Rosetta 3.3
Namespaces | Functions
src/basic/options/keys/OptionKeys.cc.gen0.hh File Reference

Namespaces

namespace  in
namespace  in::path
namespace  in::file
namespace  in::rdf
namespace  in::matdes_dock
namespace  in::matdes_design
namespace  MM
namespace  mysql
namespace  qsar
namespace  residues
namespace  PCS
namespace  inout
namespace  out
namespace  out::file
namespace  out::path
namespace  pocket_grid
namespace  fingerprint
namespace  docking
namespace  docking::ligand
namespace  docking::ligand::grid
namespace  docking::symmetry
namespace  pH
namespace  pH::calc_pka
namespace  run
namespace  jd2
namespace  evaluation
namespace  filters
namespace  MonteCarlo
namespace  frags
namespace  frags::scoring
namespace  frags::picking
namespace  frags::nonlocal
namespace  broker
namespace  chunk
namespace  nonlocal
namespace  abinitio

Functions

BooleanOptionKey const in::in ("in")
BooleanOptionKey const in::termini ("in:termini")
BooleanOptionKey const in::ignore_unrecognized_res ("in:ignore_unrecognized_res")
BooleanOptionKey const in::remember_unrecognized_res ("in:remember_unrecognized_res")
BooleanOptionKey const in::remember_unrecognized_water ("in:remember_unrecognized_water")
BooleanOptionKey const in::detect_disulf ("in:detect_disulf")
FileOptionKey const in::fix_disulf ("in:fix_disulf")
BooleanOptionKey const in::use_stupid_foldtree_format ("in:use_stupid_foldtree_format")
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")
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::l ("in:file:l")
FileVectorOptionKey const in::file::list ("in:file:list")
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_fa ("in:file:extra_res_fa")
FileVectorOptionKey const in::file::extra_res_mol ("in:file:extra_res_mol")
FileVectorOptionKey const in::file::extra_res_cen ("in:file:extra_res_cen")
PathVectorOptionKey const in::file::extra_res_path ("in:file:extra_res_path")
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::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")
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")
StringVectorOptionKey const in::file::silent_scores_wanted ("in:file:silent_scores_wanted")
BooleanOptionKey const in::file::centroid_input ("in:file:centroid_input")
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")
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::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")
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")
BooleanOptionKey const in::rdf::rdf ("in:rdf")
BooleanOptionKey const in::rdf::sep_bb_ss ("in:rdf:sep_bb_ss")
BooleanOptionKey const in::matdes_dock::matdes_dock ("in:matdes_dock")
RealVectorOptionKey const in::matdes_dock::radial_disp ("in:matdes_dock:radial_disp")
RealOptionKey const in::matdes_dock::neg_r ("in:matdes_dock:neg_r")
RealVectorOptionKey const in::matdes_dock::angle ("in:matdes_dock:angle")
BooleanOptionKey const in::matdes_dock::dump_pdb ("in:matdes_dock:dump_pdb")
BooleanOptionKey const in::matdes_dock::dump_chainA_only ("in:matdes_dock:dump_chainA_only")
StringOptionKey const in::matdes_dock::pdbID ("in:matdes_dock:pdbID")
StringOptionKey const in::matdes_dock::prefix ("in:matdes_dock:prefix")
IntegerOptionKey const in::matdes_dock::num_subs_building_block ("in:matdes_dock:num_subs_building_block")
IntegerOptionKey const in::matdes_dock::num_subs_total ("in:matdes_dock:num_subs_total")
BooleanOptionKey const in::matdes_design::matdes_design ("in:matdes_design")
RealOptionKey const in::matdes_design::contact_dist ("in:matdes_design:contact_dist")
RealOptionKey const in::matdes_design::grid_size_angle ("in:matdes_design:grid_size_angle")
RealOptionKey const in::matdes_design::grid_size_radius ("in:matdes_design:grid_size_radius")
IntegerOptionKey const in::matdes_design::grid_nsamp_angle ("in:matdes_design:grid_nsamp_angle")
IntegerOptionKey const in::matdes_design::grid_nsamp_radius ("in:matdes_design:grid_nsamp_radius")
IntegerOptionKey const in::matdes_design::num_subs_building_block ("in:matdes_design:num_subs_building_block")
RealOptionKey const in::matdes_design::fav_nat_bonus ("in:matdes_design:fav_nat_bonus")
IntegerVectorOptionKey const in::matdes_design::revert_pos ("in:matdes_design:revert_pos")
StringVectorOptionKey const in::matdes_design::revert_ids ("in:matdes_design:revert_ids")
BooleanOptionKey const MM::MM ("MM")
BooleanOptionKey const MM::ignore_missing_bondangle_params ("MM:ignore_missing_bondangle_params")
BooleanOptionKey const mysql::mysql ("mysql")
StringOptionKey const mysql::host ("mysql:host")
StringOptionKey const mysql::user ("mysql:user")
StringOptionKey const mysql::password ("mysql:password")
IntegerOptionKey const mysql::port ("mysql:port")
BooleanOptionKey const qsar::qsar ("qsar")
StringOptionKey const qsar::weights ("qsar:weights")
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 inout::inout ("inout")
BooleanOptionKey const inout::fold_tree_io ("inout:fold_tree_io")
FileOptionKey const inout::database_filename ("inout:database_filename")
StringOptionKey const inout::database_mode ("inout:database_mode")
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::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")
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::mute_warning ("out:mute_warning")
StringVectorOptionKey const out::mute_info ("out:mute_info")
StringVectorOptionKey const out::mute_debug ("out:mute_debug")
StringVectorOptionKey const out::unmute_error ("out:unmute_error")
StringVectorOptionKey const out::unmute_warning ("out:unmute_warning")
StringVectorOptionKey const out::unmute_info ("out:unmute_info")
StringVectorOptionKey const out::unmute_debug ("out:unmute_debug")
