OptionKeys.cc.gen2.hh File Reference

Namespaces
	pose_metrics
	ddg
	murphp
	motifs
	constraints
	dna
	dna::specificity
	dna::design
	dna::design::specificity
	dna::design::reversion
	flxbb
	flxbb::layer
	fldsgn
	rna
	cm
	cm::sanitize
	cm::hybridize
	ms
	ms::checkpoint
	loops
	loops::loop_closure
	assembly
	fast_loops
	SSrbrelax
	boinc
	LoopModel
	AnchoredDesign
	AnchoredDesign::filters
	AnchoredDesign::akash
	AnchoredDesign::testing
	chemically_conjugated_docking
	FloppyTail
	FloppyTail::short_tail
	DenovoProteinDesign
	RBSegmentRelax
	edensity
	patterson
	cryst
	optE
	optE::rescore
	backrub
	bbg
	flexpack
	flexpack::annealer
	hotspot
	parser
	DomainAssembly

Functions
RealOptionKey const	pose_metrics::contact_cutoffE ("pose_metrics:contact_cutoffE")
RealOptionKey const	pose_metrics::neighbor_by_distance_cutoff ("pose_metrics:neighbor_by_distance_cutoff")
RealOptionKey const	pose_metrics::inter_group_neighbors_cutoff ("pose_metrics:inter_group_neighbors_cutoff")
RealOptionKey const	pose_metrics::semiex_water_burial_cutoff ("pose_metrics:semiex_water_burial_cutoff")
BooleanOptionKey const	ddg::ddg ("ddg")
BooleanOptionKey const	ddg::avg_rot_cst_enrg ("ddg:avg_rot_cst_enrg")
BooleanOptionKey const	ddg::use_bound_cst ("ddg:use_bound_cst")
RealOptionKey const	ddg::cap_rot_cst_enrg ("ddg:cap_rot_cst_enrg")
BooleanOptionKey const	ddg::opt_input_structure ("ddg:opt_input_structure")
BooleanOptionKey const	ddg::pack_until_converge ("ddg:pack_until_converge")
BooleanOptionKey const	ddg::no_constraints ("ddg:no_constraints")
RealOptionKey const	ddg::apply_rot_cst_to_mutation_region_only ("ddg:apply_rot_cst_to_mutation_region_only")
RealOptionKey const	ddg::rot_cst_enrg_cutoff ("ddg:rot_cst_enrg_cutoff")
BooleanOptionKey const	ddg::use_rotamer_constraints_to_native ("ddg:use_rotamer_constraints_to_native")
BooleanOptionKey const	ddg::single_res_scoring ("ddg:single_res_scoring")
BooleanOptionKey const	ddg::downweight_by_sasa ("ddg:downweight_by_sasa")
BooleanOptionKey const	ddg::global ("ddg:global")
BooleanOptionKey const	ddg::exclude_solvent_exposed_res ("ddg:exclude_solvent_exposed_res")
RealOptionKey const	ddg::radius ("ddg:radius")
StringOptionKey const	ddg::wt ("ddg:wt")
StringOptionKey const	ddg::mut ("ddg:mut")
BooleanOptionKey const	ddg::suppress_checkpointing ("ddg:suppress_checkpointing")
BooleanOptionKey const	ddg::wt_only ("ddg:wt_only")
BooleanOptionKey const	ddg::mut_only ("ddg:mut_only")
BooleanOptionKey const	ddg::output_silent ("ddg:output_silent")
StringOptionKey const	ddg::minimization_scorefunction ("ddg:minimization_scorefunction")
StringOptionKey const	ddg::minimization_patch ("ddg:minimization_patch")
BooleanOptionKey const	ddg::min_cst ("ddg:min_cst")
IntegerOptionKey const	ddg::lowest_x_decoys ("ddg:lowest_x_decoys")
BooleanOptionKey const	ddg::local_opt_only ("ddg:local_opt_only")
BooleanOptionKey const	ddg::print_per_res_diff ("ddg:print_per_res_diff")
BooleanOptionKey const	ddg::mean ("ddg:mean")
BooleanOptionKey const	ddg::min ("ddg:min")
BooleanOptionKey const	ddg::rb_restrict_to_mutsite_nbrs ("ddg:rb_restrict_to_mutsite_nbrs")
BooleanOptionKey const	ddg::no_bb_movement ("ddg:no_bb_movement")
BooleanOptionKey const	ddg::initial_repack ("ddg:initial_repack")
StringOptionKey const	ddg::rb_file ("ddg:rb_file")
IntegerOptionKey const	ddg::interface_ddg ("ddg:interface_ddg")
RealOptionKey const	ddg::ens_variation ("ddg:ens_variation")
BooleanOptionKey const	ddg::sc_min_only ("ddg:sc_min_only")
StringOptionKey const	ddg::min_cst_weights ("ddg:min_cst_weights")
RealOptionKey const	ddg::opt_radius ("ddg:opt_radius")
StringOptionKey const	ddg::output_dir ("ddg:output_dir")
StringOptionKey const	ddg::last_accepted_pose_dir ("ddg:last_accepted_pose_dir")
BooleanOptionKey const	ddg::min_with_cst ("ddg:min_with_cst")
RealOptionKey const	ddg::temperature ("ddg:temperature")
BooleanOptionKey const	ddg::ramp_repulsive ("ddg:ramp_repulsive")
StringOptionKey const	ddg::mut_file ("ddg:mut_file")
StringOptionKey const	ddg::out_pdb_prefix ("ddg:out_pdb_prefix")
RealOptionKey const	ddg::constraint_weight ("ddg:constraint_weight")
RealOptionKey const	ddg::harmonic_ca_tether ("ddg:harmonic_ca_tether")
IntegerOptionKey const	ddg::iterations ("ddg:iterations")
StringOptionKey const	ddg::out ("ddg:out")
BooleanOptionKey const	ddg::debug_output ("ddg:debug_output")
BooleanOptionKey const	ddg::dump_pdbs ("ddg:dump_pdbs")
StringOptionKey const	ddg::weight_file ("ddg:weight_file")
IntegerOptionKey const	ddg::translate_by ("ddg:translate_by")
BooleanOptionKey const	murphp::murphp ("murphp")
StringOptionKey const	murphp::inv_kin_lig_loop_design_filename ("murphp:inv_kin_lig_loop_design_filename")
BooleanOptionKey const	motifs::motifs ("motifs")
RealOptionKey const	motifs::close_enough ("motifs:close_enough")
IntegerOptionKey const	motifs::max_depth ("motifs:max_depth")
BooleanOptionKey const	motifs::keep_motif_xtal_location ("motifs:keep_motif_xtal_location")
RealOptionKey const	motifs::pack_score_cutoff ("motifs:pack_score_cutoff")
RealOptionKey const	motifs::hb_score_cutoff ("motifs:hb_score_cutoff")
RealOptionKey const	motifs::water_score_cutoff ("motifs:water_score_cutoff")
RealOptionKey const	motifs::pack_min_threshold ("motifs:pack_min_threshold")
RealOptionKey const	motifs::pack_max_threshold ("motifs:pack_max_threshold")
RealOptionKey const	motifs::hbond_min_threshold ("motifs:hbond_min_threshold")
RealOptionKey const	motifs::hbond_max_threshold ("motifs:hbond_max_threshold")
RealOptionKey const	motifs::elec_min_threshold ("motifs:elec_min_threshold")
RealOptionKey const	motifs::elec_max_threshold ("motifs:elec_max_threshold")
RealOptionKey const	motifs::duplicate_dist_cutoff ("motifs:duplicate_dist_cutoff")
RealOptionKey const	motifs::duplicate_angle_cutoff ("motifs:duplicate_angle_cutoff")
StringOptionKey const	motifs::motif_output_directory ("motifs:motif_output_directory")
BooleanOptionKey const	motifs::eliminate_weak_motifs ("motifs:eliminate_weak_motifs")
RealOptionKey const	motifs::duplicate_motif_cutoff ("motifs:duplicate_motif_cutoff")
BooleanOptionKey const	motifs::preminimize_motif_pdbs ("motifs:preminimize_motif_pdbs")
BooleanOptionKey const	motifs::preminimize_motif_pdbs_sconly ("motifs:preminimize_motif_pdbs_sconly")
BooleanOptionKey const	motifs::place_adduct_waters ("motifs:place_adduct_waters")
FileVectorOptionKey const	motifs::list_motifs ("motifs:list_motifs")
StringOptionKey const	motifs::motif_filename ("motifs:motif_filename")
StringOptionKey const	motifs::file_prefix ("motifs:file_prefix")
StringOptionKey const	motifs::build_residue_file ("motifs:build_residue_file")
StringOptionKey const	motifs::motif_flexible_loop_file ("motifs:motif_flexible_loop_file")
StringOptionKey const	motifs::residue_trim_file ("motifs:residue_trim_file")
StringOptionKey const	motifs::BPData ("motifs:BPData")
FileVectorOptionKey const	motifs::list_dnaconformers ("motifs:list_dnaconformers")
StringVectorOptionKey const	motifs::target_dna_defs ("motifs:target_dna_defs")
StringVectorOptionKey const	motifs::motif_build_defs ("motifs:motif_build_defs")
StringOptionKey const	motifs::motif_build_position_chain ("motifs:motif_build_position_chain")
IntegerVectorOptionKey const	motifs::motif_build_positions ("motifs:motif_build_positions")
RealOptionKey const	motifs::r1 ("motifs:r1")
RealOptionKey const	motifs::r2 ("motifs:r2")
RealOptionKey const	motifs::z1 ("motifs:z1")
RealOptionKey const	motifs::z2 ("motifs:z2")
RealOptionKey const	motifs::dtest ("motifs:dtest")
IntegerOptionKey const	motifs::rotlevel ("motifs:rotlevel")
IntegerOptionKey const	motifs::num_repacks ("motifs:num_repacks")
BooleanOptionKey const	motifs::minimize ("motifs:minimize")
