooleanOptionKey const	fold_cst::skip_on_noviolation_in_stage1 ("fold_cst:skip_on_noviolation_in_stage1")
RealOptionKey const	fold_cst::stage1_ramp_cst_cycle_factor ("fold_cst:stage1_ramp_cst_cycle_factor")
RealOptionKey const	fold_cst::stage2_constraint_threshold ("fold_cst:stage2_constraint_threshold")
BooleanOptionKey const	fold_cst::ignore_sequence_seperation ("fold_cst:ignore_sequence_seperation")
BooleanOptionKey const	fold_cst::no_recover_low_at_constraint_switch ("fold_cst:no_recover_low_at_constraint_switch")
BooleanOptionKey const	fold_cst::ramp_coord_cst ("fold_cst:ramp_coord_cst")
BooleanOptionKey const	resample::resample ("resample")
FileOptionKey const	resample::silent ("resample:silent")
StringOptionKey const	resample::tag ("resample:tag")
BooleanOptionKey const	resample::stage1 ("resample:stage1")
BooleanOptionKey const	resample::stage2 ("resample:stage2")
BooleanOptionKey const	resample::jumps ("resample:jumps")
RealVectorOptionKey const	resample::min_max_start_seq_sep ("resample:min_max_start_seq_sep")
BooleanOptionKey const	loopfcst::loopfcst ("loopfcst")
RealOptionKey const	loopfcst::coord_cst_weight ("loopfcst:coord_cst_weight")
BooleanOptionKey const	loopfcst::coord_cst_all_atom ("loopfcst:coord_cst_all_atom")
BooleanOptionKey const	loopfcst::use_general_protocol ("loopfcst:use_general_protocol")
FileOptionKey const	loopfcst::coord_cst_weight_array ("loopfcst:coord_cst_weight_array")
FileOptionKey const	loopfcst::dump_coord_cst_weight_array ("loopfcst:dump_coord_cst_weight_array")
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")