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Namespaces | Functions
OptionKeys.cc.gen11.hh File Reference

Namespaces

 nmr
 
 nmr::pre
 
 nmr::spinlabel
 
 nmr::score
 
 nonlocal
 
 optE
 
 optE::rescore
 
 packstat
 
 patterson
 
 pb_potential
 
 PCS
 
 PCSTS1
 
 PCSTS2
 
 PCSTS3
 
 PCSTS4
 
 pepspec
 
 pH
 
 pH::calc_pka
 
 pocket_grid
 
 gen_pharmacophore
 
 fingerprint
 
 ProQ
 
 qsar
 

Functions

BooleanOptionKey const nmr::pre::show_info ("nmr:pre:show_info")
 
BooleanOptionKey const nmr::spinlabel::spinlabel ("nmr:spinlabel")
 
IntegerOptionKey const nmr::spinlabel::max_ensemble_size ("nmr:spinlabel:max_ensemble_size")
 
StringOptionKey const nmr::spinlabel::highres_conformer_filter_type ("nmr:spinlabel:highres_conformer_filter_type")
 
BooleanOptionKey const nmr::spinlabel::elaborate_rotamer_clash_check ("nmr:spinlabel:elaborate_rotamer_clash_check")
 
RealOptionKey const nmr::spinlabel::boltzmann_kt ("nmr:spinlabel:boltzmann_kt")
 
BooleanOptionKey const nmr::score::score ("nmr:score")
 
BooleanOptionKey const nmr::score::verbose ("nmr:score:verbose")
 
BooleanOptionKey const nmr::score::output_exp_calc ("nmr:score:output_exp_calc")
 
BooleanOptionKey const nmr::score::output_tensor_info ("nmr:score:output_tensor_info")
 
BooleanOptionKey const nonlocal::nonlocal ("nonlocal")
 
FileOptionKey const nonlocal::chunks ("nonlocal:chunks")
 
BooleanOptionKey const nonlocal::randomize_missing ("nonlocal:randomize_missing")
 
BooleanOptionKey const optE::optE ("optE")
 
StringOptionKey const optE::load_from_silent ("optE:load_from_silent")
 
StringOptionKey const optE::data_in ("optE:data_in")
 
StringOptionKey const optE::data_out ("optE:data_out")
 
StringOptionKey const optE::weights ("optE:weights")
 
StringVectorOptionKey const optE::fix ("optE:fix")
 
FileOptionKey const optE::free ("optE:free")
 
FileOptionKey const optE::fixed ("optE:fixed")
 
FileOptionKey const optE::parse_tagfile ("optE:parse_tagfile")
 
FileOptionKey const optE::constant_logic_taskops_file ("optE:constant_logic_taskops_file")
 
BooleanOptionKey const optE::optE_soft_rep ("optE:optE_soft_rep")
 
BooleanOptionKey const optE::no_hb_env_dependence ("optE:no_hb_env_dependence")
 
BooleanOptionKey const optE::no_hb_env_dependence_DNA ("optE:no_hb_env_dependence_DNA")
 
BooleanOptionKey const optE::optE_no_protein_fa_elec ("optE:optE_no_protein_fa_elec")
 
BooleanOptionKey const optE::include_intra_res_protein ("optE:include_intra_res_protein")
 
BooleanOptionKey const optE::centroid_rot ("optE:centroid_rot")
 
BooleanOptionKey const optE::centroid_rot_min ("optE:centroid_rot_min")
 
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::design_with_fast_design ("optE:design_with_fast_design")
 
BooleanOptionKey const optE::design_with_offrotpack ("optE:design_with_offrotpack")
 
BooleanOptionKey const optE::limit_bad_scores ("optE:limit_bad_scores")
 
BooleanOptionKey const optE::no_design_pdb_output ("optE:no_design_pdb_output")
 
BooleanOptionKey const optE::rescore::rescore ("optE:rescore")
 
FileOptionKey const optE::rescore::weights ("optE:rescore:weights")
 
IntegerOptionKey const optE::rescore::context_round ("optE:rescore:context_round")
 
FileOptionKey const optE::rescore::outlog ("optE:rescore:outlog")
 
BooleanOptionKey const optE::rescore::measure_sequence_recovery ("optE:rescore:measure_sequence_recovery")
 
BooleanOptionKey const packstat::packstat ("packstat")
 
BooleanOptionKey const packstat::include_water ("packstat:include_water")
 
IntegerOptionKey const packstat::oversample ("packstat:oversample")
 
BooleanOptionKey const packstat::packstat_pdb ("packstat:packstat_pdb")
 
BooleanOptionKey const packstat::surface_accessibility ("packstat:surface_accessibility")
 
BooleanOptionKey const packstat::residue_scores ("packstat:residue_scores")
 
RealOptionKey const packstat::cavity_burial_probe_radius ("packstat:cavity_burial_probe_radius")
 
BooleanOptionKey const packstat::raw_stats ("packstat:raw_stats")
 
IntegerOptionKey const packstat::threads ("packstat:threads")
 
RealOptionKey const packstat::cluster_min_volume ("packstat:cluster_min_volume")
 
RealOptionKey const packstat::min_surface_accessibility ("packstat:min_surface_accessibility")
 
RealOptionKey const packstat::min_cluster_overlap ("packstat:min_cluster_overlap")
 
RealOptionKey const packstat::min_cav_ball_radius ("packstat:min_cav_ball_radius")
 
BooleanOptionKey const patterson::patterson ("patterson")
 
RealOptionKey const patterson::weight ("patterson:weight")
 
RealOptionKey const patterson::sc_scaling ("patterson:sc_scaling")
 
RealVectorOptionKey const patterson::radius_cutoffs ("patterson:radius_cutoffs")
 
RealVectorOptionKey const patterson::resolution_cutoffs ("patterson:resolution_cutoffs")
 
RealOptionKey const patterson::Bsol ("patterson:Bsol")
 
RealOptionKey const patterson::Fsol ("patterson:Fsol")
 
RealOptionKey const patterson::model_B ("patterson:model_B")
 
RealOptionKey const patterson::rmsd ("patterson:rmsd")
 
BooleanOptionKey const patterson::no_ecalc ("patterson:no_ecalc")
 
IntegerOptionKey const patterson::nshells ("patterson:nshells")
 
BooleanOptionKey const patterson::use_spline_interpolation ("patterson:use_spline_interpolation")
 
BooleanOptionKey const patterson::use_on_repack ("patterson:use_on_repack")
 
BooleanOptionKey const patterson::dont_use_symm_in_pcalc ("patterson:dont_use_symm_in_pcalc")
 
BooleanOptionKey const pb_potential::pb_potential ("pb_potential")
 
IntegerVectorOptionKey const pb_potential::charged_chains ("pb_potential:charged_chains")
 
BooleanOptionKey const pb_potential::sidechain_only ("pb_potential:sidechain_only")
 
IntegerVectorOptionKey const pb_potential::revamp_near_chain ("pb_potential:revamp_near_chain")
 
StringOptionKey const pb_potential::apbs_path ("pb_potential:apbs_path")
 
RealOptionKey const pb_potential::potential_cap ("pb_potential:potential_cap")
 
RealOptionKey const pb_potential::tolerance ("pb_potential:tolerance")
 
IntegerOptionKey const pb_potential::apbs_debug ("pb_potential:apbs_debug")
 
BooleanOptionKey const pb_potential::calcenergy ("pb_potential:calcenergy")
 
BooleanOptionKey const PCS::PCS ("PCS")
 
FileOptionKey const PCS::write_extra ("PCS:write_extra")
 
IntegerOptionKey const PCS::normalization_id ("PCS:normalization_id")
 
BooleanOptionKey const PCSTS1::PCSTS1 ("PCSTS1")
 
FileOptionKey const PCSTS1::write_extra ("PCSTS1:write_extra")
 
IntegerOptionKey const PCSTS1::normalization_id ("PCSTS1:normalization_id")
 
BooleanOptionKey const PCSTS2::PCSTS2 ("PCSTS2")
 