BooleanOptionKey const	motifs::minimize_dna ("motifs:minimize_dna")
BooleanOptionKey const	motifs::run_motifs ("motifs:run_motifs")
BooleanOptionKey const	motifs::expand_motifs ("motifs:expand_motifs")
BooleanOptionKey const	motifs::aromatic_motifs ("motifs:aromatic_motifs")
BooleanOptionKey const	motifs::dump_motifs ("motifs:dump_motifs")
BooleanOptionKey const	motifs::quick_and_dirty ("motifs:quick_and_dirty")
RealOptionKey const	motifs::special_rotweight ("motifs:special_rotweight")
StringOptionKey const	motifs::output_file ("motifs:output_file")
StringOptionKey const	motifs::data_file ("motifs:data_file")
StringOptionKey const	motifs::target_aa ("motifs:target_aa")
RealOptionKey const	motifs::constraint_max ("motifs:constraint_max")
BooleanOptionKey const	motifs::flex_sugar ("motifs:flex_sugar")
BooleanOptionKey const	motifs::clear_bprots ("motifs:clear_bprots")
IntegerOptionKey const	motifs::rots2add ("motifs:rots2add")
BooleanOptionKey const	motifs::restrict_to_wt ("motifs:restrict_to_wt")
BooleanOptionKey const	motifs::rerun_motifsearch ("motifs:rerun_motifsearch")
BooleanOptionKey const	motifs::no_rotamer_bump ("motifs:no_rotamer_bump")
RealOptionKey const	motifs::ligand_motif_sphere ("motifs:ligand_motif_sphere")
BooleanOptionKey const	constraints::constraints ("constraints")
RealOptionKey const	constraints::CA_tether ("constraints:CA_tether")
BooleanOptionKey const	constraints::exit_on_bad_read ("constraints:exit_on_bad_read")
StringVectorOptionKey const	constraints::cst_file ("constraints:cst_file")
RealOptionKey const	constraints::cst_weight ("constraints:cst_weight")
RealOptionKey const	constraints::max_cst_dist ("constraints:max_cst_dist")
StringVectorOptionKey const	constraints::cst_fa_file ("constraints:cst_fa_file")
RealOptionKey const	constraints::cst_fa_weight ("constraints:cst_fa_weight")
BooleanOptionKey const	constraints::normalize_mixture_func ("constraints:normalize_mixture_func")
BooleanOptionKey const	constraints::penalize_mixture_func ("constraints:penalize_mixture_func")
FileOptionKey const	constraints::forest_file ("constraints:forest_file")
BooleanOptionKey const	constraints::compute_total_dist_cst ("constraints:compute_total_dist_cst")
IntegerOptionKey const	constraints::cull_with_native ("constraints:cull_with_native")
FileOptionKey const	constraints::dump_cst_set ("constraints:dump_cst_set")
IntegerVectorOptionKey const	constraints::evaluate_max_seq_sep ("constraints:evaluate_max_seq_sep")
BooleanOptionKey const	constraints::named ("constraints:named")
BooleanOptionKey const	constraints::no_cst_in_relax ("constraints:no_cst_in_relax")
BooleanOptionKey const	constraints::no_linearize_bounded ("constraints:no_linearize_bounded")
RealOptionKey const	constraints::pocket_constraint_weight ("constraints:pocket_constraint_weight")
BooleanOptionKey const	constraints::pocket_zero_derivatives ("constraints:pocket_zero_derivatives")
BooleanOptionKey const	constraints::viol ("constraints:viol")
IntegerOptionKey const	constraints::viol_level ("constraints:viol_level")
StringOptionKey const	constraints::viol_type ("constraints:viol_type")
RealOptionKey const	constraints::sog_cst_param ("constraints:sog_cst_param")
RealOptionKey const	constraints::sog_upper_bound ("constraints:sog_upper_bound")
BooleanOptionKey const	constraints::epr_distance ("constraints:epr_distance")
IntegerOptionKey const	constraints::combine ("constraints:combine")
FileOptionKey const	constraints::combine_exclude_region ("constraints:combine_exclude_region")
BooleanOptionKey const	constraints::skip_redundant ("constraints:skip_redundant")
IntegerOptionKey const	constraints::skip_redundant_width ("constraints:skip_redundant_width")
RealOptionKey const	constraints::increase_constraints ("constraints:increase_constraints")
BooleanOptionKey const	dna::dna ("dna")
BooleanOptionKey const	dna::specificity::specificity ("dna:specificity")
BooleanOptionKey const	dna::specificity::exclude_dna_dna ("dna:specificity:exclude_dna_dna")
RealVectorOptionKey const	dna::specificity::params ("dna:specificity:params")
FileVectorOptionKey const	dna::specificity::frag_files ("dna:specificity:frag_files")
BooleanOptionKey const	dna::specificity::exclude_bb_sc_hbonds ("dna:specificity:exclude_bb_sc_hbonds")
BooleanOptionKey const	dna::specificity::only_repack ("dna:specificity:only_repack")
BooleanOptionKey const	dna::specificity::design_DNA ("dna:specificity:design_DNA")
BooleanOptionKey const	dna::specificity::run_test ("dna:specificity:run_test")
BooleanOptionKey const	dna::specificity::soft_rep ("dna:specificity:soft_rep")
BooleanOptionKey const	dna::specificity::dump_pdbs ("dna:specificity:dump_pdbs")
BooleanOptionKey const	dna::specificity::fast ("dna:specificity:fast")
BooleanOptionKey const	dna::specificity::randomize_motif ("dna:specificity:randomize_motif")
RealOptionKey const	dna::specificity::Wfa_elec ("dna:specificity:Wfa_elec")
RealOptionKey const	dna::specificity::Wdna_bs ("dna:specificity:Wdna_bs")
RealOptionKey const	dna::specificity::Wdna_bp ("dna:specificity:Wdna_bp")
RealOptionKey const	dna::specificity::minimize_tolerance ("dna:specificity:minimize_tolerance")
StringOptionKey const	dna::specificity::weights_tag ("dna:specificity:weights_tag")
StringOptionKey const	dna::specificity::weights_tag_list ("dna:specificity:weights_tag_list")
StringOptionKey const	dna::specificity::min_type ("dna:specificity:min_type")
StringOptionKey const	dna::specificity::tf ("dna:specificity:tf")
StringOptionKey const	dna::specificity::mode ("dna:specificity:mode")
StringOptionKey const	dna::specificity::score_function ("dna:specificity:score_function")
BooleanOptionKey const	dna::specificity::pre_minimize ("dna:specificity:pre_minimize")
BooleanOptionKey const	dna::specificity::post_minimize ("dna:specificity:post_minimize")
BooleanOptionKey const	dna::specificity::pre_pack ("dna:specificity:pre_pack")
IntegerOptionKey const	dna::specificity::nloop ("dna:specificity:nloop")
IntegerOptionKey const	dna::specificity::n_inner ("dna:specificity:n_inner")
IntegerOptionKey const	dna::specificity::n_outer ("dna:specificity:n_outer")
IntegerOptionKey const	dna::specificity::nstep_water ("dna:specificity:nstep_water")
IntegerOptionKey const	dna::specificity::moving_jump ("dna:specificity:moving_jump")
IntegerOptionKey const	dna::specificity::motif_begin ("dna:specificity:motif_begin")
IntegerOptionKey const	dna::specificity::motif_size ("dna:specificity:motif_size")
StringVectorOptionKey const	dna::specificity::pdb_pos ("dna:specificity:pdb_pos")
StringVectorOptionKey const	dna::specificity::methylate ("dna:specificity:methylate")
BooleanOptionKey const	dna::design::design ("dna:design")
BooleanOptionKey const	dna::design::output_initial_pdb ("dna:design:output_initial_pdb")
BooleanOptionKey const	dna::design::output_unbound_pdb ("dna:design:output_unbound_pdb")
RealOptionKey const	dna::design::z_cutoff ("dna:design:z_cutoff")
StringOptionKey const	dna::design::protein_scan ("dna:design:protein_scan")
StringOptionKey const	dna::design::checkpoint ("dna:design:checkpoint")
BooleanOptionKey const	dna::design::minimize ("dna:design:minimize")
IntegerOptionKey const	dna::design::iterations ("dna:design:iterations")
StringOptionKey const	dna::design::bb_moves ("dna:design:bb_moves")
StringVectorOptionKey const	dna::design::dna_defs ("dna:design:dna_defs")
StringOptionKey const	dna::design::dna_defs_file ("dna:design:dna_defs_file")
BooleanOptionKey const	dna::design::preminimize_interface ("dna:design:preminimize_interface")
BooleanOptionKey const	dna::design::prepack_interface ("dna:design:prepack_interface")
