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OptionKeys.cc.gen9.hh File Reference

Namespaces

 fold_from_loops
 
 frags
 
 frags::scoring
 
 frags::picking
 
 frags::nonlocal
 
 frags::contacts
 
 frags::ABEGO
 
 helical_bundle_predict
 
 holes
 
 hotspot
 
 indexed_structure_store
 
 lh
 
 lh::fragpdb
 
 lh::symfragrm
 
 loopfcst
 
 LoopModel
 
 make_rot_lib
 
 make_mainchain_potential
 
 match
 
 matdes
 
 matdes::dock
 
 matdes::design
 

Functions

IntegerOptionKey const fold_from_loops::loop_mov_nterm ("fold_from_loops:loop_mov_nterm")
 
IntegerOptionKey const fold_from_loops::loop_mov_cterm ("fold_from_loops:loop_mov_cterm")
 
RealOptionKey const fold_from_loops::ca_rmsd_cutoff ("fold_from_loops:ca_rmsd_cutoff")
 
IntegerVectorOptionKey const fold_from_loops::res_design_bs ("fold_from_loops:res_design_bs")
 
FileOptionKey const fold_from_loops::clear_csts ("fold_from_loops:clear_csts")
 
BooleanOptionKey const fold_from_loops::output_centroid ("fold_from_loops:output_centroid")
 
BooleanOptionKey const fold_from_loops::add_cst_loop ("fold_from_loops:add_cst_loop")
 
BooleanOptionKey const frags::frags ("frags")
 
IntegerOptionKey const frags::j ("frags:j")
 
BooleanOptionKey const frags::filter_JC ("frags:filter_JC")
 
BooleanOptionKey const frags::bounded_protocol ("frags:bounded_protocol")
 
BooleanOptionKey const frags::keep_all_protocol ("frags:keep_all_protocol")
 
BooleanOptionKey const frags::quota_protocol ("frags:quota_protocol")
 
BooleanOptionKey const frags::nonlocal_pairs ("frags:nonlocal_pairs")
 
BooleanOptionKey const frags::fragment_contacts ("frags:fragment_contacts")
 
BooleanOptionKey const frags::p_value_selection ("frags:p_value_selection")
 
IntegerOptionKey const frags::n_frags ("frags:n_frags")
 
FileOptionKey const frags::allowed_pdb ("frags:allowed_pdb")
 
StringVectorOptionKey const frags::ss_pred ("frags:ss_pred")
 
FileOptionKey const frags::spine_x ("frags:spine_x")
 
FileOptionKey const frags::depth ("frags:depth")
 
FileOptionKey const frags::denied_pdb ("frags:denied_pdb")
 
IntegerVectorOptionKey const frags::frag_sizes ("frags:frag_sizes")
 
BooleanOptionKey const frags::write_ca_coordinates ("frags:write_ca_coordinates")
 
BooleanOptionKey const frags::write_scores ("frags:write_scores")
 
BooleanOptionKey const frags::annotate ("frags:annotate")
 
IntegerOptionKey const frags::nr_large_copies ("frags:nr_large_copies")
 
IntegerOptionKey const frags::n_candidates ("frags:n_candidates")
 
BooleanOptionKey const frags::write_rama_tables ("frags:write_rama_tables")
 
RealOptionKey const frags::rama_C ("frags:rama_C")
 
RealOptionKey const frags::rama_B ("frags:rama_B")
 
RealOptionKey const frags::sigmoid_cs_A ("frags:sigmoid_cs_A")
 
RealOptionKey const frags::sigmoid_cs_B ("frags:sigmoid_cs_B")
 
RealOptionKey const frags::seqsim_H ("frags:seqsim_H")
 
RealOptionKey const frags::seqsim_E ("frags:seqsim_E")
 
RealOptionKey const frags::seqsim_L ("frags:seqsim_L")
 
RealOptionKey const frags::rama_norm ("frags:rama_norm")
 
StringOptionKey const frags::describe_fragments ("frags:describe_fragments")
 
RealOptionKey const frags::picking_old_max_score ("frags:picking_old_max_score")
 
BooleanOptionKey const frags::write_sequence_only ("frags:write_sequence_only")
 
BooleanOptionKey const frags::output_silent ("frags:output_silent")
 
BooleanOptionKey const frags::output_index ("frags:output_index")
 
BooleanOptionKey const frags::score_output_silent ("frags:score_output_silent")
 
BooleanOptionKey const frags::scoring::scoring ("frags:scoring")
 
FileOptionKey const frags::scoring::config ("frags:scoring:config")
 
StringOptionKey const frags::scoring::profile_score ("frags:scoring:profile_score")
 
BooleanOptionKey const frags::picking::picking ("frags:picking")
 
StringOptionKey const frags::picking::selecting_rule ("frags:picking:selecting_rule")
 
StringOptionKey const frags::picking::selecting_scorefxn ("frags:picking:selecting_scorefxn")
 
FileOptionKey const frags::picking::quota_config_file ("frags:picking:quota_config_file")
 
IntegerVectorOptionKey const frags::picking::query_pos ("frags:picking:query_pos")
 
BooleanOptionKey const frags::nonlocal::nonlocal ("frags:nonlocal")
 
BooleanOptionKey const frags::nonlocal::relax_input ("frags:nonlocal:relax_input")
 
BooleanOptionKey const frags::nonlocal::relax_input_with_coordinate_constraints ("frags:nonlocal:relax_input_with_coordinate_constraints")
 
IntegerOptionKey const frags::nonlocal::relax_frags_repeats ("frags:nonlocal:relax_frags_repeats")
 
BooleanOptionKey const frags::nonlocal::single_chain ("frags:nonlocal:single_chain")
 
RealOptionKey const frags::nonlocal::min_contacts_per_res ("frags:nonlocal:min_contacts_per_res")
 
RealOptionKey const frags::nonlocal::max_ddg_score ("frags:nonlocal:max_ddg_score")
 
RealOptionKey const frags::nonlocal::max_rmsd_after_relax ("frags:nonlocal:max_rmsd_after_relax")
 
BooleanOptionKey const frags::nonlocal::output_frags_pdbs ("frags:nonlocal:output_frags_pdbs")
 
BooleanOptionKey const frags::nonlocal::output_idealized ("frags:nonlocal:output_idealized")
 
BooleanOptionKey const frags::nonlocal::output_silent ("frags:nonlocal:output_silent")
 
BooleanOptionKey const frags::contacts::contacts ("frags:contacts")
 
IntegerOptionKey const frags::contacts::min_seq_sep ("frags:contacts:min_seq_sep")
 
RealVectorOptionKey const frags::contacts::dist_cutoffs ("frags:contacts:dist_cutoffs")
 
RealOptionKey const frags::contacts::centroid_distance_scale_factor ("frags:contacts:centroid_distance_scale_factor")
 
StringVectorOptionKey const frags::contacts::type ("frags:contacts:type")
 
IntegerOptionKey const frags::contacts::neighbors ("frags:contacts:neighbors")
 
BooleanOptionKey const frags::contacts::output_all ("frags:contacts:output_all")
 
BooleanOptionKey const frags::ABEGO::ABEGO ("frags:ABEGO")
 
RealOptionKey const frags::ABEGO::phi_psi_range_A ("frags:ABEGO:phi_psi_range_A")
 
BooleanOptionKey const helical_bundle_predict::helical_bundle_predict ("helical_bundle_predict")
 
StringOptionKey const helical_bundle_predict::sequence_file ("helical_bundle_predict:sequence_file")
 
FileOptionKey const helical_bundle_predict::helix_assignment_file ("helical_bundle_predict:helix_assignment_file")
 
IntegerOptionKey const helical_bundle_predict::num_simulated_annealing_rounds_centroid ("helical_bundle_predict:num_simulated_annealing_rounds_centroid")
 
IntegerOptionKey const helical_bundle_predict::num_steps_per_simulated_annealing_round_centroid ("helical_bundle_predict:num_steps_per_simulated_annealing_round_centroid")
 
RealOptionKey const helical_bundle_predict::centroid_max_temperature ("helical_bundle_predict:centroid_max_temperature")
 
RealOptionKey const helical_bundle_predict::centroid_min_temperature ("helical_bundle_predict:centroid_min_temperature")
 
BooleanOptionKey const helical_bundle_predict::do_final_fullatom_refinement ("helical_bundle_predict:do_final_fullatom_refinement")
 
IntegerOptionKey const helical_bundle_predict::fast_relax_rounds ("helical_bundle_predict:fast_relax_rounds")
 
BooleanOptionKey const helical_bundle_predict::find_disulfides ("helical_bundle_predict:find_disulfides")
 
IntegerVectorOptionKey const helical_bundle_predict::ignore_native_residues_in_rmsd ("helical_bundle_predict:ignore_native_residues_in_rmsd")
 
IntegerVectorOptionKey const helical_bundle_predict::ignore_prediction_residues_in_rmsd ("helical_bundle_predict:ignore_prediction_residues_in_rmsd")
 
BooleanOptionKey const holes::holes ("holes")
 
FileOptionKey const holes::dalphaball ("holes:dalphaball")
 
FileOptionKey const holes::params ("holes:params")
 
IntegerOptionKey const holes::h_mode ("holes:h_mode")
 
BooleanOptionKey const holes::water ("holes:water")
 
BooleanOptionKey const holes::make_pdb ("holes:make_pdb")
 
BooleanOptionKey const holes::make_voids ("holes:make_voids")
 
BooleanOptionKey const holes::atom_scores ("holes:atom_scores")
 
BooleanOptionKey const holes::residue_scores ("holes:residue_scores")
 
StringOptionKey const holes::minimize ("holes:minimize")
 
BooleanOptionKey const holes::debug ("holes:debug")
 
BooleanOptionKey const hotspot::hotspot ("hotspot")
 
BooleanOptionKey const hotspot::allow_gly ("hotspot:allow_gly")
 
BooleanOptionKey const hotspot::allow_proline ("hotspot:allow_proline")
 
BooleanOptionKey const hotspot::benchmark ("hotspot:benchmark")
 
StringVectorOptionKey const hotspot::residue ("hotspot:residue")
 
FileOptionKey const hotspot::hashfile ("hotspot:hashfile")
 
FileOptionKey const hotspot::target ("hotspot:target")
 
IntegerOptionKey const hotspot::target_res ("hotspot:target_res")
 
RealOptionKey const hotspot::target_dist ("hotspot:target_dist")
 
FileOptionKey const hotspot::density ("hotspot:density")
 
FileOptionKey const hotspot::weighted_density ("hotspot:weighted_density")
 
FileOptionKey const hotspot::rms_target ("hotspot:rms_target")
 
FileOptionKey const hotspot::rms_hotspot ("hotspot:rms_hotspot")
 
IntegerOptionKey const hotspot::rms_hotspot_res ("hotspot:rms_hotspot_res")
 
BooleanOptionKey const hotspot::rescore ("hotspot:rescore")
 
RealOptionKey const hotspot::threshold ("hotspot:threshold")
 
BooleanOptionKey const hotspot::sc_only ("hotspot:sc_only")
 
BooleanOptionKey const hotspot::fxnal_group ("hotspot:fxnal_group")
 
BooleanOptionKey const hotspot::cluster ("hotspot:cluster")
 
BooleanOptionKey const hotspot::colonyE ("hotspot:colonyE")
 
IntegerOptionKey const hotspot::length ("hotspot:length")
 
BooleanOptionKey const hotspot::envhb ("hotspot:envhb")
 
RealOptionKey const hotspot::angle ("hotspot:angle")
 
IntegerOptionKey const hotspot::angle_res ("hotspot:angle_res")
 
IntegerOptionKey const hotspot::batch_size ("hotspot:batch_size")
 
BooleanOptionKey const indexed_structure_store::indexed_structure_store ("indexed_structure_store")
 
FileOptionKey const indexed_structure_store::fragment_store ("indexed_structure_store:fragment_store")
 
RealOptionKey const indexed_structure_store::fragment_threshold_distance ("indexed_structure_store:fragment_threshold_distance")
 
StringOptionKey const indexed_structure_store::store_name ("indexed_structure_store:store_name")
 
StringOptionKey const indexed_structure_store::exclude_homo ("indexed_structure_store:exclude_homo")
 
BooleanOptionKey const lh::lh ("lh")
 
IntegerVectorOptionKey const lh::loopsizes ("lh:loopsizes")
 
IntegerOptionKey const lh::num_partitions ("lh:num_partitions")
 
PathOptionKey const lh::db_path ("lh:db_path")
 
BooleanOptionKey const lh::exclude_homo ("lh:exclude_homo")
 
BooleanOptionKey const lh::bss ("lh:bss")
 
StringOptionKey const lh::refstruct ("lh:refstruct")
 
StringOptionKey const lh::homo_file ("lh:homo_file")
 
RealVectorOptionKey const lh::createdb_rms_cutoff ("lh:createdb_rms_cutoff")
 
RealOptionKey const lh::min_bbrms ("lh:min_bbrms")
 
RealOptionKey const lh::max_bbrms ("lh:max_bbrms")
 
RealOptionKey const lh::min_rms ("lh:min_rms")
 
RealOptionKey const lh::max_rms ("lh:max_rms")
 
BooleanOptionKey const lh::filter_by_phipsi ("lh:filter_by_phipsi")
 
IntegerOptionKey const lh::max_radius ("lh:max_radius")
 
IntegerOptionKey const lh::max_struct ("lh:max_struct")
 
IntegerOptionKey const lh::max_struct_per_radius ("lh:max_struct_per_radius")
 
RealOptionKey const lh::grid_space_multiplier ("lh:grid_space_multiplier")
 
RealOptionKey const lh::grid_angle_multiplier ("lh:grid_angle_multiplier")
 
IntegerOptionKey const lh::skim_size ("lh:skim_size")
 
IntegerOptionKey const lh::rounds ("lh:rounds")
 
StringOptionKey const lh::jobname ("lh:jobname")
 
IntegerOptionKey const lh::max_lib_size ("lh:max_lib_size")
 
IntegerOptionKey const lh::max_emperor_lib_size ("lh:max_emperor_lib_size")
 
IntegerOptionKey const lh::max_emperor_lib_round ("lh:max_emperor_lib_round")
 
IntegerOptionKey const lh::library_expiry_time ("lh:library_expiry_time")
 
StringOptionKey const lh::objective_function ("lh:objective_function")
 
IntegerOptionKey const lh::expire_after_rounds ("lh:expire_after_rounds")
 
StringOptionKey const lh::mpi_resume ("lh:mpi_resume")
 
StringOptionKey const lh::mpi_feedback ("lh:mpi_feedback")
 
IntegerOptionKey const lh::mpi_batch_relax_chunks ("lh:mpi_batch_relax_chunks")
 
IntegerOptionKey const lh::mpi_batch_relax_absolute_max ("lh:mpi_batch_relax_absolute_max")
 
IntegerOptionKey const lh::mpi_outbound_wu_buffer_size ("lh:mpi_outbound_wu_buffer_size")
 
IntegerOptionKey const lh::mpi_loophash_split_size ("lh:mpi_loophash_split_size ")
 
RealOptionKey const lh::mpi_metropolis_temp ("lh:mpi_metropolis_temp")
 
IntegerOptionKey const lh::mpi_save_state_interval ("lh:mpi_save_state_interval")
 
BooleanOptionKey const lh::mpi_master_save_score_only ("lh:mpi_master_save_score_only")
 
IntegerOptionKey const lh::max_loophash_per_structure ("lh:max_loophash_per_structure")
 
RealOptionKey const lh::prob_terminus_ramapert ("lh:prob_terminus_ramapert")
 
RealOptionKey const lh::rms_limit ("lh:rms_limit")
 
RealOptionKey const lh::similarity_reference ("lh:similarity_reference")
 
BooleanOptionKey const lh::centroid_only ("lh:centroid_only")
 
BooleanOptionKey const lh::write_centroid_structs ("lh:write_centroid_structs")
 
BooleanOptionKey const lh::write_all_fa_structs ("lh:write_all_fa_structs")
 
BooleanOptionKey const lh::sandbox ("lh:sandbox")
 
BooleanOptionKey const lh::create_db ("lh:create_db")
 
FileOptionKey const lh::sample_weight_file ("lh:sample_weight_file")
 
RealOptionKey const lh::radius_size ("lh:radius_size")
 
IntegerOptionKey const lh::max_ref_lib_size ("lh:max_ref_lib_size")
 
StringVectorOptionKey const lh::multi_objective_functions ("lh:multi_objective_functions")
 
StringVectorOptionKey const lh::additional_objective_functions ("lh:additional_objective_functions")
 
RealOptionKey const lh::edensity_weight_for_sampling ("lh:edensity_weight_for_sampling")
 
StringOptionKey const lh::mpi_master_schfile ("lh:mpi_master_schfile")
 
IntegerVectorOptionKey const lh::mpi_master_cpu_weight ("lh:mpi_master_cpu_weight")
 
StringOptionKey const lh::mpi_loophash_scan_type ("lh:mpi_loophash_scan_type")
 
BooleanOptionKey const lh::mpi_read_structure_for_emperor ("lh:mpi_read_structure_for_emperor")
 
BooleanOptionKey const lh::mpi_packmin_init ("lh:mpi_packmin_init")
 
IntegerOptionKey const lh::max_sample_per_structure ("lh:max_sample_per_structure")
 
StringOptionKey const lh::loop_string ("lh:loop_string")
 
StringOptionKey const lh::seg_string ("lh:seg_string")
 
StringVectorOptionKey const lh::loopresdef ("lh:loopresdef")
 
BooleanOptionKey const lh::pert_init_loop ("lh:pert_init_loop")
 
RealOptionKey const lh::NMdist ("lh:NMdist")
 
RealVectorOptionKey const lh::objective_dominate_cut ("lh:objective_dominate_cut")
 
RealVectorOptionKey const lh::objective_cut_increment ("lh:objective_cut_increment")
 
StringOptionKey const lh::similarity_method ("lh:similarity_method")
 
StringOptionKey const lh::similarity_measure ("lh:similarity_measure")
 
RealOptionKey const lh::similarity_tolerance ("lh:similarity_tolerance")
 
RealOptionKey const lh::parent_selection_kT ("lh:parent_selection_kT")
 
StringOptionKey const lh::sim_replace_obj ("lh:sim_replace_obj")
 
RealOptionKey const lh::ulr_mulfactor ("lh:ulr_mulfactor")
 
BooleanOptionKey const lh::filter_up_to_maxlib ("lh:filter_up_to_maxlib")
 
BooleanOptionKey const lh::minimize_after_nmsearch ("lh:minimize_after_nmsearch")
 
BooleanOptionKey const lh::fragpdb::fragpdb ("lh:fragpdb")
 
StringOptionKey const lh::fragpdb::out_path ("lh:fragpdb:out_path")
 
IntegerVectorOptionKey const lh::fragpdb::indexoffset ("lh:fragpdb:indexoffset")
 
StringVectorOptionKey const lh::fragpdb::bin ("lh:fragpdb:bin")
 
BooleanOptionKey const lh::symfragrm::symfragrm ("lh:symfragrm")
 
FileVectorOptionKey const lh::symfragrm::pdblist ("lh:symfragrm:pdblist")
 
BooleanOptionKey const loopfcst::loopfcst ("loopfcst")
 
RealOptionKey const loopfcst::coord_cst_weight ("loopfcst:coord_cst_weight")
 
BooleanOptionKey const loopfcst::coord_cst_all_atom ("loopfcst:coord_cst_all_atom")
 
BooleanOptionKey const loopfcst::use_general_protocol ("loopfcst:use_general_protocol")
 
FileOptionKey const loopfcst::coord_cst_weight_array ("loopfcst:coord_cst_weight_array")
 
FileOptionKey const loopfcst::dump_coord_cst_weight_array ("loopfcst:dump_coord_cst_weight_array")
 
BooleanOptionKey const LoopModel::LoopModel ("LoopModel")
 
FileOptionKey const LoopModel::input_pdb ("LoopModel:input_pdb")
 
BooleanOptionKey const make_rot_lib::make_rot_lib ("make_rot_lib")
 
FileOptionKey const make_rot_lib::options_file ("make_rot_lib:options_file")
 
BooleanOptionKey const make_rot_lib::output_logging ("make_rot_lib:output_logging")
 
IntegerVectorOptionKey const make_rot_lib::two_fold_symmetry_135_315 ("make_rot_lib:two_fold_symmetry_135_315")
 
IntegerVectorOptionKey const make_rot_lib::two_fold_symmetry_0_180 ("make_rot_lib:two_fold_symmetry_0_180")
 
IntegerVectorOptionKey const make_rot_lib::three_fold_symmetry_90_210_330 ("make_rot_lib:three_fold_symmetry_90_210_330")
 
BooleanOptionKey const make_rot_lib::use_terminal_residues ("make_rot_lib:use_terminal_residues")
 
BooleanOptionKey const make_rot_lib::k_medoids ("make_rot_lib:k_medoids")
 
StringOptionKey const make_rot_lib::patch_name_for_residue ("make_rot_lib:patch_name_for_residue")
 
FileOptionKey const make_rot_lib::polymeric_context ("make_rot_lib:polymeric_context")
 
BooleanOptionKey const make_mainchain_potential::make_mainchain_potential ("make_mainchain_potential")
 
BooleanOptionKey const make_mainchain_potential::do_minimization ("make_mainchain_potential:do_minimization")
 
IntegerVectorOptionKey const make_mainchain_potential::mainchain_potential_points_per_dimension ("make_mainchain_potential:mainchain_potential_points_per_dimension")
 
IntegerVectorOptionKey const make_mainchain_potential::mainchain_torsions_covered ("make_mainchain_potential:mainchain_torsions_covered")
 
BooleanOptionKey const make_mainchain_potential::make_pre_proline_potential ("make_mainchain_potential:make_pre_proline_potential")
 
FileOptionKey const make_mainchain_potential::output_filename ("make_mainchain_potential:output_filename")
 
StringOptionKey const make_mainchain_potential::residue_name ("make_mainchain_potential:residue_name")
 
BooleanOptionKey const make_mainchain_potential::symmetrize_output ("make_mainchain_potential:symmetrize_output")
 
BooleanOptionKey const make_mainchain_potential::write_potentials_for_individual_scoreterms ("make_mainchain_potential:write_potentials_for_individual_scoreterms")
 
BooleanOptionKey const match::match ("match")
 
StringOptionKey const match::lig_name ("match:lig_name")
 
RealOptionKey const match::bump_tolerance ("match:bump_tolerance")
 
FileOptionKey const match::active_site_definition_by_residue ("match:active_site_definition_by_residue")
 
FileOptionKey const match::active_site_definition_by_gridlig ("match:active_site_definition_by_gridlig")
 
FileOptionKey const match::required_active_site_atom_names ("match:required_active_site_atom_names")
 
FileOptionKey const match::grid_boundary ("match:grid_boundary")
 
FileOptionKey const match::geometric_constraint_file ("match:geometric_constraint_file")
 
FileOptionKey const match::scaffold_active_site_residues ("match:scaffold_active_site_residues")
 
FileOptionKey const match::scaffold_active_site_residues_for_geomcsts ("match:scaffold_active_site_residues_for_geomcsts")
 
RealOptionKey const match::euclid_bin_size ("match:euclid_bin_size")
 
RealOptionKey const match::euler_bin_size ("match:euler_bin_size")
 
BooleanOptionKey const match::consolidate_matches ("match:consolidate_matches")
 
IntegerOptionKey const match::output_matches_per_group ("match:output_matches_per_group")
 
StringVectorOptionKey const match::orientation_atoms ("match:orientation_atoms")
 
StringOptionKey const match::output_format ("match:output_format")
 
StringOptionKey const match::match_grouper ("match:match_grouper")
 
RealOptionKey const match::grouper_downstream_rmsd ("match:grouper_downstream_rmsd")
 
BooleanOptionKey const match::output_matchres_only ("match:output_matchres_only")
 
IntegerVectorOptionKey const match::geom_csts_downstream_output ("match:geom_csts_downstream_output")
 
BooleanOptionKey const match::filter_colliding_upstream_residues ("match:filter_colliding_upstream_residues")
 
RealOptionKey const match::upstream_residue_collision_tolerance ("match:upstream_residue_collision_tolerance")
 
RealOptionKey const match::upstream_residue_collision_score_cutoff ("match:upstream_residue_collision_score_cutoff")
 
RealOptionKey const match::upstream_residue_collision_Wfa_atr ("match:upstream_residue_collision_Wfa_atr")
 
RealOptionKey const match::upstream_residue_collision_Wfa_rep ("match:upstream_residue_collision_Wfa_rep")
 
RealOptionKey const match::upstream_residue_collision_Wfa_sol ("match:upstream_residue_collision_Wfa_sol")
 
BooleanOptionKey const match::filter_upstream_downstream_collisions ("match:filter_upstream_downstream_collisions")
 
RealOptionKey const match::updown_collision_tolerance ("match:updown_collision_tolerance")
 
RealOptionKey const match::updown_residue_collision_score_cutoff ("match:updown_residue_collision_score_cutoff")
 
RealOptionKey const match::updown_residue_collision_Wfa_atr ("match:updown_residue_collision_Wfa_atr")
 
RealOptionKey const match::updown_residue_collision_Wfa_rep ("match:updown_residue_collision_Wfa_rep")
 
RealOptionKey const match::updown_residue_collision_Wfa_sol ("match:updown_residue_collision_Wfa_sol")
 
BooleanOptionKey const match::define_match_by_single_downstream_positioning ("match:define_match_by_single_downstream_positioning")
 
IntegerOptionKey const match::ligand_rotamer_index ("match:ligand_rotamer_index")
 
BooleanOptionKey const match::enumerate_ligand_rotamers ("match:enumerate_ligand_rotamers")
 
BooleanOptionKey const match::only_enumerate_non_match_redundant_ligand_rotamers ("match:only_enumerate_non_match_redundant_ligand_rotamers")
 
BooleanOptionKey const match::dynamic_grid_refinement ("match:dynamic_grid_refinement")
 
BooleanOptionKey const match::build_round1_hits_twice ("match:build_round1_hits_twice")
 
BooleanOptionKey const matdes::matdes ("matdes")
 
IntegerOptionKey const matdes::num_subs_building_block ("matdes:num_subs_building_block")
 
IntegerOptionKey const matdes::num_subs_total ("matdes:num_subs_total")
 
StringOptionKey const matdes::pdbID ("matdes:pdbID")
 
StringOptionKey const matdes::prefix ("matdes:prefix")
 
RealVectorOptionKey const matdes::radial_disp ("matdes:radial_disp")
 
RealVectorOptionKey const matdes::angle ("matdes:angle")
 
StringOptionKey const matdes::tag ("matdes:tag")
 
BooleanOptionKey const matdes::dock::dock ("matdes:dock")
 
RealOptionKey const matdes::dock::neg_r ("matdes:dock:neg_r")
 
BooleanOptionKey const matdes::dock::dump_pdb ("matdes:dock:dump_pdb")
 
BooleanOptionKey const matdes::dock::dump_chainA_only ("matdes:dock:dump_chainA_only")
 
BooleanOptionKey const matdes::design::design ("matdes:design")
 
RealOptionKey const matdes::design::contact_dist ("matdes:design:contact_dist")
 
RealOptionKey const matdes::design::grid_size_angle ("matdes:design:grid_size_angle")
 
RealOptionKey const matdes::design::grid_size_radius ("matdes:design:grid_size_radius")
 
IntegerOptionKey const matdes::design::grid_nsamp_angle ("matdes:design:grid_nsamp_angle")
 
IntegerOptionKey const matdes::design::grid_nsamp_radius ("matdes:design:grid_nsamp_radius")
 
RealOptionKey const matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus")