Rosetta Utilities  2014.35
Namespaces | Functions
OptionKeys.cc.gen1.hh File Reference

Namespaces

 loops
 
 loops::ccd
 
 membrane_new
 
 membrane_new::viewer
 
 membrane_new::visualize
 
 membrane_new::scoring
 
 membrane_new::setup
 
 membrane
 
 mistakes
 
 mistakes::chemical
 
 MM
 
 MonteCarlo
 
 optimization
 
 orbitals
 
 pose_metrics
 
 rigid
 
 sasa
 
 symmetry
 
 abinitio
 
 abinitio::star
 
 abrelax
 
 AnchoredDesign
 
 AnchoredDesign::filters
 
 AnchoredDesign::akash
 
 AnchoredDesign::testing
 
 antibody
 
 antibody::design
 
 assembly
 
 backrub
 
 batch_relax
 
 bbg
 
 boinc
 
 broker
 
 bunsat_calc2
 
 canonical_sampling
 
 canonical_sampling::probabilities
 
 canonical_sampling::sampling
 
 canonical_sampling::out
 
 casp
 
 chemically_conjugated_docking
 
 chunk
 
 cluster
 
 cm
 
 cm::sanitize
 
 cm::hybridize
 
 contactMap
 
 cp
 
 cryst
 
 csa
 
 cutoutdomain
 
 cyclization
 
 dc
 
 ddg
 
 DenovoProteinDesign
 
 dna
 
 dna::specificity
 
 dna::design
 
 dna::design::specificity
 
 dna::design::reversion
 
 docking
 
 docking::ligand
 

Functions

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_leave_centroid_after_initial_closure ("loops:kic_leave_centroid_after_initial_closure")
 
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::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::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::ccd::ccd ("loops:ccd")
 
RealOptionKey const loops::ccd::max_rama_score_increase ("loops:ccd:max_rama_score_increase")
 
RealVectorOptionKey const loops::ccd::max_torsion_delta_per_move ("loops:ccd:max_torsion_delta_per_move")
 
RealVectorOptionKey const loops::ccd::max_torsion_delta ("loops:ccd:max_torsion_delta")
 
RealOptionKey const loops::ccd::tolerance ("loops:ccd:tolerance")
 
IntegerOptionKey const loops::ccd::max_cycles ("loops:ccd:max_cycles")
 
BooleanOptionKey const loops::ccd::check_rama_scores ("loops:ccd:check_rama_scores")
 
BooleanOptionKey const loops::ccd::rama_2b ("loops:ccd:rama_2b")
 
RealOptionKey const loops::ccd::temperature ("loops:ccd:temperature")
 
BooleanOptionKey const membrane_new::membrane_new ("membrane_new")
 
BooleanOptionKey const membrane_new::anchored_foldtree ("membrane_new:anchored_foldtree")
 
RealOptionKey const membrane_new::thickness ("membrane_new:thickness")
 
RealVectorOptionKey const membrane_new::center_start ("membrane_new:center_start")
 
RealOptionKey const membrane_new::center_delta ("membrane_new:center_delta")
 
RealOptionKey const membrane_new::center_search_cycles ("membrane_new:center_search_cycles")
 
RealVectorOptionKey const membrane_new::normal_start ("membrane_new:normal_start")
 
RealOptionKey const membrane_new::normal_angle_start ("membrane_new:normal_angle_start")
 
RealOptionKey const membrane_new::normal_angle_delta ("membrane_new:normal_angle_delta")
 
RealOptionKey const membrane_new::normal_search_cycles ("membrane_new:normal_search_cycles")
 
RealOptionKey const membrane_new::chain_normal_angle_max ("membrane_new:chain_normal_angle_max")
 
RealOptionKey const membrane_new::pose_normal_angle_max ("membrane_new:pose_normal_angle_max")
 
BooleanOptionKey const membrane_new::no_interpolate_Mpair ("membrane_new:no_interpolate_Mpair")
 
BooleanOptionKey const membrane_new::Hbond_depth_correction ("membrane_new:Hbond_depth_correction")
 
BooleanOptionKey const membrane_new::TMprojection ("membrane_new:TMprojection")
 
RealOptionKey const membrane_new::wt_TMprojection ("membrane_new:wt_TMprojection")
 
BooleanOptionKey const membrane_new::non_helix ("membrane_new:non_helix")
 
RealOptionKey const membrane_new::wt_non_helix ("membrane_new:wt_non_helix")
 
BooleanOptionKey const membrane_new::termini ("membrane_new:termini")
 
RealOptionKey const membrane_new::wt_termini ("membrane_new:wt_termini")
 
BooleanOptionKey const membrane_new::secstruct ("membrane_new:secstruct")
 
RealOptionKey const membrane_new::wt_secstruct ("membrane_new:wt_secstruct")
 
BooleanOptionKey const membrane_new::spanning ("membrane_new:spanning")
 
RealOptionKey const membrane_new::wt_spanning ("membrane_new:wt_spanning")
 
BooleanOptionKey const membrane_new::view_in_pymol ("membrane_new:view_in_pymol")
 
BooleanOptionKey const membrane_new::viewer::viewer ("membrane_new:viewer")
 
RealOptionKey const membrane_new::viewer::thickness ("membrane_new:viewer:thickness")
 
IntegerOptionKey const membrane_new::viewer::num_points ("membrane_new:viewer:num_points")
 
BooleanOptionKey const membrane_new::visualize::visualize ("membrane_new:visualize")
 
RealOptionKey const membrane_new::visualize::spacing ("membrane_new:visualize:spacing")
 
RealOptionKey const membrane_new::visualize::width ("membrane_new:visualize:width")
 
RealOptionKey const membrane_new::visualize::thickness ("membrane_new:visualize:thickness")
 
RealOptionKey const membrane_new::visualize::plane_radius ("membrane_new:visualize:plane_radius")
 
BooleanOptionKey const membrane_new::scoring::scoring ("membrane_new:scoring")
 
BooleanOptionKey const membrane_new::scoring::hbond ("membrane_new:scoring:hbond")
 
BooleanOptionKey const membrane_new::setup::setup ("membrane_new:setup")
 
StringVectorOptionKey const membrane_new::setup::spanfiles ("membrane_new:setup:spanfiles")
 
StringOptionKey const membrane_new::setup::lipsfile ("membrane_new:setup:lipsfile")
 
RealVectorOptionKey const membrane_new::setup::center ("membrane_new:setup:center")
 
RealVectorOptionKey const membrane_new::setup::normal ("membrane_new:setup:normal")
 
BooleanOptionKey const membrane::membrane ("membrane")
 
IntegerOptionKey const membrane::normal_cycles ("membrane:normal_cycles")
 
RealOptionKey const membrane::normal_mag ("membrane:normal_mag")
 
RealOptionKey const membrane::center_mag ("membrane:center_mag")
 
RealOptionKey const membrane::smooth_move_frac ("membrane:smooth_move_frac")
 
BooleanOptionKey const membrane::no_interpolate_Mpair ("membrane:no_interpolate_Mpair")
 
BooleanOptionKey const membrane::Menv_penalties ("membrane:Menv_penalties")
 
BooleanOptionKey const membrane::Membed_init ("membrane:Membed_init")
 
BooleanOptionKey const membrane::Fa_Membed_update ("membrane:Fa_Membed_update")
 
BooleanOptionKey const membrane::center_search ("membrane:center_search")
 
BooleanOptionKey const membrane::normal_search ("membrane:normal_search")
 
IntegerOptionKey const membrane::center_max_delta ("membrane:center_max_delta")
 
IntegerOptionKey const membrane::normal_start_angle ("membrane:normal_start_angle")
 
IntegerOptionKey const membrane::normal_delta_angle ("membrane:normal_delta_angle")
 
IntegerOptionKey const membrane::normal_max_angle ("membrane:normal_max_angle")
 
BooleanOptionKey const membrane::debug ("membrane:debug")
 
BooleanOptionKey const membrane::fixed_membrane ("membrane:fixed_membrane")
 
RealVectorOptionKey const membrane::membrane_center ("membrane:membrane_center")
 
RealVectorOptionKey const membrane::membrane_normal ("membrane:membrane_normal")
 
BooleanOptionKey const membrane::view ("membrane:view")
 
BooleanOptionKey const membrane::Mhbond_depth ("membrane:Mhbond_depth")
 
RealOptionKey const membrane::thickness ("membrane:thickness")
 
BooleanOptionKey const mistakes::mistakes ("mistakes")
 
BooleanOptionKey const mistakes::restore_pre_talaris_2013_behavior ("mistakes:restore_pre_talaris_2013_behavior")
 
BooleanOptionKey const mistakes::chemical::chemical ("mistakes:chemical")
 
BooleanOptionKey const mistakes::chemical::pre_talaris2013_geometries ("mistakes:chemical:pre_talaris2013_geometries")
 
BooleanOptionKey const MM::MM ("MM")
 
BooleanOptionKey const MM::ignore_missing_bondangle_params ("MM:ignore_missing_bondangle_params")
 
BooleanOptionKey const MonteCarlo::MonteCarlo ("MonteCarlo")
 
RealOptionKey const MonteCarlo::temp_initial ("MonteCarlo:temp_initial")
 
RealOptionKey const MonteCarlo::temp_final ("MonteCarlo:temp_final")
 
BooleanOptionKey const optimization::optimization ("optimization")
 
IntegerOptionKey const optimization::default_max_cycles ("optimization:default_max_cycles")
 
RealOptionKey const optimization::armijo_min_stepsize ("optimization:armijo_min_stepsize")
 
RealOptionKey const optimization::scale_normalmode_dampen ("optimization:scale_normalmode_dampen")
 
IntegerOptionKey const optimization::lbfgs_M ("optimization:lbfgs_M")
 
RealOptionKey const optimization::scale_d ("optimization:scale_d")
 
RealOptionKey const optimization::scale_theta ("optimization:scale_theta")
 
RealOptionKey const optimization::scale_rb ("optimization:scale_rb")
 
RealOptionKey const optimization::scale_rbangle ("optimization:scale_rbangle")
 
BooleanOptionKey const optimization::scmin_nonideal ("optimization:scmin_nonideal")
 
BooleanOptionKey const optimization::scmin_cartesian ("optimization:scmin_cartesian")
 
BooleanOptionKey const optimization::nonideal ("optimization:nonideal")
 
BooleanOptionKey const optimization::new_sym_min ("optimization:new_sym_min")
 
BooleanOptionKey const orbitals::orbitals ("orbitals")
 
BooleanOptionKey const orbitals::Hpol ("orbitals:Hpol")
 
BooleanOptionKey const orbitals::Haro ("orbitals:Haro")
 
BooleanOptionKey const orbitals::bb_stats ("orbitals:bb_stats")
 
BooleanOptionKey const orbitals::sc_stats ("orbitals:sc_stats")
 
BooleanOptionKey const pose_metrics::pose_metrics ("pose_metrics")
 
RealOptionKey const pose_metrics::atomic_burial_cutoff ("pose_metrics:atomic_burial_cutoff")
 
RealOptionKey const pose_metrics::sasa_calculator_probe_radius ("pose_metrics:sasa_calculator_probe_radius")
 
RealOptionKey const pose_metrics::interface_cutoff ("pose_metrics:interface_cutoff")
 
IntegerOptionKey const pose_metrics::min_sequence_separation ("pose_metrics:min_sequence_separation")
 
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 rigid::rigid ("rigid")
 
RealOptionKey const rigid::chainbreak_bias ("rigid:chainbreak_bias")
 
BooleanOptionKey const rigid::close_loops ("rigid:close_loops")
 
IntegerOptionKey const rigid::fragment_cycles ("rigid:fragment_cycles")
 
BooleanOptionKey const rigid::log_accepted_moves ("rigid:log_accepted_moves")
 
RealOptionKey const rigid::max_ca_ca_dist ("rigid:max_ca_ca_dist")
 
FileOptionKey const rigid::patch ("rigid:patch")
 
IntegerOptionKey const rigid::residues_backbone_move ("rigid:residues_backbone_move")
 
RealOptionKey const rigid::rotation ("rigid:rotation")
 
FileOptionKey const rigid::sampling_prob ("rigid:sampling_prob")
 
StringOptionKey const rigid::score ("rigid:score")
 
IntegerOptionKey const rigid::sequence_separation ("rigid:sequence_separation")
 
IntegerOptionKey const rigid::small_cycles ("rigid:small_cycles")
 
IntegerOptionKey const rigid::stages ("rigid:stages")
 
RealOptionKey const rigid::temperature ("rigid:temperature")
 
RealOptionKey const rigid::translation ("rigid:translation")
 
BooleanOptionKey const sasa::sasa ("sasa")
 
StringOptionKey const sasa::method ("sasa:method")
 
BooleanOptionKey const sasa::include_hydrogens_explicitly ("sasa:include_hydrogens_explicitly")
 
RealOptionKey const sasa::probe_radius ("sasa:probe_radius")
 
BooleanOptionKey const sasa::include_probe_radius_in_atom_radii ("sasa:include_probe_radius_in_atom_radii")
 
BooleanOptionKey const sasa::include_only_C_S_in_hsasa ("sasa:include_only_C_S_in_hsasa")
 
BooleanOptionKey const sasa::exclude_polar_atoms_by_charge_in_hsasa ("sasa:exclude_polar_atoms_by_charge_in_hsasa")
 
RealOptionKey const sasa::polar_charge_cutoff ("sasa:polar_charge_cutoff")
 
StringOptionKey const sasa::implicit_hydrogen_radii_set ("sasa:implicit_hydrogen_radii_set")
 
StringOptionKey const sasa::explicit_hydrogen_radii_set ("sasa:explicit_hydrogen_radii_set")
 
BooleanOptionKey const symmetry::symmetry ("symmetry")
 
StringOptionKey const symmetry::symmetry_definition ("symmetry:symmetry_definition")
 
RealOptionKey const symmetry::reweight_symm_interactions ("symmetry:reweight_symm_interactions")
 
BooleanOptionKey const symmetry::initialize_rigid_body_dofs ("symmetry:initialize_rigid_body_dofs")
 
BooleanOptionKey const symmetry::detect_bonds ("symmetry:detect_bonds")
 
RealVectorOptionKey const symmetry::perturb_rigid_body_dofs ("symmetry:perturb_rigid_body_dofs")
 
BooleanOptionKey const symmetry::symmetric_rmsd ("symmetry:symmetric_rmsd")
 
BooleanOptionKey const abinitio::abinitio ("abinitio")
 
BooleanOptionKey const abinitio::membrane ("abinitio:membrane")
 
BooleanOptionKey const abinitio::use_loophash_filter ("abinitio:use_loophash_filter")
 
RealOptionKey const abinitio::loophash_filter_acceptance_rate ("abinitio:loophash_filter_acceptance_rate")
 
FileOptionKey const abinitio::kill_hairpins ("abinitio:kill_hairpins")
 
RealOptionKey const abinitio::kill_hairpins_frequency ("abinitio:kill_hairpins_frequency")
 
BooleanOptionKey const abinitio::smooth_cycles_only ("abinitio:smooth_cycles_only")
 
BooleanOptionKey const abinitio::relax ("abinitio:relax")
 
BooleanOptionKey const abinitio::final_clean_relax ("abinitio:final_clean_relax")
 
BooleanOptionKey const abinitio::fastrelax ("abinitio:fastrelax")
 
BooleanOptionKey const abinitio::multifastrelax ("abinitio:multifastrelax")
 
BooleanOptionKey const abinitio::debug ("abinitio:debug")
 
BooleanOptionKey const abinitio::clear_pose_cache ("abinitio:clear_pose_cache")
 
BooleanOptionKey const abinitio::explicit_pdb_debug ("abinitio:explicit_pdb_debug")
 
BooleanOptionKey const abinitio::use_filters ("abinitio:use_filters")
 
RealOptionKey const abinitio::increase_cycles ("abinitio:increase_cycles")
 
IntegerOptionKey const abinitio::number_3mer_frags ("abinitio:number_3mer_frags")
 
IntegerOptionKey const abinitio::number_9mer_frags ("abinitio:number_9mer_frags")
 
RealOptionKey const abinitio::temperature ("abinitio:temperature")
 
RealOptionKey const abinitio::rg_reweight ("abinitio:rg_reweight")
 
RealOptionKey const abinitio::rsd_wt_helix ("abinitio:rsd_wt_helix")
 
RealOptionKey const abinitio::rsd_wt_strand ("abinitio:rsd_wt_strand")
 
RealOptionKey const abinitio::rsd_wt_loop ("abinitio:rsd_wt_loop")
 
BooleanOptionKey const abinitio::skip_convergence_check ("abinitio:skip_convergence_check")
 
FileVectorOptionKey const abinitio::stage1_patch ("abinitio:stage1_patch")
 
FileVectorOptionKey const abinitio::stage2_patch ("abinitio:stage2_patch")
 
FileVectorOptionKey const abinitio::stage3a_patch ("abinitio:stage3a_patch")
 
FileVectorOptionKey const abinitio::stage3b_patch ("abinitio:stage3b_patch")
 
FileVectorOptionKey const abinitio::stage4_patch ("abinitio:stage4_patch")
 
FileVectorOptionKey const abinitio::stage5_patch ("abinitio:stage5_patch")
 
BooleanOptionKey const abinitio::steal_3mers ("abinitio:steal_3mers")
 
BooleanOptionKey const abinitio::steal_9mers ("abinitio:steal_9mers")
 
BooleanOptionKey const abinitio::no_write_failures ("abinitio:no_write_failures")
 
BooleanOptionKey const abinitio::relax_failures ("abinitio:relax_failures")
 
BooleanOptionKey const abinitio::relax_with_jumps ("abinitio:relax_with_jumps")
 
BooleanOptionKey const abinitio::process_store ("abinitio:process_store")
 
IntegerVectorOptionKey const abinitio::fix_residues_to_native ("abinitio:fix_residues_to_native")
 
BooleanOptionKey const abinitio::return_full_atom ("abinitio:return_full_atom")
 
BooleanOptionKey const abinitio::detect_disulfide_before_relax ("abinitio:detect_disulfide_before_relax")
 
BooleanOptionKey const abinitio::close_loops ("abinitio:close_loops")
 
BooleanOptionKey const abinitio::bGDT ("abinitio:bGDT")
 
BooleanOptionKey const abinitio::dump_frags ("abinitio:dump_frags")
 
BooleanOptionKey const abinitio::jdist_rerun ("abinitio:jdist_rerun")
 
RealOptionKey const abinitio::perturb ("abinitio:perturb")
 
BooleanOptionKey const abinitio::rerun ("abinitio:rerun")
 
IntegerVectorOptionKey const abinitio::rmsd_residues ("abinitio:rmsd_residues")
 
BooleanOptionKey const abinitio::start_native ("abinitio:start_native")
 
BooleanOptionKey const abinitio::debug_structures ("abinitio:debug_structures")
 
FileOptionKey const abinitio::log_frags ("abinitio:log_frags")
 
BooleanOptionKey const abinitio::only_stage1 ("abinitio:only_stage1")
 
RealOptionKey const abinitio::end_bias ("abinitio:end_bias")
 
IntegerOptionKey const abinitio::symmetry_residue ("abinitio:symmetry_residue")
 
RealOptionKey const abinitio::vdw_weight_stage1 ("abinitio:vdw_weight_stage1")
 
BooleanOptionKey const abinitio::override_vdw_all_stages ("abinitio:override_vdw_all_stages")
 
IntegerVectorOptionKey const abinitio::recover_low_in_stages ("abinitio:recover_low_in_stages")
 
IntegerVectorOptionKey const abinitio::skip_stages ("abinitio:skip_stages")
 
BooleanOptionKey const abinitio::close_chbrk ("abinitio:close_chbrk")
 
BooleanOptionKey const abinitio::include_stage5 ("abinitio:include_stage5")
 
BooleanOptionKey const abinitio::close_loops_by_idealizing ("abinitio:close_loops_by_idealizing")
 
BooleanOptionKey const abinitio::optimize_cutpoints_using_kic ("abinitio:optimize_cutpoints_using_kic")
 
IntegerOptionKey const abinitio::optimize_cutpoints_margin ("abinitio:optimize_cutpoints_margin")
 
BooleanOptionKey const abinitio::star::star ("abinitio:star")
 
RealOptionKey const abinitio::star::initial_dist_cutoff ("abinitio:star:initial_dist_cutoff")
 
IntegerOptionKey const abinitio::star::min_unaligned_len ("abinitio:star:min_unaligned_len")
 
BooleanOptionKey const abrelax::abrelax ("abrelax")
 
BooleanOptionKey const abrelax::fail_unclosed ("abrelax:fail_unclosed")
 
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 antibody::antibody ("antibody")
 
StringOptionKey const antibody::numbering_scheme ("antibody:numbering_scheme")
 
StringOptionKey const antibody::cdr_definition ("antibody:cdr_definition")
 
BooleanOptionKey const antibody::check_cdr_chainbreaks ("antibody:check_cdr_chainbreaks")
 
BooleanOptionKey const antibody::check_cdr_pep_bond_geom ("antibody:check_cdr_pep_bond_geom")
 
BooleanOptionKey const antibody::graft_l1 ("antibody:graft_l1")
 
BooleanOptionKey const antibody::graft_l2 ("antibody:graft_l2")
 
BooleanOptionKey const antibody::graft_l3 ("antibody:graft_l3")
 
BooleanOptionKey const antibody::graft_h1 ("antibody:graft_h1")
 
BooleanOptionKey const antibody::graft_h2 ("antibody:graft_h2")
 
BooleanOptionKey const antibody::graft_h3 ("antibody:graft_h3")
 
BooleanOptionKey const antibody::h3_no_stem_graft ("antibody:h3_no_stem_graft")
 
BooleanOptionKey const antibody::packonly_after_graft ("antibody:packonly_after_graft")
 
BooleanOptionKey const antibody::stem_optimize ("antibody:stem_optimize")
 
IntegerOptionKey const antibody::stem_optimize_size ("antibody:stem_optimize_size")
 
StringOptionKey const antibody::preprocessing_script_version ("antibody:preprocessing_script_version")
 
BooleanOptionKey const antibody::model_h3 ("antibody:model_h3")
 
BooleanOptionKey const antibody::snugfit ("antibody:snugfit")
 
BooleanOptionKey const antibody::refine_h3 ("antibody:refine_h3")
 
BooleanOptionKey const antibody::h3_filter ("antibody:h3_filter")
 
RealOptionKey const antibody::h3_filter_tolerance ("antibody:h3_filter_tolerance")
 
BooleanOptionKey const antibody::cter_insert ("antibody:cter_insert")
 
BooleanOptionKey const antibody::flank_residue_min ("antibody:flank_residue_min")
 
BooleanOptionKey const antibody::sc_min ("antibody:sc_min")
 
BooleanOptionKey const antibody::rt_min ("antibody:rt_min")
 
BooleanOptionKey const antibody::bad_nter ("antibody:bad_nter")
 
BooleanOptionKey const antibody::extend_h3_before_modeling ("antibody:extend_h3_before_modeling")
 
BooleanOptionKey const antibody::idealize_h3_stems_before_modeling ("antibody:idealize_h3_stems_before_modeling")
 
StringOptionKey const antibody::remodel ("antibody:remodel")
 
StringOptionKey const antibody::refine ("antibody:refine")
 
StringOptionKey const antibody::centroid_refine ("antibody:centroid_refine")
 
BooleanOptionKey const antibody::constrain_cter ("antibody:constrain_cter")
 
BooleanOptionKey const antibody::constrain_vlvh_qq ("antibody:constrain_vlvh_qq")
 
BooleanOptionKey const antibody::camelid ("antibody:camelid")
 
BooleanOptionKey const antibody::camelid_constraints ("antibody:camelid_constraints")
 
BooleanOptionKey const antibody::design::design ("antibody:design")
 
StringOptionKey const antibody::design::instructions ("antibody:design:instructions")
 
StringOptionKey const antibody::design::antibody_database ("antibody:design:antibody_database")
 
StringVectorOptionKey const antibody::design::design_cdrs ("antibody:design:design_cdrs")
 
BooleanOptionKey const antibody::design::do_graft_design ("antibody:design:do_graft_design")
 
BooleanOptionKey const antibody::design::do_post_graft_design_modeling ("antibody:design:do_post_graft_design_modeling")
 
BooleanOptionKey const antibody::design::do_sequence_design ("antibody:design:do_sequence_design")
 
BooleanOptionKey const antibody::design::do_post_design_modeling ("antibody:design:do_post_design_modeling")
 
IntegerOptionKey const antibody::design::graft_rounds ("antibody:design:graft_rounds")
 
IntegerOptionKey const antibody::design::top_graft_designs ("antibody:design:top_graft_designs")
 
BooleanOptionKey const antibody::design::initial_perturb ("antibody:design:initial_perturb")
 
BooleanOptionKey const antibody::design::use_deterministic ("antibody:design:use_deterministic")
 
BooleanOptionKey const antibody::design::dump_post_graft_designs ("antibody:design:dump_post_graft_designs")
 
RealOptionKey const antibody::design::interface_dis ("antibody:design:interface_dis")
 
RealOptionKey const antibody::design::neighbor_dis ("antibody:design:neighbor_dis")
 
BooleanOptionKey const antibody::design::dock_post_graft ("antibody:design:dock_post_graft")
 
BooleanOptionKey const antibody::design::pack_post_graft ("antibody:design:pack_post_graft")
 
BooleanOptionKey const antibody::design::rb_min_post_graft ("antibody:design:rb_min_post_graft")
 
IntegerOptionKey const antibody::design::dock_rounds ("antibody:design:dock_rounds")
 
StringOptionKey const antibody::design::ab_dock_chains ("antibody:design:ab_dock_chains")
 
StringOptionKey const antibody::design::design_method ("antibody:design:design_method")
 
IntegerOptionKey const antibody::design::design_rounds ("antibody:design:design_rounds")
 
StringOptionKey const antibody::design::design_scorefxn ("antibody:design:design_scorefxn")
 
BooleanOptionKey const antibody::design::benchmark_basic_design ("antibody:design:benchmark_basic_design")
 
IntegerOptionKey const antibody::design::stats_cutoff ("antibody:design:stats_cutoff")
 
IntegerOptionKey const antibody::design::sample_zero_probs_at ("antibody:design:sample_zero_probs_at")
 
BooleanOptionKey const antibody::design::conservative_h3_design ("antibody:design:conservative_h3_design")
 
BooleanOptionKey const antibody::design::turn_conservation ("antibody:design:turn_conservation")
 
BooleanOptionKey const antibody::design::extend_native_cdrs ("antibody:design:extend_native_cdrs")
 
BooleanOptionKey const assembly::assembly ("assembly")
 
FileOptionKey const assembly::pdb1 ("assembly:pdb1")
 
FileOptionKey const assembly::pdb2 ("assembly:pdb2")
 
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 batch_relax::batch_relax ("batch_relax")
 
IntegerOptionKey const batch_relax::batch_size ("batch_relax:batch_size")
 
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 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 broker::broker ("broker")
 
FileVectorOptionKey const broker::setup ("broker:setup")
 
RealOptionKey const broker::rb_mover_stage1_weight ("broker:rb_mover_stage1_weight")
 
RealOptionKey const broker::large_frag_mover_stage1_weight ("broker:large_frag_mover_stage1_weight")
 
RealOptionKey const broker::small_frag_mover_stage1_weight ("broker:small_frag_mover_stage1_weight")
 
BooleanOptionKey const bunsat_calc2::bunsat_calc2 ("bunsat_calc2")
 
RealOptionKey const bunsat_calc2::sasa_burial_cutoff ("bunsat_calc2:sasa_burial_cutoff")
 
BooleanOptionKey const bunsat_calc2::layered_sasa ("bunsat_calc2:layered_sasa")
 
BooleanOptionKey const bunsat_calc2::generous_hbonds ("bunsat_calc2:generous_hbonds")
 
RealOptionKey const bunsat_calc2::AHD_cutoff ("bunsat_calc2:AHD_cutoff")
 
RealOptionKey const bunsat_calc2::dist_cutoff ("bunsat_calc2:dist_cutoff")
 
RealOptionKey const bunsat_calc2::hxl_dist_cutoff ("bunsat_calc2:hxl_dist_cutoff")
 
RealOptionKey const bunsat_calc2::sulph_dist_cutoff ("bunsat_calc2:sulph_dist_cutoff")
 
RealOptionKey const bunsat_calc2::metal_dist_cutoff ("bunsat_calc2:metal_dist_cutoff")
 
BooleanOptionKey const canonical_sampling::canonical_sampling ("canonical_sampling")
 
BooleanOptionKey const canonical_sampling::probabilities::probabilities ("canonical_sampling:probabilities")
 
RealOptionKey const canonical_sampling::probabilities::sc ("canonical_sampling:probabilities:sc")
 
RealOptionKey const canonical_sampling::probabilities::localbb ("canonical_sampling:probabilities:localbb")
 
RealOptionKey const canonical_sampling::probabilities::sc_prob_uniform ("canonical_sampling:probabilities:sc_prob_uniform")
 
RealOptionKey const canonical_sampling::probabilities::sc_prob_withinrot ("canonical_sampling:probabilities:sc_prob_withinrot")
 
RealOptionKey const canonical_sampling::probabilities::sc_prob_perturbcurrent ("canonical_sampling:probabilities:sc_prob_perturbcurrent")
 
BooleanOptionKey const canonical_sampling::probabilities::MPI_sync_pools ("canonical_sampling:probabilities:MPI_sync_pools")
 
BooleanOptionKey const canonical_sampling::probabilities::MPI_bcast ("canonical_sampling:probabilities:MPI_bcast")
 
BooleanOptionKey const canonical_sampling::probabilities::fast_sc_moves ("canonical_sampling:probabilities:fast_sc_moves")
 
RealOptionKey const canonical_sampling::probabilities::fast_sc_moves_ntrials ("canonical_sampling:probabilities:fast_sc_moves_ntrials")
 
BooleanOptionKey const canonical_sampling::probabilities::no_jd2_output ("canonical_sampling:probabilities:no_jd2_output")
 
BooleanOptionKey const canonical_sampling::probabilities::use_hierarchical_clustering ("canonical_sampling:probabilities:use_hierarchical_clustering")
 
RealOptionKey const canonical_sampling::probabilities::backrub ("canonical_sampling:probabilities:backrub")
 
RealOptionKey const canonical_sampling::probabilities::conrot ("canonical_sampling:probabilities:conrot")
 
BooleanOptionKey const canonical_sampling::sampling::sampling ("canonical_sampling:sampling")
 
BooleanOptionKey const canonical_sampling::sampling::no_detailed_balance ("canonical_sampling:sampling:no_detailed_balance")
 
IntegerOptionKey const canonical_sampling::sampling::ntrials ("canonical_sampling:sampling:ntrials")
 
RealOptionKey const canonical_sampling::sampling::mc_kt ("canonical_sampling:sampling:mc_kt")
 
IntegerOptionKey const canonical_sampling::sampling::interval_pose_dump ("canonical_sampling:sampling:interval_pose_dump")
 
IntegerOptionKey const canonical_sampling::sampling::interval_data_dump ("canonical_sampling:sampling:interval_data_dump")
 
BooleanOptionKey const canonical_sampling::sampling::output_only_cluster_transitions ("canonical_sampling:sampling:output_only_cluster_transitions")
 
RealOptionKey const canonical_sampling::sampling::transition_threshold ("canonical_sampling:sampling:transition_threshold")
 
IntegerOptionKey const canonical_sampling::sampling::max_files_per_dir ("canonical_sampling:sampling:max_files_per_dir")
 
BooleanOptionKey const canonical_sampling::sampling::save_loops_only ("canonical_sampling:sampling:save_loops_only")
 
BooleanOptionKey const canonical_sampling::sampling::dump_loops_only ("canonical_sampling:sampling:dump_loops_only")
 
BooleanOptionKey const canonical_sampling::out::out ("canonical_sampling:out")
 
FileOptionKey const canonical_sampling::out::new_structures ("canonical_sampling:out:new_structures")
 
BooleanOptionKey const casp::casp ("casp")
 
RealOptionKey const casp::opt_radius ("casp:opt_radius")
 
BooleanOptionKey const casp::repack ("casp:repack")
 
BooleanOptionKey const casp::sc_min ("casp:sc_min")
 
BooleanOptionKey const casp::sequential ("casp:sequential")
 
RealOptionKey const casp::num_iterations ("casp:num_iterations")
 
StringOptionKey const casp::refine_res ("casp:refine_res")
 
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 chunk::chunk ("chunk")
 
FileOptionKey const chunk::pdb2 ("chunk:pdb2")
 
FileOptionKey const chunk::loop2 ("chunk:loop2")
 
BooleanOptionKey const cluster::cluster ("cluster")
 
BooleanOptionKey const cluster::lite ("cluster:lite")
 
RealOptionKey const cluster::input_score_filter ("cluster:input_score_filter")
 
RealOptionKey const cluster::output_score_filter ("cluster:output_score_filter")
 
IntegerVectorOptionKey const cluster::exclude_res ("cluster:exclude_res")
 
RealOptionKey const cluster::thinout_factor ("cluster:thinout_factor")
 
RealOptionKey const cluster::radius ("cluster:radius")
 
IntegerOptionKey const cluster::limit_cluster_size ("cluster:limit_cluster_size")
 
RealOptionKey const cluster::limit_cluster_size_percent ("cluster:limit_cluster_size_percent")
 
RealOptionKey const cluster::random_limit_cluster_size_percent ("cluster:random_limit_cluster_size_percent")
 
IntegerOptionKey const cluster::limit_clusters ("cluster:limit_clusters")
 
IntegerOptionKey const cluster::limit_total_structures ("cluster:limit_total_structures")
 
IntegerOptionKey const cluster::max_total_cluster ("cluster:max_total_cluster")
 
BooleanOptionKey const cluster::gdtmm ("cluster:gdtmm")
 
BooleanOptionKey const cluster::sort_groups_by_energy ("cluster:sort_groups_by_energy")
 
BooleanOptionKey const cluster::sort_groups_by_size ("cluster:sort_groups_by_size")
 
BooleanOptionKey const cluster::remove_singletons ("cluster:remove_singletons")
 
BooleanOptionKey const cluster::export_only_low ("cluster:export_only_low")
 
BooleanOptionKey const cluster::remove_highest_energy_member ("cluster:remove_highest_energy_member")
 
BooleanOptionKey const cluster::idealize_final_structures ("cluster:idealize_final_structures")
 
IntegerOptionKey const cluster::limit_dist_matrix ("cluster:limit_dist_matrix")
 
BooleanOptionKey const cluster::make_ensemble_cst ("cluster:make_ensemble_cst")
 
BooleanOptionKey const cluster::hotspot_hash ("cluster:hotspot_hash")
 
BooleanOptionKey const cluster::loops ("cluster:loops")
 
RealOptionKey const cluster::population_weight ("cluster:population_weight")
 
StringOptionKey const cluster::template_scores ("cluster:template_scores")
 
IntegerOptionKey const cluster::K_level ("cluster:K_level")
 
RealVectorOptionKey const cluster::K_radius ("cluster:K_radius")
 
IntegerVectorOptionKey const cluster::K_n_cluster ("cluster:K_n_cluster")
 
StringVectorOptionKey const cluster::K_style ("cluster:K_style")
 
IntegerOptionKey const cluster::K_n_sub ("cluster:K_n_sub")
 
IntegerOptionKey const cluster::K_deque_size ("cluster:K_deque_size")
 
IntegerOptionKey const cluster::K_deque_level ("cluster:K_deque_level")
 
BooleanOptionKey const cluster::K_redundant ("cluster:K_redundant")
 
BooleanOptionKey const cluster::K_not_fit_xyz ("cluster:K_not_fit_xyz")
 
BooleanOptionKey const cluster::K_save_headers ("cluster:K_save_headers")
 
RealOptionKey const cluster::score_diff_cut ("cluster:score_diff_cut")
 
BooleanOptionKey const cluster::auto_tune ("cluster:auto_tune")
 
BooleanOptionKey const cm::cm ("cm")
 
BooleanOptionKey const cm::sanitize::sanitize ("cm:sanitize")
 
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::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")
 
FileVectorOptionKey const cm::ev_map ("cm:ev_map")
 
FileVectorOptionKey const cm::hh_map ("cm:hh_map")
 
BooleanOptionKey const cm::hybridize::hybridize ("cm:hybridize")
 
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")
 
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")
 
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::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 contactMap::contactMap ("contactMap")
 
StringOptionKey const contactMap::prefix ("contactMap:prefix")
 
RealOptionKey const contactMap::distance_cutoff ("contactMap:distance_cutoff")
 
RealOptionKey const contactMap::energy_cutoff ("contactMap:energy_cutoff")
 
StringOptionKey const contactMap::region_def ("contactMap:region_def")
 
BooleanOptionKey const contactMap::row_format ("contactMap:row_format")
 
BooleanOptionKey const contactMap::distance_matrix ("contactMap:distance_matrix")
 
BooleanOptionKey const cp::cp ("cp")
 
RealOptionKey const cp::cutoff ("cp:cutoff")
 
StringOptionKey const cp::relax_sfxn ("cp:relax_sfxn")
 
StringOptionKey const cp::pack_sfxn ("cp:pack_sfxn")
 
StringOptionKey const cp::minimizer_score_fxn ("cp:minimizer_score_fxn")
 
StringOptionKey const cp::output ("cp:output")
 
IntegerOptionKey const cp::ncycles ("cp:ncycles")
 
IntegerOptionKey const cp::max_failures ("cp:max_failures")
 
BooleanOptionKey const cp::print_reports ("cp:print_reports")
 
StringOptionKey const cp::vipReportFile ("cp:vipReportFile")
 
StringOptionKey const cp::exclude_file ("cp:exclude_file")
 
StringOptionKey const cp::relax_mover ("cp:relax_mover")
 
BooleanOptionKey const cp::skip_relax ("cp:skip_relax")
 
BooleanOptionKey const cp::local_relax ("cp:local_relax")
 
BooleanOptionKey const cp::print_intermediate_pdbs ("cp:print_intermediate_pdbs")
 
BooleanOptionKey const cp::use_unrelaxed_starting_points ("cp:use_unrelaxed_starting_points")
 
BooleanOptionKey const cp::easy_vip_acceptance ("cp:easy_vip_acceptance")
 
BooleanOptionKey const cryst::cryst ("cryst")
 
StringOptionKey const cryst::mtzfile ("cryst:mtzfile")
 
BooleanOptionKey const cryst::crystal_refine ("cryst:crystal_refine")
 
BooleanOptionKey const csa::csa ("csa")
 
BooleanOptionKey const csa::useZ ("csa:useZ")
 
BooleanOptionKey const cutoutdomain::cutoutdomain ("cutoutdomain")
 
IntegerOptionKey const cutoutdomain::start ("cutoutdomain:start")
 
IntegerOptionKey const cutoutdomain::end ("cutoutdomain:end")
 
BooleanOptionKey const cyclization::cyclization ("cyclization")
 
IntegerVectorOptionKey const cyclization::chains_to_cyclize ("cyclization:chains_to_cyclize")
 
IntegerOptionKey const cyclization::num_min_rebuild ("cyclization:num_min_rebuild")
 
BooleanOptionKey const dc::dc ("dc")
 
BooleanOptionKey const dc::useZ ("dc:useZ")
 
BooleanOptionKey const ddg::ddg ("ddg")
 
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")
 
BooleanOptionKey const ddg::use_rotamer_constraints_to_native ("ddg:use_rotamer_constraints_to_native")
 
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::no_bb_movement ("ddg:no_bb_movement")
 
BooleanOptionKey const ddg::initial_repack ("ddg:initial_repack")
 
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")
 
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::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 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::only_repack ("dna:specificity:only_repack")
 
BooleanOptionKey const dna::specificity::design_DNA ("dna:specificity:design_DNA")
 
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::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_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")
 
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::nopdb ("dna:design:nopdb")
 
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::reversion_scan ("dna:design:reversion_scan")
 
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 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::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 docking::kick_relax ("docking:kick_relax")
 
BooleanOptionKey const docking::docking ("docking")
 
BooleanOptionKey const docking::view ("docking:view")
 
BooleanOptionKey const docking::no_filters ("docking:no_filters")
 
StringVectorOptionKey const docking::design_chains ("docking:design_chains")
 
FileOptionKey const docking::recover_sidechains ("docking:recover_sidechains")
 
StringOptionKey const docking::partners ("docking:partners")
 
BooleanOptionKey const docking::docking_local_refine ("docking:docking_local_refine")
 
BooleanOptionKey const docking::low_res_protocol_only ("docking:low_res_protocol_only")
 
BooleanOptionKey const docking::randomize1 ("docking:randomize1")
 
BooleanOptionKey const docking::randomize2 ("docking:randomize2")
 
BooleanOptionKey const docking::use_ellipsoidal_randomization ("docking:use_ellipsoidal_randomization")
 
BooleanOptionKey const docking::spin ("docking:spin")
 
RealVectorOptionKey const docking::dock_pert ("docking:dock_pert")
 
RealOptionKey const docking::uniform_trans ("docking:uniform_trans")
 
BooleanOptionKey const docking::center_at_interface ("docking:center_at_interface")
 
IntegerOptionKey const docking::dock_mcm_first_cycles ("docking:dock_mcm_first_cycles")
 
IntegerOptionKey const docking::dock_mcm_second_cycles ("docking:dock_mcm_second_cycles")
 
IntegerOptionKey const docking::docking_centroid_outer_cycles ("docking:docking_centroid_outer_cycles")
 
IntegerOptionKey const docking::docking_centroid_inner_cycles ("docking:docking_centroid_inner_cycles")
 
BooleanOptionKey const docking::dock_min ("docking:dock_min")
 
StringOptionKey const docking::flexible_bb_docking ("docking:flexible_bb_docking")
 
RealOptionKey const docking::flexible_bb_docking_interface_dist ("docking:flexible_bb_docking_interface_dist")
 
StringOptionKey const docking::ensemble1 ("docking:ensemble1")
 
StringOptionKey const docking::ensemble2 ("docking:ensemble2")
 
RealOptionKey const docking::dock_mcm_trans_magnitude ("docking:dock_mcm_trans_magnitude")
 
RealOptionKey const docking::dock_mcm_rot_magnitude ("docking:dock_mcm_rot_magnitude")
 
RealOptionKey const docking::minimization_threshold ("docking:minimization_threshold")
 
RealOptionKey const docking::temperature ("docking:temperature")
 
IntegerOptionKey const docking::repack_period ("docking:repack_period")
 
BooleanOptionKey const docking::extra_rottrial ("docking:extra_rottrial")
 
BooleanOptionKey const docking::dock_rtmin ("docking:dock_rtmin")
 
BooleanOptionKey const docking::sc_min ("docking:sc_min")
 
BooleanOptionKey const docking::norepack1 ("docking:norepack1")
 
BooleanOptionKey const docking::norepack2 ("docking:norepack2")
 
IntegerVectorOptionKey const docking::bb_min_res ("docking:bb_min_res")
 
IntegerVectorOptionKey const docking::sc_min_res ("docking:sc_min_res")
 
BooleanOptionKey const docking::dock_ppk ("docking:dock_ppk")
 
IntegerOptionKey const docking::max_repeats ("docking:max_repeats")
 
RealVectorOptionKey const docking::dock_lowres_filter ("docking:dock_lowres_filter")
 
IntegerVectorOptionKey const docking::multibody ("docking:multibody")
 
BooleanOptionKey const docking::ignore_default_docking_task ("docking:ignore_default_docking_task")
 
StringOptionKey const docking::low_patch ("docking:low_patch")
 
StringOptionKey const docking::high_patch ("docking:high_patch")
 
StringOptionKey const docking::high_min_patch ("docking:high_min_patch")
 
StringOptionKey const docking::pack_patch ("docking:pack_patch")
 
BooleanOptionKey const docking::use_legacy_protocol ("docking:use_legacy_protocol")
 
RealOptionKey const docking::docklowres_trans_magnitude ("docking:docklowres_trans_magnitude")
 
RealOptionKey const docking::docklowres_rot_magnitude ("docking:docklowres_rot_magnitude")
 
BooleanOptionKey const docking::ligand::ligand ("docking:ligand")
 
StringOptionKey const docking::ligand::protocol ("docking:ligand:protocol")
 
BooleanOptionKey const docking::ligand::soft_rep ("docking:ligand:soft_rep")
 
BooleanOptionKey const docking::ligand::tweak_sxfn ("docking:ligand:tweak_sxfn")
 
BooleanOptionKey const docking::ligand::old_estat ("docking:ligand:old_estat")
 
BooleanOptionKey const docking::ligand::random_conformer ("docking:ligand:random_conformer")
 
IntegerOptionKey const docking::ligand::improve_orientation ("docking:ligand:improve_orientation")
 
BooleanOptionKey const docking::ligand::mutate_same_name3 ("docking:ligand:mutate_same_name3")
 
RealOptionKey const docking::ligand::subset_to_keep ("docking:ligand:subset_to_keep")
 
RealOptionKey const docking::ligand::min_rms ("docking:ligand:min_rms")
 
IntegerOptionKey const docking::ligand::max_poses ("docking:ligand:max_poses")
 
BooleanOptionKey const docking::ligand::minimize_ligand ("docking:ligand:minimize_ligand")
 
RealOptionKey const docking::ligand::harmonic_torsions ("docking:ligand:harmonic_torsions")
 
BooleanOptionKey const docking::ligand::use_ambig_constraints ("docking:ligand:use_ambig_constraints")
 
IntegerOptionKey const docking::ligand::shear_moves ("docking:ligand:shear_moves")
 
BooleanOptionKey const docking::ligand::minimize_backbone ("docking:ligand:minimize_backbone")