Rosetta Utilities  2014.35
Namespaces | Functions
OptionKeys.cc.gen2.hh File Reference

Namespaces

 docking
 
 docking::ligand
 
 docking::ligand::grid
 
 DomainAssembly
 
 edensity
 
 els
 
 enzdes
 
 fast_loops
 
 fingerprint
 
 flexpack
 
 flexpack::annealer
 
 flexPepDocking
 
 FloppyTail
 
 FloppyTail::short_tail
 
 flxbb
 
 flxbb::layer
 
 fold_and_dock
 
 fold_cst
 
 fold_from_loops
 
 frags
 
 frags::scoring
 
 frags::picking
 
 frags::nonlocal
 
 frags::contacts
 
 frags::ABEGO
 
 holes
 
 hotspot
 
 indexed_structure_store
 
 lh
 
 lh::fragpdb
 
 lh::symfragrm
 
 loopfcst
 
 LoopModel
 
 make_rot_lib
 
 match
 
 matdes
 
 matdes::dock
 
 matdes::design
 
 matdes::mutalyze
 
 mc
 
 mh
 
 mh::score
 
 mh::filter
 
 motifs
 
 ms
 
 ms::checkpoint
 
 nonlocal
 
 optE
 
 optE::rescore
 
 packstat
 
 parser
 
 patterson
 
 pb_potential
 

Functions

RealOptionKey const docking::ligand::harmonic_Calphas ("docking:ligand:harmonic_Calphas")
 
RealOptionKey const docking::ligand::tether_ligand ("docking:ligand:tether_ligand")
 
RealVectorOptionKey const docking::ligand::start_from ("docking:ligand:start_from")
 
StringOptionKey const docking::ligand::option_file ("docking:ligand:option_file")
 
BooleanOptionKey const docking::ligand::grid::grid ("docking:ligand:grid")
 
FileOptionKey const docking::ligand::grid::grid_kin ("docking:ligand:grid:grid_kin")
 
FileOptionKey const docking::ligand::grid::grid_map ("docking:ligand:grid:grid_map")
 
BooleanOptionKey const 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")
 
FileOptionKey const DomainAssembly::da_eval_pose_map ("DomainAssembly:da_eval_pose_map")
 
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::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")
 
BooleanOptionKey const edensity::unmask_bb ("edensity:unmask_bb")
 
BooleanOptionKey const els::els ("els")
 
IntegerOptionKey const els::master_wu_per_send ("els:master_wu_per_send")
 
StringOptionKey const els::vars ("els:vars")
 
FileOptionKey const els::script ("els:script")
 
IntegerOptionKey const els::num_traj ("els:num_traj")
 
IntegerOptionKey const els::traj_per_master ("els:traj_per_master")
 
IntegerOptionKey const els::shortest_wu ("els:shortest_wu")
 
BooleanOptionKey const els::pool ("els:pool")
 
BooleanOptionKey const els::singlenode ("els:singlenode")
 
BooleanOptionKey const enzdes::enzdes ("enzdes")
 
StringOptionKey const enzdes::checkpoint ("enzdes:checkpoint")
 
BooleanOptionKey const enzdes::enz_score ("enzdes:enz_score")
 
BooleanOptionKey const enzdes::enz_repack ("enzdes:enz_repack")
 
BooleanOptionKey const enzdes::cst_opt ("enzdes:cst_opt")
 
BooleanOptionKey const enzdes::cst_predock ("enzdes:cst_predock")
 
RealOptionKey const enzdes::trans_magnitude ("enzdes:trans_magnitude")
 
RealOptionKey const enzdes::rot_magnitude ("enzdes:rot_magnitude")
 
RealOptionKey const enzdes::dock_trials ("enzdes:dock_trials")
 
BooleanOptionKey const enzdes::cst_min ("enzdes:cst_min")
 
BooleanOptionKey const enzdes::cst_design ("enzdes:cst_design")
 
IntegerOptionKey const enzdes::design_min_cycles ("enzdes:design_min_cycles")
 
BooleanOptionKey const enzdes::make_consensus_mutations ("enzdes:make_consensus_mutations")
 
BooleanOptionKey const enzdes::bb_min ("enzdes:bb_min")
 
RealOptionKey const enzdes::bb_min_allowed_dev ("enzdes:bb_min_allowed_dev")
 
RealOptionKey const enzdes::loop_bb_min_allowed_dev ("enzdes:loop_bb_min_allowed_dev")
 
RealOptionKey const enzdes::minimize_ligand_torsions ("enzdes:minimize_ligand_torsions")
 
RealOptionKey const enzdes::minimize_all_ligand_torsions ("enzdes:minimize_all_ligand_torsions")
 
BooleanOptionKey const enzdes::chi_min ("enzdes:chi_min")
 
BooleanOptionKey const enzdes::min_all_jumps ("enzdes:min_all_jumps")
 
BooleanOptionKey const enzdes::cst_dock ("enzdes:cst_dock")
 
BooleanOptionKey const enzdes::run_ligand_motifs ("enzdes:run_ligand_motifs")
 
BooleanOptionKey const enzdes::enz_debug ("enzdes:enz_debug")
 
FileOptionKey const enzdes::cstfile ("enzdes:cstfile")
 
FileOptionKey const enzdes::enz_loops_file ("enzdes:enz_loops_file")
 
BooleanOptionKey const enzdes::flexbb_protocol ("enzdes:flexbb_protocol")
 
BooleanOptionKey const enzdes::remodel_protocol ("enzdes:remodel_protocol")
 
BooleanOptionKey const enzdes::kic_loop_sampling ("enzdes:kic_loop_sampling")
 
StringOptionKey const enzdes::dump_loop_samples ("enzdes:dump_loop_samples")
 
BooleanOptionKey const enzdes::fix_catalytic_aa ("enzdes:fix_catalytic_aa")
 
IntegerOptionKey const enzdes::additional_packing_ligand_rb_confs ("enzdes:additional_packing_ligand_rb_confs")
 
IntegerOptionKey const enzdes::ex_catalytic_rot ("enzdes:ex_catalytic_rot")
 
