#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option.cc.include.gen.hh>
#include <platform/types.hh>
#include <utility/down_cast.hh>
#include <utility/keys/AutoKey.fwd.hh>
#include <utility/keys/AutoKey.hh>
#include <utility/keys/Key.fwd.hh>
#include <utility/keys/Key.hh>
#include <utility/keys/KeyLess.fwd.hh>
#include <utility/keys/KeyLookup.fwd.hh>
#include <utility/keys/KeyLookup.hh>
#include <utility/keys/NoClient.fwd.hh>
#include <utility/keys/NoClient.hh>
#include <utility/keys/SmallKeyVector.fwd.hh>
#include <utility/keys/UserKey.fwd.hh>
#include <utility/keys/VariantKey.fwd.hh>
#include <utility/keys/VariantKey.hh>
#include <utility/options/AnyOption.fwd.hh>
#include <utility/options/BooleanOption.fwd.hh>
#include <utility/options/BooleanVectorOption.fwd.hh>
#include <utility/options/FileOption.fwd.hh>
#include <utility/options/FileVectorOption.fwd.hh>
#include <utility/options/IntegerOption.fwd.hh>
#include <utility/options/IntegerVectorOption.fwd.hh>
#include <utility/options/Option.fwd.hh>
#include <utility/options/PathOption.fwd.hh>
#include <utility/options/PathVectorOption.fwd.hh>
#include <utility/options/RealOption.fwd.hh>
#include <utility/options/RealVectorOption.fwd.hh>
#include <utility/options/StringOption.fwd.hh>
#include <utility/options/StringVectorOption.fwd.hh>
#include <utility/options/keys/AnyOptionKey.fwd.hh>
#include <utility/options/keys/AnyOptionKey.hh>
#include <utility/options/keys/AnyVectorOptionKey.fwd.hh>
#include <utility/options/keys/AnyVectorOptionKey.hh>
#include <utility/options/keys/BooleanOptionKey.fwd.hh>
#include <utility/options/keys/BooleanOptionKey.hh>
#include <utility/options/keys/BooleanVectorOptionKey.fwd.hh>
#include <utility/options/keys/BooleanVectorOptionKey.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <utility/options/keys/FileVectorOptionKey.fwd.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <utility/options/keys/IntegerOptionKey.fwd.hh>
#include <utility/options/keys/IntegerOptionKey.hh>
#include <utility/options/keys/IntegerVectorOptionKey.fwd.hh>
#include <utility/options/keys/IntegerVectorOptionKey.hh>
#include <utility/options/keys/OptionKey.fwd.hh>
#include <utility/options/keys/OptionKey.hh>
#include <utility/options/keys/OptionKeys.hh>
#include <utility/options/keys/PathOptionKey.fwd.hh>
#include <utility/options/keys/PathOptionKey.hh>
#include <utility/options/keys/PathVectorOptionKey.fwd.hh>
#include <utility/options/keys/PathVectorOptionKey.hh>
#include <utility/options/keys/RealOptionKey.fwd.hh>
#include <utility/options/keys/RealOptionKey.hh>
#include <utility/options/keys/RealVectorOptionKey.fwd.hh>
#include <utility/options/keys/RealVectorOptionKey.hh>
#include <utility/options/keys/ScalarOptionKey.fwd.hh>
#include <utility/options/keys/ScalarOptionKey.hh>
#include <utility/options/keys/StringOptionKey.fwd.hh>
#include <utility/options/keys/StringOptionKey.hh>
#include <utility/options/keys/StringVectorOptionKey.fwd.hh>
#include <utility/options/keys/StringVectorOptionKey.hh>
#include <utility/options/keys/VectorOptionKey.fwd.hh>
#include <utility/options/keys/VectorOptionKey.hh>
#include <utility/options/keys/all.hh>
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <map>
#include <set>
#include <string>
#include <utility>
#include <basic/options/keys/OptionKeys.cc.gen3.hh>

Namespaces
	basic

	basic::options

	basic::options::OptionKeys

	basic::options::OptionKeys::DomainAssembly

	basic::options::OptionKeys::remodel

	basic::options::OptionKeys::remodel::staged_sampling

	basic::options::OptionKeys::remodel::domainFusion

	basic::options::OptionKeys::remodel::design

	basic::options::OptionKeys::remodel::RemodelLoopMover

	basic::options::OptionKeys::fold_from_loops

	basic::options::OptionKeys::symmetry

	basic::options::OptionKeys::fold_and_dock

	basic::options::OptionKeys::match

	basic::options::OptionKeys::canonical_sampling

	basic::options::OptionKeys::canonical_sampling::probabilities

	basic::options::OptionKeys::canonical_sampling::sampling

	basic::options::OptionKeys::canonical_sampling::out

	basic::options::OptionKeys::rdc

	basic::options::OptionKeys::csa

	basic::options::OptionKeys::dc

	basic::options::OptionKeys::antibody

	basic::options::OptionKeys::antibody::design

	basic::options::OptionKeys::flexPepDocking

	basic::options::OptionKeys::threadsc

	basic::options::OptionKeys::cp

	basic::options::OptionKeys::archive

	basic::options::OptionKeys::optimization

	basic::options::OptionKeys::stepwise

	basic::options::OptionKeys::stepwise::monte_carlo

	basic::options::OptionKeys::stepwise::rna

	basic::options::OptionKeys::stepwise::protein

	basic::options::OptionKeys::full_model

	basic::options::OptionKeys::ufv

	basic::options::OptionKeys::ufv::insert

	basic::options::OptionKeys::chrisk

	basic::options::OptionKeys::rot_anl

	basic::options::OptionKeys::sewing

	basic::options::OptionKeys::strand_assembly

	basic::options::OptionKeys::pepspec

	basic::options::OptionKeys::sicdock

	basic::options::OptionKeys::mh

	basic::options::OptionKeys::mh::score

	basic::options::OptionKeys::mh::filter

	basic::options::OptionKeys::orbitals

	basic::options::OptionKeys::cutoutdomain

	basic::options::OptionKeys::carbohydrates

	basic::options::OptionKeys::dwkulp

	basic::options::OptionKeys::matdes

	basic::options::OptionKeys::matdes::dock

	basic::options::OptionKeys::matdes::design

	basic::options::OptionKeys::matdes::mutalyze

	basic::options::OptionKeys::gpu

	basic::options::OptionKeys::pb_potential

	basic::options::OptionKeys::bunsat_calc2

Functions
FileOptionKey const	basic::options::OptionKeys::DomainAssembly::da_eval_pose_map ("DomainAssembly:da_eval_pose_map")

BooleanOptionKey const	basic::options::OptionKeys::fold_from_loops::fold_from_loops ("fold_from_loops")

BooleanOptionKey const	basic::options::OptionKeys::fold_from_loops::native_ca_cst ("fold_from_loops:native_ca_cst")

FileOptionKey const	basic::options::OptionKeys::fold_from_loops::swap_loops ("fold_from_loops:swap_loops")

StringOptionKey const	basic::options::OptionKeys::fold_from_loops::checkpoint ("fold_from_loops:checkpoint")

RealOptionKey const	basic::options::OptionKeys::fold_from_loops::ca_csts_dev ("fold_from_loops:ca_csts_dev")

IntegerOptionKey const	basic::options::OptionKeys::fold_from_loops::add_relax_cycles ("fold_from_loops:add_relax_cycles")

IntegerOptionKey const	basic::options::OptionKeys::fold_from_loops::loop_mov_nterm ("fold_from_loops:loop_mov_nterm")

IntegerOptionKey const	basic::options::OptionKeys::fold_from_loops::loop_mov_cterm ("fold_from_loops:loop_mov_cterm")

RealOptionKey const	basic::options::OptionKeys::fold_from_loops::ca_rmsd_cutoff ("fold_from_loops:ca_rmsd_cutoff")

IntegerVectorOptionKey const	basic::options::OptionKeys::fold_from_loops::res_design_bs ("fold_from_loops:res_design_bs")

FileOptionKey const	basic::options::OptionKeys::fold_from_loops::clear_csts ("fold_from_loops:clear_csts")

BooleanOptionKey const	basic::options::OptionKeys::fold_from_loops::output_centroid ("fold_from_loops:output_centroid")

BooleanOptionKey const	basic::options::OptionKeys::fold_from_loops::add_cst_loop ("fold_from_loops:add_cst_loop")

BooleanOptionKey const	basic::options::OptionKeys::fold_and_dock::fold_and_dock ("fold_and_dock")

BooleanOptionKey const	basic::options::OptionKeys::fold_and_dock::move_anchor_points ("fold_and_dock:move_anchor_points")

BooleanOptionKey const	basic::options::OptionKeys::fold_and_dock::set_anchor_at_closest_point ("fold_and_dock:set_anchor_at_closest_point")

BooleanOptionKey const	basic::options::OptionKeys::fold_and_dock::rotate_anchor_to_x ("fold_and_dock:rotate_anchor_to_x")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::trans_mag_smooth ("fold_and_dock:trans_mag_smooth")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::rot_mag_smooth ("fold_and_dock:rot_mag_smooth")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::rb_rot_magnitude ("fold_and_dock:rb_rot_magnitude")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::rb_trans_magnitude ("fold_and_dock:rb_trans_magnitude")

IntegerOptionKey const	basic::options::OptionKeys::fold_and_dock::rigid_body_cycles ("fold_and_dock:rigid_body_cycles")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::move_anchor_frequency ("fold_and_dock:move_anchor_frequency")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::rigid_body_frequency ("fold_and_dock:rigid_body_frequency")

BooleanOptionKey const	basic::options::OptionKeys::fold_and_dock::rigid_body_disable_mc ("fold_and_dock:rigid_body_disable_mc")

RealOptionKey const	basic::options::OptionKeys::fold_and_dock::slide_contact_frequency ("fold_and_dock:slide_contact_frequency")

BooleanOptionKey const	basic::options::OptionKeys::match::match ("match")

StringOptionKey const	basic::options::OptionKeys::match::lig_name ("match:lig_name")

RealOptionKey const	basic::options::OptionKeys::match::bump_tolerance ("match:bump_tolerance")

FileOptionKey const	basic::options::OptionKeys::match::active_site_definition_by_residue ("match:active_site_definition_by_residue")

FileOptionKey const	basic::options::OptionKeys::match::active_site_definition_by_gridlig ("match:active_site_definition_by_gridlig")