BooleanOptionKey const	dna::design::flush ("dna:design:flush")
BooleanOptionKey const	dna::design::nopdb ("dna:design:nopdb")
BooleanOptionKey const	dna::design::nopack ("dna:design:nopack")
BooleanOptionKey const	dna::design::more_stats ("dna:design:more_stats")
BooleanOptionKey const	dna::design::pdb_each_iteration ("dna:design:pdb_each_iteration")
BooleanOptionKey const	dna::design::designable_second_shell ("dna:design:designable_second_shell")
BooleanOptionKey const	dna::design::base_contacts_only ("dna:design:base_contacts_only")
IntegerOptionKey const	dna::design::probe_specificity ("dna:design:probe_specificity")
BooleanOptionKey const	dna::design::specificity::specificity ("dna:design:specificity")
BooleanOptionKey const	dna::design::specificity::output_structures ("dna:design:specificity:output_structures")
BooleanOptionKey const	dna::design::specificity::include_dna_potentials ("dna:design:specificity:include_dna_potentials")
BooleanOptionKey const	dna::design::reversion_scan ("dna:design:reversion_scan")
BooleanOptionKey const	dna::design::reversion::reversion ("dna:design:reversion")
RealOptionKey const	dna::design::reversion::dscore_cutoff ("dna:design:reversion:dscore_cutoff")
RealOptionKey const	dna::design::reversion::dspec_cutoff ("dna:design:reversion:dspec_cutoff")
BooleanOptionKey const	dna::design::binding ("dna:design:binding")
RealOptionKey const	dna::design::Boltz_temp ("dna:design:Boltz_temp")
BooleanOptionKey const	dna::design::repack_only ("dna:design:repack_only")
BooleanOptionKey const	dna::design::sparse_pdb_output ("dna:design:sparse_pdb_output")
BooleanOptionKey const	flxbb::flxbb ("flxbb")
BooleanOptionKey const	flxbb::view ("flxbb:view")
IntegerOptionKey const	flxbb::ncycle ("flxbb:ncycle")
RealOptionKey const	flxbb::constraints_sheet ("flxbb:constraints_sheet")
BooleanOptionKey const	flxbb::constraints_sheet_include_cacb_pseudotorsion ("flxbb:constraints_sheet_include_cacb_pseudotorsion")
RealOptionKey const	flxbb::constraints_NtoC ("flxbb:constraints_NtoC")
IntegerOptionKey const	flxbb::filter_trial ("flxbb:filter_trial")
StringOptionKey const	flxbb::filter_type ("flxbb:filter_type")
BooleanOptionKey const	flxbb::exclude_Met ("flxbb:exclude_Met")
BooleanOptionKey const	flxbb::exclude_Ala ("flxbb:exclude_Ala")
FileOptionKey const	flxbb::blueprint ("flxbb:blueprint")
BooleanOptionKey const	flxbb::movemap_from_blueprint ("flxbb:movemap_from_blueprint")
StringOptionKey const	flxbb::layer::layer ("flxbb:layer")
RealOptionKey const	flxbb::layer::pore_radius ("flxbb:layer:pore_radius")
RealOptionKey const	flxbb::layer::burial ("flxbb:layer:burial")
RealOptionKey const	flxbb::layer::surface ("flxbb:layer:surface")
BooleanOptionKey const	fldsgn::fldsgn ("fldsgn")
BooleanOptionKey const	fldsgn::view ("fldsgn:view")
FileVectorOptionKey const	fldsgn::blueprint ("fldsgn:blueprint")
IntegerOptionKey const	fldsgn::dr_cycles ("fldsgn:dr_cycles")
StringOptionKey const	fldsgn::centroid_sfx ("fldsgn:centroid_sfx")
StringOptionKey const	fldsgn::centroid_sfx_patch ("fldsgn:centroid_sfx_patch")
StringOptionKey const	fldsgn::fullatom_sfx ("fldsgn:fullatom_sfx")
StringOptionKey const	fldsgn::fullatom_sfx_patch ("fldsgn:fullatom_sfx_patch")
IntegerOptionKey const	fldsgn::run_flxbb ("fldsgn:run_flxbb")
BooleanOptionKey const	rna::rna ("rna")
IntegerOptionKey const	rna::minimize_rounds ("rna:minimize_rounds")
BooleanOptionKey const	rna::corrected_geo ("rna:corrected_geo")
BooleanOptionKey const	rna::vary_geometry ("rna:vary_geometry")
BooleanOptionKey const	rna::skip_coord_constraints ("rna:skip_coord_constraints")
BooleanOptionKey const	rna::skip_o2prime_trials ("rna:skip_o2prime_trials")
StringOptionKey const	rna::vall_torsions ("rna:vall_torsions")
BooleanOptionKey const	rna::jump_database ("rna:jump_database")
BooleanOptionKey const	rna::bps_database ("rna:bps_database")
BooleanOptionKey const	rna::rna_prot_erraser ("rna:rna_prot_erraser")
BooleanOptionKey const	rna::deriv_check ("rna:deriv_check")
BooleanOptionKey const	cm::cm ("cm")
BooleanOptionKey const	cm::sanitize::sanitize ("cm:sanitize")
RealOptionKey const	cm::sanitize::bound_delta ("cm:sanitize:bound_delta")
RealOptionKey const	cm::sanitize::bound_sd ("cm:sanitize:bound_sd")
IntegerOptionKey const	cm::sanitize::num_fragments ("cm:sanitize:num_fragments")
RealOptionKey const	cm::sanitize::cst_weight_pair ("cm:sanitize:cst_weight_pair")
RealOptionKey const	cm::sanitize::cst_weight_coord ("cm:sanitize:cst_weight_coord")
BooleanOptionKey const	cm::start_models_only ("cm:start_models_only")
StringOptionKey const	cm::aln_format ("cm:aln_format")
BooleanOptionKey const	cm::recover_side_chains ("cm:recover_side_chains")
FileVectorOptionKey const	cm::steal_extra_residues ("cm:steal_extra_residues")
StringOptionKey const	cm::loop_mover ("cm:loop_mover")
IntegerOptionKey const	cm::loop_close_level ("cm:loop_close_level")
IntegerOptionKey const	cm::min_loop_size ("cm:min_loop_size")
IntegerOptionKey const	cm::max_loop_rebuild ("cm:max_loop_rebuild")
RealOptionKey const	cm::loop_rebuild_filter ("cm:loop_rebuild_filter")
RealOptionKey const	cm::aln_length_filter_quantile ("cm:aln_length_filter_quantile")
IntegerOptionKey const	cm::aln_length_filter ("cm:aln_length_filter")
StringVectorOptionKey const	cm::template_ids ("cm:template_ids")
FileOptionKey const	cm::ligand_pdb ("cm:ligand_pdb")
StringVectorOptionKey const	cm::seq_score ("cm:seq_score")
StringOptionKey const	cm::aligner ("cm:aligner")
RealOptionKey const	cm::min_gap_open ("cm:min_gap_open")
RealOptionKey const	cm::max_gap_open ("cm:max_gap_open")
RealOptionKey const	cm::min_gap_extend ("cm:min_gap_extend")
RealOptionKey const	cm::max_gap_extend ("cm:max_gap_extend")
IntegerOptionKey const	cm::nn ("cm:nn")
RealOptionKey const	cm::fr_temperature ("cm:fr_temperature")
FileVectorOptionKey const	cm::ev_map ("cm:ev_map")
FileVectorOptionKey const	cm::hh_map ("cm:hh_map")
BooleanOptionKey const	cm::hybridize::hybridize ("cm:hybridize")
FileVectorOptionKey const	cm::hybridize::templates ("cm:hybridize:templates")
FileOptionKey const	cm::hybridize::template_list ("cm:hybridize:template_list")
IntegerVectorOptionKey const	cm::hybridize::starting_template ("cm:hybridize:starting_template")
BooleanOptionKey const	cm::hybridize::realign_domains ("cm:hybridize:realign_domains")
BooleanOptionKey const	cm::hybridize::add_non_init_chunks ("cm:hybridize:add_non_init_chunks")
StringOptionKey const	cm::hybridize::ss ("cm:hybridize:ss")
RealOptionKey const	cm::hybridize::stage1_increase_cycles ("cm:hybridize:stage1_increase_cycles")
RealOptionKey const	cm::hybridize::stage2_increase_cycles ("cm:hybridize:stage2_increase_cycles")
RealOptionKey const	cm::hybridize::stage2min_increase_cycles ("cm:hybridize:stage2min_increase_cycles")
RealOptionKey const	cm::hybridize::stage1_probability ("cm:hybridize:stage1_probability")
StringOptionKey const	cm::hybridize::stage1_weights ("cm:hybridize:stage1_weights")
StringOptionKey const	cm::hybridize::stage1_patch ("cm:hybridize:stage1_patch")
BooleanOptionKey const	cm::hybridize::skip_stage2 ("cm:hybridize:skip_stage2")
BooleanOptionKey const	cm::hybridize::no_global_frame ("cm:hybridize:no_global_frame")
BooleanOptionKey const	cm::hybridize::linmin_only ("cm:hybridize:linmin_only")
StringOptionKey const	cm::hybridize::stage2_weights ("cm:hybridize:stage2_weights")
StringOptionKey const	cm::hybridize::stage2_patch ("cm:hybridize:stage2_patch")
IntegerOptionKey const	cm::hybridize::relax ("cm:hybridize:relax")
RealOptionKey const	cm::hybridize::frag_weight_aligned ("cm:hybridize:frag_weight_aligned")
BooleanOptionKey const	cm::hybridize::move_anchor ("cm:hybridize:move_anchor")
IntegerOptionKey const	cm::hybridize::max_registry_shift ("cm:hybridize:max_registry_shift")
BooleanOptionKey const	cm::hybridize::alignment_from_template_seqpos ("cm:hybridize:alignment_from_template_seqpos")
IntegerVectorOptionKey const	cm::hybridize::alignment_from_chunk_mapping ("cm:hybridize:alignment_from_chunk_mapping")
BooleanOptionKey const	cm::hybridize::virtual_loops ("cm:hybridize:virtual_loops")
BooleanOptionKey const	cm::hybridize::revert_real_loops ("cm:hybridize:revert_real_loops")
BooleanOptionKey const	cm::hybridize::realign_domains_stage2 ("cm:hybridize:realign_domains_stage2")
RealOptionKey const	cm::hybridize::frag_1mer_insertion_weight ("cm:hybridize:frag_1mer_insertion_weight")
RealOptionKey const	cm::hybridize::small_frag_insertion_weight ("cm:hybridize:small_frag_insertion_weight")
RealOptionKey const	cm::hybridize::big_frag_insertion_weight ("cm:hybridize:big_frag_insertion_weight")
BooleanOptionKey const	cm::hybridize::auto_frag_insertion_weight ("cm:hybridize:auto_frag_insertion_weight")
IntegerOptionKey const	cm::hybridize::stage1_1_cycles ("cm:hybridize:stage1_1_cycles")
IntegerOptionKey const	cm::hybridize::stage1_2_cycles ("cm:hybridize:stage1_2_cycles")
IntegerOptionKey const	cm::hybridize::stage1_3_cycles ("cm:hybridize:stage1_3_cycles")
IntegerOptionKey const	cm::hybridize::stage1_4_cycles ("cm:hybridize:stage1_4_cycles")
RealOptionKey const	cm::hybridize::stage2_temperature ("cm:hybridize:stage2_temperature")
StringOptionKey const	cm::hybridize::stage1_4_cenrot_score ("cm:hybridize:stage1_4_cenrot_score")
BooleanOptionKey const	ms::ms ("ms")
BooleanOptionKey const	ms::share_data ("ms:share_data")
BooleanOptionKey const	ms::verbose ("ms:verbose")
BooleanOptionKey const	ms::restrict_to_canonical ("ms:restrict_to_canonical")
IntegerOptionKey const	ms::pop_from_ss ("ms:pop_from_ss")
IntegerOptionKey const	ms::pop_size ("ms:pop_size")
IntegerOptionKey const	ms::generations ("ms:generations")
IntegerOptionKey const	ms::num_packs ("ms:num_packs")
IntegerOptionKey const	ms::numresults ("ms:numresults")
RealOptionKey const	ms::anchor_offset ("ms:anchor_offset")
RealOptionKey const	ms::Boltz_temp ("ms:Boltz_temp")
RealOptionKey const	ms::mutate_rate ("ms:mutate_rate")
RealOptionKey const	ms::fraction_by_recombination ("ms:fraction_by_recombination")
BooleanOptionKey const	ms::checkpoint::checkpoint ("ms:checkpoint")
StringOptionKey const	ms::checkpoint::prefix ("ms:checkpoint:prefix")
IntegerOptionKey const	ms::checkpoint::interval ("ms:checkpoint:interval")
BooleanOptionKey const	ms::checkpoint::gz ("ms:checkpoint:gz")
BooleanOptionKey const	ms::checkpoint::rename ("ms:checkpoint:rename")
BooleanOptionKey const	loops::loops ("loops")
StringOptionKey const	loops::cen_weights ("loops:cen_weights")
StringOptionKey const	loops::cen_patch ("loops:cen_patch")
FileOptionKey const	loops::input_pdb ("loops:input_pdb")
StringVectorOptionKey const	loops::loop_file ("loops:loop_file")
FileOptionKey const	loops::extended_loop_file ("loops:extended_loop_file")
FileOptionKey const	loops::mm_loop_file ("loops:mm_loop_file")
BooleanOptionKey const	loops::fix_natsc ("loops:fix_natsc")
BooleanOptionKey const	loops::refine_only ("loops:refine_only")
BooleanOptionKey const	loops::fa_input ("loops:fa_input")
BooleanOptionKey const	loops::fast ("loops:fast")
FileOptionKey const	loops::vall_file ("loops:vall_file")
IntegerVectorOptionKey const	loops::frag_sizes ("loops:frag_sizes")
FileVectorOptionKey const	loops::frag_files ("loops:frag_files")
FileOptionKey const	loops::output_pdb ("loops:output_pdb")
BooleanOptionKey const	loops::debug ("loops:debug")
BooleanOptionKey const	loops::build_initial ("loops:build_initial")
BooleanOptionKey const	loops::extended ("loops:extended")
BooleanOptionKey const	loops::remove_extended_loops ("loops:remove_extended_loops")
BooleanOptionKey const	loops::idealize_after_loop_close ("loops:idealize_after_loop_close")
BooleanOptionKey const	loops::idealize_before_loop_close ("loops:idealize_before_loop_close")
IntegerOptionKey const	loops::select_best_loop_from ("loops:select_best_loop_from")
IntegerOptionKey const	loops::build_attempts ("loops:build_attempts")
IntegerOptionKey const	loops::grow_attempts ("loops:grow_attempts")
RealOptionKey const	loops::random_grow_loops_by ("loops:random_grow_loops_by")
BooleanOptionKey const	loops::accept_aborted_loops ("loops:accept_aborted_loops")
BooleanOptionKey const	loops::strict_loops ("loops:strict_loops")
BooleanOptionKey const	loops::superimpose_native ("loops:superimpose_native")
IntegerVectorOptionKey const	loops::build_specific_loops ("loops:build_specific_loops")
BooleanOptionKey const	loops::random_order ("loops:random_order")
BooleanOptionKey const	loops::build_all_loops ("loops:build_all_loops")
BooleanOptionKey const	loops::fa_closure_protocol ("loops:fa_closure_protocol")
RealOptionKey const	loops::combine_rate ("loops:combine_rate")
StringOptionKey const	loops::remodel ("loops:remodel")
StringOptionKey const	loops::intermedrelax ("loops:intermedrelax")
StringOptionKey const	loops::refine ("loops:refine")
StringOptionKey const	loops::relax ("loops:relax")
IntegerOptionKey const	loops::n_rebuild_tries ("loops:n_rebuild_tries")
BooleanOptionKey const	loops::final_clean_fastrelax ("loops:final_clean_fastrelax")
BooleanOptionKey const	loops::relax_with_foldtree ("loops:relax_with_foldtree")
RealOptionKey const	loops::constrain_rigid_segments ("loops:constrain_rigid_segments")
StringOptionKey const	loops::loopscores ("loops:loopscores")
BooleanOptionKey const	loops::timer ("loops:timer")
BooleanOptionKey const	loops::vicinity_sampling ("loops:vicinity_sampling")
RealOptionKey const	loops::vicinity_degree ("loops:vicinity_degree")
RealOptionKey const	loops::neighbor_dist ("loops:neighbor_dist")
IntegerOptionKey const	loops::kic_max_seglen ("loops:kic_max_seglen")
BooleanOptionKey const	loops::kic_recover_last ("loops:kic_recover_last")
BooleanOptionKey const	loops::kic_min_after_repack ("loops:kic_min_after_repack")
BooleanOptionKey const	loops::optimize_only_kic_region_sidechains_after_move ("loops:optimize_only_kic_region_sidechains_after_move")
IntegerOptionKey const	loops::max_kic_build_attempts ("loops:max_kic_build_attempts")
IntegerOptionKey const	loops::remodel_kic_attempts ("loops:remodel_kic_attempts")
IntegerOptionKey const	loops::max_kic_perturber_samples ("loops:max_kic_perturber_samples")
BooleanOptionKey const	loops::nonpivot_torsion_sampling ("loops:nonpivot_torsion_sampling")
BooleanOptionKey const	loops::fix_ca_bond_angles ("loops:fix_ca_bond_angles")
BooleanOptionKey const	loops::kic_use_linear_chainbreak ("loops:kic_use_linear_chainbreak")
BooleanOptionKey const	loops::sample_omega_at_pre_prolines ("loops:sample_omega_at_pre_prolines")
BooleanOptionKey const	loops::allow_omega_move ("loops:allow_omega_move")
BooleanOptionKey const	loops::kic_with_cartmin ("loops:kic_with_cartmin")
BooleanOptionKey const	loops::allow_takeoff_torsion_move ("loops:allow_takeoff_torsion_move")
IntegerOptionKey const	loops::extend_length ("loops:extend_length")
IntegerOptionKey const	loops::outer_cycles ("loops:outer_cycles")
IntegerOptionKey const	loops::max_inner_cycles ("loops:max_inner_cycles")
IntegerOptionKey const	loops::repack_period ("loops:repack_period")
BooleanOptionKey const	loops::repack_never ("loops:repack_never")
RealOptionKey const	loops::remodel_init_temp ("loops:remodel_init_temp")
RealOptionKey const	loops::remodel_final_temp ("loops:remodel_final_temp")
RealOptionKey const	loops::refine_init_temp ("loops:refine_init_temp")
RealOptionKey const	loops::refine_final_temp ("loops:refine_final_temp")
IntegerOptionKey const	loops::gapspan ("loops:gapspan")
IntegerOptionKey const	loops::spread ("loops:spread")
IntegerOptionKey const	loops::kinematic_wrapper_cycles ("loops:kinematic_wrapper_cycles")
IntegerOptionKey const	loops::kic_num_rotamer_trials ("loops:kic_num_rotamer_trials")
BooleanOptionKey const	loops::kic_omega_sampling ("loops:kic_omega_sampling")
RealOptionKey const	loops::kic_bump_overlap_factor ("loops:kic_bump_overlap_factor")
StringOptionKey const	loops::kic_cen_weights ("loops:kic_cen_weights")
StringOptionKey const	loops::kic_cen_patch ("loops:kic_cen_patch")
StringOptionKey const	loops::restrict_kic_sampling_to_torsion_string ("loops:restrict_kic_sampling_to_torsion_string")
BooleanOptionKey const	loops::derive_torsion_string_from_native_pose ("loops:derive_torsion_string_from_native_pose")
BooleanOptionKey const	loops::always_remodel_full_loop ("loops:always_remodel_full_loop")
BooleanOptionKey const	loops::taboo_sampling ("loops:taboo_sampling")
BooleanOptionKey const	loops::taboo_in_fa ("loops:taboo_in_fa")
BooleanOptionKey const	loops::ramp_fa_rep ("loops:ramp_fa_rep")
BooleanOptionKey const	loops::ramp_rama ("loops:ramp_rama")
BooleanOptionKey const	loops::kic_rama2b ("loops:kic_rama2b")
BooleanOptionKey const	loops::kic_small_moves ("loops:kic_small_moves")
RealOptionKey const	loops::kic_small_move_magnitude ("loops:kic_small_move_magnitude")
BooleanOptionKey const	loops::kic_pivot_based ("loops:kic_pivot_based")
BooleanOptionKey const	loops::kic_no_centroid_min ("loops:kic_no_centroid_min")
BooleanOptionKey const	loops::kic_leave_centroid_after_initial_closure ("loops:kic_leave_centroid_after_initial_closure")
BooleanOptionKey const	loops::kic_repack_neighbors_only ("loops:kic_repack_neighbors_only")
BooleanOptionKey const	loops::legacy_kic ("loops:legacy_kic")
BooleanOptionKey const	loops::alternative_closure_protocol ("loops:alternative_closure_protocol")
RealOptionKey const	loops::chainbreak_max_accept ("loops:chainbreak_max_accept")
BooleanOptionKey const	loops::debug_loop_closure ("loops:debug_loop_closure")
BooleanOptionKey const	loops::non_ideal_loop_closing ("loops:non_ideal_loop_closing")
RealOptionKey const	loops::scored_frag_cycles ("loops:scored_frag_cycles")
RealOptionKey const	loops::short_frag_cycles ("loops:short_frag_cycles")
RealOptionKey const	loops::rmsd_tol ("loops:rmsd_tol")
RealOptionKey const	loops::chain_break_tol ("loops:chain_break_tol")
BooleanOptionKey const	loops::random_loop ("loops:random_loop")
FileVectorOptionKey const	loops::stealfrags ("loops:stealfrags")
IntegerOptionKey const	loops::stealfrags_times ("loops:stealfrags_times")
RealOptionKey const	loops::coord_cst ("loops:coord_cst")
RealOptionKey const	loops::skip_1mers ("loops:skip_1mers")
RealOptionKey const	loops::skip_3mers ("loops:skip_3mers")
RealOptionKey const	loops::skip_9mers ("loops:skip_9mers")
BooleanOptionKey const	loops::loop_model ("loops:loop_model")
RealOptionKey const	loops::score_filter_cutoff ("loops:score_filter_cutoff")
BooleanOptionKey const	loops::loop_farlx ("loops:loop_farlx")
BooleanOptionKey const	loops::ccd_closure ("loops:ccd_closure")
BooleanOptionKey const	loops::skip_ccd_moves ("loops:skip_ccd_moves")
BooleanOptionKey const	loops::no_randomize_loop ("loops:no_randomize_loop")
BooleanOptionKey const	loops::loops_subset ("loops:loops_subset")
IntegerOptionKey const	loops::num_desired_loops ("loops:num_desired_loops")
RealOptionKey const	loops::loop_combine_rate ("loops:loop_combine_rate")
RealOptionKey const	loops::final_score_filter ("loops:final_score_filter")
BooleanOptionKey const	loops::no_combine_if_fail ("loops:no_combine_if_fail")
BooleanOptionKey const	loops::shorten_long_terminal_loop ("loops:shorten_long_terminal_loop")
IntegerOptionKey const	loops::backrub_trials ("loops:backrub_trials")
RealOptionKey const	loops::looprlx_cycle_ratio ("loops:looprlx_cycle_ratio")
RealOptionKey const	loops::extended_beta ("loops:extended_beta")
BooleanOptionKey const	loops::shortrelax ("loops:shortrelax")
BooleanOptionKey const	loops::fastrelax ("loops:fastrelax")
BooleanOptionKey const	loops::no_looprebuild ("loops:no_looprebuild")
BooleanOptionKey const	loops::allow_lig_move ("loops:allow_lig_move")
FileOptionKey const	loops::keep_natro ("loops:keep_natro")
IntegerOptionKey const	loops::refine_design_iterations ("loops:refine_design_iterations")
BooleanOptionKey const	loops::loop_closure::loop_closure ("loops:loop_closure")
StringOptionKey const	loops::loop_closure::loop_insert ("loops:loop_closure:loop_insert")
StringOptionKey const	loops::loop_closure::loop_insert_rclrc ("loops:loop_closure:loop_insert_rclrc")
StringOptionKey const	loops::loop_closure::blueprint ("loops:loop_closure:blueprint")
BooleanOptionKey const	assembly::assembly ("assembly")
FileOptionKey const	assembly::pdb1 ("assembly:pdb1")
FileOptionKey const	assembly::pdb2 ("assembly:pdb2")
StringOptionKey const	assembly::nterm_seq ("assembly:nterm_seq")
StringOptionKey const	assembly::cterm_seq ("assembly:cterm_seq")
IntegerVectorOptionKey const	assembly::linkers_pdb1 ("assembly:linkers_pdb1")
IntegerVectorOptionKey const	assembly::linkers_pdb2 ("assembly:linkers_pdb2")
IntegerVectorOptionKey const	assembly::preserve_sidechains_pdb1 ("assembly:preserve_sidechains_pdb1")
IntegerVectorOptionKey const	assembly::preserve_sidechains_pdb2 ("assembly:preserve_sidechains_pdb2")
BooleanOptionKey const	fast_loops::fast_loops ("fast_loops")
RealOptionKey const	fast_loops::window_accept_ratio ("fast_loops:window_accept_ratio")
IntegerOptionKey const	fast_loops::nr_scored_sampling_passes ("fast_loops:nr_scored_sampling_passes")
IntegerOptionKey const	fast_loops::nr_scored_fragments ("fast_loops:nr_scored_fragments")
IntegerOptionKey const	fast_loops::min_breakout_good_loops ("fast_loops:min_breakout_good_loops")
IntegerOptionKey const	fast_loops::min_breakout_fast_loops ("fast_loops:min_breakout_fast_loops")
IntegerOptionKey const	fast_loops::min_good_loops ("fast_loops:min_good_loops")
IntegerOptionKey const	fast_loops::min_fast_loops ("fast_loops:min_fast_loops")
RealOptionKey const	fast_loops::vdw_delta ("fast_loops:vdw_delta")
IntegerOptionKey const	fast_loops::give_up ("fast_loops:give_up")
RealOptionKey const	fast_loops::chainbreak_max ("fast_loops:chainbreak_max")
FileOptionKey const	fast_loops::fragsample_score ("fast_loops:fragsample_score")
FileOptionKey const	fast_loops::fragsample_patch ("fast_loops:fragsample_patch")
FileOptionKey const	fast_loops::overwrite_filter_scorefxn ("fast_loops:overwrite_filter_scorefxn")
FileOptionKey const	fast_loops::patch_filter_scorefxn ("fast_loops:patch_filter_scorefxn")
FileOptionKey const	fast_loops::filter_cst_file ("fast_loops:filter_cst_file")
RealOptionKey const	fast_loops::filter_cst_weight ("fast_loops:filter_cst_weight")
FileOptionKey const	fast_loops::fast_relax_sequence_file ("fast_loops:fast_relax_sequence_file")
BooleanOptionKey const	SSrbrelax::SSrbrelax ("SSrbrelax")
FileOptionKey const	SSrbrelax::input_pdb ("SSrbrelax:input_pdb")
FileOptionKey const	SSrbrelax::rb_file ("SSrbrelax:rb_file")
FileOptionKey const	SSrbrelax::rb_param_file ("SSrbrelax:rb_param_file")
IntegerVectorOptionKey const	SSrbrelax::frag_sizes ("SSrbrelax:frag_sizes")
FileVectorOptionKey const	SSrbrelax::frag_files ("SSrbrelax:frag_files")
BooleanOptionKey const	boinc::boinc ("boinc")
BooleanOptionKey const	boinc::graphics ("boinc:graphics")
BooleanOptionKey const	boinc::fullscreen ("boinc:fullscreen")
IntegerOptionKey const	boinc::max_fps ("boinc:max_fps")
IntegerOptionKey const	boinc::max_cpu ("boinc:max_cpu")
BooleanOptionKey const	boinc::noshmem ("boinc:noshmem")
IntegerOptionKey const	boinc::cpu_run_time ("boinc:cpu_run_time")
IntegerOptionKey const	boinc::max_nstruct ("boinc:max_nstruct")
RealOptionKey const	boinc::cpu_frac ("boinc:cpu_frac")
RealOptionKey const	boinc::frame_rate ("boinc:frame_rate")
BooleanOptionKey const	boinc::watchdog ("boinc:watchdog")
IntegerOptionKey const	boinc::watchdog_time ("boinc:watchdog_time")
IntegerOptionKey const	boinc::cpu_run_timeout ("boinc:cpu_run_timeout")
FileOptionKey const	boinc::description_file ("boinc:description_file")
RealOptionKey const	boinc::score_cut_pct ("boinc:score_cut_pct")
FileOptionKey const	boinc::score_cut_fl ("boinc:score_cut_fl")
BooleanOptionKey const	boinc::score_cut_smart_throttle ("boinc:score_cut_smart_throttle")
BooleanOptionKey const	LoopModel::LoopModel ("LoopModel")
FileOptionKey const	LoopModel::input_pdb ("LoopModel:input_pdb")
FileOptionKey const	LoopModel::loop_file ("LoopModel:loop_file")
BooleanOptionKey const	AnchoredDesign::AnchoredDesign ("AnchoredDesign")
FileOptionKey const	AnchoredDesign::anchor ("AnchoredDesign:anchor")
BooleanOptionKey const	AnchoredDesign::allow_anchor_repack ("AnchoredDesign:allow_anchor_repack")
BooleanOptionKey const	AnchoredDesign::vary_cutpoints ("AnchoredDesign:vary_cutpoints")
BooleanOptionKey const	AnchoredDesign::no_frags ("AnchoredDesign:no_frags")
BooleanOptionKey const	AnchoredDesign::debug ("AnchoredDesign:debug")
BooleanOptionKey const	AnchoredDesign::show_extended ("AnchoredDesign:show_extended")
BooleanOptionKey const	AnchoredDesign::refine_only ("AnchoredDesign:refine_only")
BooleanOptionKey const	AnchoredDesign::perturb_show ("AnchoredDesign:perturb_show")
IntegerOptionKey const	AnchoredDesign::perturb_cycles ("AnchoredDesign:perturb_cycles")
RealOptionKey const	AnchoredDesign::perturb_temp ("AnchoredDesign:perturb_temp")
BooleanOptionKey const	AnchoredDesign::perturb_CCD_off ("AnchoredDesign:perturb_CCD_off")
BooleanOptionKey const	AnchoredDesign::perturb_KIC_off ("AnchoredDesign:perturb_KIC_off")
BooleanOptionKey const	AnchoredDesign::refine_CCD_off ("AnchoredDesign:refine_CCD_off")
BooleanOptionKey const	AnchoredDesign::refine_KIC_off ("AnchoredDesign:refine_KIC_off")
IntegerOptionKey const	AnchoredDesign::refine_cycles ("AnchoredDesign:refine_cycles")
RealOptionKey const	AnchoredDesign::refine_temp ("AnchoredDesign:refine_temp")
IntegerOptionKey const	AnchoredDesign::refine_repack_cycles ("AnchoredDesign:refine_repack_cycles")
BooleanOptionKey const	AnchoredDesign::rmsd ("AnchoredDesign:rmsd")
BooleanOptionKey const	AnchoredDesign::unbound_mode ("AnchoredDesign:unbound_mode")
RealOptionKey const	AnchoredDesign::chainbreak_weight ("AnchoredDesign:chainbreak_weight")
BooleanOptionKey const	AnchoredDesign::filters::filters ("AnchoredDesign:filters")
RealOptionKey const	AnchoredDesign::filters::score ("AnchoredDesign:filters:score")
RealOptionKey const	AnchoredDesign::filters::sasa ("AnchoredDesign:filters:sasa")
BooleanOptionKey const	AnchoredDesign::filters::omega ("AnchoredDesign:filters:omega")
BooleanOptionKey const	AnchoredDesign::akash::akash ("AnchoredDesign:akash")
IntegerOptionKey const	AnchoredDesign::akash::dyepos ("AnchoredDesign:akash:dyepos")
BooleanOptionKey const	AnchoredDesign::testing::testing ("AnchoredDesign:testing")
RealOptionKey const	AnchoredDesign::testing::VDW_weight ("AnchoredDesign:testing:VDW_weight")
BooleanOptionKey const	AnchoredDesign::testing::anchor_via_constraints ("AnchoredDesign:testing:anchor_via_constraints")
BooleanOptionKey const	AnchoredDesign::testing::delete_interface_native_sidechains ("AnchoredDesign:testing:delete_interface_native_sidechains")
FileOptionKey const	AnchoredDesign::testing::RMSD_only_this ("AnchoredDesign:testing:RMSD_only_this")
BooleanOptionKey const	AnchoredDesign::testing::anchor_noise_constraints_mode ("AnchoredDesign:testing:anchor_noise_constraints_mode")
BooleanOptionKey const	AnchoredDesign::testing::super_secret_fixed_interface_mode ("AnchoredDesign:testing:super_secret_fixed_interface_mode")
BooleanOptionKey const	AnchoredDesign::testing::randomize_input_sequence ("AnchoredDesign:testing:randomize_input_sequence")
BooleanOptionKey const	chemically_conjugated_docking::chemically_conjugated_docking ("chemically_conjugated_docking")
FileOptionKey const	chemically_conjugated_docking::UBQpdb ("chemically_conjugated_docking:UBQpdb")
FileOptionKey const	chemically_conjugated_docking::E2pdb ("chemically_conjugated_docking:E2pdb")
IntegerOptionKey const	chemically_conjugated_docking::E2_residue ("chemically_conjugated_docking:E2_residue")
RealOptionKey const	chemically_conjugated_docking::SASAfilter ("chemically_conjugated_docking:SASAfilter")
RealOptionKey const	chemically_conjugated_docking::scorefilter ("chemically_conjugated_docking:scorefilter")
BooleanOptionKey const	chemically_conjugated_docking::publication ("chemically_conjugated_docking:publication")
IntegerOptionKey const	chemically_conjugated_docking::n_tail_res ("chemically_conjugated_docking:n_tail_res")
BooleanOptionKey const	chemically_conjugated_docking::two_ubiquitins ("chemically_conjugated_docking:two_ubiquitins")
FileVectorOptionKey const	chemically_conjugated_docking::extra_bodies ("chemically_conjugated_docking:extra_bodies")
IntegerOptionKey const	chemically_conjugated_docking::UBQ2_lys ("chemically_conjugated_docking:UBQ2_lys")
FileOptionKey const	chemically_conjugated_docking::UBQ2_pdb ("chemically_conjugated_docking:UBQ2_pdb")
BooleanOptionKey const	chemically_conjugated_docking::dont_minimize_omega ("chemically_conjugated_docking:dont_minimize_omega")
BooleanOptionKey const	chemically_conjugated_docking::pdz ("chemically_conjugated_docking:pdz")
FileOptionKey const	chemically_conjugated_docking::GTPasepdb ("chemically_conjugated_docking:GTPasepdb")
IntegerOptionKey const	chemically_conjugated_docking::GTPase_residue ("chemically_conjugated_docking:GTPase_residue")
BooleanOptionKey const	FloppyTail::FloppyTail ("FloppyTail")
IntegerOptionKey const	FloppyTail::flexible_start_resnum ("FloppyTail:flexible_start_resnum")
IntegerOptionKey const	FloppyTail::flexible_stop_resnum ("FloppyTail:flexible_stop_resnum")
StringOptionKey const	FloppyTail::flexible_chain ("FloppyTail:flexible_chain")
RealOptionKey const	FloppyTail::shear_on ("FloppyTail:shear_on")
BooleanOptionKey const	FloppyTail::short_tail::short_tail ("FloppyTail:short_tail")
RealOptionKey const	FloppyTail::short_tail::short_tail_fraction ("FloppyTail:short_tail:short_tail_fraction")
RealOptionKey const	FloppyTail::short_tail::short_tail_off ("FloppyTail:short_tail:short_tail_off")
BooleanOptionKey const	FloppyTail::pair_off ("FloppyTail:pair_off")
BooleanOptionKey const	FloppyTail::publication ("FloppyTail:publication")
BooleanOptionKey const	FloppyTail::C_root ("FloppyTail:C_root")
BooleanOptionKey const	FloppyTail::force_linear_fold_tree ("FloppyTail:force_linear_fold_tree")
BooleanOptionKey const	FloppyTail::debug ("FloppyTail:debug")
StringOptionKey const	FloppyTail::cen_weights ("FloppyTail:cen_weights")
BooleanOptionKey const	FloppyTail::perturb_show ("FloppyTail:perturb_show")
IntegerOptionKey const	FloppyTail::perturb_cycles ("FloppyTail:perturb_cycles")
RealOptionKey const	FloppyTail::perturb_temp ("FloppyTail:perturb_temp")
IntegerOptionKey const	FloppyTail::refine_cycles ("FloppyTail:refine_cycles")
RealOptionKey const	FloppyTail::refine_temp ("FloppyTail:refine_temp")
IntegerOptionKey const	FloppyTail::refine_repack_cycles ("FloppyTail:refine_repack_cycles")
BooleanOptionKey const	DenovoProteinDesign::DenovoProteinDesign ("DenovoProteinDesign")
BooleanOptionKey const	DenovoProteinDesign::redesign_core ("DenovoProteinDesign:redesign_core")
BooleanOptionKey const	DenovoProteinDesign::redesign_loops ("DenovoProteinDesign:redesign_loops")
BooleanOptionKey const	DenovoProteinDesign::redesign_surface ("DenovoProteinDesign:redesign_surface")
BooleanOptionKey const	DenovoProteinDesign::redesign_complete ("DenovoProteinDesign:redesign_complete")
BooleanOptionKey const	DenovoProteinDesign::disallow_native_aa ("DenovoProteinDesign:disallow_native_aa")
BooleanOptionKey const	DenovoProteinDesign::optimize_loops ("DenovoProteinDesign:optimize_loops")
FileOptionKey const	DenovoProteinDesign::secondary_structure_file ("DenovoProteinDesign:secondary_structure_file")
FileOptionKey const	DenovoProteinDesign::hydrophobic_polar_pattern ("DenovoProteinDesign:hydrophobic_polar_pattern")
BooleanOptionKey const	DenovoProteinDesign::use_template_sequence ("DenovoProteinDesign:use_template_sequence")
BooleanOptionKey const	DenovoProteinDesign::use_template_topology ("DenovoProteinDesign:use_template_topology")
FileOptionKey const	DenovoProteinDesign::create_from_template_pdb ("DenovoProteinDesign:create_from_template_pdb")
BooleanOptionKey const	DenovoProteinDesign::create_from_secondary_structure ("DenovoProteinDesign:create_from_secondary_structure")
BooleanOptionKey const	RBSegmentRelax::RBSegmentRelax ("RBSegmentRelax")
FileOptionKey const	RBSegmentRelax::input_pdb ("RBSegmentRelax:input_pdb")
FileOptionKey const	RBSegmentRelax::rb_file ("RBSegmentRelax:rb_file")
RealOptionKey const	RBSegmentRelax::cst_wt ("RBSegmentRelax:cst_wt")
RealOptionKey const	RBSegmentRelax::cst_width ("RBSegmentRelax:cst_width")
StringOptionKey const	RBSegmentRelax::cst_pdb ("RBSegmentRelax:cst_pdb")
IntegerOptionKey const	RBSegmentRelax::nrbmoves ("RBSegmentRelax:nrbmoves")
IntegerOptionKey const	RBSegmentRelax::nrboutercycles ("RBSegmentRelax:nrboutercycles")
StringOptionKey const	RBSegmentRelax::rb_scorefxn ("RBSegmentRelax:rb_scorefxn")
BooleanOptionKey const	RBSegmentRelax::skip_fragment_moves ("RBSegmentRelax:skip_fragment_moves")
BooleanOptionKey const	RBSegmentRelax::skip_seqshift_moves ("RBSegmentRelax:skip_seqshift_moves")
BooleanOptionKey const	RBSegmentRelax::skip_rb_moves ("RBSegmentRelax:skip_rb_moves")
RealVectorOptionKey const	RBSegmentRelax::helical_movement_params ("RBSegmentRelax:helical_movement_params")
RealVectorOptionKey const	RBSegmentRelax::strand_movement_params ("RBSegmentRelax:strand_movement_params")
RealVectorOptionKey const	RBSegmentRelax::default_movement_params ("RBSegmentRelax:default_movement_params")
IntegerOptionKey const	RBSegmentRelax::cst_seqwidth ("RBSegmentRelax:cst_seqwidth")
BooleanOptionKey const	edensity::edensity ("edensity")
BooleanOptionKey const	edensity::debug ("edensity:debug")
StringOptionKey const	edensity::mapfile ("edensity:mapfile")
RealOptionKey const	edensity::mapreso ("edensity:mapreso")
RealOptionKey const	edensity::grid_spacing ("edensity:grid_spacing")
RealOptionKey const	edensity::centroid_density_mass ("edensity:centroid_density_mass")
IntegerOptionKey const	edensity::sliding_window ("edensity:sliding_window")
BooleanOptionKey const	edensity::cryoem_scatterers ("edensity:cryoem_scatterers")
RealOptionKey const	edensity::force_apix ("edensity:force_apix")
RealOptionKey const	edensity::fastdens_wt ("edensity:fastdens_wt")
RealVectorOptionKey const	edensity::fastdens_params ("edensity:fastdens_params")
BooleanOptionKey const	edensity::legacy_fastdens_score ("edensity:legacy_fastdens_score")
RealOptionKey const	edensity::sliding_window_wt ("edensity:sliding_window_wt")
BooleanOptionKey const	edensity::score_sliding_window_context ("edensity:score_sliding_window_context")
RealOptionKey const	edensity::whole_structure_ca_wt ("edensity:whole_structure_ca_wt")
RealOptionKey const	edensity::whole_structure_allatom_wt ("edensity:whole_structure_allatom_wt")
BooleanOptionKey const	edensity::no_edens_in_minimizer ("edensity:no_edens_in_minimizer")
BooleanOptionKey const	edensity::debug_derivatives ("edensity:debug_derivatives")
StringOptionKey const	edensity::realign ("edensity:realign")
StringOptionKey const	edensity::membrane_axis ("edensity:membrane_axis")
RealOptionKey const	edensity::atom_mask ("edensity:atom_mask")
RealOptionKey const	edensity::atom_mask_min ("edensity:atom_mask_min")
RealOptionKey const	edensity::ca_mask ("edensity:ca_mask")
BooleanOptionKey const	edensity::score_symm_complex ("edensity:score_symm_complex")
RealOptionKey const	edensity::sc_scaling ("edensity:sc_scaling")
IntegerOptionKey const	edensity::n_kbins ("edensity:n_kbins")
RealOptionKey const	edensity::render_sigma ("edensity:render_sigma")
BooleanOptionKey const	edensity::unmask_bb ("edensity:unmask_bb")
BooleanOptionKey const	patterson::patterson ("patterson")
BooleanOptionKey const	patterson::debug ("patterson:debug")
RealOptionKey const	patterson::weight ("patterson:weight")
RealOptionKey const	patterson::sc_scaling ("patterson:sc_scaling")
RealVectorOptionKey const	patterson::radius_cutoffs ("patterson:radius_cutoffs")
RealVectorOptionKey const	patterson::resolution_cutoffs ("patterson:resolution_cutoffs")
RealOptionKey const	patterson::Bsol ("patterson:Bsol")
RealOptionKey const	patterson::Fsol ("patterson:Fsol")
RealOptionKey const	patterson::model_B ("patterson:model_B")
RealOptionKey const	patterson::rmsd ("patterson:rmsd")
BooleanOptionKey const	patterson::no_ecalc ("patterson:no_ecalc")
IntegerOptionKey const	patterson::nshells ("patterson:nshells")
BooleanOptionKey const	patterson::use_spline_interpolation ("patterson:use_spline_interpolation")
BooleanOptionKey const	patterson::use_on_repack ("patterson:use_on_repack")
BooleanOptionKey const	patterson::dont_use_symm_in_pcalc ("patterson:dont_use_symm_in_pcalc")
BooleanOptionKey const	cryst::cryst ("cryst")
StringOptionKey const	cryst::mtzfile ("cryst:mtzfile")
BooleanOptionKey const	cryst::crystal_refine ("cryst:crystal_refine")
BooleanOptionKey const	optE::optE ("optE")
StringOptionKey const	optE::load_from_silent ("optE:load_from_silent")
StringOptionKey const	optE::data_in ("optE:data_in")
StringOptionKey const	optE::data_out ("optE:data_out")
StringOptionKey const	optE::weights ("optE:weights")
StringVectorOptionKey const	optE::fix ("optE:fix")
FileOptionKey const	optE::free ("optE:free")
FileOptionKey const	optE::fixed ("optE:fixed")
FileOptionKey const	optE::parse_tagfile ("optE:parse_tagfile")
FileOptionKey const	optE::constant_logic_taskops_file ("optE:constant_logic_taskops_file")
BooleanOptionKey const	optE::optE_soft_rep ("optE:optE_soft_rep")
BooleanOptionKey const	optE::no_hb_env_dependence ("optE:no_hb_env_dependence")
BooleanOptionKey const	optE::no_hb_env_dependence_DNA ("optE:no_hb_env_dependence_DNA")
BooleanOptionKey const	optE::optE_no_protein_fa_elec ("optE:optE_no_protein_fa_elec")
BooleanOptionKey const	optE::design_first ("optE:design_first")
IntegerOptionKey const	optE::n_design_cycles ("optE:n_design_cycles")
BooleanOptionKey const	optE::recover_nat_rot ("optE:recover_nat_rot")
FileOptionKey const	optE::component_weights ("optE:component_weights")
BooleanOptionKey const	optE::optimize_nat_aa ("optE:optimize_nat_aa")
BooleanOptionKey const	optE::optimize_nat_rot ("optE:optimize_nat_rot")
FileOptionKey const	optE::optimize_ligand_rot ("optE:optimize_ligand_rot")
BooleanOptionKey const	optE::optimize_pssm ("optE:optimize_pssm")
FileOptionKey const	optE::optimize_dGbinding ("optE:optimize_dGbinding")
FileOptionKey const	optE::optimize_ddG_bind_correlation ("optE:optimize_ddG_bind_correlation")
FileOptionKey const	optE::optimize_ddGmutation ("optE:optimize_ddGmutation")
BooleanOptionKey const	optE::optimize_ddGmutation_straight_mean ("optE:optimize_ddGmutation_straight_mean")
BooleanOptionKey const	optE::optimize_ddGmutation_boltzman_average ("optE:optimize_ddGmutation_boltzman_average")
RealOptionKey const	optE::exclude_badrep_ddGs ("optE:exclude_badrep_ddGs")
BooleanOptionKey const	optE::pretend_no_ddG_repulsion ("optE:pretend_no_ddG_repulsion")
FileOptionKey const	optE::optimize_decoy_discrimination ("optE:optimize_decoy_discrimination")
StringOptionKey const	optE::normalize_decoy_score_spread ("optE:normalize_decoy_score_spread")
BooleanOptionKey const	optE::ramp_nativeness ("optE:ramp_nativeness")
IntegerOptionKey const	optE::n_top_natives_to_optimize ("optE:n_top_natives_to_optimize")
RealOptionKey const	optE::approximate_decoy_entropy ("optE:approximate_decoy_entropy")
BooleanOptionKey const	optE::repack_and_minimize_decoys ("optE:repack_and_minimize_decoys")
BooleanOptionKey const	optE::repack_and_minimize_input_structures ("optE:repack_and_minimize_input_structures")
IntegerOptionKey const	optE::output_top_n_new_decoys ("optE:output_top_n_new_decoys")
FileOptionKey const	optE::optimize_ligand_discrimination ("optE:optimize_ligand_discrimination")
BooleanOptionKey const	optE::no_design ("optE:no_design")
BooleanOptionKey const	optE::sqrt_pssm ("optE:sqrt_pssm")
RealOptionKey const	optE::min_decoy_rms_to_native ("optE:min_decoy_rms_to_native")
RealOptionKey const	optE::max_rms_from_native ("optE:max_rms_from_native")
BooleanOptionKey const	optE::optimize_starting_free_weights ("optE:optimize_starting_free_weights")
FileOptionKey const	optE::wrap_dof_optimization ("optE:wrap_dof_optimization")
RealOptionKey const	optE::randomly_perturb_starting_free_weights ("optE:randomly_perturb_starting_free_weights")
RealOptionKey const	optE::inv_kT_natrot ("optE:inv_kT_natrot")
RealOptionKey const	optE::inv_kT_nataa ("optE:inv_kT_nataa")
RealOptionKey const	optE::inv_kT_natstruct ("optE:inv_kT_natstruct")
BooleanOptionKey const	optE::mpi_weight_minimization ("optE:mpi_weight_minimization")
BooleanOptionKey const	optE::dont_use_reference_energies ("optE:dont_use_reference_energies")
IntegerOptionKey const	optE::number_of_swarm_particles ("optE:number_of_swarm_particles")
IntegerOptionKey const	optE::number_of_swarm_cycles ("optE:number_of_swarm_cycles")
FileOptionKey const	optE::constrain_weights ("optE:constrain_weights")
BooleanOptionKey const	optE::fit_reference_energies_to_aa_profile_recovery ("optE:fit_reference_energies_to_aa_profile_recovery")
FileOptionKey const	optE::starting_refEs ("optE:starting_refEs")
BooleanOptionKey const	optE::repeat_swarm_optimization_until_fitness_improves ("optE:repeat_swarm_optimization_until_fitness_improves")
BooleanOptionKey const	optE::design_with_minpack ("optE:design_with_minpack")
BooleanOptionKey const	optE::limit_bad_scores ("optE:limit_bad_scores")
BooleanOptionKey const	optE::rescore::rescore ("optE:rescore")
FileOptionKey const	optE::rescore::weights ("optE:rescore:weights")
IntegerOptionKey const	optE::rescore::context_round ("optE:rescore:context_round")
FileOptionKey const	optE::rescore::outlog ("optE:rescore:outlog")
BooleanOptionKey const	optE::rescore::measure_sequence_recovery ("optE:rescore:measure_sequence_recovery")
BooleanOptionKey const	optE::no_design_pdb_output ("optE:no_design_pdb_output")
BooleanOptionKey const	backrub::backrub ("backrub")
IntegerVectorOptionKey const	backrub::pivot_residues ("backrub:pivot_residues")
StringVectorOptionKey const	backrub::pivot_atoms ("backrub:pivot_atoms")
IntegerOptionKey const	backrub::min_atoms ("backrub:min_atoms")
IntegerOptionKey const	backrub::max_atoms ("backrub:max_atoms")
BooleanOptionKey const	bbg::bbg ("bbg")
RealOptionKey const	bbg::factorA ("bbg:factorA")
RealOptionKey const	bbg::factorB ("bbg:factorB")
BooleanOptionKey const	bbg::ignore_improper_res ("bbg:ignore_improper_res")
BooleanOptionKey const	bbg::fix_short_segment ("bbg:fix_short_segment")
BooleanOptionKey const	flexpack::flexpack ("flexpack")
BooleanOptionKey const	flexpack::annealer::annealer ("flexpack:annealer")
RealOptionKey const	flexpack::annealer::inner_iteration_scale ("flexpack:annealer:inner_iteration_scale")
RealOptionKey const	flexpack::annealer::outer_iteration_scale ("flexpack:annealer:outer_iteration_scale")
RealOptionKey const	flexpack::annealer::fixbb_substitutions_scale ("flexpack:annealer:fixbb_substitutions_scale")
RealOptionKey const	flexpack::annealer::pure_movebb_substitutions_scale ("flexpack:annealer:pure_movebb_substitutions_scale")
RealOptionKey const	flexpack::annealer::rotsub_movebb_substitutions_scale ("flexpack:annealer:rotsub_movebb_substitutions_scale")
BooleanOptionKey const	hotspot::hotspot ("hotspot")
BooleanOptionKey const	hotspot::allow_gly ("hotspot:allow_gly")
BooleanOptionKey const	hotspot::allow_proline ("hotspot:allow_proline")
BooleanOptionKey const	hotspot::benchmark ("hotspot:benchmark")
StringVectorOptionKey const	hotspot::residue ("hotspot:residue")
FileOptionKey const	hotspot::hashfile ("hotspot:hashfile")
FileOptionKey const	hotspot::target ("hotspot:target")
IntegerOptionKey const	hotspot::target_res ("hotspot:target_res")
RealOptionKey const	hotspot::target_dist ("hotspot:target_dist")
FileOptionKey const	hotspot::density ("hotspot:density")
FileOptionKey const	hotspot::weighted_density ("hotspot:weighted_density")
FileOptionKey const	hotspot::rms_target ("hotspot:rms_target")
FileOptionKey const	hotspot::rms_hotspot ("hotspot:rms_hotspot")
IntegerOptionKey const	hotspot::rms_hotspot_res ("hotspot:rms_hotspot_res")
BooleanOptionKey const	hotspot::rescore ("hotspot:rescore")
RealOptionKey const	hotspot::threshold ("hotspot:threshold")
BooleanOptionKey const	hotspot::sc_only ("hotspot:sc_only")
BooleanOptionKey const	hotspot::fxnal_group ("hotspot:fxnal_group")
BooleanOptionKey const	hotspot::cluster ("hotspot:cluster")
BooleanOptionKey const	hotspot::colonyE ("hotspot:colonyE")
IntegerOptionKey const	hotspot::length ("hotspot:length")
BooleanOptionKey const	hotspot::envhb ("hotspot:envhb")
RealOptionKey const	hotspot::angle ("hotspot:angle")
IntegerOptionKey const	hotspot::angle_res ("hotspot:angle_res")
BooleanOptionKey const	parser::parser ("parser")
StringOptionKey const	parser::protocol ("parser:protocol")
StringVectorOptionKey const	parser::script_vars ("parser:script_vars")
BooleanOptionKey const	parser::view ("parser:view")
StringOptionKey const	parser::patchdock ("parser:patchdock")
IntegerVectorOptionKey const	parser::patchdock_random_entry ("parser:patchdock_random_entry")
BooleanOptionKey const	DomainAssembly::DomainAssembly ("DomainAssembly")
BooleanOptionKey const	DomainAssembly::da_setup ("DomainAssembly:da_setup")
FileOptionKey const	DomainAssembly::da_setup_option_file ("DomainAssembly:da_setup_option_file")
FileOptionKey const	DomainAssembly::da_setup_output_pdb ("DomainAssembly:da_setup_output_pdb")
FileOptionKey const	DomainAssembly::da_linker_file ("DomainAssembly:da_linker_file")
FileOptionKey const	DomainAssembly::da_require_buried ("DomainAssembly:da_require_buried")
FileOptionKey const	DomainAssembly::da_start_pdb ("DomainAssembly:da_start_pdb")
BooleanOptionKey const	DomainAssembly::run_fullatom ("DomainAssembly:run_fullatom")
BooleanOptionKey const	DomainAssembly::run_centroid ("DomainAssembly:run_centroid")
BooleanOptionKey const	DomainAssembly::run_centroid_abinitio ("DomainAssembly:run_centroid_abinitio")
IntegerOptionKey const	DomainAssembly::da_nruns ("DomainAssembly:da_nruns")
IntegerOptionKey const	DomainAssembly::da_start_pdb_num ("DomainAssembly:da_start_pdb_num")
FileOptionKey const	DomainAssembly::da_linker_file_rna ("DomainAssembly:da_linker_file_rna")
StringOptionKey const	DomainAssembly::residues_repack_only ("DomainAssembly:residues_repack_only")