FileOptionKey const PCSTS2::write_extra ("PCSTS2:write_extra")
 
IntegerOptionKey const PCSTS2::normalization_id ("PCSTS2:normalization_id")
 
BooleanOptionKey const PCSTS3::PCSTS3 ("PCSTS3")
 
FileOptionKey const PCSTS3::write_extra ("PCSTS3:write_extra")
 
IntegerOptionKey const PCSTS3::normalization_id ("PCSTS3:normalization_id")
 
BooleanOptionKey const PCSTS4::PCSTS4 ("PCSTS4")
 
FileOptionKey const PCSTS4::write_extra ("PCSTS4:write_extra")
 
IntegerOptionKey const PCSTS4::normalization_id ("PCSTS4:normalization_id")
 
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")
 
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")
 
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 pH::pH ("pH")
 
BooleanOptionKey const pH::pH_mode ("pH:pH_mode")
 
BooleanOptionKey const pH::keep_input_protonation_state ("pH:keep_input_protonation_state")
 
RealOptionKey const pH::value_pH ("pH:value_pH")
 
BooleanOptionKey const pH::calc_pka::calc_pka ("pH:calc_pka")
 
BooleanOptionKey const pH::calc_pka::pka_all ("pH:calc_pka:pka_all")
 
RealVectorOptionKey const pH::calc_pka::pka_for_resnos ("pH:calc_pka:pka_for_resnos")
 
StringOptionKey const pH::calc_pka::pka_for_chainno ("pH:calc_pka:pka_for_chainno")
 
BooleanOptionKey const pH::calc_pka::pH_neighbor_pack ("pH:calc_pka:pH_neighbor_pack")
 
RealOptionKey const pH::calc_pka::pka_rad ("pH:calc_pka:pka_rad")
 
BooleanOptionKey const pH::calc_pka::pH_prepack ("pH:calc_pka:pH_prepack")
 
BooleanOptionKey const pH::calc_pka::pH_relax ("pH:calc_pka:pH_relax")
 
BooleanOptionKey const pH::calc_pka::rotamer_prot_stats ("pH:calc_pka:rotamer_prot_stats")
 
FileVectorOptionKey const pH::pH_unbound ("pH:pH_unbound")
 
BooleanOptionKey const pH::output_raw_scores ("pH:output_raw_scores")
 
BooleanOptionKey const pH::pre_process ("pH:pre_process")
 
StringOptionKey const pH::cognate_partners ("pH:cognate_partners")
 
FileOptionKey const pH::cognate_pdb ("pH:cognate_pdb")
 
BooleanOptionKey const pocket_grid::pocket_grid ("pocket_grid")
 
RealOptionKey const pocket_grid::pocket_grid_size ("pocket_grid:pocket_grid_size")
 
RealOptionKey const pocket_grid::pocket_grid_size_x ("pocket_grid:pocket_grid_size_x")
 
RealOptionKey const pocket_grid::pocket_grid_size_y ("pocket_grid:pocket_grid_size_y")
 
RealOptionKey const pocket_grid::pocket_grid_size_z ("pocket_grid:pocket_grid_size_z")
 
RealOptionKey const pocket_grid::pocket_grid_spacing ("pocket_grid:pocket_grid_spacing")
 
RealOptionKey const pocket_grid::pocket_max_spacing ("pocket_grid:pocket_max_spacing")
 
RealOptionKey const pocket_grid::pocket_min_size ("pocket_grid:pocket_min_size")
 
RealOptionKey const pocket_grid::pocket_max_size ("pocket_grid:pocket_max_size")
 
RealOptionKey const pocket_grid::pocket_probe_radius ("pocket_grid:pocket_probe_radius")
 
StringOptionKey const pocket_grid::central_relax_pdb_num ("pocket_grid:central_relax_pdb_num")
 
IntegerOptionKey const pocket_grid::pocket_ntrials ("pocket_grid:pocket_ntrials")
 
IntegerOptionKey const pocket_grid::pocket_num_angles ("pocket_grid:pocket_num_angles")
 
BooleanOptionKey const pocket_grid::pocket_side ("pocket_grid:pocket_side")
 
BooleanOptionKey const pocket_grid::pocket_dump_pdbs ("pocket_grid:pocket_dump_pdbs")
 
BooleanOptionKey const pocket_grid::pocket_dump_exemplars ("pocket_grid:pocket_dump_exemplars")
 
BooleanOptionKey const pocket_grid::pocket_filter_by_exemplar ("pocket_grid:pocket_filter_by_exemplar")
 
BooleanOptionKey const pocket_grid::pocket_limit_exemplar_color ("pocket_grid:pocket_limit_exemplar_color")
 
BooleanOptionKey const pocket_grid::pocket_limit_small_exemplars ("pocket_grid:pocket_limit_small_exemplars")
 
BooleanOptionKey const pocket_grid::pocket_dump_rama ("pocket_grid:pocket_dump_rama")
 
BooleanOptionKey const pocket_grid::pocket_restrict_size ("pocket_grid:pocket_restrict_size")
 
BooleanOptionKey const pocket_grid::pocket_ignore_buried ("pocket_grid:pocket_ignore_buried")
 
BooleanOptionKey const pocket_grid::pocket_only_buried ("pocket_grid:pocket_only_buried")
 
BooleanOptionKey const pocket_grid::pocket_psp ("pocket_grid:pocket_psp")
 
BooleanOptionKey const pocket_grid::pocket_sps ("pocket_grid:pocket_sps")
 
BooleanOptionKey const pocket_grid::pocket_search13 ("pocket_grid:pocket_search13")
 
RealOptionKey const pocket_grid::pocket_surface_score ("pocket_grid:pocket_surface_score")
 
RealOptionKey const pocket_grid::pocket_surface_dist ("pocket_grid:pocket_surface_dist")
 
RealOptionKey const pocket_grid::pocket_buried_score ("pocket_grid:pocket_buried_score")
 
RealOptionKey const pocket_grid::pocket_buried_dist ("pocket_grid:pocket_buried_dist")
 
RealOptionKey const pocket_grid::pocket_exemplar_vdw_pen ("pocket_grid:pocket_exemplar_vdw_pen")
 
BooleanOptionKey const pocket_grid::pocket_debug_output ("pocket_grid:pocket_debug_output")
 
BooleanOptionKey const pocket_grid::dump_pocketGrid ("pocket_grid:dump_pocketGrid")
 
BooleanOptionKey const pocket_grid::dump_Grid ("pocket_grid:dump_Grid")
 
BooleanOptionKey const pocket_grid::extend_eggshell ("pocket_grid:extend_eggshell")
 
RealOptionKey const pocket_grid::extend_eggshell_dist ("pocket_grid:extend_eggshell_dist")
 
RealOptionKey const pocket_grid::extra_eggshell_dist ("pocket_grid:extra_eggshell_dist")
 
RealOptionKey const pocket_grid::eggshell_dist ("pocket_grid:eggshell_dist")
 
BooleanOptionKey const pocket_grid::reduce_rays ("pocket_grid:reduce_rays")
 
BooleanOptionKey const pocket_grid::pocket_static_grid ("pocket_grid:pocket_static_grid")
 
BooleanOptionKey const pocket_grid::dump_espGrid ("pocket_grid:dump_espGrid")
 
BooleanOptionKey const pocket_grid::dump_connollySurface ("pocket_grid:dump_connollySurface")
 
RealOptionKey const pocket_grid::esp_buffer_dist ("pocket_grid:esp_buffer_dist")
 
BooleanOptionKey const pocket_grid::round_pocketGrid_center ("pocket_grid:round_pocketGrid_center")
 
BooleanOptionKey const gen_pharmacophore::gen_pharmacophore ("gen_pharmacophore")
 
RealOptionKey const gen_pharmacophore::clash_distance_cutoff ("gen_pharmacophore:clash_distance_cutoff")
 
IntegerOptionKey const gen_pharmacophore::ring_sasa_cutoff ("gen_pharmacophore:ring_sasa_cutoff")
 
IntegerOptionKey const gen_pharmacophore::min_num_ring ("gen_pharmacophore:min_num_ring")
 
RealOptionKey const gen_pharmacophore::ring_ring_dist_cutoff ("gen_pharmacophore:ring_ring_dist_cutoff")
 
RealOptionKey const gen_pharmacophore::ring_atm_dist_cutoff ("gen_pharmacophore:ring_atm_dist_cutoff")
 
BooleanOptionKey const fingerprint::fingerprint ("fingerprint")
 
BooleanOptionKey const fingerprint::print_eggshell ("fingerprint:print_eggshell")
 
RealOptionKey const fingerprint::atom_radius_scale ("fingerprint:atom_radius_scale")
 
RealOptionKey const fingerprint::atom_radius_buffer ("fingerprint:atom_radius_buffer")
 
RealOptionKey const fingerprint::packing_weight ("fingerprint:packing_weight")
 
RealOptionKey const fingerprint::dist_cut_off ("fingerprint:dist_cut_off")
 
BooleanOptionKey const fingerprint::include_extrashell_to_set_origin ("fingerprint:include_extrashell_to_set_origin")
 
BooleanOptionKey const fingerprint::include_hydrogens ("fingerprint:include_hydrogens")
 
BooleanOptionKey const fingerprint::multiple_origin ("fingerprint:multiple_origin")
 
BooleanOptionKey const fingerprint::use_DARC_gpu ("fingerprint:use_DARC_gpu")
 
BooleanOptionKey const fingerprint::square_score ("fingerprint:square_score")
 
BooleanOptionKey const fingerprint::darc_components ("fingerprint:darc_components")
 
IntegerOptionKey const fingerprint::set_origin ("fingerprint:set_origin")
 
StringOptionKey const fingerprint::origin_res_num ("fingerprint:origin_res_num")
 
BooleanOptionKey const fingerprint::add_esp ("fingerprint:add_esp")
 
BooleanOptionKey const fingerprint::darc_shape_only ("fingerprint:darc_shape_only")
 
BooleanOptionKey const fingerprint::darc_elsts_only ("fingerprint:darc_elsts_only")
 
RealOptionKey const fingerprint::esp_weight ("fingerprint:esp_weight")
 
RealOptionKey const fingerprint::esp_protein_wt ("fingerprint:esp_protein_wt")
 
RealOptionKey const fingerprint::esp_surface_wt ("fingerprint:esp_surface_wt")
 
BooleanOptionKey const fingerprint::delphi_grid ("fingerprint:delphi_grid")
 
RealOptionKey const fingerprint::cap_e_potential ("fingerprint:cap_e_potential")
 
BooleanOptionKey const fingerprint::return_zero_darc_score ("fingerprint:return_zero_darc_score")
 
BooleanOptionKey const fingerprint::set_surface_esp_to_zero ("fingerprint:set_surface_esp_to_zero")
 
BooleanOptionKey const fingerprint::set_protein_esp_to_zero ("fingerprint:set_protein_esp_to_zero")
 
StringOptionKey const fingerprint::inp_lig ("fingerprint:inp_lig")
 
StringOptionKey const fingerprint::ref_lig ("fingerprint:ref_lig")
 
BooleanOptionKey const ProQ::ProQ ("ProQ")
 
IntegerOptionKey const ProQ::svmmodel ("ProQ:svmmodel")
 
StringOptionKey const ProQ::basename ("ProQ:basename")
 
BooleanOptionKey const ProQ::membrane ("ProQ:membrane")
 
BooleanOptionKey const ProQ::prof_bug ("ProQ:prof_bug")
 
BooleanOptionKey const ProQ::output_feature_vector ("ProQ:output_feature_vector")
 
BooleanOptionKey const ProQ::output_local_prediction ("ProQ:output_local_prediction")
 
StringOptionKey const ProQ::prefix ("ProQ:prefix")
 
BooleanOptionKey const ProQ::use_gzip ("ProQ:use_gzip")
 
RealOptionKey const ProQ::normalize ("ProQ:normalize")
 
BooleanOptionKey const qsar::qsar ("qsar")