FileOptionKey const	basic::options::OptionKeys::match::required_active_site_atom_names ("match:required_active_site_atom_names")

FileOptionKey const	basic::options::OptionKeys::match::grid_boundary ("match:grid_boundary")

FileOptionKey const	basic::options::OptionKeys::match::geometric_constraint_file ("match:geometric_constraint_file")

FileOptionKey const	basic::options::OptionKeys::match::scaffold_active_site_residues ("match:scaffold_active_site_residues")

FileOptionKey const	basic::options::OptionKeys::match::scaffold_active_site_residues_for_geomcsts ("match:scaffold_active_site_residues_for_geomcsts")

RealOptionKey const	basic::options::OptionKeys::match::euclid_bin_size ("match:euclid_bin_size")

RealOptionKey const	basic::options::OptionKeys::match::euler_bin_size ("match:euler_bin_size")

BooleanOptionKey const	basic::options::OptionKeys::match::consolidate_matches ("match:consolidate_matches")

IntegerOptionKey const	basic::options::OptionKeys::match::output_matches_per_group ("match:output_matches_per_group")

StringVectorOptionKey const	basic::options::OptionKeys::match::orientation_atoms ("match:orientation_atoms")

StringOptionKey const	basic::options::OptionKeys::match::output_format ("match:output_format")

StringOptionKey const	basic::options::OptionKeys::match::match_grouper ("match:match_grouper")

RealOptionKey const	basic::options::OptionKeys::match::grouper_downstream_rmsd ("match:grouper_downstream_rmsd")

BooleanOptionKey const	basic::options::OptionKeys::match::output_matchres_only ("match:output_matchres_only")

IntegerVectorOptionKey const	basic::options::OptionKeys::match::geom_csts_downstream_output ("match:geom_csts_downstream_output")

BooleanOptionKey const	basic::options::OptionKeys::match::filter_colliding_upstream_residues ("match:filter_colliding_upstream_residues")

RealOptionKey const	basic::options::OptionKeys::match::upstream_residue_collision_tolerance ("match:upstream_residue_collision_tolerance")

RealOptionKey const	basic::options::OptionKeys::match::upstream_residue_collision_score_cutoff ("match:upstream_residue_collision_score_cutoff")

RealOptionKey const	basic::options::OptionKeys::match::upstream_residue_collision_Wfa_atr ("match:upstream_residue_collision_Wfa_atr")

RealOptionKey const	basic::options::OptionKeys::match::upstream_residue_collision_Wfa_rep ("match:upstream_residue_collision_Wfa_rep")

RealOptionKey const	basic::options::OptionKeys::match::upstream_residue_collision_Wfa_sol ("match:upstream_residue_collision_Wfa_sol")

BooleanOptionKey const	basic::options::OptionKeys::match::filter_upstream_downstream_collisions ("match:filter_upstream_downstream_collisions")

RealOptionKey const	basic::options::OptionKeys::match::updown_collision_tolerance ("match:updown_collision_tolerance")

RealOptionKey const	basic::options::OptionKeys::match::updown_residue_collision_score_cutoff ("match:updown_residue_collision_score_cutoff")

RealOptionKey const	basic::options::OptionKeys::match::updown_residue_collision_Wfa_atr ("match:updown_residue_collision_Wfa_atr")

RealOptionKey const	basic::options::OptionKeys::match::updown_residue_collision_Wfa_rep ("match:updown_residue_collision_Wfa_rep")

RealOptionKey const	basic::options::OptionKeys::match::updown_residue_collision_Wfa_sol ("match:updown_residue_collision_Wfa_sol")

BooleanOptionKey const	basic::options::OptionKeys::match::define_match_by_single_downstream_positioning ("match:define_match_by_single_downstream_positioning")

IntegerOptionKey const	basic::options::OptionKeys::match::ligand_rotamer_index ("match:ligand_rotamer_index")

BooleanOptionKey const	basic::options::OptionKeys::match::enumerate_ligand_rotamers ("match:enumerate_ligand_rotamers")

BooleanOptionKey const	basic::options::OptionKeys::match::only_enumerate_non_match_redundant_ligand_rotamers ("match:only_enumerate_non_match_redundant_ligand_rotamers")

BooleanOptionKey const	basic::options::OptionKeys::match::dynamic_grid_refinement ("match:dynamic_grid_refinement")

BooleanOptionKey const	basic::options::OptionKeys::match::build_round1_hits_twice ("match:build_round1_hits_twice")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::canonical_sampling ("canonical_sampling")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::probabilities ("canonical_sampling:probabilities")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::sc ("canonical_sampling:probabilities:sc")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::localbb ("canonical_sampling:probabilities:localbb")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_uniform ("canonical_sampling:probabilities:sc_prob_uniform")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_withinrot ("canonical_sampling:probabilities:sc_prob_withinrot")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::sc_prob_perturbcurrent ("canonical_sampling:probabilities:sc_prob_perturbcurrent")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::MPI_sync_pools ("canonical_sampling:probabilities:MPI_sync_pools")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::MPI_bcast ("canonical_sampling:probabilities:MPI_bcast")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves ("canonical_sampling:probabilities:fast_sc_moves")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::fast_sc_moves_ntrials ("canonical_sampling:probabilities:fast_sc_moves_ntrials")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::no_jd2_output ("canonical_sampling:probabilities:no_jd2_output")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::use_hierarchical_clustering ("canonical_sampling:probabilities:use_hierarchical_clustering")

IntegerOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::hierarchical_max_cache_size ("canonical_sampling:probabilities:hierarchical_max_cache_size")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::backrub ("canonical_sampling:probabilities:backrub")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::probabilities::conrot ("canonical_sampling:probabilities:conrot")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::sampling ("canonical_sampling:sampling")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::no_detailed_balance ("canonical_sampling:sampling:no_detailed_balance")

IntegerOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::ntrials ("canonical_sampling:sampling:ntrials")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::mc_kt ("canonical_sampling:sampling:mc_kt")

IntegerOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::interval_pose_dump ("canonical_sampling:sampling:interval_pose_dump")

IntegerOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::interval_data_dump ("canonical_sampling:sampling:interval_data_dump")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::output_only_cluster_transitions ("canonical_sampling:sampling:output_only_cluster_transitions")

RealOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::transition_threshold ("canonical_sampling:sampling:transition_threshold")

IntegerOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::max_files_per_dir ("canonical_sampling:sampling:max_files_per_dir")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::save_loops_only ("canonical_sampling:sampling:save_loops_only")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::sampling::dump_loops_only ("canonical_sampling:sampling:dump_loops_only")

BooleanOptionKey const	basic::options::OptionKeys::canonical_sampling::out::out ("canonical_sampling:out")

FileOptionKey const	basic::options::OptionKeys::canonical_sampling::out::new_structures ("canonical_sampling:out:new_structures")

BooleanOptionKey const	basic::options::OptionKeys::csa::csa ("csa")

BooleanOptionKey const	basic::options::OptionKeys::csa::useZ ("csa:useZ")

BooleanOptionKey const	basic::options::OptionKeys::dc::dc ("dc")

BooleanOptionKey const	basic::options::OptionKeys::dc::useZ ("dc:useZ")

BooleanOptionKey const	basic::options::OptionKeys::antibody::antibody ("antibody")

StringOptionKey const	basic::options::OptionKeys::antibody::numbering_scheme ("antibody:numbering_scheme")

StringOptionKey const	basic::options::OptionKeys::antibody::cdr_definition ("antibody:cdr_definition")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_l1 ("antibody:graft_l1")

StringOptionKey const	basic::options::OptionKeys::antibody::l1_template ("antibody:l1_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_l2 ("antibody:graft_l2")

StringOptionKey const	basic::options::OptionKeys::antibody::l2_template ("antibody:l2_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_l3 ("antibody:graft_l3")

StringOptionKey const	basic::options::OptionKeys::antibody::l3_template ("antibody:l3_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_h1 ("antibody:graft_h1")

StringOptionKey const	basic::options::OptionKeys::antibody::h1_template ("antibody:h1_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_h2 ("antibody:graft_h2")

StringOptionKey const	basic::options::OptionKeys::antibody::h2_template ("antibody:h2_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::graft_h3 ("antibody:graft_h3")

StringOptionKey const	basic::options::OptionKeys::antibody::h3_template ("antibody:h3_template")

BooleanOptionKey const	basic::options::OptionKeys::antibody::h3_no_stem_graft ("antibody:h3_no_stem_graft")

BooleanOptionKey const	basic::options::OptionKeys::antibody::packonly_after_graft ("antibody:packonly_after_graft")

BooleanOptionKey const	basic::options::OptionKeys::antibody::stem_optimize ("antibody:stem_optimize")

IntegerOptionKey const	basic::options::OptionKeys::antibody::stem_optimize_size ("antibody:stem_optimize_size")

StringOptionKey const	basic::options::OptionKeys::antibody::preprocessing_script_version ("antibody:preprocessing_script_version")

BooleanOptionKey const	basic::options::OptionKeys::antibody::model_h3 ("antibody:model_h3")

BooleanOptionKey const	basic::options::OptionKeys::antibody::snugfit ("antibody:snugfit")

BooleanOptionKey const	basic::options::OptionKeys::antibody::refine_h3 ("antibody:refine_h3")

BooleanOptionKey const	basic::options::OptionKeys::antibody::h3_filter ("antibody:h3_filter")

RealOptionKey const	basic::options::OptionKeys::antibody::h3_filter_tolerance ("antibody:h3_filter_tolerance")

BooleanOptionKey const	basic::options::OptionKeys::antibody::cter_insert ("antibody:cter_insert")

BooleanOptionKey const	basic::options::OptionKeys::antibody::flank_residue_min ("antibody:flank_residue_min")

BooleanOptionKey const	basic::options::OptionKeys::antibody::sc_min ("antibody:sc_min")

BooleanOptionKey const	basic::options::OptionKeys::antibody::rt_min ("antibody:rt_min")

BooleanOptionKey const	basic::options::OptionKeys::antibody::bad_nter ("antibody:bad_nter")

BooleanOptionKey const	basic::options::OptionKeys::antibody::extend_h3_before_modeling ("antibody:extend_h3_before_modeling")

BooleanOptionKey const	basic::options::OptionKeys::antibody::idealize_h3_stems_before_modeling ("antibody:idealize_h3_stems_before_modeling")

StringOptionKey const	basic::options::OptionKeys::antibody::remodel ("antibody:remodel")

StringOptionKey const	basic::options::OptionKeys::antibody::refine ("antibody:refine")

StringOptionKey const	basic::options::OptionKeys::antibody::centroid_refine ("antibody:centroid_refine")

BooleanOptionKey const	basic::options::OptionKeys::antibody::constrain_cter ("antibody:constrain_cter")

BooleanOptionKey const	basic::options::OptionKeys::antibody::constrain_vlvh_qq ("antibody:constrain_vlvh_qq")

BooleanOptionKey const	basic::options::OptionKeys::antibody::snug_loops ("antibody:snug_loops")

FileOptionKey const	basic::options::OptionKeys::antibody::input_fv ("antibody:input_fv")

BooleanOptionKey const	basic::options::OptionKeys::antibody::camelid ("antibody:camelid")

BooleanOptionKey const	basic::options::OptionKeys::antibody::camelid_constraints ("antibody:camelid_constraints")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::design ("antibody:design")

StringOptionKey const	basic::options::OptionKeys::antibody::design::instructions ("antibody:design:instructions")

StringOptionKey const	basic::options::OptionKeys::antibody::design::antibody_database ("antibody:design:antibody_database")

StringVectorOptionKey const	basic::options::OptionKeys::antibody::design::design_cdrs ("antibody:design:design_cdrs")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::do_graft_design ("antibody:design:do_graft_design")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::do_post_graft_design_modeling ("antibody:design:do_post_graft_design_modeling")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::do_sequence_design ("antibody:design:do_sequence_design")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::do_post_design_modeling ("antibody:design:do_post_design_modeling")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::graft_rounds ("antibody:design:graft_rounds")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::top_graft_designs ("antibody:design:top_graft_designs")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::initial_perturb ("antibody:design:initial_perturb")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::use_deterministic ("antibody:design:use_deterministic")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::dump_post_graft_designs ("antibody:design:dump_post_graft_designs")

RealOptionKey const	basic::options::OptionKeys::antibody::design::interface_dis ("antibody:design:interface_dis")

RealOptionKey const	basic::options::OptionKeys::antibody::design::neighbor_dis ("antibody:design:neighbor_dis")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::dock_post_graft ("antibody:design:dock_post_graft")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::pack_post_graft ("antibody:design:pack_post_graft")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::rb_min_post_graft ("antibody:design:rb_min_post_graft")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::design_post_graft ("antibody:design:design_post_graft")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::dock_rounds ("antibody:design:dock_rounds")

StringOptionKey const	basic::options::OptionKeys::antibody::design::ab_dock_chains ("antibody:design:ab_dock_chains")

StringOptionKey const	basic::options::OptionKeys::antibody::design::design_method ("antibody:design:design_method")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::design_rounds ("antibody:design:design_rounds")

StringOptionKey const	basic::options::OptionKeys::antibody::design::design_scorefxn ("antibody:design:design_scorefxn")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::benchmark_basic_design ("antibody:design:benchmark_basic_design")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::use_filters ("antibody:design:use_filters")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::stats_cutoff ("antibody:design:stats_cutoff")

IntegerOptionKey const	basic::options::OptionKeys::antibody::design::sample_zero_probs_at ("antibody:design:sample_zero_probs_at")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::conservative_h3_design ("antibody:design:conservative_h3_design")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::turn_conservation ("antibody:design:turn_conservation")

BooleanOptionKey const	basic::options::OptionKeys::antibody::design::extend_native_cdrs ("antibody:design:extend_native_cdrs")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexPepDocking ("flexPepDocking")

StringOptionKey const	basic::options::OptionKeys::flexPepDocking::params_file ("flexPepDocking:params_file")

IntegerOptionKey const	basic::options::OptionKeys::flexPepDocking::peptide_anchor ("flexPepDocking:peptide_anchor")

StringOptionKey const	basic::options::OptionKeys::flexPepDocking::receptor_chain ("flexPepDocking:receptor_chain")

StringOptionKey const	basic::options::OptionKeys::flexPepDocking::peptide_chain ("flexPepDocking:peptide_chain")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::pep_fold_only ("flexPepDocking:pep_fold_only")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::lowres_abinitio ("flexPepDocking:lowres_abinitio")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::lowres_preoptimize ("flexPepDocking:lowres_preoptimize")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexPepDockingMinimizeOnly ("flexPepDocking:flexPepDockingMinimizeOnly")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::extend_peptide ("flexPepDocking:extend_peptide")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::pep_refine ("flexPepDocking:pep_refine")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::rbMCM ("flexPepDocking:rbMCM")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::torsionsMCM ("flexPepDocking:torsionsMCM")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::peptide_loop_model ("flexPepDocking:peptide_loop_model")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::backrub_peptide ("flexPepDocking:backrub_peptide")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::boost_fa_atr ("flexPepDocking:boost_fa_atr")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::ramp_fa_rep ("flexPepDocking:ramp_fa_rep")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::ramp_rama ("flexPepDocking:ramp_rama")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexpep_score_only ("flexPepDocking:flexpep_score_only")

FileOptionKey const	basic::options::OptionKeys::flexPepDocking::ref_startstruct ("flexPepDocking:ref_startstruct")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::use_cen_score ("flexPepDocking:use_cen_score")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::design_peptide ("flexPepDocking:design_peptide")

IntegerOptionKey const	basic::options::OptionKeys::flexPepDocking::rep_ramp_cycles ("flexPepDocking:rep_ramp_cycles")

IntegerOptionKey const	basic::options::OptionKeys::flexPepDocking::mcm_cycles ("flexPepDocking:mcm_cycles")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::random_phi_psi_preturbation ("flexPepDocking:random_phi_psi_preturbation")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::smove_angle_range ("flexPepDocking:smove_angle_range")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::min_receptor_bb ("flexPepDocking:min_receptor_bb")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::random_trans_start ("flexPepDocking:random_trans_start")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::random_rot_start ("flexPepDocking:random_rot_start")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexpep_prepack ("flexPepDocking:flexpep_prepack")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexpep_noprepack1 ("flexPepDocking:flexpep_noprepack1")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::flexpep_noprepack2 ("flexPepDocking:flexpep_noprepack2")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::score_filter ("flexPepDocking:score_filter")

IntegerOptionKey const	basic::options::OptionKeys::flexPepDocking::hb_filter ("flexPepDocking:hb_filter")

IntegerOptionKey const	basic::options::OptionKeys::flexPepDocking::hotspot_filter ("flexPepDocking:hotspot_filter")

StringOptionKey const	basic::options::OptionKeys::flexPepDocking::frag5 ("flexPepDocking:frag5")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::frag9_weight ("flexPepDocking:frag9_weight")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::frag5_weight ("flexPepDocking:frag5_weight")

RealOptionKey const	basic::options::OptionKeys::flexPepDocking::frag3_weight ("flexPepDocking:frag3_weight")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::pSer2Asp_centroid ("flexPepDocking:pSer2Asp_centroid")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::pSer2Glu_centroid ("flexPepDocking:pSer2Glu_centroid")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::dumpPDB_abinitio ("flexPepDocking:dumpPDB_abinitio")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::dumpPDB_lowres ("flexPepDocking:dumpPDB_lowres")

BooleanOptionKey const	basic::options::OptionKeys::flexPepDocking::dumpPDB_hires ("flexPepDocking:dumpPDB_hires")

BooleanOptionKey const	basic::options::OptionKeys::cp::cp ("cp")

RealOptionKey const	basic::options::OptionKeys::cp::cutoff ("cp:cutoff")

StringOptionKey const	basic::options::OptionKeys::cp::minimizer ("cp:minimizer")

StringOptionKey const	basic::options::OptionKeys::cp::relax_sfxn ("cp:relax_sfxn")

StringOptionKey const	basic::options::OptionKeys::cp::pack_sfxn ("cp:pack_sfxn")

RealOptionKey const	basic::options::OptionKeys::cp::minimizer_tol ("cp:minimizer_tol")

StringOptionKey const	basic::options::OptionKeys::cp::minimizer_score_fxn ("cp:minimizer_score_fxn")

StringOptionKey const	basic::options::OptionKeys::cp::output ("cp:output")

IntegerOptionKey const	basic::options::OptionKeys::cp::ncycles ("cp:ncycles")

IntegerOptionKey const	basic::options::OptionKeys::cp::max_failures ("cp:max_failures")

BooleanOptionKey const	basic::options::OptionKeys::cp::print_reports ("cp:print_reports")

StringOptionKey const	basic::options::OptionKeys::cp::vipReportFile ("cp:vipReportFile")

StringOptionKey const	basic::options::OptionKeys::cp::exclude_file ("cp:exclude_file")

StringOptionKey const	basic::options::OptionKeys::cp::relax_mover ("cp:relax_mover")

BooleanOptionKey const	basic::options::OptionKeys::cp::skip_relax ("cp:skip_relax")

BooleanOptionKey const	basic::options::OptionKeys::cp::local_relax ("cp:local_relax")

BooleanOptionKey const	basic::options::OptionKeys::cp::print_intermediate_pdbs ("cp:print_intermediate_pdbs")

BooleanOptionKey const	basic::options::OptionKeys::cp::use_unrelaxed_starting_points ("cp:use_unrelaxed_starting_points")

BooleanOptionKey const	basic::options::OptionKeys::cp::easy_vip_acceptance ("cp:easy_vip_acceptance")

BooleanOptionKey const	basic::options::OptionKeys::archive::archive ("archive")

BooleanOptionKey const	basic::options::OptionKeys::archive::reread_all_structures ("archive:reread_all_structures")

IntegerOptionKey const	basic::options::OptionKeys::archive::completion_notify_frequency ("archive:completion_notify_frequency")

BooleanOptionKey const	basic::options::OptionKeys::optimization::optimization ("optimization")

IntegerOptionKey const	basic::options::OptionKeys::optimization::default_max_cycles ("optimization:default_max_cycles")

RealOptionKey const	basic::options::OptionKeys::optimization::armijo_min_stepsize ("optimization:armijo_min_stepsize")

RealOptionKey const	basic::options::OptionKeys::optimization::scale_normalmode_dampen ("optimization:scale_normalmode_dampen")

