Rosetta 3.3
Namespaces | Functions
src/basic/options/keys/OptionKeys.cc.gen3.hh File Reference

Namespaces

namespace  DenovoProteinDesign
namespace  RBSegmentRelax
namespace  edensity
namespace  patterson
namespace  optE
namespace  optE::rescore
namespace  backrub
namespace  bbg
namespace  flexpack
namespace  flexpack::annealer
namespace  hotspot
namespace  parser
namespace  DomainAssembly
namespace  remodel
namespace  remodel::domainFusion
namespace  remodel::design
namespace  remodel::RemodelLoopMover
namespace  fold_from_loops
namespace  symmetry
namespace  fold_and_dock
namespace  match
namespace  canonical_sampling
namespace  canonical_sampling::probabilities
namespace  canonical_sampling::sampling
namespace  canonical_sampling::out
namespace  rdc
namespace  antibody
namespace  flexPepDocking
namespace  threadsc
namespace  archive
namespace  optimization
namespace  ufv
namespace  ufv::insert
namespace  chrisk
namespace  rot_anl
namespace  pepspec
namespace  orbitals
namespace  dwkulp
namespace  matdes
namespace  matdes::dock
namespace  matdes::design

Functions

BooleanOptionKey const DenovoProteinDesign::disallow_native_aa ("DenovoProteinDesign:disallow_native_aa")
BooleanOptionKey const DenovoProteinDesign::optimize_loops ("DenovoProteinDesign:optimize_loops")
FileOptionKey const DenovoProteinDesign::secondary_structure_file ("DenovoProteinDesign:secondary_structure_file")
FileOptionKey const DenovoProteinDesign::hydrophobic_polar_pattern ("DenovoProteinDesign:hydrophobic_polar_pattern")
BooleanOptionKey const DenovoProteinDesign::use_template_sequence ("DenovoProteinDesign:use_template_sequence")
BooleanOptionKey const DenovoProteinDesign::use_template_topology ("DenovoProteinDesign:use_template_topology")
FileOptionKey const DenovoProteinDesign::create_from_template_pdb ("DenovoProteinDesign:create_from_template_pdb")
BooleanOptionKey const DenovoProteinDesign::create_from_secondary_structure ("DenovoProteinDesign:create_from_secondary_structure")
BooleanOptionKey const RBSegmentRelax::RBSegmentRelax ("RBSegmentRelax")
FileOptionKey const RBSegmentRelax::input_pdb ("RBSegmentRelax:input_pdb")
FileOptionKey const RBSegmentRelax::rb_file ("RBSegmentRelax:rb_file")
RealOptionKey const RBSegmentRelax::cst_wt ("RBSegmentRelax:cst_wt")
RealOptionKey const RBSegmentRelax::cst_width ("RBSegmentRelax:cst_width")
StringOptionKey const RBSegmentRelax::cst_pdb ("RBSegmentRelax:cst_pdb")
IntegerOptionKey const RBSegmentRelax::nrbmoves ("RBSegmentRelax:nrbmoves")
IntegerOptionKey const RBSegmentRelax::nrboutercycles ("RBSegmentRelax:nrboutercycles")
StringOptionKey const RBSegmentRelax::rb_scorefxn ("RBSegmentRelax:rb_scorefxn")
BooleanOptionKey const RBSegmentRelax::skip_fragment_moves ("RBSegmentRelax:skip_fragment_moves")
BooleanOptionKey const RBSegmentRelax::skip_seqshift_moves ("RBSegmentRelax:skip_seqshift_moves")
BooleanOptionKey const RBSegmentRelax::skip_rb_moves ("RBSegmentRelax:skip_rb_moves")
RealVectorOptionKey const RBSegmentRelax::helical_movement_params ("RBSegmentRelax:helical_movement_params")
RealVectorOptionKey const RBSegmentRelax::strand_movement_params ("RBSegmentRelax:strand_movement_params")
RealVectorOptionKey const RBSegmentRelax::default_movement_params ("RBSegmentRelax:default_movement_params")
IntegerOptionKey const RBSegmentRelax::cst_seqwidth ("RBSegmentRelax:cst_seqwidth")
BooleanOptionKey const edensity::edensity ("edensity")
BooleanOptionKey const edensity::debug ("edensity:debug")
StringOptionKey const edensity::mapfile ("edensity:mapfile")
RealOptionKey const edensity::mapreso ("edensity:mapreso")
RealOptionKey const edensity::grid_spacing ("edensity:grid_spacing")
RealOptionKey const edensity::centroid_density_mass ("edensity:centroid_density_mass")
IntegerOptionKey const edensity::sliding_window ("edensity:sliding_window")
RealOptionKey const edensity::sliding_window_wt ("edensity:sliding_window_wt")
RealOptionKey const edensity::whole_structure_ca_wt ("edensity:whole_structure_ca_wt")
RealOptionKey const edensity::whole_structure_allatom_wt ("edensity:whole_structure_allatom_wt")
BooleanOptionKey const edensity::no_edens_in_minimizer ("edensity:no_edens_in_minimizer")
BooleanOptionKey const edensity::debug_derivatives ("edensity:debug_derivatives")
StringOptionKey const edensity::realign ("edensity:realign")
StringOptionKey const edensity::membrane_axis ("edensity:membrane_axis")
RealOptionKey const edensity::atom_mask ("edensity:atom_mask")
RealOptionKey const edensity::ca_mask ("edensity:ca_mask")
BooleanOptionKey const edensity::score_symm_complex ("edensity:score_symm_complex")
RealOptionKey const edensity::sc_scaling ("edensity:sc_scaling")
RealOptionKey const edensity::render_sigma ("edensity:render_sigma")
BooleanOptionKey const patterson::patterson ("patterson")
BooleanOptionKey const patterson::debug ("patterson:debug")
RealOptionKey const patterson::weight ("patterson:weight")
RealOptionKey const patterson::sc_scaling ("patterson:sc_scaling")
RealVectorOptionKey const patterson::radius_cutoffs ("patterson:radius_cutoffs")
RealVectorOptionKey const patterson::resolution_cutoffs ("patterson:resolution_cutoffs")
RealOptionKey const patterson::Bsol ("patterson:Bsol")
RealOptionKey const patterson::Fsol ("patterson:Fsol")
RealOptionKey const patterson::model_B ("patterson:model_B")
RealOptionKey const patterson::rmsd ("patterson:rmsd")
BooleanOptionKey const patterson::no_ecalc ("patterson:no_ecalc")
IntegerOptionKey const patterson::nshells ("patterson:nshells")
BooleanOptionKey const patterson::use_spline_interpolation ("patterson:use_spline_interpolation")
BooleanOptionKey const patterson::use_on_repack ("patterson:use_on_repack")
BooleanOptionKey const patterson::dont_use_symm_in_pcalc ("patterson:dont_use_symm_in_pcalc")
BooleanOptionKey const optE::optE ("optE")
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_hack_elec ("optE:optE_no_protein_hack_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::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 backrub::backrub ("backrub")
IntegerVectorOptionKey const backrub::pivot_residues ("backrub:pivot_residues")
StringVectorOptionKey const backrub::pivot_atoms ("backrub:pivot_atoms")
IntegerOptionKey const backrub::min_atoms ("backrub:min_atoms")
IntegerOptionKey const backrub::max_atoms ("backrub:max_atoms")
BooleanOptionKey const bbg::bbg ("bbg")
RealOptionKey const bbg::factorA ("bbg:factorA")
RealOptionKey const bbg::factorB ("bbg:factorB")
BooleanOptionKey const bbg::ignore_improper_res ("bbg:ignore_improper_res")
BooleanOptionKey const bbg::fix_short_segment ("bbg:fix_short_segment")
BooleanOptionKey const flexpack::flexpack ("flexpack")
BooleanOptionKey const flexpack::annealer::annealer ("flexpack:annealer")
RealOptionKey const flexpack::annealer::inner_iteration_scale ("flexpack:annealer:inner_iteration_scale")
RealOptionKey const flexpack::annealer::outer_iteration_scale ("flexpack:annealer:outer_iteration_scale")
RealOptionKey const flexpack::annealer::fixbb_substitutions_scale ("flexpack:annealer:fixbb_substitutions_scale")
RealOptionKey const flexpack::annealer::pure_movebb_substitutions_scale ("flexpack:annealer:pure_movebb_substitutions_scale")
RealOptionKey const flexpack::annealer::rotsub_movebb_substitutions_scale ("flexpack:annealer:rotsub_movebb_substitutions_scale")
BooleanOptionKey const hotspot::hotspot ("hotspot")
BooleanOptionKey const hotspot::allow_gly ("hotspot:allow_gly")
BooleanOptionKey const hotspot::allow_proline ("hotspot:allow_proline")
BooleanOptionKey const hotspot::benchmark ("hotspot:benchmark")
StringVectorOptionKey const hotspot::residue ("hotspot:residue")
FileOptionKey const hotspot::hashfile ("hotspot:hashfile")
FileOptionKey const hotspot::target ("hotspot:target")
IntegerOptionKey const hotspot::target_res ("hotspot:target_res")
RealOptionKey const hotspot::target_dist ("hotspot:target_dist")
FileOptionKey const hotspot::density ("hotspot:density")
FileOptionKey const hotspot::weighted_density ("hotspot:weighted_density")
FileOptionKey const hotspot::rms_target ("hotspot:rms_target")
FileOptionKey const hotspot::rms_hotspot ("hotspot:rms_hotspot")
IntegerOptionKey const hotspot::rms_hotspot_res ("hotspot:rms_hotspot_res")
BooleanOptionKey const hotspot::rescore ("hotspot:rescore")
RealOptionKey const hotspot::threshold ("hotspot:threshold")
BooleanOptionKey const hotspot::sc_only ("hotspot:sc_only")
BooleanOptionKey const hotspot::fxnal_group ("hotspot:fxnal_group")
BooleanOptionKey const hotspot::cluster ("hotspot:cluster")
BooleanOptionKey const hotspot::colonyE ("hotspot:colonyE")
IntegerOptionKey const hotspot::length ("hotspot:length")
BooleanOptionKey const hotspot::envhb ("hotspot:envhb")
RealOptionKey const hotspot::angle ("hotspot:angle")
IntegerOptionKey const hotspot::angle_res ("hotspot:angle_res")
BooleanOptionKey const parser::parser ("parser")
StringOptionKey const parser::protocol ("parser:protocol")
StringVectorOptionKey const parser::script_vars ("parser:script_vars")
BooleanOptionKey const parser::view ("parser:view")
StringOptionKey const parser::patchdock ("parser:patchdock")
IntegerVectorOptionKey const parser::patchdock_random_entry ("parser:patchdock_random_entry")
BooleanOptionKey const DomainAssembly::DomainAssembly ("DomainAssembly")
BooleanOptionKey const DomainAssembly::da_setup ("DomainAssembly:da_setup")
FileOptionKey const DomainAssembly::da_setup_option_file ("DomainAssembly:da_setup_option_file")
FileOptionKey const DomainAssembly::da_setup_output_pdb ("DomainAssembly:da_setup_output_pdb")
FileOptionKey const DomainAssembly::da_linker_file ("DomainAssembly:da_linker_file")
FileOptionKey const DomainAssembly::da_start_pdb ("DomainAssembly:da_start_pdb")
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")
BooleanOptionKey const remodel::remodel ("remodel")
BooleanOptionKey const remodel::help ("remodel:help")
BooleanOptionKey const remodel::autopilot ("remodel:autopilot")
FileOptionKey const remodel::blueprint ("remodel:blueprint")
FileOptionKey const remodel::cstfile ("remodel:cstfile")
IntegerOptionKey const remodel::num_trajectory ("remodel:num_trajectory")
IntegerOptionKey const remodel::save_top ("remodel:save_top")
BooleanOptionKey const remodel::swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols")
IntegerOptionKey const remodel::num_frag_moves ("remodel:num_frag_moves")
BooleanOptionKey const remodel::bypass_fragments ("remodel:bypass_fragments")
BooleanOptionKey const remodel::use_same_length_fragments ("remodel:use_same_length_fragments")
BooleanOptionKey const remodel::enable_ligand_aa ("remodel:enable_ligand_aa")
BooleanOptionKey const remodel::no_jumps ("remodel:no_jumps")
BooleanOptionKey const remodel::backrub ("remodel:backrub")
BooleanOptionKey const remodel::use_blueprint_sequence ("remodel:use_blueprint_sequence ")
BooleanOptionKey const remodel::randomize_equivalent_fragments ("remodel:randomize_equivalent_fragments ")
BooleanOptionKey const remodel::quick_and_dirty ("remodel:quick_and_dirty ")
BooleanOptionKey const remodel::checkpoint ("remodel:checkpoint ")
BooleanOptionKey const remodel::use_ccd_refine ("remodel:use_ccd_refine ")
BooleanOptionKey const remodel::use_pose_relax ("remodel:use_pose_relax ")
BooleanOptionKey const remodel::use_dssp_assignment ("remodel:use_dssp_assignment")
BooleanOptionKey const remodel::keep_jumps_in_minimizer ("remodel:keep_jumps_in_minimizer ")
FileOptionKey const remodel::output_fragfiles ("remodel:output_fragfiles")
FileOptionKey const remodel::read_fragfile ("remodel:read_fragfile")
StringOptionKey const remodel::generic_aa ("remodel:generic_aa")
RealOptionKey const remodel::cluster_radius ("remodel:cluster_radius")
BooleanOptionKey const remodel::use_clusters ("remodel:use_clusters")
BooleanOptionKey const remodel::run_confirmation ("remodel:run_confirmation")
BooleanOptionKey const remodel::cluster_on_entire_pose ("remodel:cluster_on_entire_pose")
IntegerOptionKey const remodel::collect_clustered_top ("remodel:collect_clustered_top")
IntegerOptionKey const remodel::dr_cycles ("remodel:dr_cycles")
IntegerOptionKey const remodel::two_chain_tree ("remodel:two_chain_tree")
BooleanOptionKey const remodel::domainFusion::domainFusion ("remodel:domainFusion")
FileOptionKey const remodel::domainFusion::insert_segment_from_pdb ("remodel:domainFusion:insert_segment_from_pdb")
RealOptionKey const remodel::hb_lrbb ("remodel:hb_lrbb")
RealOptionKey const remodel::hb_srbb ("remodel:hb_srbb")
RealOptionKey const remodel::rg ("remodel:rg")
RealOptionKey const remodel::rsigma ("remodel:rsigma")
RealOptionKey const remodel::ss_pair ("remodel:ss_pair")
BooleanOptionKey const remodel::build_disulf ("remodel:build_disulf")
IntegerOptionKey const remodel::max_disulf_allowed ("remodel:max_disulf_allowed")
RealOptionKey const remodel::match_rt_limit ("remodel:match_rt_limit")
IntegerVectorOptionKey const remodel::disulf_landing_range ("remodel:disulf_landing_range")
BooleanOptionKey const remodel::design::design ("remodel:design")
BooleanOptionKey const remodel::design::no_design ("remodel:design:no_design ")
BooleanOptionKey const remodel::design::silent ("remodel:design:silent")
BooleanOptionKey const remodel::design::skip_partial ("remodel:design:skip_partial")
BooleanOptionKey const remodel::design::design_neighbors ("remodel:design:design_neighbors")
BooleanOptionKey const remodel::design::find_neighbors ("remodel:design:find_neighbors")
BooleanOptionKey const remodel::RemodelLoopMover::RemodelLoopMover ("remodel:RemodelLoopMover")
IntegerOptionKey const remodel::RemodelLoopMover::max_linear_chainbreak ("remodel:RemodelLoopMover:max_linear_chainbreak")
BooleanOptionKey const remodel::RemodelLoopMover::randomize_loops ("remodel:RemodelLoopMover:randomize_loops")
IntegerOptionKey const remodel::RemodelLoopMover::allowed_closure_attempts ("remodel:RemodelLoopMover:allowed_closure_attempts")
IntegerOptionKey const remodel::RemodelLoopMover::simultaneous_cycles ("remodel:RemodelLoopMover:simultaneous_cycles")
IntegerOptionKey const remodel::RemodelLoopMover::independent_cycles ("remodel:RemodelLoopMover:independent_cycles")
IntegerOptionKey const remodel::RemodelLoopMover::lockdown_cycles ("remodel:RemodelLoopMover:lockdown_cycles")
BooleanOptionKey const remodel::RemodelLoopMover::force_cutting_N ("remodel:RemodelLoopMover:force_cutting_N")
BooleanOptionKey const remodel::RemodelLoopMover::bypass_closure ("remodel:RemodelLoopMover:bypass_closure")
BooleanOptionKey const remodel::rank_by_bsasa ("remodel:rank_by_bsasa")
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 symmetry::symmetry ("symmetry")
StringOptionKey const symmetry::symmetry_definition ("symmetry:symmetry_definition")
BooleanOptionKey const symmetry::initialize_rigid_body_dofs ("symmetry:initialize_rigid_body_dofs")
RealVectorOptionKey const symmetry::perturb_rigid_body_dofs ("symmetry:perturb_rigid_body_dofs")
BooleanOptionKey const symmetry::symmetric_rmsd ("symmetry:symmetric_rmsd")
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::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 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 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")
IntegerOptionKey const canonical_sampling::probabilities::hierarchical_max_cache_size ("canonical_sampling:probabilities:hierarchical_max_cache_size")
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 rdc::rdc ("rdc")
BooleanOptionKey const rdc::correct_NH_length ("rdc:correct_NH_length")
BooleanOptionKey const rdc::reduced_couplings ("rdc:reduced_couplings")
FileOptionKey const rdc::weights ("rdc:weights")
RealOptionKey const rdc::iterate_weights ("rdc:iterate_weights")
FileOptionKey const rdc::segment_file ("rdc:segment_file")
StringOptionKey const rdc::segment_scoring_mode ("rdc:segment_scoring_mode")
RealOptionKey const rdc::total_weight ("rdc:total_weight")
RealOptionKey const rdc::tensor_weight ("rdc:tensor_weight")
FileOptionKey const rdc::print_rdc_values ("rdc:print_rdc_values")
RealOptionKey const rdc::iterate_tol ("rdc:iterate_tol")
BooleanOptionKey const rdc::iterate_reset ("rdc:iterate_reset")
FileOptionKey const rdc::dump_weight_trajectory ("rdc:dump_weight_trajectory")
RealVectorOptionKey const rdc::fix_normAzz ("rdc:fix_normAzz")
FileOptionKey const rdc::select_residues_file ("rdc:select_residues_file")
BooleanOptionKey const antibody::antibody ("antibody")
BooleanOptionKey const antibody::graft_l1 ("antibody:graft_l1")
StringOptionKey const antibody::l1_template ("antibody:l1_template")
BooleanOptionKey const antibody::graft_l2 ("antibody:graft_l2")
StringOptionKey const antibody::l2_template ("antibody:l2_template")
BooleanOptionKey const antibody::graft_l3 ("antibody:graft_l3")
StringOptionKey const antibody::l3_template ("antibody:l3_template")
BooleanOptionKey const antibody::graft_h1 ("antibody:graft_h1")
StringOptionKey const antibody::h1_template ("antibody:h1_template")
BooleanOptionKey const antibody::graft_h2 ("antibody:graft_h2")
StringOptionKey const antibody::h2_template ("antibody:h2_template")
BooleanOptionKey const antibody::graft_h3 ("antibody:graft_h3")
StringOptionKey const antibody::h3_template ("antibody:h3_template")
BooleanOptionKey const antibody::model_h3 ("antibody:model_h3")
BooleanOptionKey const antibody::snugfit ("antibody:snugfit")
BooleanOptionKey const antibody::snug_loops ("antibody:snug_loops")
FileOptionKey const antibody::input_fv ("antibody:input_fv")
BooleanOptionKey const antibody::camelid ("antibody:camelid")
BooleanOptionKey const antibody::camelid_constraints ("antibody:camelid_constraints")
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 threadsc::threadsc ("threadsc")
StringOptionKey const threadsc::src_chain ("threadsc:src_chain")
StringOptionKey const threadsc::trg_chain ("threadsc:trg_chain")
IntegerOptionKey const threadsc::src_first_resid ("threadsc:src_first_resid")
IntegerOptionKey const threadsc::trg_first_resid ("threadsc:trg_first_resid")
IntegerOptionKey const threadsc::nres ("threadsc:nres")
IntegerOptionKey const threadsc::trg_anchor ("threadsc:trg_anchor")
BooleanOptionKey const archive::archive ("archive")
BooleanOptionKey const archive::reread_all_structures ("archive:reread_all_structures")
IntegerOptionKey const archive::completion_notify_frequency ("archive:completion_notify_frequency")
BooleanOptionKey const optimization::optimization ("optimization")
IntegerOptionKey const optimization::dfpmin_max_cycles ("optimization:dfpmin_max_cycles")
RealOptionKey const optimization::armijo_min_stepsize ("optimization:armijo_min_stepsize")
IntegerOptionKey const optimization::lbfgs_max_cycles ("optimization:lbfgs_max_cycles")
IntegerOptionKey const optimization::lbfgs_M ("optimization:lbfgs_M")
BooleanOptionKey const ufv::ufv ("ufv")
IntegerOptionKey const ufv::left ("ufv:left")
IntegerOptionKey const ufv::right ("ufv:right")
StringOptionKey const ufv::ss ("ufv:ss")
StringOptionKey const ufv::aa_during_build ("ufv:aa_during_build")
StringOptionKey const ufv::aa_during_design_refine ("ufv:aa_during_design_refine")
BooleanOptionKey const ufv::keep_junction_torsions ("ufv:keep_junction_torsions")
FileOptionKey const ufv::ufv_loops ("ufv:ufv_loops")
BooleanOptionKey const ufv::use_fullmer ("ufv:use_fullmer")
StringOptionKey const ufv::centroid_loop_mover ("ufv:centroid_loop_mover")
BooleanOptionKey const ufv::no_neighborhood_design ("ufv:no_neighborhood_design")
IntegerOptionKey const ufv::dr_cycles ("ufv:dr_cycles")
StringOptionKey const ufv::centroid_sfx ("ufv:centroid_sfx")
StringOptionKey const ufv::centroid_sfx_patch ("ufv:centroid_sfx_patch")
StringOptionKey const ufv::fullatom_sfx ("ufv:fullatom_sfx")
StringOptionKey const ufv::fullatom_sfx_patch ("ufv:fullatom_sfx_patch")
BooleanOptionKey const ufv::insert::insert ("ufv:insert")
FileOptionKey const ufv::insert::insert_pdb ("ufv:insert:insert_pdb")
FileOptionKey const ufv::insert::attached_pdb ("ufv:insert:attached_pdb")
StringOptionKey const ufv::insert::connection_scheme ("ufv:insert:connection_scheme")
BooleanOptionKey const chrisk::chrisk ("chrisk")
BooleanOptionKey const chrisk::hb_elec ("chrisk:hb_elec")
BooleanOptionKey const rot_anl::rot_anl ("rot_anl")
StringOptionKey const rot_anl::tag ("rot_anl:tag")
BooleanOptionKey const rot_anl::premin ("rot_anl:premin")
BooleanOptionKey const rot_anl::min ("rot_anl:min")
BooleanOptionKey const rot_anl::diff_to_min ("rot_anl:diff_to_min")
BooleanOptionKey const rot_anl::repack ("rot_anl:repack")
BooleanOptionKey const rot_anl::rtmin ("rot_anl:rtmin")
BooleanOptionKey const rot_anl::scmove ("rot_anl:scmove")
BooleanOptionKey const rot_anl::design ("rot_anl:design")
RealOptionKey const rot_anl::score_tol ("rot_anl:score_tol")
RealOptionKey const rot_anl::rmsd_tol ("rot_anl:rmsd_tol")
BooleanOptionKey const rot_anl::dump_pdb ("rot_anl:dump_pdb")
IntegerOptionKey const rot_anl::nloop_scmove ("rot_anl:nloop_scmove")
BooleanOptionKey const pepspec::pepspec ("pepspec")
StringOptionKey const pepspec::soft_wts ("pepspec:soft_wts")
StringOptionKey const pepspec::cen_wts ("pepspec:cen_wts")
BooleanOptionKey const pepspec::binding_score ("pepspec:binding_score")
BooleanOptionKey const pepspec::no_cen ("pepspec:no_cen")
BooleanOptionKey const pepspec::no_cen_rottrials ("pepspec:no_cen_rottrials")
BooleanOptionKey const pepspec::run_sequential ("pepspec:run_sequential")
IntegerOptionKey const pepspec::pep_anchor ("pepspec:pep_anchor")
StringOptionKey const pepspec::pep_chain ("pepspec:pep_chain")
IntegerOptionKey const pepspec::n_peptides ("pepspec:n_peptides")
IntegerOptionKey const pepspec::n_build_loop ("pepspec:n_build_loop")
IntegerOptionKey const pepspec::n_cgrelax_loop ("pepspec:n_cgrelax_loop")
IntegerOptionKey const pepspec::n_dock_loop ("pepspec:n_dock_loop")
RealOptionKey const pepspec::interface_cutoff ("pepspec:interface_cutoff")
BooleanOptionKey const pepspec::use_input_bb ("pepspec:use_input_bb")
BooleanOptionKey const pepspec::remove_input_bb ("pepspec:remove_input_bb")
StringOptionKey const pepspec::homol_csts ("pepspec:homol_csts")
RealOptionKey const pepspec::p_homol_csts ("pepspec:p_homol_csts")
StringOptionKey const pepspec::frag_file ("pepspec:frag_file")
BooleanOptionKey const pepspec::gen_pep_bb_sequential ("pepspec:gen_pep_bb_sequential")
StringOptionKey const pepspec::input_seq ("pepspec:input_seq")
StringOptionKey const pepspec::ss_type ("pepspec:ss_type")
BooleanOptionKey const pepspec::upweight_interface ("pepspec:upweight_interface")
BooleanOptionKey const pepspec::calc_sasa ("pepspec:calc_sasa")
BooleanOptionKey const pepspec::diversify_pep_seqs ("pepspec:diversify_pep_seqs")
IntegerOptionKey const pepspec::diversify_lvl ("pepspec:diversify_lvl")
BooleanOptionKey const pepspec::dump_cg_bb ("pepspec:dump_cg_bb")
BooleanOptionKey const pepspec::save_low_pdbs ("pepspec:save_low_pdbs")
BooleanOptionKey const pepspec::save_all_pdbs ("pepspec:save_all_pdbs")
BooleanOptionKey const pepspec::no_design ("pepspec:no_design")
StringOptionKey const pepspec::pdb_list ("pepspec:pdb_list")
StringOptionKey const pepspec::ref_pdb_list ("pepspec:ref_pdb_list")
BooleanOptionKey const pepspec::add_buffer_res ("pepspec:add_buffer_res")
StringOptionKey const pepspec::cg_res_type ("pepspec:cg_res_type")
IntegerOptionKey const pepspec::native_pep_anchor ("pepspec:native_pep_anchor")
StringOptionKey const pepspec::native_pep_chain ("pepspec:native_pep_chain")
BooleanOptionKey const pepspec::native_align ("pepspec:native_align")
BooleanOptionKey const pepspec::rmsd_analysis ("pepspec:rmsd_analysis")
BooleanOptionKey const pepspec::phipsi_analysis ("pepspec:phipsi_analysis")
StringOptionKey const pepspec::anchor_type ("pepspec:anchor_type")
BooleanOptionKey const pepspec::no_prepack_prot ("pepspec:no_prepack_prot")
BooleanOptionKey const pepspec::prep_use_ref_rotamers ("pepspec:prep_use_ref_rotamers")
IntegerOptionKey const pepspec::n_prepend ("pepspec:n_prepend")
IntegerOptionKey const pepspec::n_append ("pepspec:n_append")
RealOptionKey const pepspec::clash_cutoff ("pepspec:clash_cutoff")
RealOptionKey const pepspec::n_anchor_dock_std_devs ("pepspec:n_anchor_dock_std_devs")
RealOptionKey const pepspec::prep_trans_std_dev ("pepspec:prep_trans_std_dev")
RealOptionKey const pepspec::prep_rot_std_dev ("pepspec:prep_rot_std_dev")
BooleanOptionKey const pepspec::seq_align ("pepspec:seq_align")
StringOptionKey const pepspec::prep_align_prot_to ("pepspec:prep_align_prot_to")
BooleanOptionKey const orbitals::orbitals ("orbitals")
BooleanOptionKey const orbitals::Hpol ("orbitals:Hpol")
BooleanOptionKey const orbitals::Haro ("orbitals:Haro")
BooleanOptionKey const orbitals::orbital ("orbitals:orbital")
RealOptionKey const orbitals::atomic_cutoff ("orbitals:atomic_cutoff")
BooleanOptionKey const orbitals::verbose ("orbitals:verbose")
BooleanOptionKey const orbitals::bb_stats ("orbitals:bb_stats")
BooleanOptionKey const orbitals::sc_stats ("orbitals:sc_stats")
BooleanOptionKey const orbitals::orb_orb_stats ("orbitals:orb_orb_stats")
BooleanOptionKey const orbitals::threeA ("orbitals:threeA")
BooleanOptionKey const orbitals::fiveA ("orbitals:fiveA")
BooleanOptionKey const orbitals::no_pos_bonus ("orbitals:no_pos_bonus")
BooleanOptionKey const orbitals::sc_bb ("orbitals:sc_bb")
BooleanOptionKey const orbitals::ten ("orbitals:ten")
BooleanOptionKey const orbitals::dist ("orbitals:dist")
RealOptionKey const orbitals::nbr_distance_squared ("orbitals:nbr_distance_squared")
BooleanOptionKey const orbitals::bb_smooth ("orbitals:bb_smooth")
BooleanOptionKey const dwkulp::dwkulp ("dwkulp")
StringOptionKey const dwkulp::forcePolyAAfragments ("dwkulp:forcePolyAAfragments")
BooleanOptionKey const matdes::matdes ("matdes")
BooleanOptionKey const matdes::dock::dock ("matdes:dock")
RealVectorOptionKey const matdes::dock::radial_disp ("matdes:dock:radial_disp")
RealOptionKey const matdes::dock::neg_r ("matdes:dock:neg_r")
RealVectorOptionKey const matdes::dock::angle ("matdes:dock:angle")
BooleanOptionKey const matdes::dock::dump_pdb ("matdes:dock:dump_pdb")
BooleanOptionKey const matdes::dock::dump_chainA_only ("matdes:dock:dump_chainA_only")
StringOptionKey const matdes::dock::pdbID ("matdes:dock:pdbID")
StringOptionKey const matdes::dock::prefix ("matdes:dock:prefix")
IntegerOptionKey const matdes::dock::num_subs_building_block ("matdes:dock:num_subs_building_block")
IntegerOptionKey const matdes::dock::num_subs_total ("matdes:dock:num_subs_total")
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")
IntegerOptionKey const matdes::design::num_subs_building_block ("matdes:design:num_subs_building_block")
RealOptionKey const matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus")
IntegerVectorOptionKey const matdes::design::revert_pos ("matdes:design:revert_pos")
StringVectorOptionKey const matdes::design::revert_ids ("matdes:design:revert_ids")
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