IntegerOptionKey const enzdes::single_loop_ensemble_size ("enzdes:single_loop_ensemble_size")
 
IntegerOptionKey const enzdes::loop_generator_trials ("enzdes:loop_generator_trials")
 
BooleanOptionKey const enzdes::no_catres_min_in_loopgen ("enzdes:no_catres_min_in_loopgen")
 
RealOptionKey const enzdes::mc_kt_low ("enzdes:mc_kt_low")
 
RealOptionKey const enzdes::mc_kt_high ("enzdes:mc_kt_high")
 
RealOptionKey const enzdes::min_cacb_deviation ("enzdes:min_cacb_deviation")
 
RealOptionKey const enzdes::max_bb_deviation ("enzdes:max_bb_deviation")
 
RealOptionKey const enzdes::max_bb_deviation_from_startstruct ("enzdes:max_bb_deviation_from_startstruct")
 
IntegerOptionKey const enzdes::remodel_trials ("enzdes:remodel_trials")
 
BooleanOptionKey const enzdes::remodel_secmatch ("enzdes:remodel_secmatch")
 
BooleanOptionKey const enzdes::dump_inverse_rotamers ("enzdes:dump_inverse_rotamers")
 
RealOptionKey const enzdes::remodel_aggressiveness ("enzdes:remodel_aggressiveness")
 
RealOptionKey const enzdes::favor_native_res ("enzdes:favor_native_res")
 
BooleanOptionKey const enzdes::detect_design_interface ("enzdes:detect_design_interface")
 
BooleanOptionKey const enzdes::include_catres_in_interface_detection ("enzdes:include_catres_in_interface_detection")
 
BooleanOptionKey const enzdes::arg_sweep_interface ("enzdes:arg_sweep_interface")
 
RealOptionKey const enzdes::arg_sweep_cutoff ("enzdes:arg_sweep_cutoff")
 
RealOptionKey const enzdes::cut1 ("enzdes:cut1")
 
RealOptionKey const enzdes::cut2 ("enzdes:cut2")
 
RealOptionKey const enzdes::cut3 ("enzdes:cut3")
 
RealOptionKey const enzdes::cut4 ("enzdes:cut4")
 
RealOptionKey const enzdes::lig_packer_weight ("enzdes:lig_packer_weight")
 
BooleanOptionKey const enzdes::no_unconstrained_repack ("enzdes:no_unconstrained_repack")
 
RealOptionKey const enzdes::secmatch_Ecutoff ("enzdes:secmatch_Ecutoff")
 
FileOptionKey const enzdes::change_lig ("enzdes:change_lig")
 
StringOptionKey const enzdes::process_ligrot_separately ("enzdes:process_ligrot_separately")
 
BooleanOptionKey const enzdes::start_from_random_rb_conf ("enzdes:start_from_random_rb_conf")
 
RealOptionKey const enzdes::bb_bump_cutoff ("enzdes:bb_bump_cutoff")
 
RealOptionKey const enzdes::sc_sc_bump_cutoff ("enzdes:sc_sc_bump_cutoff")
 
BooleanOptionKey const enzdes::no_packstat_calculation ("enzdes:no_packstat_calculation")
 
StringOptionKey const enzdes::compare_native ("enzdes:compare_native")
 
BooleanOptionKey const enzdes::final_repack_without_ligand ("enzdes:final_repack_without_ligand")
 
BooleanOptionKey const enzdes::dump_final_repack_without_ligand_pdb ("enzdes:dump_final_repack_without_ligand_pdb")
 
BooleanOptionKey const enzdes::parser_read_cloud_pdb ("enzdes:parser_read_cloud_pdb")
 
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 fingerprint::fingerprint ("fingerprint")
 
RealOptionKey const fingerprint::atom_radius_scale ("fingerprint:atom_radius_scale")
 
RealOptionKey const fingerprint::atom_radius_buffer ("fingerprint:atom_radius_buffer")
 
BooleanOptionKey const fingerprint::include_hydrogens ("fingerprint:include_hydrogens")
 
BooleanOptionKey const fingerprint::square_score ("fingerprint:square_score")
 
IntegerOptionKey const fingerprint::set_origin ("fingerprint:set_origin")
 
IntegerOptionKey const fingerprint::origin_res_num ("fingerprint:origin_res_num")
 
BooleanOptionKey const 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 flexPepDocking::flexPepDocking ("flexPepDocking")
 
StringOptionKey const flexPepDocking::params_file ("flexPepDocking:params_file")
 
IntegerOptionKey const flexPepDocking::peptide_anchor ("flexPepDocking:peptide_anchor")
 
StringOptionKey const flexPepDocking::receptor_chain ("flexPepDocking:receptor_chain")
 
StringOptionKey const flexPepDocking::peptide_chain ("flexPepDocking:peptide_chain")
 
BooleanOptionKey const flexPepDocking::pep_fold_only ("flexPepDocking:pep_fold_only")
 
BooleanOptionKey const flexPepDocking::lowres_abinitio ("flexPepDocking:lowres_abinitio")
 
BooleanOptionKey const flexPepDocking::lowres_preoptimize ("flexPepDocking:lowres_preoptimize")
 
BooleanOptionKey const flexPepDocking::flexPepDockingMinimizeOnly ("flexPepDocking:flexPepDockingMinimizeOnly")
 
BooleanOptionKey const flexPepDocking::extend_peptide ("flexPepDocking:extend_peptide")
 
BooleanOptionKey const flexPepDocking::pep_refine ("flexPepDocking:pep_refine")
 
BooleanOptionKey const flexPepDocking::rbMCM ("flexPepDocking:rbMCM")
 
BooleanOptionKey const flexPepDocking::torsionsMCM ("flexPepDocking:torsionsMCM")
 
BooleanOptionKey const flexPepDocking::peptide_loop_model ("flexPepDocking:peptide_loop_model")
 
BooleanOptionKey const flexPepDocking::backrub_peptide ("flexPepDocking:backrub_peptide")
 
BooleanOptionKey const flexPepDocking::boost_fa_atr ("flexPepDocking:boost_fa_atr")
 