IntegerOptionKey const	basic::options::OptionKeys::optimization::lbfgs_M ("optimization:lbfgs_M")

RealOptionKey const	basic::options::OptionKeys::optimization::scale_d ("optimization:scale_d")

RealOptionKey const	basic::options::OptionKeys::optimization::scale_theta ("optimization:scale_theta")

RealOptionKey const	basic::options::OptionKeys::optimization::scale_rb ("optimization:scale_rb")

RealOptionKey const	basic::options::OptionKeys::optimization::scale_rbangle ("optimization:scale_rbangle")

BooleanOptionKey const	basic::options::OptionKeys::optimization::scmin_nonideal ("optimization:scmin_nonideal")

BooleanOptionKey const	basic::options::OptionKeys::optimization::scmin_cartesian ("optimization:scmin_cartesian")

BooleanOptionKey const	basic::options::OptionKeys::optimization::nonideal ("optimization:nonideal")

BooleanOptionKey const	basic::options::OptionKeys::full_model::full_model ("full_model")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::cutpoint_open ("full_model:cutpoint_open")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::cutpoint_closed ("full_model:cutpoint_closed")

StringVectorOptionKey const	basic::options::OptionKeys::full_model::other_poses ("full_model:other_poses")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::extra_min_res ("full_model:extra_min_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::jump_res ("full_model:jump_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::root_res ("full_model:root_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::virtual_sugar_res ("full_model:virtual_sugar_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::virtual_res ("full_model:virtual_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::sample_res ("full_model:sample_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::full_model::calc_rms_res ("full_model:calc_rms_res")

BooleanOptionKey const	basic::options::OptionKeys::chrisk::chrisk ("chrisk")

BooleanOptionKey const	basic::options::OptionKeys::chrisk::hb_elec ("chrisk:hb_elec")

BooleanOptionKey const	basic::options::OptionKeys::mh::mh ("mh")

StringOptionKey const	basic::options::OptionKeys::mh::motif_out_file ("mh:motif_out_file")

FileVectorOptionKey const	basic::options::OptionKeys::mh::harvest_motifs ("mh:harvest_motifs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::print_motifs ("mh:print_motifs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::dump_motif_pdbs ("mh:dump_motif_pdbs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::merge_motifs ("mh:merge_motifs")

BooleanOptionKey const	basic::options::OptionKeys::mh::merge_motifs_one_per_bin ("mh:merge_motifs_one_per_bin")

BooleanOptionKey const	basic::options::OptionKeys::mh::generate_reverse_motifs ("mh:generate_reverse_motifs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::dump_input_pdb ("mh:dump_input_pdb")

FileVectorOptionKey const	basic::options::OptionKeys::mh::score_pdbs ("mh:score_pdbs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data ("mh:xform_score_data")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data_ee ("mh:xform_score_data_ee")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data_eh ("mh:xform_score_data_eh")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data_he ("mh:xform_score_data_he")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data_hh ("mh:xform_score_data_hh")

FileVectorOptionKey const	basic::options::OptionKeys::mh::xform_score_data_sspair ("mh:xform_score_data_sspair")

FileVectorOptionKey const	basic::options::OptionKeys::mh::sequence_recovery ("mh:sequence_recovery")

FileVectorOptionKey const	basic::options::OptionKeys::mh::explicit_motif_score ("mh:explicit_motif_score")

FileVectorOptionKey const	basic::options::OptionKeys::mh::input_motifs ("mh:input_motifs")

FileVectorOptionKey const	basic::options::OptionKeys::mh::harvest_scores ("mh:harvest_scores")

FileOptionKey const	basic::options::OptionKeys::mh::print_scores ("mh:print_scores")

FileVectorOptionKey const	basic::options::OptionKeys::mh::dump_matching_motifs ("mh:dump_matching_motifs")

RealOptionKey const	basic::options::OptionKeys::mh::dump_matching_motifs_cutoff ("mh:dump_matching_motifs_cutoff")

BooleanOptionKey const	basic::options::OptionKeys::mh::score_across_chains_only ("mh:score_across_chains_only")

BooleanOptionKey const	basic::options::OptionKeys::mh::normalize_score_ncontact ("mh:normalize_score_ncontact")

IntegerOptionKey const	basic::options::OptionKeys::mh::dump_motif_pdbs_min_counts ("mh:dump_motif_pdbs_min_counts")

RealOptionKey const	basic::options::OptionKeys::mh::hash_cart_size ("mh:hash_cart_size")

RealOptionKey const	basic::options::OptionKeys::mh::hash_cart_resl ("mh:hash_cart_resl")

RealOptionKey const	basic::options::OptionKeys::mh::hash_angle_resl ("mh:hash_angle_resl")

IntegerOptionKey const	basic::options::OptionKeys::mh::harvest_motifs_min_hh_ends ("mh:harvest_motifs_min_hh_ends")

IntegerOptionKey const	basic::options::OptionKeys::mh::harvest_scores_min_count ("mh:harvest_scores_min_count")

BooleanOptionKey const	basic::options::OptionKeys::mh::ignore_io_errors ("mh:ignore_io_errors")

RealOptionKey const	basic::options::OptionKeys::mh::motif_match_radius ("mh:motif_match_radius")

RealVectorOptionKey const	basic::options::OptionKeys::mh::merge_similar_motifs ("mh:merge_similar_motifs")

BooleanOptionKey const	basic::options::OptionKeys::mh::score::score ("mh:score")

BooleanOptionKey const	basic::options::OptionKeys::mh::score::noloops ("mh:score:noloops")

BooleanOptionKey const	basic::options::OptionKeys::mh::score::spread_ss_element ("mh:score:spread_ss_element")

RealOptionKey const	basic::options::OptionKeys::mh::score::min_cover_fraction ("mh:score:min_cover_fraction")

RealOptionKey const	basic::options::OptionKeys::mh::score::strand_pair_weight ("mh:score:strand_pair_weight")

RealOptionKey const	basic::options::OptionKeys::mh::score::min_contact_pairs ("mh:score:min_contact_pairs")

RealOptionKey const	basic::options::OptionKeys::mh::score::max_contact_pairs ("mh:score:max_contact_pairs")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::filter ("mh:filter")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::filter_harvest ("mh:filter:filter_harvest")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::filter_io ("mh:filter:filter_io")

StringOptionKey const	basic::options::OptionKeys::mh::filter::restype ("mh:filter:restype")

StringOptionKey const	basic::options::OptionKeys::mh::filter::restype_one ("mh:filter:restype_one")

StringOptionKey const	basic::options::OptionKeys::mh::filter::not_restype ("mh:filter:not_restype")

StringOptionKey const	basic::options::OptionKeys::mh::filter::not_restype_one ("mh:filter:not_restype_one")

IntegerOptionKey const	basic::options::OptionKeys::mh::filter::seqsep ("mh:filter:seqsep")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::no_hb_bb ("mh:filter:no_hb_bb")

RealOptionKey const	basic::options::OptionKeys::mh::filter::mindist2 ("mh:filter:mindist2")

RealOptionKey const	basic::options::OptionKeys::mh::filter::maxdist2 ("mh:filter:maxdist2")

StringOptionKey const	basic::options::OptionKeys::mh::filter::ss1 ("mh:filter:ss1")

StringOptionKey const	basic::options::OptionKeys::mh::filter::ss2 ("mh:filter:ss2")

StringOptionKey const	basic::options::OptionKeys::mh::filter::dssp1 ("mh:filter:dssp1")

StringOptionKey const	basic::options::OptionKeys::mh::filter::dssp2 ("mh:filter:dssp2")

StringOptionKey const	basic::options::OptionKeys::mh::filter::aa1 ("mh:filter:aa1")

StringOptionKey const	basic::options::OptionKeys::mh::filter::aa2 ("mh:filter:aa2")

RealOptionKey const	basic::options::OptionKeys::mh::filter::sasa ("mh:filter:sasa")

RealOptionKey const	basic::options::OptionKeys::mh::filter::faatr ("mh:filter:faatr")

RealOptionKey const	basic::options::OptionKeys::mh::filter::hb_sc ("mh:filter:hb_sc")

RealOptionKey const	basic::options::OptionKeys::mh::filter::hb_bb_sc ("mh:filter:hb_bb_sc")

RealOptionKey const	basic::options::OptionKeys::mh::filter::hb_bb ("mh:filter:hb_bb")

RealOptionKey const	basic::options::OptionKeys::mh::filter::occupancy ("mh:filter:occupancy")

RealOptionKey const	basic::options::OptionKeys::mh::filter::coorderr ("mh:filter:coorderr")

RealOptionKey const	basic::options::OptionKeys::mh::filter::faatr_or_hbbb ("mh:filter:faatr_or_hbbb")

RealOptionKey const	basic::options::OptionKeys::mh::filter::faatr_or_hb ("mh:filter:faatr_or_hb")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::noloops ("mh:filter:noloops")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::oneloop ("mh:filter:oneloop")

BooleanOptionKey const	basic::options::OptionKeys::mh::filter::nodisulf ("mh:filter:nodisulf")

BooleanOptionKey const	basic::options::OptionKeys::cutoutdomain::cutoutdomain ("cutoutdomain")

IntegerOptionKey const	basic::options::OptionKeys::cutoutdomain::start ("cutoutdomain:start")

IntegerOptionKey const	basic::options::OptionKeys::cutoutdomain::end ("cutoutdomain:end")

BooleanOptionKey const	basic::options::OptionKeys::carbohydrates::carbohydrates ("carbohydrates")

BooleanOptionKey const	basic::options::OptionKeys::carbohydrates::lock_rings ("carbohydrates:lock_rings")

BooleanOptionKey const	basic::options::OptionKeys::dwkulp::dwkulp ("dwkulp")

StringOptionKey const	basic::options::OptionKeys::dwkulp::forcePolyAAfragments ("dwkulp:forcePolyAAfragments")

BooleanOptionKey const	basic::options::OptionKeys::matdes::matdes ("matdes")

IntegerOptionKey const	basic::options::OptionKeys::matdes::num_subs_building_block ("matdes:num_subs_building_block")

IntegerOptionKey const	basic::options::OptionKeys::matdes::num_subs_total ("matdes:num_subs_total")

StringOptionKey const	basic::options::OptionKeys::matdes::pdbID ("matdes:pdbID")

StringOptionKey const	basic::options::OptionKeys::matdes::prefix ("matdes:prefix")

RealVectorOptionKey const	basic::options::OptionKeys::matdes::radial_disp ("matdes:radial_disp")

RealVectorOptionKey const	basic::options::OptionKeys::matdes::angle ("matdes:angle")

StringOptionKey const	basic::options::OptionKeys::matdes::tag ("matdes:tag")

BooleanOptionKey const	basic::options::OptionKeys::matdes::dock::dock ("matdes:dock")

RealOptionKey const	basic::options::OptionKeys::matdes::dock::neg_r ("matdes:dock:neg_r")

BooleanOptionKey const	basic::options::OptionKeys::matdes::dock::dump_pdb ("matdes:dock:dump_pdb")

BooleanOptionKey const	basic::options::OptionKeys::matdes::dock::dump_chainA_only ("matdes:dock:dump_chainA_only")

BooleanOptionKey const	basic::options::OptionKeys::matdes::design::design ("matdes:design")

RealOptionKey const	basic::options::OptionKeys::matdes::design::contact_dist ("matdes:design:contact_dist")

RealOptionKey const	basic::options::OptionKeys::matdes::design::grid_size_angle ("matdes:design:grid_size_angle")

RealOptionKey const	basic::options::OptionKeys::matdes::design::grid_size_radius ("matdes:design:grid_size_radius")

IntegerOptionKey const	basic::options::OptionKeys::matdes::design::grid_nsamp_angle ("matdes:design:grid_nsamp_angle")

IntegerOptionKey const	basic::options::OptionKeys::matdes::design::grid_nsamp_radius ("matdes:design:grid_nsamp_radius")

RealOptionKey const	basic::options::OptionKeys::matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus")

BooleanOptionKey const	basic::options::OptionKeys::matdes::mutalyze::mutalyze ("matdes:mutalyze")

BooleanOptionKey const	basic::options::OptionKeys::matdes::mutalyze::calc_rot_boltz ("matdes:mutalyze:calc_rot_boltz")

BooleanOptionKey const	basic::options::OptionKeys::matdes::mutalyze::ala_scan ("matdes:mutalyze:ala_scan")

BooleanOptionKey const	basic::options::OptionKeys::matdes::mutalyze::revert_scan ("matdes:mutalyze:revert_scan")

BooleanOptionKey const	basic::options::OptionKeys::matdes::mutalyze::min_rb ("matdes:mutalyze:min_rb")

BooleanOptionKey const	basic::options::OptionKeys::gpu::gpu ("gpu")

IntegerOptionKey const	basic::options::OptionKeys::gpu::device ("gpu:device")

IntegerOptionKey const	basic::options::OptionKeys::gpu::threads ("gpu:threads")

BooleanOptionKey const	basic::options::OptionKeys::bunsat_calc2::bunsat_calc2 ("bunsat_calc2")

BooleanOptionKey const	basic::options::OptionKeys::bunsat_calc2::layered_sasa ("bunsat_calc2:layered_sasa")

BooleanOptionKey const	basic::options::OptionKeys::bunsat_calc2::generous_hbonds ("bunsat_calc2:generous_hbonds")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::sasa_burial_cutoff ("bunsat_calc2:sasa_burial_cutoff")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::AHD_cutoff ("bunsat_calc2:AHD_cutoff")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::dist_cutoff ("bunsat_calc2:dist_cutoff")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::hxl_dist_cutoff ("bunsat_calc2:hxl_dist_cutoff")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::sulph_dist_cutoff ("bunsat_calc2:sulph_dist_cutoff")

RealOptionKey const	basic::options::OptionKeys::bunsat_calc2::metal_dist_cutoff ("bunsat_calc2:metal_dist_cutoff")

Variables
BooleanOptionKey const	basic::options::OptionKeys::remodel::remodel ("remodel")

BooleanOptionKey const	basic::options::OptionKeys::remodel::help ("remodel:help")

BooleanOptionKey const	basic::options::OptionKeys::remodel::autopilot ("remodel:autopilot")

FileOptionKey const	basic::options::OptionKeys::remodel::blueprint ("remodel:blueprint")

FileOptionKey const	basic::options::OptionKeys::remodel::cstfile ("remodel:cstfile")

IntegerOptionKey const	basic::options::OptionKeys::remodel::cstfilter ("remodel:cstfilter")

StringOptionKey const	basic::options::OptionKeys::remodel::cen_sfxn ("remodel:cen_sfxn")

BooleanOptionKey const	basic::options::OptionKeys::remodel::check_scored_centroid ("remodel:check_scored_centroid")

IntegerOptionKey const	basic::options::OptionKeys::remodel::num_trajectory ("remodel:num_trajectory")

IntegerOptionKey const	basic::options::OptionKeys::remodel::save_top ("remodel:save_top")

BooleanOptionKey const	basic::options::OptionKeys::remodel::swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols")

IntegerOptionKey const	basic::options::OptionKeys::remodel::num_frag_moves ("remodel:num_frag_moves")

BooleanOptionKey const	basic::options::OptionKeys::remodel::bypass_fragments ("remodel:bypass_fragments")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_same_length_fragments ("remodel:use_same_length_fragments")

BooleanOptionKey const	basic::options::OptionKeys::remodel::enable_ligand_aa ("remodel:enable_ligand_aa")

BooleanOptionKey const	basic::options::OptionKeys::remodel::no_jumps ("remodel:no_jumps")

BooleanOptionKey const	basic::options::OptionKeys::remodel::backrub ("remodel:backrub")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_blueprint_sequence ("remodel:use_blueprint_sequence ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::randomize_equivalent_fragments ("remodel:randomize_equivalent_fragments ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::quick_and_dirty ("remodel:quick_and_dirty ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::checkpoint ("remodel:checkpoint ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_ccd_refine ("remodel:use_ccd_refine ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_pose_relax ("remodel:use_pose_relax ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_cart_relax ("remodel:use_cart_relax ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::free_relax ("remodel:free_relax ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_dssp_assignment ("remodel:use_dssp_assignment")

BooleanOptionKey const	basic::options::OptionKeys::remodel::keep_jumps_in_minimizer ("remodel:keep_jumps_in_minimizer ")

FileOptionKey const	basic::options::OptionKeys::remodel::output_fragfiles ("remodel:output_fragfiles")

FileOptionKey const	basic::options::OptionKeys::remodel::read_fragfile ("remodel:read_fragfile")

StringOptionKey const	basic::options::OptionKeys::remodel::generic_aa ("remodel:generic_aa")

RealOptionKey const	basic::options::OptionKeys::remodel::cluster_radius ("remodel:cluster_radius")

BooleanOptionKey const	basic::options::OptionKeys::remodel::use_clusters ("remodel:use_clusters")

BooleanOptionKey const	basic::options::OptionKeys::remodel::run_confirmation ("remodel:run_confirmation")

BooleanOptionKey const	basic::options::OptionKeys::remodel::cluster_on_entire_pose ("remodel:cluster_on_entire_pose")

IntegerOptionKey const	basic::options::OptionKeys::remodel::collect_clustered_top ("remodel:collect_clustered_top")

IntegerOptionKey const	basic::options::OptionKeys::remodel::dr_cycles ("remodel:dr_cycles")

IntegerOptionKey const	basic::options::OptionKeys::remodel::two_chain_tree ("remodel:two_chain_tree")

IntegerOptionKey const	basic::options::OptionKeys::remodel::repeat_structure ("remodel:repeat_structure")

IntegerOptionKey const	basic::options::OptionKeys::remodel::lh_ex_limit ("remodel:lh_ex_limit")

StringVectorOptionKey const	basic::options::OptionKeys::remodel::lh_filter_string ("remodel:lh_filter_string")

IntegerOptionKey const	basic::options::OptionKeys::remodel::lh_cbreak_selection ("remodel:lh_cbreak_selection")

BooleanOptionKey const	basic::options::OptionKeys::remodel::lh_closure_filter ("remodel:lh_closure_filter")

BooleanOptionKey const	basic::options::OptionKeys::remodel::cen_minimize ("remodel:cen_minimize")

IntegerOptionKey const	basic::options::OptionKeys::remodel::core_cutoff ("remodel:core_cutoff")

IntegerOptionKey const	basic::options::OptionKeys::remodel::boundary_cutoff ("remodel:boundary_cutoff")

BooleanOptionKey const	basic::options::OptionKeys::remodel::resclass_by_sasa ("remodel:resclass_by_sasa")

RealOptionKey const	basic::options::OptionKeys::remodel::helical_rise ("remodel:helical_rise")

RealOptionKey const	basic::options::OptionKeys::remodel::helical_radius ("remodel:helical_radius")

RealOptionKey const	basic::options::OptionKeys::remodel::helical_omega ("remodel:helical_omega")

RealOptionKey const	basic::options::OptionKeys::remodel::COM_sd ("remodel:COM_sd")

RealOptionKey const	basic::options::OptionKeys::remodel::COM_tolerance ("remodel:COM_tolerance")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::staged_sampling ("remodel:staged_sampling")

FileOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::residues_to_sample ("remodel:staged_sampling:residues_to_sample")

StringOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::starting_sequence ("remodel:staged_sampling:starting_sequence")

FileOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::starting_pdb ("remodel:staged_sampling:starting_pdb")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::require_frags_match_blueprint ("remodel:staged_sampling:require_frags_match_blueprint")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::start_w_ideal_helices ("remodel:staged_sampling:start_w_ideal_helices")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::sample_over_loops ("remodel:staged_sampling:sample_over_loops")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::small_moves ("remodel:staged_sampling:small_moves")

BooleanOptionKey const	basic::options::OptionKeys::remodel::staged_sampling::fa_relax_moves ("remodel:staged_sampling:fa_relax_moves")

BooleanOptionKey const	basic::options::OptionKeys::remodel::domainFusion::domainFusion ("remodel:domainFusion")

FileOptionKey const	basic::options::OptionKeys::remodel::domainFusion::insert_segment_from_pdb ("remodel:domainFusion:insert_segment_from_pdb")

RealOptionKey const	basic::options::OptionKeys::remodel::vdw ("remodel:vdw")

RealOptionKey const	basic::options::OptionKeys::remodel::rama ("remodel:rama")

RealOptionKey const	basic::options::OptionKeys::remodel::cbeta ("remodel:cbeta")

RealOptionKey const	basic::options::OptionKeys::remodel::cenpack ("remodel:cenpack")

RealOptionKey const	basic::options::OptionKeys::remodel::rg_local ("remodel:rg_local")

RealOptionKey const	basic::options::OptionKeys::remodel::hb_lrbb ("remodel:hb_lrbb")

RealOptionKey const	basic::options::OptionKeys::remodel::hb_srbb ("remodel:hb_srbb")

RealOptionKey const	basic::options::OptionKeys::remodel::rg ("remodel:rg")

RealOptionKey const	basic::options::OptionKeys::remodel::rsigma ("remodel:rsigma")

RealOptionKey const	basic::options::OptionKeys::remodel::ss_pair ("remodel:ss_pair")

BooleanOptionKey const	basic::options::OptionKeys::remodel::build_disulf ("remodel:build_disulf")

IntegerOptionKey const	basic::options::OptionKeys::remodel::max_disulf_allowed ("remodel:max_disulf_allowed")

RealOptionKey const	basic::options::OptionKeys::remodel::match_rt_limit ("remodel:match_rt_limit")

IntegerVectorOptionKey const	basic::options::OptionKeys::remodel::disulf_landing_range ("remodel:disulf_landing_range")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::design ("remodel:design")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::no_design ("remodel:design:no_design ")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::design_all ("remodel:design:design_all")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::allow_rare_aro_chi ("remodel:design:allow_rare_aro_chi")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::silent ("remodel:design:silent")
	Named verbosity levels. More...

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::skip_partial ("remodel:design:skip_partial")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::design_neighbors ("remodel:design:design_neighbors")

BooleanOptionKey const	basic::options::OptionKeys::remodel::design::find_neighbors ("remodel:design:find_neighbors")

BooleanOptionKey const	basic::options::OptionKeys::remodel::rank_by_bsasa ("remodel:rank_by_bsasa")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::RemodelLoopMover ("remodel:RemodelLoopMover")

RealOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::max_linear_chainbreak ("remodel:RemodelLoopMover:max_linear_chainbreak")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::randomize_loops ("remodel:RemodelLoopMover:randomize_loops")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::use_loop_hash ("remodel:RemodelLoopMover:use_loop_hash")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::allowed_closure_attempts ("remodel:RemodelLoopMover:allowed_closure_attempts")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::loophash_cycles ("remodel:RemodelLoopMover:loophash_cycles")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::simultaneous_cycles ("remodel:RemodelLoopMover:simultaneous_cycles")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::independent_cycles ("remodel:RemodelLoopMover:independent_cycles")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::boost_closure_cycles ("remodel:RemodelLoopMover:boost_closure_cycles")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::force_cutting_N ("remodel:RemodelLoopMover:force_cutting_N")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::bypass_closure ("remodel:RemodelLoopMover:bypass_closure")

BooleanOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::cyclic_peptide ("remodel:RemodelLoopMover:cyclic_peptide")

RealOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::temperature ("remodel:RemodelLoopMover:temperature")

IntegerOptionKey const	basic::options::OptionKeys::remodel::RemodelLoopMover::max_chews ("remodel:RemodelLoopMover:max_chews")

BooleanOptionKey const	basic::options::OptionKeys::symmetry::symmetry ("symmetry")

StringOptionKey const	basic::options::OptionKeys::symmetry::symmetry_definition ("symmetry:symmetry_definition")

RealOptionKey const	basic::options::OptionKeys::symmetry::reweight_symm_interactions ("symmetry:reweight_symm_interactions")

BooleanOptionKey const	basic::options::OptionKeys::symmetry::initialize_rigid_body_dofs ("symmetry:initialize_rigid_body_dofs")

BooleanOptionKey const	basic::options::OptionKeys::symmetry::detect_bonds ("symmetry:detect_bonds")

RealVectorOptionKey const	basic::options::OptionKeys::symmetry::perturb_rigid_body_dofs ("symmetry:perturb_rigid_body_dofs")

BooleanOptionKey const	basic::options::OptionKeys::symmetry::symmetric_rmsd ("symmetry:symmetric_rmsd")

BooleanOptionKey const	basic::options::OptionKeys::rdc::rdc ("rdc")

BooleanOptionKey const	basic::options::OptionKeys::rdc::correct_NH_length ("rdc:correct_NH_length")

BooleanOptionKey const	basic::options::OptionKeys::rdc::reduced_couplings ("rdc:reduced_couplings")

FileOptionKey const	basic::options::OptionKeys::rdc::weights ("rdc:weights")

RealOptionKey const	basic::options::OptionKeys::rdc::iterate_weights ("rdc:iterate_weights")

FileOptionKey const	basic::options::OptionKeys::rdc::segment_file ("rdc:segment_file")

StringOptionKey const	basic::options::OptionKeys::rdc::segment_scoring_mode ("rdc:segment_scoring_mode")

RealOptionKey const	basic::options::OptionKeys::rdc::total_weight ("rdc:total_weight")

RealOptionKey const	basic::options::OptionKeys::rdc::tensor_weight ("rdc:tensor_weight")

FileOptionKey const	basic::options::OptionKeys::rdc::print_rdc_values ("rdc:print_rdc_values")

RealOptionKey const	basic::options::OptionKeys::rdc::iterate_tol ("rdc:iterate_tol")

BooleanOptionKey const	basic::options::OptionKeys::rdc::iterate_reset ("rdc:iterate_reset")

FileOptionKey const	basic::options::OptionKeys::rdc::dump_weight_trajectory ("rdc:dump_weight_trajectory")

RealVectorOptionKey const	basic::options::OptionKeys::rdc::fix_normAzz ("rdc:fix_normAzz")

FileOptionKey const	basic::options::OptionKeys::rdc::select_residues_file ("rdc:select_residues_file")

StringOptionKey const	basic::options::OptionKeys::rdc::fit_method ("rdc:fit_method")

RealVectorOptionKey const	basic::options::OptionKeys::rdc::fixDa ("rdc:fixDa")

RealVectorOptionKey const	basic::options::OptionKeys::rdc::fixR ("rdc:fixR")

IntegerOptionKey const	basic::options::OptionKeys::rdc::nlsrepeat ("rdc:nlsrepeat")

BooleanOptionKey const	basic::options::OptionKeys::threadsc::threadsc ("threadsc")

StringOptionKey const	basic::options::OptionKeys::threadsc::src_chain ("threadsc:src_chain")

StringOptionKey const	basic::options::OptionKeys::threadsc::trg_chain ("threadsc:trg_chain")

IntegerOptionKey const	basic::options::OptionKeys::threadsc::src_first_resid ("threadsc:src_first_resid")

IntegerOptionKey const	basic::options::OptionKeys::threadsc::trg_first_resid ("threadsc:trg_first_resid")

IntegerOptionKey const	basic::options::OptionKeys::threadsc::nres ("threadsc:nres")

IntegerOptionKey const	basic::options::OptionKeys::threadsc::trg_anchor ("threadsc:trg_anchor")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::stepwise ("stepwise")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::s1 ("stepwise:s1")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::s2 ("stepwise:s2")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::silent1 ("stepwise:silent1")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::silent2 ("stepwise:silent2")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::tags1 ("stepwise:tags1")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::tags2 ("stepwise:tags2")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::slice_res1 ("stepwise:slice_res1")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::slice_res2 ("stepwise:slice_res2")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::input_res1 ("stepwise:input_res1")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::input_res2 ("stepwise:input_res2")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::backbone_only1 ("stepwise:backbone_only1")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::backbone_only2 ("stepwise:backbone_only2")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::fixed_res ("stepwise:fixed_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::working_res ("stepwise:working_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::test_encapsulation ("stepwise:test_encapsulation")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::choose_random ("stepwise:choose_random")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::num_random_samples ("stepwise:num_random_samples")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::num_pose_minimize ("stepwise:num_pose_minimize")

StringOptionKey const	basic::options::OptionKeys::stepwise::align_pdb ("stepwise:align_pdb")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::enumerate ("stepwise:enumerate")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::preminimize ("stepwise:preminimize")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::monte_carlo ("stepwise:monte_carlo")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::verbose_scores ("stepwise:monte_carlo:verbose_scores")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::skip_deletions ("stepwise:monte_carlo:skip_deletions")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::erraser ("stepwise:monte_carlo:erraser")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_hinge_moves ("stepwise:monte_carlo:allow_internal_hinge_moves")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_internal_local_moves ("stepwise:monte_carlo:allow_internal_local_moves")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_skip_bulge ("stepwise:monte_carlo:allow_skip_bulge")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::from_scratch_frequency ("stepwise:monte_carlo:from_scratch_frequency")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_split_off ("stepwise:monte_carlo:allow_split_off")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::cycles ("stepwise:monte_carlo:cycles")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::temperature ("stepwise:monte_carlo:temperature")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::add_delete_frequency ("stepwise:monte_carlo:add_delete_frequency")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::intermolecular_frequency ("stepwise:monte_carlo:intermolecular_frequency")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::minimize_single_res_frequency ("stepwise:monte_carlo:minimize_single_res_frequency")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::allow_variable_bond_geometry ("stepwise:monte_carlo:allow_variable_bond_geometry")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::switch_focus_frequency ("stepwise:monte_carlo:switch_focus_frequency")

RealOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::just_min_after_mutation_frequency ("stepwise:monte_carlo:just_min_after_mutation_frequency")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::local_redock_only ("stepwise:monte_carlo:local_redock_only")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::monte_carlo::make_movie ("stepwise:monte_carlo:make_movie")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::move ("stepwise:move")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::use_green_packer ("stepwise:use_green_packer")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rna ("stepwise:rna")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_native_rmsd_screen ("stepwise:rna:sampler_native_rmsd_screen")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_native_screen_rmsd_cutoff ("stepwise:rna:sampler_native_screen_rmsd_cutoff")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_cluster_rmsd ("stepwise:rna:sampler_cluster_rmsd")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_perform_o2prime_pack ("stepwise:rna:sampler_perform_o2prime_pack")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::VERBOSE ("stepwise:rna:VERBOSE")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::distinguish_pucker ("stepwise:rna:distinguish_pucker")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::finer_sampling_at_chain_closure ("stepwise:rna:finer_sampling_at_chain_closure")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::PBP_clustering_at_chain_closure ("stepwise:rna:PBP_clustering_at_chain_closure")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_allow_syn_pyrimidine ("stepwise:rna:sampler_allow_syn_pyrimidine")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_chi_rotamer ("stepwise:rna:sampler_extra_chi_rotamer")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_beta_rotamer ("stepwise:rna:sampler_extra_beta_rotamer")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_extra_epsilon_rotamer ("stepwise:rna:sampler_extra_epsilon_rotamer")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::force_centroid_interaction ("stepwise:rna:force_centroid_interaction")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_legacy_mode ("stepwise:rna:virtual_sugar_legacy_mode")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::erraser ("stepwise:rna:erraser")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::centroid_screen ("stepwise:rna:centroid_screen")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_atr_rep_screen ("stepwise:rna:VDW_atr_rep_screen")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::skip_sampling ("stepwise:rna:skip_sampling")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimizer_perform_minimize ("stepwise:rna:minimizer_perform_minimize")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF ("stepwise:rna:VDW_rep_alignment_RMSD_CUTOFF")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_delete_matching_res ("stepwise:rna:VDW_rep_delete_matching_res")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff ("stepwise:rna:VDW_rep_screen_physical_pose_clash_dist_cutoff")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::integration_test ("stepwise:rna:integration_test")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_bulge_at_chainbreak ("stepwise:rna:allow_bulge_at_chainbreak")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::parin_favorite_output ("stepwise:rna:parin_favorite_output")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::reinitialize_CCD_torsions ("stepwise:rna:reinitialize_CCD_torsions")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sample_both_sugar_base_rotamer ("stepwise:rna:sample_both_sugar_base_rotamer")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_include_torsion_value_in_tag ("stepwise:rna:sampler_include_torsion_value_in_tag")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_assert_no_virt_sugar_sampling ("stepwise:rna:sampler_assert_no_virt_sugar_sampling")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_try_sugar_instantiation ("stepwise:rna:sampler_try_sugar_instantiation")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::do_not_sample_multiple_virtual_sugar ("stepwise:rna:do_not_sample_multiple_virtual_sugar")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::sample_ONLY_multiple_virtual_sugar ("stepwise:rna:sample_ONLY_multiple_virtual_sugar")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_base_pair_only_centroid_screen ("stepwise:rna:allow_base_pair_only_centroid_screen")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimizer_output_before_o2prime_pack ("stepwise:rna:minimizer_output_before_o2prime_pack")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimizer_perform_o2prime_pack ("stepwise:rna:minimizer_perform_o2prime_pack")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimizer_rename_tag ("stepwise:rna:minimizer_rename_tag")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_res ("stepwise:rna:minimize_res")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::alignment_res ("stepwise:rna:alignment_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::native_alignment_res ("stepwise:rna:native_alignment_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::rmsd_res ("stepwise:rna:rmsd_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::missing_res ("stepwise:rna:missing_res")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::missing_res2 ("stepwise:rna:missing_res2")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::job_queue_ID ("stepwise:rna:job_queue_ID")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::minimize_and_score_sugar ("stepwise:rna:minimize_and_score_sugar")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::global_sample_res_list ("stepwise:rna:global_sample_res_list")

FileOptionKey const	basic::options::OptionKeys::stepwise::rna::filter_output_filename ("stepwise:rna:filter_output_filename")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::combine_long_loop_mode ("stepwise:rna:combine_long_loop_mode")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::combine_helical_silent_file ("stepwise:rna:combine_helical_silent_file")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::output_extra_RMSDs ("stepwise:rna:output_extra_RMSDs")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::force_syn_chi_res_list ("stepwise:rna:force_syn_chi_res_list")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::force_north_sugar_list ("stepwise:rna:force_north_sugar_list")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::force_south_sugar_list ("stepwise:rna:force_south_sugar_list")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::protonated_H1_adenosine_list ("stepwise:rna:protonated_H1_adenosine_list")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::native_virtual_res ("stepwise:rna:native_virtual_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::simple_append_map ("stepwise:rna:simple_append_map")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_fixed_res_at_moving_res ("stepwise:rna:allow_fixed_res_at_moving_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::force_user_defined_jumps ("stepwise:rna:force_user_defined_jumps")

StringVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::jump_point_pairs ("stepwise:rna:jump_point_pairs")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::terminal_res ("stepwise:rna:terminal_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::add_virt_root ("stepwise:rna:add_virt_root")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::floating_base ("stepwise:rna:floating_base")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::rna::floating_base_anchor_res ("stepwise:rna:floating_base_anchor_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP ("stepwise:rna:allow_chain_boundary_jump_partner_right_at_fixed_BP")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::rna::bulge_res ("stepwise:rna:bulge_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::rebuild_bulge_mode ("stepwise:rna:rebuild_bulge_mode")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_keep_base_fixed ("stepwise:rna:virtual_sugar_keep_base_fixed")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::virtual_sugar_do_minimize ("stepwise:rna:virtual_sugar_do_minimize")

RealOptionKey const	basic::options::OptionKeys::stepwise::rna::sampler_max_centroid_distance ("stepwise:rna:sampler_max_centroid_distance")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::filter_user_alignment_res ("stepwise:rna:filter_user_alignment_res")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::output_pdb ("stepwise:rna:output_pdb")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::tether_jump ("stepwise:rna:tether_jump")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::rna::unified_framework ("stepwise:rna:unified_framework")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::protein ("stepwise:protein")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::global_optimize ("stepwise:protein:global_optimize")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::disallow_backbone_sampling ("stepwise:protein:disallow_backbone_sampling")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff ("stepwise:protein:disable_sampling_of_loop_takeoff")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::dump ("stepwise:protein:dump")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::sample_beta ("stepwise:protein:sample_beta")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::ghost_loops ("stepwise:protein:ghost_loops")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::rescore_only ("stepwise:protein:rescore_only")

StringOptionKey const	basic::options::OptionKeys::stepwise::protein::min_type ("stepwise:protein:min_type")

RealOptionKey const	basic::options::OptionKeys::stepwise::protein::min_tolerance ("stepwise:protein:min_tolerance")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_screen ("stepwise:protein:centroid_screen")

RealOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut ("stepwise:protein:centroid_score_diff_cut")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::skip_minimize ("stepwise:protein:skip_minimize")

StringOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_weights ("stepwise:protein:centroid_weights")

RealOptionKey const	basic::options::OptionKeys::stepwise::protein::score_diff_cut ("stepwise:protein:score_diff_cut")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::filter_native_big_bins ("stepwise:protein:filter_native_big_bins")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd ("stepwise:protein:cluster_by_all_atom_rmsd")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::centroid_output ("stepwise:protein:centroid_output")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::protein::n_sample ("stepwise:protein:n_sample")

IntegerOptionKey const	basic::options::OptionKeys::stepwise::protein::nstruct_centroid ("stepwise:protein:nstruct_centroid")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::ccd_close ("stepwise:protein:ccd_close")

IntegerVectorOptionKey const	basic::options::OptionKeys::stepwise::protein::bridge_res ("stepwise:protein:bridge_res")

RealOptionKey const	basic::options::OptionKeys::stepwise::protein::rmsd_screen ("stepwise:protein:rmsd_screen")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::cart_min ("stepwise:protein:cart_min")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains ("stepwise:protein:move_jumps_between_chains")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials ("stepwise:protein:use_packer_instead_of_rotamer_trials")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::expand_loop_takeoff ("stepwise:protein:expand_loop_takeoff")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::skip_coord_constraints ("stepwise:protein:skip_coord_constraints")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains ("stepwise:protein:allow_virtual_side_chains")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::protein_prepack ("stepwise:protein:protein_prepack")

BooleanOptionKey const	basic::options::OptionKeys::stepwise::protein::protein_atr_rep_screen ("stepwise:protein:protein_atr_rep_screen")

BooleanOptionKey const	basic::options::OptionKeys::ufv::ufv ("ufv")

IntegerOptionKey const	basic::options::OptionKeys::ufv::left ("ufv:left")

IntegerOptionKey const	basic::options::OptionKeys::ufv::right ("ufv:right")

StringOptionKey const	basic::options::OptionKeys::ufv::ss ("ufv:ss")

StringOptionKey const	basic::options::OptionKeys::ufv::aa_during_build ("ufv:aa_during_build")

StringOptionKey const	basic::options::OptionKeys::ufv::aa_during_design_refine ("ufv:aa_during_design_refine")

BooleanOptionKey const	basic::options::OptionKeys::ufv::keep_junction_torsions ("ufv:keep_junction_torsions")

FileOptionKey const	basic::options::OptionKeys::ufv::ufv_loops ("ufv:ufv_loops")

BooleanOptionKey const	basic::options::OptionKeys::ufv::use_fullmer ("ufv:use_fullmer")

StringOptionKey const	basic::options::OptionKeys::ufv::centroid_loop_mover ("ufv:centroid_loop_mover")

BooleanOptionKey const	basic::options::OptionKeys::ufv::no_neighborhood_design ("ufv:no_neighborhood_design")

IntegerOptionKey const	basic::options::OptionKeys::ufv::dr_cycles ("ufv:dr_cycles")

StringOptionKey const	basic::options::OptionKeys::ufv::centroid_sfx ("ufv:centroid_sfx")

StringOptionKey const	basic::options::OptionKeys::ufv::centroid_sfx_patch ("ufv:centroid_sfx_patch")

StringOptionKey const	basic::options::OptionKeys::ufv::fullatom_sfx ("ufv:fullatom_sfx")

StringOptionKey const	basic::options::OptionKeys::ufv::fullatom_sfx_patch ("ufv:fullatom_sfx_patch")

BooleanOptionKey const	basic::options::OptionKeys::ufv::insert::insert ("ufv:insert")

FileOptionKey const	basic::options::OptionKeys::ufv::insert::insert_pdb ("ufv:insert:insert_pdb")

FileOptionKey const	basic::options::OptionKeys::ufv::insert::attached_pdb ("ufv:insert:attached_pdb")

StringOptionKey const	basic::options::OptionKeys::ufv::insert::connection_scheme ("ufv:insert:connection_scheme")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::rot_anl ("rot_anl")

StringOptionKey const	basic::options::OptionKeys::rot_anl::tag ("rot_anl:tag")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::premin ("rot_anl:premin")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::min ("rot_anl:min")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::diff_to_min ("rot_anl:diff_to_min")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::repack ("rot_anl:repack")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::rtmin ("rot_anl:rtmin")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::scmove ("rot_anl:scmove")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::design ("rot_anl:design")

RealOptionKey const	basic::options::OptionKeys::rot_anl::score_tol ("rot_anl:score_tol")

RealOptionKey const	basic::options::OptionKeys::rot_anl::rmsd_tol ("rot_anl:rmsd_tol")

BooleanOptionKey const	basic::options::OptionKeys::rot_anl::dump_pdb ("rot_anl:dump_pdb")

IntegerOptionKey const	basic::options::OptionKeys::rot_anl::nloop_scmove ("rot_anl:nloop_scmove")

BooleanOptionKey const	basic::options::OptionKeys::sewing::sewing ("sewing")

FileOptionKey const	basic::options::OptionKeys::sewing::query_structure_path ("sewing:query_structure_path")

IntegerOptionKey const	basic::options::OptionKeys::sewing::frag1_start ("sewing:frag1_start")

IntegerOptionKey const	basic::options::OptionKeys::sewing::frag1_end ("sewing:frag1_end")

IntegerOptionKey const	basic::options::OptionKeys::sewing::frag2_start ("sewing:frag2_start")

IntegerOptionKey const	basic::options::OptionKeys::sewing::frag2_end ("sewing:frag2_end")

IntegerOptionKey const	basic::options::OptionKeys::sewing::minimum_helix_contacts ("sewing:minimum_helix_contacts")

IntegerOptionKey const	basic::options::OptionKeys::sewing::helices_to_add ("sewing:helices_to_add")

RealOptionKey const	basic::options::OptionKeys::sewing::single_helix_rmsd_cutoff ("sewing:single_helix_rmsd_cutoff")

RealOptionKey const	basic::options::OptionKeys::sewing::helix_pair_rmsd_cutoff ("sewing:helix_pair_rmsd_cutoff")

FileOptionKey const	basic::options::OptionKeys::sewing::nat_ro_file ("sewing:nat_ro_file")

RealOptionKey const	basic::options::OptionKeys::sewing::helix_cap_dist_cutoff ("sewing:helix_cap_dist_cutoff")

RealOptionKey const	basic::options::OptionKeys::sewing::helix_contact_dist_cutoff ("sewing:helix_contact_dist_cutoff")

IntegerOptionKey const	basic::options::OptionKeys::sewing::min_helix_size ("sewing:min_helix_size")

BooleanOptionKey const	basic::options::OptionKeys::strand_assembly::strand_assembly ("strand_assembly")

IntegerOptionKey const	basic::options::OptionKeys::strand_assembly::min_num_strands_to_deal ("strand_assembly:min_num_strands_to_deal")

IntegerOptionKey const	basic::options::OptionKeys::strand_assembly::max_num_strands_to_deal ("strand_assembly:max_num_strands_to_deal")

BooleanOptionKey const	basic::options::OptionKeys::strand_assembly::extract_native_only ("strand_assembly:extract_native_only")

IntegerOptionKey const	basic::options::OptionKeys::strand_assembly::min_res_in_strand ("strand_assembly:min_res_in_strand")

IntegerOptionKey const	basic::options::OptionKeys::strand_assembly::max_res_in_strand ("strand_assembly:max_res_in_strand")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::min_O_N_dis ("strand_assembly:min_O_N_dis")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::max_O_N_dis ("strand_assembly:max_O_N_dis")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::min_sheet_dis ("strand_assembly:min_sheet_dis")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::max_sheet_dis ("strand_assembly:max_sheet_dis")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::min_sheet_torsion ("strand_assembly:min_sheet_torsion")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::max_sheet_torsion ("strand_assembly:max_sheet_torsion")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::min_sheet_angle ("strand_assembly:min_sheet_angle")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::max_sheet_angle ("strand_assembly:max_sheet_angle")

RealOptionKey const	basic::options::OptionKeys::strand_assembly::min_shortest_dis_sidechain_inter_sheet ("strand_assembly:min_shortest_dis_sidechain_inter_sheet")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::pepspec ("pepspec")

StringOptionKey const	basic::options::OptionKeys::pepspec::soft_wts ("pepspec:soft_wts")

StringOptionKey const	basic::options::OptionKeys::pepspec::cen_wts ("pepspec:cen_wts")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::binding_score ("pepspec:binding_score")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::no_cen ("pepspec:no_cen")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::no_cen_rottrials ("pepspec:no_cen_rottrials")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::run_sequential ("pepspec:run_sequential")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::pep_anchor ("pepspec:pep_anchor")

StringOptionKey const	basic::options::OptionKeys::pepspec::pep_chain ("pepspec:pep_chain")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_peptides ("pepspec:n_peptides")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_build_loop ("pepspec:n_build_loop")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_cgrelax_loop ("pepspec:n_cgrelax_loop")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_dock_loop ("pepspec:n_dock_loop")

RealOptionKey const	basic::options::OptionKeys::pepspec::interface_cutoff ("pepspec:interface_cutoff")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::use_input_bb ("pepspec:use_input_bb")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::remove_input_bb ("pepspec:remove_input_bb")

StringOptionKey const	basic::options::OptionKeys::pepspec::homol_csts ("pepspec:homol_csts")

RealOptionKey const	basic::options::OptionKeys::pepspec::p_homol_csts ("pepspec:p_homol_csts")

StringOptionKey const	basic::options::OptionKeys::pepspec::frag_file ("pepspec:frag_file")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::gen_pep_bb_sequential ("pepspec:gen_pep_bb_sequential")

StringOptionKey const	basic::options::OptionKeys::pepspec::input_seq ("pepspec:input_seq")

StringOptionKey const	basic::options::OptionKeys::pepspec::ss_type ("pepspec:ss_type")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::upweight_interface ("pepspec:upweight_interface")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::calc_sasa ("pepspec:calc_sasa")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::diversify_pep_seqs ("pepspec:diversify_pep_seqs")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::diversify_lvl ("pepspec:diversify_lvl")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::dump_cg_bb ("pepspec:dump_cg_bb")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::save_low_pdbs ("pepspec:save_low_pdbs")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::save_all_pdbs ("pepspec:save_all_pdbs")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::no_design ("pepspec:no_design")

StringOptionKey const	basic::options::OptionKeys::pepspec::pdb_list ("pepspec:pdb_list")

StringOptionKey const	basic::options::OptionKeys::pepspec::ref_pdb_list ("pepspec:ref_pdb_list")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::add_buffer_res ("pepspec:add_buffer_res")

StringOptionKey const	basic::options::OptionKeys::pepspec::cg_res_type ("pepspec:cg_res_type")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::native_pep_anchor ("pepspec:native_pep_anchor")

StringOptionKey const	basic::options::OptionKeys::pepspec::native_pep_chain ("pepspec:native_pep_chain")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::native_align ("pepspec:native_align")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::rmsd_analysis ("pepspec:rmsd_analysis")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::phipsi_analysis ("pepspec:phipsi_analysis")

StringOptionKey const	basic::options::OptionKeys::pepspec::anchor_type ("pepspec:anchor_type")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::no_prepack_prot ("pepspec:no_prepack_prot")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::prep_use_ref_rotamers ("pepspec:prep_use_ref_rotamers")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_prepend ("pepspec:n_prepend")

IntegerOptionKey const	basic::options::OptionKeys::pepspec::n_append ("pepspec:n_append")

RealOptionKey const	basic::options::OptionKeys::pepspec::clash_cutoff ("pepspec:clash_cutoff")

RealOptionKey const	basic::options::OptionKeys::pepspec::n_anchor_dock_std_devs ("pepspec:n_anchor_dock_std_devs")

RealOptionKey const	basic::options::OptionKeys::pepspec::prep_trans_std_dev ("pepspec:prep_trans_std_dev")

RealOptionKey const	basic::options::OptionKeys::pepspec::prep_rot_std_dev ("pepspec:prep_rot_std_dev")

BooleanOptionKey const	basic::options::OptionKeys::pepspec::seq_align ("pepspec:seq_align")

StringOptionKey const	basic::options::OptionKeys::pepspec::prep_align_prot_to ("pepspec:prep_align_prot_to")

BooleanOptionKey const	basic::options::OptionKeys::sicdock::sicdock ("sicdock")

RealOptionKey const	basic::options::OptionKeys::sicdock::clash_dis ("sicdock:clash_dis")

RealOptionKey const	basic::options::OptionKeys::sicdock::contact_dis ("sicdock:contact_dis")

RealOptionKey const	basic::options::OptionKeys::sicdock::hash_2D_vs_3D ("sicdock:hash_2D_vs_3D")

RealOptionKey const	basic::options::OptionKeys::sicdock::term_min_expose ("sicdock:term_min_expose")

RealOptionKey const	basic::options::OptionKeys::sicdock::term_max_angle ("sicdock:term_max_angle")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::orbitals ("orbitals")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::Hpol ("orbitals:Hpol")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::Haro ("orbitals:Haro")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::bb_stats ("orbitals:bb_stats")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::sc_stats ("orbitals:sc_stats")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::orb_orb_stats ("orbitals:orb_orb_stats")

BooleanOptionKey const	basic::options::OptionKeys::orbitals::sc_bb ("orbitals:sc_bb")

BooleanOptionKey const	basic::options::OptionKeys::pb_potential::pb_potential ("pb_potential")

IntegerVectorOptionKey const	basic::options::OptionKeys::pb_potential::charged_chains ("pb_potential:charged_chains")

BooleanOptionKey const	basic::options::OptionKeys::pb_potential::sidechain_only ("pb_potential:sidechain_only")

IntegerVectorOptionKey const	basic::options::OptionKeys::pb_potential::revamp_near_chain ("pb_potential:revamp_near_chain")

StringOptionKey const	basic::options::OptionKeys::pb_potential::apbs_path ("pb_potential:apbs_path")

RealOptionKey const	basic::options::OptionKeys::pb_potential::potential_cap ("pb_potential:potential_cap")

RealOptionKey const	basic::options::OptionKeys::pb_potential::epsilon ("pb_potential:epsilon")

IntegerOptionKey const	basic::options::OptionKeys::pb_potential::apbs_debug ("pb_potential:apbs_debug")

BooleanOptionKey const	basic::options::OptionKeys::pb_potential::calcenergy ("pb_potential:calcenergy")

Namespaces

Functions

Variables