BooleanOptionKey const out::chname ("out:chname")
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")
StringOptionKey const out::file::silent ("out:file:silent")
StringOptionKey const out::file::score_only ("out:file:score_only")
StringOptionKey const out::file::atom_tree_diff ("out:file:atom_tree_diff")
StringOptionKey const out::file::alignment ("out:file:alignment")
StringOptionKey const out::file::scorefile ("out:file:scorefile")
StringOptionKey const out::file::silent_struct_type ("out:file:silent_struct_type")
BooleanOptionKey const out::file::silent_preserve_H ("out:file:silent_preserve_H")
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::fullatom ("out:file:fullatom")
BooleanOptionKey const out::file::output_virtual ("out:file:output_virtual")
BooleanOptionKey const out::file::output_orbitals ("out:file:output_orbitals")
BooleanOptionKey const out::file::weight_silent_scores ("out:file:weight_silent_scores")
FileOptionKey const out::file::design_contrast ("out:file:design_contrast")
BooleanOptionKey const out::file::dont_rewrite_dunbrack_database ("out:file:dont_rewrite_dunbrack_database")
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")
StringOptionKey const out::file::residue_type_set ("out:file:residue_type_set")
StringOptionKey const out::file::frag_prefix ("out:file:frag_prefix")
BooleanOptionKey const out::file::output_torsions ("out:file:output_torsions")
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 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_rama ("pocket_grid:pocket_dump_rama")
BooleanOptionKey const pocket_grid::pocket_restrict_size ("pocket_grid:pocket_restrict_size")
BooleanOptionKey const pocket_grid::pocket_psp ("pocket_grid:pocket_psp")
BooleanOptionKey const pocket_grid::pocket_sps ("pocket_grid:pocket_sps")
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")
BooleanOptionKey const fingerprint::fingerprint ("fingerprint")
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 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")
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::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::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")
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")
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")
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")
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::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::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")
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")
StringOptionKey const docking::ligand::option_file ("docking:ligand:option_file")
BooleanOptionKey const docking::ligand::rescore ("docking:ligand:rescore")
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")
RealOptionKey const pH::value_pH ("pH:value_pH")
BooleanOptionKey const pH::calc_pka::calc_pka ("pH:calc_pka")
IntegerOptionKey const pH::calc_pka::pka_for_resno ("pH:calc_pka:pka_for_resno")
StringOptionKey const pH::calc_pka::pka_for_chainno ("pH:calc_pka:pka_for_chainno")
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")
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")
IntegerOptionKey const run::benchmark_scale ("run:benchmark_scale")
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::trust_missing_coords ("run:trust_missing_coords")
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")
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")
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")
BooleanOptionKey const jd2::delete_old_poses ("jd2:delete_old_poses")
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")
FileOptionKey const evaluation::pool ("evaluation:pool")
FileVectorOptionKey const evaluation::rmsd ("evaluation:rmsd")
BooleanOptionKey const evaluation::gdtmm ("evaluation:gdtmm")
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")
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")
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")
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::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::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::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")
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")
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")
IntegerOptionKey const frags::nonlocal::min_seq_sep ("frags:nonlocal:min_seq_sep")
IntegerOptionKey const frags::nonlocal::ca_dist ("frags:nonlocal:ca_dist")
IntegerOptionKey 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 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")
FileOptionKey const nonlocal::moves ("nonlocal:moves")
StringOptionKey const nonlocal::mode ("nonlocal:mode")
StringOptionKey const nonlocal::builder ("nonlocal:builder")
StringOptionKey const nonlocal::search ("nonlocal:search")
BooleanOptionKey const nonlocal::randomize_missing ("nonlocal:randomize_missing")
IntegerOptionKey const nonlocal::gap_sampling_extension ("nonlocal:gap_sampling_extension")
IntegerOptionKey const nonlocal::min_chunk_size ("nonlocal:min_chunk_size")
IntegerOptionKey const nonlocal::max_chunk_size ("nonlocal:max_chunk_size")
RealOptionKey const nonlocal::rdc_weight ("nonlocal:rdc_weight")
IntegerOptionKey const nonlocal::ramp_constraints_cycles ("nonlocal:ramp_constraints_cycles")
BooleanOptionKey const nonlocal::ramp_chainbreaks ("nonlocal:ramp_chainbreaks")
BooleanOptionKey const nonlocal::ramp_constraints ("nonlocal:ramp_constraints")
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")
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines