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OptionKeys.cc.gen7.hh File Reference

Namespaces

 cyclic_peptide
 
 dc
 
 ddg
 
 DenovoProteinDesign
 
 dna
 
 dna::specificity
 
 dna::design
 
 dna::design::specificity
 
 dna::design::reversion
 
 DisulfideInsertion
 
 docking
 

Functions

RealOptionKey const cyclic_peptide::hbond_energy_cutoff ("cyclic_peptide:hbond_energy_cutoff")
 
BooleanOptionKey const cyclic_peptide::do_not_count_adjacent_res_hbonds ("cyclic_peptide:do_not_count_adjacent_res_hbonds")
 
IntegerOptionKey const cyclic_peptide::fast_relax_rounds ("cyclic_peptide:fast_relax_rounds")
 
BooleanOptionKey const cyclic_peptide::count_sc_hbonds ("cyclic_peptide:count_sc_hbonds")
 
BooleanOptionKey const cyclic_peptide::require_disulfides ("cyclic_peptide:require_disulfides")
 
RealOptionKey const cyclic_peptide::disulf_cutoff_prerelax ("cyclic_peptide:disulf_cutoff_prerelax")
 
RealOptionKey const cyclic_peptide::disulf_cutoff_postrelax ("cyclic_peptide:disulf_cutoff_postrelax")
 
RealVectorOptionKey const cyclic_peptide::user_set_alpha_dihedrals ("cyclic_peptide:user_set_alpha_dihedrals")
 
RealOptionKey const cyclic_peptide::user_set_alpha_dihedral_perturbation ("cyclic_peptide:user_set_alpha_dihedral_perturbation")
 
RealOptionKey const cyclic_peptide::bondlength_perturbation_magnitude ("cyclic_peptide:bondlength_perturbation_magnitude")
 
RealOptionKey const cyclic_peptide::bondangle_perturbation_magnitude ("cyclic_peptide:bondangle_perturbation_magnitude")
 
BooleanOptionKey const cyclic_peptide::filter_oversaturated_hbond_acceptors ("cyclic_peptide:filter_oversaturated_hbond_acceptors")
 
RealOptionKey const cyclic_peptide::hbond_acceptor_energy_cutoff ("cyclic_peptide:hbond_acceptor_energy_cutoff")
 
RealOptionKey const cyclic_peptide::sample_cis_pro_frequency ("cyclic_peptide:sample_cis_pro_frequency")
 
BooleanOptionKey const cyclic_peptide::design_peptide ("cyclic_peptide:design_peptide")
 
FileOptionKey const cyclic_peptide::allowed_residues_by_position ("cyclic_peptide:allowed_residues_by_position")
 
BooleanOptionKey const cyclic_peptide::prohibit_D_at_negative_phi ("cyclic_peptide:prohibit_D_at_negative_phi")
 
BooleanOptionKey const cyclic_peptide::prohibit_L_at_positive_phi ("cyclic_peptide:prohibit_L_at_positive_phi")
 
FileOptionKey const cyclic_peptide::L_alpha_comp_file ("cyclic_peptide:L_alpha_comp_file")
 
FileOptionKey const cyclic_peptide::D_alpha_comp_file ("cyclic_peptide:D_alpha_comp_file")
 
FileOptionKey const cyclic_peptide::L_beta_comp_file ("cyclic_peptide:L_beta_comp_file")
 
FileOptionKey const cyclic_peptide::D_beta_comp_file ("cyclic_peptide:D_beta_comp_file")
 
IntegerOptionKey const cyclic_peptide::angle_relax_rounds ("cyclic_peptide:angle_relax_rounds")
 
IntegerOptionKey const cyclic_peptide::angle_length_relax_rounds ("cyclic_peptide:angle_length_relax_rounds")
 
IntegerOptionKey const cyclic_peptide::cartesian_relax_rounds ("cyclic_peptide:cartesian_relax_rounds")
 
BooleanOptionKey const cyclic_peptide::use_classic_rama_for_sampling ("cyclic_peptide:use_classic_rama_for_sampling")
 
IntegerVectorOptionKey const cyclic_peptide::n_methyl_positions ("cyclic_peptide:n_methyl_positions")
 
IntegerOptionKey const cyclic_peptide::lariat_sidechain_index ("cyclic_peptide:lariat_sidechain_index")
 
IntegerVectorOptionKey const cyclic_peptide::sidechain_isopeptide_indices ("cyclic_peptide:sidechain_isopeptide_indices")
 
IntegerVectorOptionKey const cyclic_peptide::paraBBMB_positions ("cyclic_peptide:paraBBMB_positions")
 
BooleanOptionKey const cyclic_peptide::use_paraBBMB_filters ("cyclic_peptide:use_paraBBMB_filters")
 
RealOptionKey const cyclic_peptide::paraBBMB_sidechain_distance_filter_multiplier ("cyclic_peptide:paraBBMB_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::paraBBMB_constraints_energy_filter_multiplier ("cyclic_peptide:paraBBMB_constraints_energy_filter_multiplier")
 
BooleanOptionKey const cyclic_peptide::link_all_cys_with_paraBBMB ("cyclic_peptide:link_all_cys_with_paraBBMB")
 
IntegerVectorOptionKey const cyclic_peptide::TBMB_positions ("cyclic_peptide:TBMB_positions")
 
BooleanOptionKey const cyclic_peptide::use_TBMB_filters ("cyclic_peptide:use_TBMB_filters")
 
RealOptionKey const cyclic_peptide::TBMB_sidechain_distance_filter_multiplier ("cyclic_peptide:TBMB_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::TBMB_constraints_energy_filter_multiplier ("cyclic_peptide:TBMB_constraints_energy_filter_multiplier")
 
BooleanOptionKey const cyclic_peptide::link_all_cys_with_TBMB ("cyclic_peptide:link_all_cys_with_TBMB")
 
IntegerVectorOptionKey const cyclic_peptide::TMA_positions ("cyclic_peptide:TMA_positions")
 
BooleanOptionKey const cyclic_peptide::use_TMA_filters ("cyclic_peptide:use_TMA_filters")
 
RealOptionKey const cyclic_peptide::TMA_sidechain_distance_filter_multiplier ("cyclic_peptide:TMA_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::TMA_constraints_energy_filter_multiplier ("cyclic_peptide:TMA_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::square_pyramidal_metal_positions ("cyclic_peptide:square_pyramidal_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_square_pyramidal_metal_filters ("cyclic_peptide:use_square_pyramidal_metal_filters")
 
RealOptionKey const cyclic_peptide::square_pyramidal_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:square_pyramidal_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::square_pyramidal_metal_constraints_energy_filter_multiplier ("cyclic_peptide:square_pyramidal_metal_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::square_planar_metal_positions ("cyclic_peptide:square_planar_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_square_planar_metal_filters ("cyclic_peptide:use_square_planar_metal_filters")
 
RealOptionKey const cyclic_peptide::square_planar_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:square_planar_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::square_planar_metal_constraints_energy_filter_multiplier ("cyclic_peptide:square_planar_metal_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::trigonal_pyramidal_metal_positions ("cyclic_peptide:trigonal_pyramidal_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_trigonal_pyramidal_metal_filters ("cyclic_peptide:use_trigonal_pyramidal_metal_filters")
 
RealOptionKey const cyclic_peptide::trigonal_pyramidal_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:trigonal_pyramidal_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::trigonal_pyramidal_metal_constraints_energy_filter_multiplier ("cyclic_peptide:trigonal_pyramidal_metal_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::trigonal_planar_metal_positions ("cyclic_peptide:trigonal_planar_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_trigonal_planar_metal_filters ("cyclic_peptide:use_trigonal_planar_metal_filters")
 
RealOptionKey const cyclic_peptide::trigonal_planar_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:trigonal_planar_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::trigonal_planar_metal_constraints_energy_filter_multiplier ("cyclic_peptide:trigonal_planar_metal_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::tetrahedral_metal_positions ("cyclic_peptide:tetrahedral_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_tetrahedral_metal_filters ("cyclic_peptide:use_tetrahedral_metal_filters")
 
RealOptionKey const cyclic_peptide::tetrahedral_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:tetrahedral_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::tetrahedral_metal_constraints_energy_filter_multiplier ("cyclic_peptide:tetrahedral_metal_constraints_energy_filter_multiplier")
 
StringVectorOptionKey const cyclic_peptide::octahedral_metal_positions ("cyclic_peptide:octahedral_metal_positions")
 
BooleanOptionKey const cyclic_peptide::use_octahedral_metal_filters ("cyclic_peptide:use_octahedral_metal_filters")
 
RealOptionKey const cyclic_peptide::octahedral_metal_sidechain_distance_filter_multiplier ("cyclic_peptide:octahedral_metal_sidechain_distance_filter_multiplier")
 
RealOptionKey const cyclic_peptide::octahedral_metal_constraints_energy_filter_multiplier ("cyclic_peptide:octahedral_metal_constraints_energy_filter_multiplier")
 
IntegerOptionKey const cyclic_peptide::require_symmetry_repeats ("cyclic_peptide:require_symmetry_repeats")
 
BooleanOptionKey const cyclic_peptide::require_symmetry_mirroring ("cyclic_peptide:require_symmetry_mirroring")
 
RealOptionKey const cyclic_peptide::require_symmetry_angle_threshold ("cyclic_peptide:require_symmetry_angle_threshold")
 
RealOptionKey const cyclic_peptide::require_symmetry_perturbation ("cyclic_peptide:require_symmetry_perturbation")
 
BooleanOptionKey const cyclic_peptide::MPI_auto_2level_distribution ("cyclic_peptide:MPI_auto_2level_distribution")
 
IntegerVectorOptionKey const cyclic_peptide::MPI_processes_by_level ("cyclic_peptide:MPI_processes_by_level")
 
IntegerVectorOptionKey const cyclic_peptide::MPI_batchsize_by_level ("cyclic_peptide:MPI_batchsize_by_level")
 
StringOptionKey const cyclic_peptide::MPI_sort_by ("cyclic_peptide:MPI_sort_by")
 
BooleanOptionKey const cyclic_peptide::MPI_choose_highest ("cyclic_peptide:MPI_choose_highest")
 
RealOptionKey const cyclic_peptide::MPI_output_fraction ("cyclic_peptide:MPI_output_fraction")
 
IntegerOptionKey const cyclic_peptide::MPI_stop_after_time ("cyclic_peptide:MPI_stop_after_time")
 
RealOptionKey const cyclic_peptide::MPI_pnear_lambda ("cyclic_peptide:MPI_pnear_lambda")
 
RealOptionKey const cyclic_peptide::MPI_pnear_kbt ("cyclic_peptide:MPI_pnear_kbt")
 
IntegerOptionKey const cyclic_peptide::threads_per_worker ("cyclic_peptide:threads_per_worker")
 
BooleanOptionKey const cyclic_peptide::compute_rmsd_to_lowest ("cyclic_peptide:compute_rmsd_to_lowest")
 
RealOptionKey const cyclic_peptide::compute_pnear_to_this_fract ("cyclic_peptide:compute_pnear_to_this_fract")
 
BooleanOptionKey const cyclic_peptide::compute_ensemble_sasa_metrics ("cyclic_peptide:compute_ensemble_sasa_metrics")
 
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::optimize_wt ("ddg:optimize_wt")
 
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")
 
BooleanOptionKey const ddg::rna_all_prot_sc_min_only ("ddg:rna_all_prot_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")
 
BooleanOptionKey const ddg::force_iterations ("ddg:force_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")
 
RealOptionKey const ddg::cst_dist_cutoff ("ddg:cst_dist_cutoff")
 
BooleanOptionKey const ddg::cartesian ("ddg:cartesian")
 
IntegerOptionKey const ddg::extract_element_nbrs ("ddg:extract_element_nbrs")
 
IntegerOptionKey const ddg::frag_nbrs ("ddg:frag_nbrs")
 
IntegerOptionKey const ddg::bbnbrs ("ddg:bbnbrs")
 
IntegerOptionKey const ddg::nfrags ("ddg:nfrags")
 
IntegerOptionKey const ddg::ntrials ("ddg:ntrials")
 
BooleanOptionKey const ddg::optimize_proline ("ddg:optimize_proline")
 
BooleanOptionKey const ddg::flex_bb ("ddg:flex_bb")
 
BooleanOptionKey const ddg::fd_mode ("ddg:fd_mode")
 
BooleanOptionKey const ddg::legacy ("ddg:legacy")
 
BooleanOptionKey const ddg::json ("ddg:json")
 
IntegerOptionKey const ddg::n_converged ("ddg:n_converged")
 
RealOptionKey const ddg::score_cutoff ("ddg:score_cutoff")
 
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")
 
RealVectorOptionKey const dna::specificity::dna_backbone_torsion_sdevs ("dna:specificity:dna_backbone_torsion_sdevs")
 
RealOptionKey const dna::specificity::dna_sugar_torsion_sdev ("dna:specificity:dna_sugar_torsion_sdev")
 
RealOptionKey const dna::specificity::dna_chi_torsion_sdev ("dna:specificity:dna_chi_torsion_sdev")
 
StringOptionKey const dna::specificity::lk_ball_wtd_tag ("dna:specificity:lk_ball_wtd_tag")
 
BooleanOptionKey const dna::specificity::lk_ball_for_bb ("dna:specificity:lk_ball_for_bb")
 
RealOptionKey const dna::specificity::lk_ball_ramp_width_A2 ("dna:specificity:lk_ball_ramp_width_A2")
 
RealOptionKey const dna::specificity::lk_ball_overlap_gap ("dna:specificity:lk_ball_overlap_gap")
 
RealOptionKey const dna::specificity::lk_ball_overlap_width_A2 ("dna:specificity:lk_ball_overlap_width_A2")
 
RealOptionKey const dna::specificity::lk_ball_water_fade ("dna:specificity:lk_ball_water_fade")
 
RealVectorOptionKey const dna::specificity::lk_ball_wtd_prefactors ("dna:specificity:lk_ball_wtd_prefactors")
 
RealVectorOptionKey const dna::specificity::lk_ball_waters_sp2 ("dna:specificity:lk_ball_waters_sp2")
 
RealVectorOptionKey const dna::specificity::lk_ball_waters_sp3 ("dna:specificity:lk_ball_waters_sp3")
 
RealVectorOptionKey const dna::specificity::lk_ball_waters_ring ("dna:specificity:lk_ball_waters_ring")
 
RealOptionKey const dna::specificity::lk_ball_waters_donor ("dna:specificity:lk_ball_waters_donor")
 
RealOptionKey const dna::specificity::lk_ball_bridge_angle_widthscale ("dna:specificity:lk_ball_bridge_angle_widthscale")
 
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 DisulfideInsertion::DisulfideInsertion ("DisulfideInsertion")
 
IntegerOptionKey const DisulfideInsertion::peptide_chain ("DisulfideInsertion:peptide_chain")
 
IntegerOptionKey const DisulfideInsertion::n_cyd_seqpos ("DisulfideInsertion:n_cyd_seqpos")
 
IntegerOptionKey const DisulfideInsertion::c_cyd_seqpos ("DisulfideInsertion:c_cyd_seqpos")
 
RealOptionKey const DisulfideInsertion::max_dslf_pot ("DisulfideInsertion:max_dslf_pot")
 
RealOptionKey const DisulfideInsertion::max_dslf_energy ("DisulfideInsertion:max_dslf_energy")
 
RealOptionKey const DisulfideInsertion::min_dslf_dist_multiplier ("DisulfideInsertion:min_dslf_dist_multiplier")
 
RealOptionKey const DisulfideInsertion::max_dslf_dist_multiplier ("DisulfideInsertion:max_dslf_dist_multiplier")
 
StringOptionKey const DisulfideInsertion::scorefxn ("DisulfideInsertion:scorefxn")
 
RealOptionKey const DisulfideInsertion::constraint_weight ("DisulfideInsertion:constraint_weight")
 
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")
 
StringOptionKey const docking::docking_low_res_score ("docking:docking_low_res_score")
 
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::tilt ("docking:tilt")
 
StringOptionKey const docking::tilt1_center ("docking:tilt1_center")
 
StringOptionKey const docking::tilt2_center ("docking:tilt2_center")
 
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")
 
RealOptionKey const docking::SymDock_lowres_filter ("docking:SymDock_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")