BooleanOptionKey const flexPepDocking::ramp_fa_rep ("flexPepDocking:ramp_fa_rep")
 
BooleanOptionKey const flexPepDocking::ramp_rama ("flexPepDocking:ramp_rama")
 
BooleanOptionKey const flexPepDocking::flexpep_score_only ("flexPepDocking:flexpep_score_only")
 
FileOptionKey const flexPepDocking::ref_startstruct ("flexPepDocking:ref_startstruct")
 
BooleanOptionKey const flexPepDocking::use_cen_score ("flexPepDocking:use_cen_score")
 
BooleanOptionKey const flexPepDocking::design_peptide ("flexPepDocking:design_peptide")
 
IntegerOptionKey const flexPepDocking::rep_ramp_cycles ("flexPepDocking:rep_ramp_cycles")
 
IntegerOptionKey const flexPepDocking::mcm_cycles ("flexPepDocking:mcm_cycles")
 
RealOptionKey const flexPepDocking::random_phi_psi_preturbation ("flexPepDocking:random_phi_psi_preturbation")
 
RealOptionKey const flexPepDocking::smove_angle_range ("flexPepDocking:smove_angle_range")
 
BooleanOptionKey const flexPepDocking::min_receptor_bb ("flexPepDocking:min_receptor_bb")
 
RealOptionKey const flexPepDocking::random_trans_start ("flexPepDocking:random_trans_start")
 
RealOptionKey const flexPepDocking::random_rot_start ("flexPepDocking:random_rot_start")
 
BooleanOptionKey const flexPepDocking::flexpep_prepack ("flexPepDocking:flexpep_prepack")
 
BooleanOptionKey const flexPepDocking::flexpep_noprepack1 ("flexPepDocking:flexpep_noprepack1")
 
BooleanOptionKey const flexPepDocking::flexpep_noprepack2 ("flexPepDocking:flexpep_noprepack2")
 
RealOptionKey const flexPepDocking::score_filter ("flexPepDocking:score_filter")
 
IntegerOptionKey const flexPepDocking::hb_filter ("flexPepDocking:hb_filter")
 
IntegerOptionKey const flexPepDocking::hotspot_filter ("flexPepDocking:hotspot_filter")
 
StringOptionKey const flexPepDocking::frag5 ("flexPepDocking:frag5")
 
RealOptionKey const flexPepDocking::frag9_weight ("flexPepDocking:frag9_weight")
 
RealOptionKey const flexPepDocking::frag5_weight ("flexPepDocking:frag5_weight")
 
RealOptionKey const flexPepDocking::frag3_weight ("flexPepDocking:frag3_weight")
 
BooleanOptionKey const flexPepDocking::pSer2Asp_centroid ("flexPepDocking:pSer2Asp_centroid")
 
BooleanOptionKey const flexPepDocking::pSer2Glu_centroid ("flexPepDocking:pSer2Glu_centroid")
 
BooleanOptionKey const flexPepDocking::dumpPDB_abinitio ("flexPepDocking:dumpPDB_abinitio")
 
BooleanOptionKey const flexPepDocking::dumpPDB_lowres ("flexPepDocking:dumpPDB_lowres")
 
BooleanOptionKey const flexPepDocking::dumpPDB_hires ("flexPepDocking:dumpPDB_hires")
 
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::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 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 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")
 
FileOptionKey const flxbb::blueprint ("flxbb:blueprint")
 
BooleanOptionKey const flxbb::movemap_from_blueprint ("flxbb:movemap_from_blueprint")
 
StringOptionKey const flxbb::layer::layer ("flxbb:layer")
 
BooleanOptionKey const fold_and_dock::fold_and_dock ("fold_and_dock")
 
BooleanOptionKey const fold_and_dock::move_anchor_points ("fold_and_dock:move_anchor_points")
 
BooleanOptionKey const fold_and_dock::set_anchor_at_closest_point ("fold_and_dock:set_anchor_at_closest_point")
 
BooleanOptionKey const fold_and_dock::rotate_anchor_to_x ("fold_and_dock:rotate_anchor_to_x")
 
RealOptionKey const fold_and_dock::trans_mag_smooth ("fold_and_dock:trans_mag_smooth")
 
RealOptionKey const fold_and_dock::rot_mag_smooth ("fold_and_dock:rot_mag_smooth")
 
RealOptionKey const fold_and_dock::rb_rot_magnitude ("fold_and_dock:rb_rot_magnitude")
 
RealOptionKey const fold_and_dock::rb_trans_magnitude ("fold_and_dock:rb_trans_magnitude")
 
IntegerOptionKey const fold_and_dock::rigid_body_cycles ("fold_and_dock:rigid_body_cycles")
 
RealOptionKey const fold_and_dock::move_anchor_frequency ("fold_and_dock:move_anchor_frequency")
 
RealOptionKey const fold_and_dock::rigid_body_frequency ("fold_and_dock:rigid_body_frequency")
 
BooleanOptionKey const fold_and_dock::rigid_body_disable_mc ("fold_and_dock:rigid_body_disable_mc")
 
RealOptionKey const fold_and_dock::slide_contact_frequency ("fold_and_dock:slide_contact_frequency")
 
BooleanOptionKey const fold_cst::fold_cst ("fold_cst")
 
RealOptionKey const fold_cst::constraint_skip_rate ("fold_cst:constraint_skip_rate")
 
IntegerOptionKey const fold_cst::violation_skip_basis ("fold_cst:violation_skip_basis")
 
IntegerOptionKey const fold_cst::violation_skip_ignore ("fold_cst:violation_skip_ignore")
 
BooleanOptionKey const fold_cst::keep_skipped_csts ("fold_cst:keep_skipped_csts")
 
BooleanOptionKey const fold_cst::no_minimize ("fold_cst:no_minimize")
 
BooleanOptionKey const fold_cst::force_minimize ("fold_cst:force_minimize")
 
RealVectorOptionKey const fold_cst::seq_sep_stages ("fold_cst:seq_sep_stages")
 
IntegerOptionKey const fold_cst::reramp_cst_cycles ("fold_cst:reramp_cst_cycles")
 
RealOptionKey const fold_cst::reramp_start_cstweight ("fold_cst:reramp_start_cstweight")
 
IntegerOptionKey const fold_cst::reramp_iterations ("fold_cst:reramp_iterations")
 
BooleanOptionKey const fold_cst::skip_on_noviolation_in_stage1 ("fold_cst:skip_on_noviolation_in_stage1")
 
RealOptionKey const fold_cst::stage1_ramp_cst_cycle_factor ("fold_cst:stage1_ramp_cst_cycle_factor")
 
RealOptionKey const fold_cst::stage2_constraint_threshold ("fold_cst:stage2_constraint_threshold")
 
BooleanOptionKey const fold_cst::ignore_sequence_seperation ("fold_cst:ignore_sequence_seperation")
 
BooleanOptionKey const fold_cst::no_recover_low_at_constraint_switch ("fold_cst:no_recover_low_at_constraint_switch")
 
BooleanOptionKey const fold_cst::ramp_coord_cst ("fold_cst:ramp_coord_cst")
 
BooleanOptionKey const fold_from_loops::fold_from_loops ("fold_from_loops")
 
BooleanOptionKey const fold_from_loops::native_ca_cst ("fold_from_loops:native_ca_cst")
 
FileOptionKey const fold_from_loops::swap_loops ("fold_from_loops:swap_loops")
 
StringOptionKey const fold_from_loops::checkpoint ("fold_from_loops:checkpoint")
 
RealOptionKey const fold_from_loops::ca_csts_dev ("fold_from_loops:ca_csts_dev")
 
IntegerOptionKey const fold_from_loops::add_relax_cycles ("fold_from_loops:add_relax_cycles")
 
IntegerOptionKey const fold_from_loops::loop_mov_nterm ("fold_from_loops:loop_mov_nterm")
 
IntegerOptionKey const fold_from_loops::loop_mov_cterm ("fold_from_loops:loop_mov_cterm")
 
RealOptionKey const fold_from_loops::ca_rmsd_cutoff ("fold_from_loops:ca_rmsd_cutoff")
 
IntegerVectorOptionKey const fold_from_loops::res_design_bs ("fold_from_loops:res_design_bs")
 
FileOptionKey const fold_from_loops::clear_csts ("fold_from_loops:clear_csts")
 
BooleanOptionKey const fold_from_loops::output_centroid ("fold_from_loops:output_centroid")
 
BooleanOptionKey const fold_from_loops::add_cst_loop ("fold_from_loops:add_cst_loop")
 
BooleanOptionKey const frags::frags ("frags")
 
BooleanOptionKey const frags::filter_JC ("frags:filter_JC")
 
BooleanOptionKey const frags::bounded_protocol ("frags:bounded_protocol")
 
BooleanOptionKey const frags::keep_all_protocol ("frags:keep_all_protocol")
 
BooleanOptionKey const frags::quota_protocol ("frags:quota_protocol")
 
BooleanOptionKey const frags::nonlocal_pairs ("frags:nonlocal_pairs")
 
BooleanOptionKey const frags::fragment_contacts ("frags:fragment_contacts")
 
BooleanOptionKey const frags::p_value_selection ("frags:p_value_selection")
 
IntegerOptionKey const frags::n_frags ("frags:n_frags")
 
FileOptionKey const frags::allowed_pdb ("frags:allowed_pdb")
 
StringVectorOptionKey const frags::ss_pred ("frags:ss_pred")
 
FileOptionKey const frags::spine_x ("frags:spine_x")
 
FileOptionKey const frags::depth ("frags:depth")
 
FileOptionKey const frags::denied_pdb ("frags:denied_pdb")
 
IntegerVectorOptionKey const frags::frag_sizes ("frags:frag_sizes")
 
BooleanOptionKey const frags::write_ca_coordinates ("frags:write_ca_coordinates")
 
BooleanOptionKey const frags::write_scores ("frags:write_scores")
 
BooleanOptionKey const frags::annotate ("frags:annotate")
 
IntegerOptionKey const frags::nr_large_copies ("frags:nr_large_copies")
 
IntegerOptionKey const frags::n_candidates ("frags:n_candidates")
 
BooleanOptionKey const frags::write_rama_tables ("frags:write_rama_tables")
 
RealOptionKey const frags::rama_C ("frags:rama_C")
 
RealOptionKey const frags::rama_B ("frags:rama_B")
 
RealOptionKey const frags::sigmoid_cs_A ("frags:sigmoid_cs_A")
 
RealOptionKey const frags::sigmoid_cs_B ("frags:sigmoid_cs_B")
 
RealOptionKey const frags::seqsim_H ("frags:seqsim_H")
 
RealOptionKey const frags::seqsim_E ("frags:seqsim_E")
 
RealOptionKey const frags::seqsim_L ("frags:seqsim_L")
 
RealOptionKey const frags::rama_norm ("frags:rama_norm")
 
StringOptionKey const frags::describe_fragments ("frags:describe_fragments")
 
RealOptionKey const frags::picking_old_max_score ("frags:picking_old_max_score")
 
BooleanOptionKey const frags::write_sequence_only ("frags:write_sequence_only")
 
BooleanOptionKey const frags::output_silent ("frags:output_silent")
 
BooleanOptionKey const frags::score_output_silent ("frags:score_output_silent")
 
BooleanOptionKey const frags::scoring::scoring ("frags:scoring")
 
FileOptionKey const frags::scoring::config ("frags:scoring:config")
 
StringOptionKey const frags::scoring::profile_score ("frags:scoring:profile_score")
 
BooleanOptionKey const frags::picking::picking ("frags:picking")
 
StringOptionKey const frags::picking::selecting_rule ("frags:picking:selecting_rule")
 
StringOptionKey const frags::picking::selecting_scorefxn ("frags:picking:selecting_scorefxn")
 
FileOptionKey const frags::picking::quota_config_file ("frags:picking:quota_config_file")
 
IntegerVectorOptionKey const frags::picking::query_pos ("frags:picking:query_pos")
 
BooleanOptionKey const frags::nonlocal::nonlocal ("frags:nonlocal")
 
BooleanOptionKey const frags::nonlocal::relax_input ("frags:nonlocal:relax_input")
 
BooleanOptionKey const frags::nonlocal::relax_input_with_coordinate_constraints ("frags:nonlocal:relax_input_with_coordinate_constraints")
 
IntegerOptionKey const frags::nonlocal::relax_frags_repeats ("frags:nonlocal:relax_frags_repeats")
 
BooleanOptionKey const frags::nonlocal::single_chain ("frags:nonlocal:single_chain")
 
RealOptionKey const frags::nonlocal::min_contacts_per_res ("frags:nonlocal:min_contacts_per_res")
 
RealOptionKey const frags::nonlocal::max_ddg_score ("frags:nonlocal:max_ddg_score")
 
RealOptionKey const frags::nonlocal::max_rmsd_after_relax ("frags:nonlocal:max_rmsd_after_relax")
 
BooleanOptionKey const frags::nonlocal::output_frags_pdbs ("frags:nonlocal:output_frags_pdbs")
 
BooleanOptionKey const frags::nonlocal::output_idealized ("frags:nonlocal:output_idealized")
 
BooleanOptionKey const frags::nonlocal::output_silent ("frags:nonlocal:output_silent")
 
BooleanOptionKey const frags::contacts::contacts ("frags:contacts")
 
IntegerOptionKey const frags::contacts::min_seq_sep ("frags:contacts:min_seq_sep")
 
RealVectorOptionKey const frags::contacts::dist_cutoffs ("frags:contacts:dist_cutoffs")
 
RealOptionKey const frags::contacts::centroid_distance_scale_factor ("frags:contacts:centroid_distance_scale_factor")
 
StringVectorOptionKey const frags::contacts::type ("frags:contacts:type")
 
IntegerOptionKey const frags::contacts::neighbors ("frags:contacts:neighbors")
 
BooleanOptionKey const frags::contacts::output_all ("frags:contacts:output_all")
 
BooleanOptionKey const frags::ABEGO::ABEGO ("frags:ABEGO")
 
RealOptionKey const frags::ABEGO::phi_psi_range_A ("frags:ABEGO:phi_psi_range_A")
 
BooleanOptionKey const holes::holes ("holes")
 
FileOptionKey const holes::dalphaball ("holes:dalphaball")
 
FileOptionKey const holes::params ("holes:params")
 
IntegerOptionKey const holes::h_mode ("holes:h_mode")
 
BooleanOptionKey const holes::water ("holes:water")
 
BooleanOptionKey const holes::make_pdb ("holes:make_pdb")
 
BooleanOptionKey const holes::make_voids ("holes:make_voids")
 
BooleanOptionKey const holes::atom_scores ("holes:atom_scores")
 
BooleanOptionKey const holes::residue_scores ("holes:residue_scores")
 
StringOptionKey const holes::minimize ("holes:minimize")
 
BooleanOptionKey const holes::debug ("holes:debug")
 
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 indexed_structure_store::indexed_structure_store ("indexed_structure_store")
 
FileOptionKey const indexed_structure_store::fragment_store ("indexed_structure_store:fragment_store")
 
BooleanOptionKey const lh::lh ("lh")
 
IntegerVectorOptionKey const lh::loopsizes ("lh:loopsizes")
 
IntegerOptionKey const lh::num_partitions ("lh:num_partitions")
 
PathOptionKey const lh::db_path ("lh:db_path")
 
BooleanOptionKey const lh::exclude_homo ("lh:exclude_homo")
 
BooleanOptionKey const lh::bss ("lh:bss")
 
StringOptionKey const lh::refstruct ("lh:refstruct")
 
StringOptionKey const lh::homo_file ("lh:homo_file")
 
RealVectorOptionKey const lh::createdb_rms_cutoff ("lh:createdb_rms_cutoff")
 
RealOptionKey const lh::min_bbrms ("lh:min_bbrms")
 
RealOptionKey const lh::max_bbrms ("lh:max_bbrms")
 
RealOptionKey const lh::min_rms ("lh:min_rms")
 
RealOptionKey const lh::max_rms ("lh:max_rms")
 
BooleanOptionKey const lh::filter_by_phipsi ("lh:filter_by_phipsi")
 
IntegerOptionKey const lh::max_radius ("lh:max_radius")
 
IntegerOptionKey const lh::max_struct ("lh:max_struct")
 
IntegerOptionKey const lh::max_struct_per_radius ("lh:max_struct_per_radius")
 
RealOptionKey const lh::grid_space_multiplier ("lh:grid_space_multiplier")
 
RealOptionKey const lh::grid_angle_multiplier ("lh:grid_angle_multiplier")
 
IntegerOptionKey const lh::skim_size ("lh:skim_size")
 
IntegerOptionKey const lh::rounds ("lh:rounds")
 
StringOptionKey const lh::jobname ("lh:jobname")
 
IntegerOptionKey const lh::max_lib_size ("lh:max_lib_size")
 
IntegerOptionKey const lh::max_emperor_lib_size ("lh:max_emperor_lib_size")
 
IntegerOptionKey const lh::max_emperor_lib_round ("lh:max_emperor_lib_round")
 
IntegerOptionKey const lh::library_expiry_time ("lh:library_expiry_time")
 
StringOptionKey const lh::objective_function ("lh:objective_function")
 
IntegerOptionKey const lh::expire_after_rounds ("lh:expire_after_rounds")
 
StringOptionKey const lh::mpi_resume ("lh:mpi_resume")
 
StringOptionKey const lh::mpi_feedback ("lh:mpi_feedback")
 
IntegerOptionKey const lh::mpi_batch_relax_chunks ("lh:mpi_batch_relax_chunks")
 
IntegerOptionKey const lh::mpi_batch_relax_absolute_max ("lh:mpi_batch_relax_absolute_max")
 
IntegerOptionKey const lh::mpi_outbound_wu_buffer_size ("lh:mpi_outbound_wu_buffer_size")
 
IntegerOptionKey const lh::mpi_loophash_split_size ("lh:mpi_loophash_split_size ")
 
RealOptionKey const lh::mpi_metropolis_temp ("lh:mpi_metropolis_temp")
 
IntegerOptionKey const lh::mpi_save_state_interval ("lh:mpi_save_state_interval")
 
BooleanOptionKey const lh::mpi_master_save_score_only ("lh:mpi_master_save_score_only")
 
IntegerOptionKey const lh::max_loophash_per_structure ("lh:max_loophash_per_structure")
 
RealOptionKey const lh::rms_limit ("lh:rms_limit")
 
BooleanOptionKey const lh::centroid_only ("lh:centroid_only")
 
BooleanOptionKey const lh::write_centroid_structs ("lh:write_centroid_structs")
 
BooleanOptionKey const lh::write_all_fa_structs ("lh:write_all_fa_structs")
 
BooleanOptionKey const lh::sandbox ("lh:sandbox")
 
BooleanOptionKey const lh::create_db ("lh:create_db")
 
FileOptionKey const lh::sample_weight_file ("lh:sample_weight_file")
 
RealOptionKey const lh::radius_size ("lh:radius_size")
 
BooleanOptionKey const lh::fragpdb::fragpdb ("lh:fragpdb")
 
StringOptionKey const lh::fragpdb::out_path ("lh:fragpdb:out_path")
 
IntegerVectorOptionKey const lh::fragpdb::indexoffset ("lh:fragpdb:indexoffset")
 
StringVectorOptionKey const lh::fragpdb::bin ("lh:fragpdb:bin")
 
BooleanOptionKey const lh::symfragrm::symfragrm ("lh:symfragrm")
 
FileVectorOptionKey const lh::symfragrm::pdblist ("lh:symfragrm:pdblist")
 
BooleanOptionKey const loopfcst::loopfcst ("loopfcst")
 
RealOptionKey const loopfcst::coord_cst_weight ("loopfcst:coord_cst_weight")
 
BooleanOptionKey const loopfcst::coord_cst_all_atom ("loopfcst:coord_cst_all_atom")
 
BooleanOptionKey const loopfcst::use_general_protocol ("loopfcst:use_general_protocol")
 
FileOptionKey const loopfcst::coord_cst_weight_array ("loopfcst:coord_cst_weight_array")
 
FileOptionKey const loopfcst::dump_coord_cst_weight_array ("loopfcst:dump_coord_cst_weight_array")
 
BooleanOptionKey const LoopModel::LoopModel ("LoopModel")
 
FileOptionKey const LoopModel::input_pdb ("LoopModel:input_pdb")
 
BooleanOptionKey const make_rot_lib::make_rot_lib ("make_rot_lib")
 
FileOptionKey const make_rot_lib::options_file ("make_rot_lib:options_file")
 
IntegerVectorOptionKey const make_rot_lib::two_fold_symetry_135_315 ("make_rot_lib:two_fold_symetry_135_315")
 
IntegerVectorOptionKey const make_rot_lib::two_fold_symetry_0_180 ("make_rot_lib:two_fold_symetry_0_180")
 
IntegerVectorOptionKey const make_rot_lib::three_fold_symetry_90_210_330 ("make_rot_lib:three_fold_symetry_90_210_330")
 
BooleanOptionKey const match::match ("match")
 
StringOptionKey const match::lig_name ("match:lig_name")
 
RealOptionKey const match::bump_tolerance ("match:bump_tolerance")
 
FileOptionKey const match::active_site_definition_by_residue ("match:active_site_definition_by_residue")
 
FileOptionKey const match::active_site_definition_by_gridlig ("match:active_site_definition_by_gridlig")
 
FileOptionKey const match::required_active_site_atom_names ("match:required_active_site_atom_names")
 
FileOptionKey const match::grid_boundary ("match:grid_boundary")
 
FileOptionKey const match::geometric_constraint_file ("match:geometric_constraint_file")
 
FileOptionKey const match::scaffold_active_site_residues ("match:scaffold_active_site_residues")
 
FileOptionKey const match::scaffold_active_site_residues_for_geomcsts ("match:scaffold_active_site_residues_for_geomcsts")
 
RealOptionKey const match::euclid_bin_size ("match:euclid_bin_size")
 
RealOptionKey const match::euler_bin_size ("match:euler_bin_size")
 
BooleanOptionKey const match::consolidate_matches ("match:consolidate_matches")
 
IntegerOptionKey const match::output_matches_per_group ("match:output_matches_per_group")
 
StringVectorOptionKey const match::orientation_atoms ("match:orientation_atoms")
 
StringOptionKey const match::output_format ("match:output_format")
 
StringOptionKey const match::match_grouper ("match:match_grouper")
 
RealOptionKey const match::grouper_downstream_rmsd ("match:grouper_downstream_rmsd")
 
BooleanOptionKey const match::output_matchres_only ("match:output_matchres_only")
 
IntegerVectorOptionKey const match::geom_csts_downstream_output ("match:geom_csts_downstream_output")
 
BooleanOptionKey const match::filter_colliding_upstream_residues ("match:filter_colliding_upstream_residues")
 
RealOptionKey const match::upstream_residue_collision_tolerance ("match:upstream_residue_collision_tolerance")
 
RealOptionKey const match::upstream_residue_collision_score_cutoff ("match:upstream_residue_collision_score_cutoff")
 
RealOptionKey const match::upstream_residue_collision_Wfa_atr ("match:upstream_residue_collision_Wfa_atr")
 
RealOptionKey const match::upstream_residue_collision_Wfa_rep ("match:upstream_residue_collision_Wfa_rep")
 
RealOptionKey const match::upstream_residue_collision_Wfa_sol ("match:upstream_residue_collision_Wfa_sol")
 
BooleanOptionKey const match::filter_upstream_downstream_collisions ("match:filter_upstream_downstream_collisions")
 
RealOptionKey const match::updown_collision_tolerance ("match:updown_collision_tolerance")
 
RealOptionKey const match::updown_residue_collision_score_cutoff ("match:updown_residue_collision_score_cutoff")
 
RealOptionKey const match::updown_residue_collision_Wfa_atr ("match:updown_residue_collision_Wfa_atr")
 
RealOptionKey const match::updown_residue_collision_Wfa_rep ("match:updown_residue_collision_Wfa_rep")
 
RealOptionKey const match::updown_residue_collision_Wfa_sol ("match:updown_residue_collision_Wfa_sol")
 
BooleanOptionKey const match::define_match_by_single_downstream_positioning ("match:define_match_by_single_downstream_positioning")
 
IntegerOptionKey const match::ligand_rotamer_index ("match:ligand_rotamer_index")
 
BooleanOptionKey const match::enumerate_ligand_rotamers ("match:enumerate_ligand_rotamers")
 
BooleanOptionKey const match::only_enumerate_non_match_redundant_ligand_rotamers ("match:only_enumerate_non_match_redundant_ligand_rotamers")
 
BooleanOptionKey const match::dynamic_grid_refinement ("match:dynamic_grid_refinement")
 
BooleanOptionKey const match::build_round1_hits_twice ("match:build_round1_hits_twice")
 
BooleanOptionKey const matdes::matdes ("matdes")
 
IntegerOptionKey const matdes::num_subs_building_block ("matdes:num_subs_building_block")
 
IntegerOptionKey const matdes::num_subs_total ("matdes:num_subs_total")
 
StringOptionKey const matdes::pdbID ("matdes:pdbID")
 
StringOptionKey const matdes::prefix ("matdes:prefix")
 
RealVectorOptionKey const matdes::radial_disp ("matdes:radial_disp")
 
RealVectorOptionKey const matdes::angle ("matdes:angle")
 
StringOptionKey const matdes::tag ("matdes:tag")
 
BooleanOptionKey const matdes::dock::dock ("matdes:dock")
 
RealOptionKey const matdes::dock::neg_r ("matdes:dock:neg_r")
 
BooleanOptionKey const matdes::dock::dump_pdb ("matdes:dock:dump_pdb")
 
BooleanOptionKey const matdes::dock::dump_chainA_only ("matdes:dock:dump_chainA_only")
 
BooleanOptionKey const matdes::design::design ("matdes:design")
 
RealOptionKey const matdes::design::contact_dist ("matdes:design:contact_dist")
 
RealOptionKey const matdes::design::grid_size_angle ("matdes:design:grid_size_angle")
 
RealOptionKey const matdes::design::grid_size_radius ("matdes:design:grid_size_radius")
 
IntegerOptionKey const matdes::design::grid_nsamp_angle ("matdes:design:grid_nsamp_angle")
 
IntegerOptionKey const matdes::design::grid_nsamp_radius ("matdes:design:grid_nsamp_radius")
 
RealOptionKey const matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus")
 
BooleanOptionKey const matdes::mutalyze::mutalyze ("matdes:mutalyze")
 
BooleanOptionKey const matdes::mutalyze::calc_rot_boltz ("matdes:mutalyze:calc_rot_boltz")
 
BooleanOptionKey const matdes::mutalyze::ala_scan ("matdes:mutalyze:ala_scan")
 
BooleanOptionKey const matdes::mutalyze::revert_scan ("matdes:mutalyze:revert_scan")
 
BooleanOptionKey const matdes::mutalyze::min_rb ("matdes:mutalyze:min_rb")
 
BooleanOptionKey const mc::mc ("mc")
 
BooleanOptionKey const mc::log_scores_in_MC ("mc:log_scores_in_MC")
 
StringOptionKey const mc::hierarchical_pool ("mc:hierarchical_pool")
 
FileOptionKey const mc::read_structures_into_pool ("mc:read_structures_into_pool")
 
IntegerOptionKey const mc::convergence_check_frequency ("mc:convergence_check_frequency")
 
FileOptionKey const mc::known_structures ("mc:known_structures")
 
RealOptionKey const mc::max_rmsd_against_known_structures ("mc:max_rmsd_against_known_structures")
 
IntegerVectorOptionKey const mc::excluded_residues_from_rmsd ("mc:excluded_residues_from_rmsd")
 
IntegerOptionKey const mc::heat_convergence_check ("mc:heat_convergence_check")
 
BooleanOptionKey const mh::mh ("mh")
 
StringOptionKey const mh::motif_out_file ("mh:motif_out_file")
 
FileVectorOptionKey const mh::harvest_motifs ("mh:harvest_motifs")
 
FileVectorOptionKey const mh::print_motifs ("mh:print_motifs")
 
FileVectorOptionKey const mh::dump_motif_pdbs ("mh:dump_motif_pdbs")
 
FileVectorOptionKey const mh::merge_motifs ("mh:merge_motifs")
 
BooleanOptionKey const mh::generate_reverse_motifs ("mh:generate_reverse_motifs")
 
FileVectorOptionKey const mh::dump_input_pdb ("mh:dump_input_pdb")
 
FileVectorOptionKey const mh::xform_score_data ("mh:xform_score_data")
 
FileVectorOptionKey const mh::xform_score_data_ee ("mh:xform_score_data_ee")
 
FileVectorOptionKey const mh::xform_score_data_eh ("mh:xform_score_data_eh")
 
FileVectorOptionKey const mh::xform_score_data_he ("mh:xform_score_data_he")
 
FileVectorOptionKey const mh::xform_score_data_hh ("mh:xform_score_data_hh")
 
FileVectorOptionKey const mh::xform_score_data_sspair ("mh:xform_score_data_sspair")
 
FileVectorOptionKey const mh::input_motifs ("mh:input_motifs")
 
FileVectorOptionKey const mh::harvest_scores ("mh:harvest_scores")
 
FileOptionKey const mh::print_scores ("mh:print_scores")
 
FileVectorOptionKey const mh::dump_matching_motifs ("mh:dump_matching_motifs")
 
RealOptionKey const mh::dump_matching_motifs_cutoff ("mh:dump_matching_motifs_cutoff")
 
BooleanOptionKey const mh::score_across_chains_only ("mh:score_across_chains_only")
 
IntegerOptionKey const mh::dump_motif_pdbs_min_counts ("mh:dump_motif_pdbs_min_counts")
 
RealOptionKey const mh::hash_cart_size ("mh:hash_cart_size")
 
RealOptionKey const mh::hash_cart_resl ("mh:hash_cart_resl")
 
RealOptionKey const mh::hash_angle_resl ("mh:hash_angle_resl")
 
IntegerOptionKey const mh::harvest_motifs_min_hh_ends ("mh:harvest_motifs_min_hh_ends")
 
IntegerOptionKey const mh::harvest_scores_min_count ("mh:harvest_scores_min_count")
 
BooleanOptionKey const mh::ignore_io_errors ("mh:ignore_io_errors")
 
RealOptionKey const mh::motif_match_radius ("mh:motif_match_radius")
 
RealVectorOptionKey const mh::merge_similar_motifs ("mh:merge_similar_motifs")
 
BooleanOptionKey const mh::score::score ("mh:score")
 
BooleanOptionKey const mh::score::noloops ("mh:score:noloops")
 
RealOptionKey const mh::score::strand_pair_weight ("mh:score:strand_pair_weight")
 
RealOptionKey const mh::score::min_contact_pairs ("mh:score:min_contact_pairs")
 
RealOptionKey const mh::score::max_contact_pairs ("mh:score:max_contact_pairs")
 
BooleanOptionKey const mh::filter::filter ("mh:filter")
 
BooleanOptionKey const mh::filter::filter_harvest ("mh:filter:filter_harvest")
 
BooleanOptionKey const mh::filter::filter_io ("mh:filter:filter_io")
 
StringOptionKey const mh::filter::restype ("mh:filter:restype")
 
StringOptionKey const mh::filter::restype_one ("mh:filter:restype_one")
 
StringOptionKey const mh::filter::not_restype ("mh:filter:not_restype")
 
StringOptionKey const mh::filter::not_restype_one ("mh:filter:not_restype_one")
 
IntegerOptionKey const mh::filter::seqsep ("mh:filter:seqsep")
 
BooleanOptionKey const mh::filter::no_hb_bb ("mh:filter:no_hb_bb")
 
RealOptionKey const mh::filter::mindist2 ("mh:filter:mindist2")
 
RealOptionKey const mh::filter::maxdist2 ("mh:filter:maxdist2")
 
StringOptionKey const mh::filter::ss1 ("mh:filter:ss1")
 
StringOptionKey const mh::filter::ss2 ("mh:filter:ss2")
 
StringOptionKey const mh::filter::dssp1 ("mh:filter:dssp1")
 
StringOptionKey const mh::filter::dssp2 ("mh:filter:dssp2")
 
StringOptionKey const mh::filter::aa1 ("mh:filter:aa1")
 
StringOptionKey const mh::filter::aa2 ("mh:filter:aa2")
 
RealOptionKey const mh::filter::sasa ("mh:filter:sasa")
 
RealOptionKey const mh::filter::faatr ("mh:filter:faatr")
 
RealOptionKey const mh::filter::hb_sc ("mh:filter:hb_sc")
 
RealOptionKey const mh::filter::hb_bb_sc ("mh:filter:hb_bb_sc")
 
RealOptionKey const mh::filter::hb_bb ("mh:filter:hb_bb")
 
RealOptionKey const mh::filter::coorderr ("mh:filter:coorderr")
 
RealOptionKey const mh::filter::faatr_or_hbbb ("mh:filter:faatr_or_hbbb")
 
RealOptionKey const mh::filter::faatr_or_hb ("mh:filter:faatr_or_hb")
 
BooleanOptionKey const mh::filter::noloops ("mh:filter:noloops")
 
BooleanOptionKey const mh::filter::oneloop ("mh:filter:oneloop")
 
BooleanOptionKey const mh::filter::nodisulf ("mh:filter:nodisulf")
 
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")
 
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")
 
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 ms::ms ("ms")
 
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 nonlocal::nonlocal ("nonlocal")
 
FileOptionKey const nonlocal::chunks ("nonlocal:chunks")
 
BooleanOptionKey const nonlocal::randomize_missing ("nonlocal:randomize_missing")
 
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::no_design_pdb_output ("optE:no_design_pdb_output")
 
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 packstat::packstat ("packstat")
 
BooleanOptionKey const packstat::include_water ("packstat:include_water")
 
IntegerOptionKey const packstat::oversample ("packstat:oversample")
 
BooleanOptionKey const packstat::packstat_pdb ("packstat:packstat_pdb")
 
BooleanOptionKey const packstat::surface_accessibility ("packstat:surface_accessibility")
 
BooleanOptionKey const packstat::residue_scores ("packstat:residue_scores")
 
RealOptionKey const packstat::cavity_burial_probe_radius ("packstat:cavity_burial_probe_radius")
 
BooleanOptionKey const packstat::raw_stats ("packstat:raw_stats")
 
IntegerOptionKey const packstat::threads ("packstat:threads")
 
RealOptionKey const packstat::cluster_min_volume ("packstat:cluster_min_volume")
 
RealOptionKey const packstat::min_surface_accessibility ("packstat:min_surface_accessibility")
 
RealOptionKey const packstat::min_cluster_overlap ("packstat:min_cluster_overlap")
 
RealOptionKey const packstat::min_cav_ball_radius ("packstat:min_cav_ball_radius")
 
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 patterson::patterson ("patterson")
 
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 pb_potential::pb_potential ("pb_potential")
 
IntegerVectorOptionKey const pb_potential::charged_chains ("pb_potential:charged_chains")
 
BooleanOptionKey const pb_potential::sidechain_only ("pb_potential:sidechain_only")
 
IntegerVectorOptionKey const pb_potential::revamp_near_chain ("pb_potential:revamp_near_chain")
 
StringOptionKey const pb_potential::apbs_path ("pb_potential:apbs_path")
 
RealOptionKey const pb_potential::potential_cap ("pb_potential:potential_cap")
 
RealOptionKey const pb_potential::epsilon ("pb_potential:epsilon")
 
IntegerOptionKey const pb_potential::apbs_debug ("pb_potential:apbs_debug")