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Rosetta Utilities
2014.16.56682
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Rosetta Utilities
2014.16.56682
|
Functions | |
| IntegerOptionKey const | jumps::max_strand_gap_allowed ("jumps:max_strand_gap_allowed") |
| RealOptionKey const | jumps::contact_score ("jumps:contact_score") |
| BooleanOptionKey const | jumps::filter_templates ("jumps:filter_templates") |
| BooleanOptionKey const | templates::templates ("templates") |
| FileOptionKey const | templates::config ("templates:config") |
| BooleanOptionKey const | templates::fix_aligned_residues ("templates:fix_aligned_residues") |
| FileOptionKey const | templates::fix_frag_file ("templates:fix_frag_file") |
| IntegerOptionKey const | templates::fix_margin ("templates:fix_margin") |
| IntegerOptionKey const | templates::min_nr_large_frags ("templates:min_nr_large_frags") |
| IntegerOptionKey const | templates::min_nr_small_frags ("templates:min_nr_small_frags") |
| BooleanOptionKey const | templates::no_pick_fragments ("templates:no_pick_fragments") |
| IntegerOptionKey const | templates::nr_large_copies ("templates:nr_large_copies") |
| IntegerOptionKey const | templates::nr_small_copies ("templates:nr_small_copies") |
| BooleanOptionKey const | templates::pairings ("templates:pairings") |
| BooleanOptionKey const | templates::pick_multiple_sizes ("templates:pick_multiple_sizes") |
| BooleanOptionKey const | templates::strand_constraint ("templates:strand_constraint") |
| BooleanOptionKey const | templates::vary_frag_size ("templates:vary_frag_size") |
| BooleanOptionKey const | templates::no_culling ("templates:no_culling") |
| FileOptionKey const | templates::helix_pairings ("templates:helix_pairings") |
| FileOptionKey const | templates::prefix ("templates:prefix") |
| IntegerOptionKey const | templates::change_movemap ("templates:change_movemap") |
| BooleanOptionKey const | templates::force_native_topology ("templates:force_native_topology") |
| RealOptionKey const | templates::topology_rank_cutoff ("templates:topology_rank_cutoff") |
| IntegerOptionKey const | templates::min_frag_size ("templates:min_frag_size") |
| IntegerOptionKey const | templates::max_shrink ("templates:max_shrink") |
| IntegerOptionKey const | templates::shrink_step ("templates:shrink_step") |
| IntegerOptionKey const | templates::shrink_pos_step ("templates:shrink_pos_step") |
| IntegerOptionKey const | templates::min_padding ("templates:min_padding") |
| IntegerOptionKey const | templates::min_align_pos ("templates:min_align_pos") |
| IntegerOptionKey const | templates::max_align_pos ("templates:max_align_pos") |
| BooleanOptionKey const | templates::cst::cst ("templates:cst") |
| IntegerOptionKey const | templates::cst::topN ("templates:cst:topN") |
| RealOptionKey const | templates::cst::wTopol ("templates:cst:wTopol") |
| RealOptionKey const | templates::cst::wExtern ("templates:cst:wExtern") |
| BooleanOptionKey const | templates::fragsteal::fragsteal ("templates:fragsteal") |
| IntegerOptionKey const | templates::fragsteal::topN ("templates:fragsteal:topN") |
| RealOptionKey const | templates::fragsteal::wTopol ("templates:fragsteal:wTopol") |
| RealOptionKey const | templates::fragsteal::wExtern ("templates:fragsteal:wExtern") |
| BooleanOptionKey const | abrelax::abrelax ("abrelax") |
| BooleanOptionKey const | abrelax::filters ("abrelax:filters") |
| BooleanOptionKey const | abrelax::fail_unclosed ("abrelax:fail_unclosed") |
| BooleanOptionKey const | chemical::chemical ("chemical") |
| StringVectorOptionKey const | chemical::exclude_patches ("chemical:exclude_patches") |
| StringVectorOptionKey const | chemical::include_patches ("chemical:include_patches") |
| BooleanOptionKey const | chemical::enlarge_H_lj ("chemical:enlarge_H_lj") |
| StringVectorOptionKey const | chemical::add_atom_type_set_parameters ("chemical:add_atom_type_set_parameters") |
| StringVectorOptionKey const | chemical::set_atom_properties ("chemical:set_atom_properties") |
| BooleanOptionKey const | score::score_pose_cutpoint_variants ("score:score_pose_cutpoint_variants") |
| BooleanOptionKey const | score::score ("score") |
| StringOptionKey const | score::weights ("score:weights") |
| StringVectorOptionKey const | score::set_weights ("score:set_weights") |
| StringOptionKey const | score::pack_weights ("score:pack_weights") |
| StringOptionKey const | score::soft_wts ("score:soft_wts") |
| BooleanOptionKey const | score::docking_interface_score ("score:docking_interface_score") |
| RealOptionKey const | score::min_score_score ("score:min_score_score") |
| StringOptionKey const | score::custom_atom_pair ("score:custom_atom_pair") |
| FileVectorOptionKey const | score::patch ("score:patch") |
| BooleanOptionKey const | score::empty ("score:empty") |
| RealOptionKey const | score::fa_max_dis ("score:fa_max_dis") |
| BooleanOptionKey const | score::fa_Hatr ("score:fa_Hatr") |
| BooleanOptionKey const | score::no_smooth_etables ("score:no_smooth_etables") |
| RealOptionKey const | score::etable_lr ("score:etable_lr") |
| BooleanOptionKey const | score::no_lk_polar_desolvation ("score:no_lk_polar_desolvation") |
| StringOptionKey const | score::input_etables ("score:input_etables") |
| StringOptionKey const | score::output_etables ("score:output_etables") |
| BooleanOptionKey const | score::analytic_etable_evaluation ("score:analytic_etable_evaluation") |
| RealOptionKey const | score::rms_target ("score:rms_target") |
| BooleanOptionKey const | score::ramaneighbors ("score:ramaneighbors") |
| BooleanOptionKey const | score::rama_score_nonstandard_connections ("score:rama_score_nonstandard_connections") |
| StringOptionKey const | score::optH_weights ("score:optH_weights") |
| StringOptionKey const | score::optH_patch ("score:optH_patch") |
| StringOptionKey const | score::hbond_params ("score:hbond_params") |
| BooleanOptionKey const | score::hbond_disable_bbsc_exclusion_rule ("score:hbond_disable_bbsc_exclusion_rule") |
| IntegerOptionKey const | score::symE_units ("score:symE_units") |
| RealOptionKey const | score::symE_bonus ("score:symE_bonus") |
| RealOptionKey const | score::NV_lbound ("score:NV_lbound") |
| RealOptionKey const | score::NV_ubound ("score:NV_ubound") |
| StringOptionKey const | score::NV_table ("score:NV_table") |
| BooleanOptionKey const | score::disable_orientation_dependent_rna_ch_o_bonds ("score:disable_orientation_dependent_rna_ch_o_bonds") |
| StringOptionKey const | score::rna_torsion_potential ("score:rna_torsion_potential") |
| BooleanOptionKey const | score::rna_torsion_skip_chainbreak ("score:rna_torsion_skip_chainbreak") |
| StringOptionKey const | score::rna_chemical_shift_exp_data ("score:rna_chemical_shift_exp_data") |
| StringOptionKey const | score::rna_chemical_shift_H5_prime_mode ("score:rna_chemical_shift_H5_prime_mode") |
| IntegerVectorOptionKey const | score::rna_chemical_shift_include_res ("score:rna_chemical_shift_include_res") |
| BooleanOptionKey const | score::use_2prime_OH_potential ("score:use_2prime_OH_potential") |
| BooleanOptionKey const | score::include_neighbor_base_stacks ("score:include_neighbor_base_stacks") |
| BooleanOptionKey const | score::find_neighbors_3dgrid ("score:find_neighbors_3dgrid") |
| BooleanOptionKey const | score::find_neighbors_stripehash ("score:find_neighbors_stripehash") |
| StringOptionKey const | score::seqdep_refene_fname ("score:seqdep_refene_fname") |
| StringOptionKey const | score::secondary_seqdep_refene_fname ("score:secondary_seqdep_refene_fname") |
| BooleanOptionKey const | score::exact_occ_pairwise ("score:exact_occ_pairwise") |
| BooleanOptionKey const | score::exact_occ_skip_Hbonders ("score:exact_occ_skip_Hbonders") |
| BooleanOptionKey const | score::exact_occ_include_Hbond_contribution ("score:exact_occ_include_Hbond_contribution") |
| BooleanOptionKey const | score::exact_occ_pairwise_by_res ("score:exact_occ_pairwise_by_res") |
| BooleanOptionKey const | score::exact_occ_split_between_res ("score:exact_occ_split_between_res") |
| BooleanOptionKey const | score::exact_occ_self_res_no_occ ("score:exact_occ_self_res_no_occ") |
| RealOptionKey const | score::exact_occ_radius_scaling ("score:exact_occ_radius_scaling") |
| StringVectorOptionKey const | score::ref_offsets ("score:ref_offsets") |
| RealOptionKey const | score::ref_offset ("score:ref_offset") |
| BooleanOptionKey const | score::output_residue_energies ("score:output_residue_energies") |
| StringOptionKey const | score::fa_custom_pair_distance_file ("score:fa_custom_pair_distance_file") |
| RealOptionKey const | score::disulf_matching_probe ("score:disulf_matching_probe") |
| RealVectorOptionKey const | score::bonded_params ("score:bonded_params") |
| StringOptionKey const | score::bonded_params_dir ("score:bonded_params_dir") |
| StringOptionKey const | score::extra_improper_file ("score:extra_improper_file") |
| RealOptionKey const | score::pro_close_planar_constraint ("score:pro_close_planar_constraint") |
| BooleanOptionKey const | score::linear_bonded_potential ("score:linear_bonded_potential") |
| BooleanOptionKey const | score::geom_sol_correct_acceptor_base ("score:geom_sol_correct_acceptor_base") |
| RealOptionKey const | score::free_sugar_bonus ("score:free_sugar_bonus") |
| RealOptionKey const | score::syn_G_potential_bonus ("score:syn_G_potential_bonus") |
| RealOptionKey const | score::pack_phosphate_penalty ("score:pack_phosphate_penalty") |
| RealOptionKey const | score::free_side_chain_bonus ("score:free_side_chain_bonus") |
| IntegerVectorOptionKey const | score::rg_local_span ("score:rg_local_span") |
| BooleanOptionKey const | score::unmodifypot ("score:unmodifypot") |
| RealOptionKey const | score::conc ("score:conc") |
| RealOptionKey const | score::loop_fixed_cost ("score:loop_fixed_cost") |
| BooleanOptionKey const | score::saxs::saxs ("score:saxs") |
| RealOptionKey const | score::saxs::min_score ("score:saxs:min_score") |
| StringOptionKey const | score::saxs::custom_ff ("score:saxs:custom_ff") |
| StringOptionKey const | score::saxs::print_i_calc ("score:saxs:print_i_calc") |
| FileOptionKey const | score::saxs::ref_fa_spectrum ("score:saxs:ref_fa_spectrum") |
| FileOptionKey const | score::saxs::ref_cen_spectrum ("score:saxs:ref_cen_spectrum") |
| FileOptionKey const | score::saxs::ref_spectrum ("score:saxs:ref_spectrum") |
| FileOptionKey const | score::saxs::ref_pddf ("score:saxs:ref_pddf") |
| BooleanOptionKey const | score::saxs::skip_hydrogens ("score:saxs:skip_hydrogens") |
| RealOptionKey const | score::saxs::d_min ("score:saxs:d_min") |
| RealOptionKey const | score::saxs::d_max ("score:saxs:d_max") |
| RealOptionKey const | score::saxs::d_step ("score:saxs:d_step") |
| RealOptionKey const | score::saxs::q_min ("score:saxs:q_min") |
| RealOptionKey const | score::saxs::q_max ("score:saxs:q_max") |
| RealOptionKey const | score::saxs::q_step ("score:saxs:q_step") |
| BooleanOptionKey const | score::saxs::fit_pddf_area ("score:saxs:fit_pddf_area") |
| IntegerVectorOptionKey const | score::sidechain_buried ("score:sidechain_buried") |
| IntegerVectorOptionKey const | score::sidechain_exposed ("score:sidechain_exposed") |
| RealOptionKey const | score::elec_min_dis ("score:elec_min_dis") |
| RealOptionKey const | score::elec_max_dis ("score:elec_max_dis") |
| RealOptionKey const | score::elec_die ("score:elec_die") |
| BooleanOptionKey const | score::elec_r_option ("score:elec_r_option") |
| RealOptionKey const | score::intrares_elec_correction_scale ("score:intrares_elec_correction_scale") |
| BooleanOptionKey const | score::smooth_fa_elec ("score:smooth_fa_elec") |
| RealOptionKey const | score::facts_GBpair_cut ("score:facts_GBpair_cut") |
| RealOptionKey const | score::facts_kappa ("score:facts_kappa") |
| IntegerOptionKey const | score::facts_asp_patch ("score:facts_asp_patch") |
| BooleanOptionKey const | score::facts_plane_to_self ("score:facts_plane_to_self") |
| RealOptionKey const | score::facts_saltbridge_correction ("score:facts_saltbridge_correction") |
| RealVectorOptionKey const | score::facts_dshift ("score:facts_dshift") |
| RealOptionKey const | score::facts_die ("score:facts_die") |
| BooleanOptionKey const | score::facts_binding_affinity ("score:facts_binding_affinity") |
| BooleanOptionKey const | score::facts_intrascale_by_level ("score:facts_intrascale_by_level") |
| RealVectorOptionKey const | score::facts_intbb_elec_scale ("score:facts_intbb_elec_scale") |
| RealVectorOptionKey const | score::facts_intbb_solv_scale ("score:facts_intbb_solv_scale") |
| RealVectorOptionKey const | score::facts_adjbb_elec_scale ("score:facts_adjbb_elec_scale") |
| RealVectorOptionKey const | score::facts_adjbb_solv_scale ("score:facts_adjbb_solv_scale") |
| RealVectorOptionKey const | score::facts_intbs_elec_scale ("score:facts_intbs_elec_scale") |
| RealVectorOptionKey const | score::facts_intbs_solv_scale ("score:facts_intbs_solv_scale") |
| RealVectorOptionKey const | score::facts_adjbs_elec_scale ("score:facts_adjbs_elec_scale") |
| RealVectorOptionKey const | score::facts_adjbs_solv_scale ("score:facts_adjbs_solv_scale") |
| RealVectorOptionKey const | score::facts_intsc_elec_scale ("score:facts_intsc_elec_scale") |
| RealVectorOptionKey const | score::facts_intsc_solv_scale ("score:facts_intsc_solv_scale") |
| StringOptionKey const | score::facts_charge_dir ("score:facts_charge_dir") |
| StringOptionKey const | score::facts_eff_charge_dir ("score:facts_eff_charge_dir") |
| StringVectorOptionKey const | score::facts_plane_aa ("score:facts_plane_aa") |
| StringOptionKey const | score::facts_eq_type ("score:facts_eq_type") |
| BooleanOptionKey const | score::length_dep_srbb ("score:length_dep_srbb") |
| RealOptionKey const | score::ldsrbb_low_scale ("score:ldsrbb_low_scale") |
| RealOptionKey const | score::ldsrbb_high_scale ("score:ldsrbb_high_scale") |
| IntegerOptionKey const | score::ldsrbb_minlength ("score:ldsrbb_minlength") |
| IntegerOptionKey const | score::ldsrbb_maxlength ("score:ldsrbb_maxlength") |
| StringOptionKey const | score::nmer_ref_energies ("score:nmer_ref_energies") |
| StringOptionKey const | score::nmer_ref_energies_list ("score:nmer_ref_energies_list") |
| StringOptionKey const | score::nmer_pssm ("score:nmer_pssm") |
| StringOptionKey const | score::nmer_pssm_list ("score:nmer_pssm_list") |
| RealOptionKey const | score::nmer_pssm_scorecut ("score:nmer_pssm_scorecut") |
| StringOptionKey const | score::nmer_svm ("score:nmer_svm") |
| StringOptionKey const | score::nmer_svm_list ("score:nmer_svm_list") |
| RealOptionKey const | score::nmer_svm_scorecut ("score:nmer_svm_scorecut") |
| StringOptionKey const | score::nmer_svm_aa_matrix ("score:nmer_svm_aa_matrix") |
| IntegerOptionKey const | score::nmer_svm_term_length ("score:nmer_svm_term_length") |
| BooleanOptionKey const | score::nmer_svm_pssm_feat ("score:nmer_svm_pssm_feat") |
| IntegerOptionKey const | score::nmer_ref_seq_length ("score:nmer_ref_seq_length") |
| BooleanOptionKey const | score::just_calc_rmsd ("score:just_calc_rmsd") |
| 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 | corrections::corrections ("corrections") |
| BooleanOptionKey const | corrections::beta ("corrections:beta") |
| BooleanOptionKey const | corrections::correct ("corrections:correct") |
| BooleanOptionKey const | corrections::hbond_sp2_correction ("corrections:hbond_sp2_correction") |
| BooleanOptionKey const | corrections::facts_default ("corrections:facts_default") |
| BooleanOptionKey const | corrections::score::score ("corrections:score") |
| BooleanOptionKey const | corrections::score::bbdep_omega ("corrections:score:bbdep_omega") |
| BooleanOptionKey const | corrections::score::bbdep_bond_params ("corrections:score:bbdep_bond_params") |
| BooleanOptionKey const | corrections::score::bbdep_bond_devs ("corrections:score:bbdep_bond_devs") |
| BooleanOptionKey const | corrections::score::no_his_his_pairE ("corrections:score:no_his_his_pairE") |
| BooleanOptionKey const | corrections::score::no_his_DE_pairE ("corrections:score:no_his_DE_pairE") |
| BooleanOptionKey const | corrections::score::hbond_His_Phil_fix ("corrections:score:hbond_His_Phil_fix") |
| BooleanOptionKey const | corrections::score::helix_hb_06_2009 ("corrections:score:helix_hb_06_2009") |
| BooleanOptionKey const | corrections::score::use_incorrect_hbond_deriv ("corrections:score:use_incorrect_hbond_deriv") |
| StringOptionKey const | corrections::score::p_aa_pp ("corrections:score:p_aa_pp") |
| BooleanOptionKey const | corrections::score::p_aa_pp_nogridshift ("corrections:score:p_aa_pp_nogridshift") |
| BooleanOptionKey const | corrections::score::rama_not_squared ("corrections:score:rama_not_squared") |
| FileOptionKey const | corrections::score::rama_map ("corrections:score:rama_map") |
| BooleanOptionKey const | corrections::score::cenrot ("corrections:score:cenrot") |
| BooleanOptionKey const | corrections::score::dun10 ("corrections:score:dun10") |
| StringOptionKey const | corrections::score::dun10_dir ("corrections:score:dun10_dir") |
| StringOptionKey const | corrections::score::dun02_file ("corrections:score:dun02_file") |
| StringOptionKey const | corrections::score::ch_o_bond_potential ("corrections:score:ch_o_bond_potential") |
| BooleanOptionKey const | corrections::score::fa_elec_co_only ("corrections:score:fa_elec_co_only") |
| RealOptionKey const | corrections::score::lj_hbond_hdis ("corrections:score:lj_hbond_hdis") |
| RealOptionKey const | corrections::score::lj_hbond_OH_donor_dis ("corrections:score:lj_hbond_OH_donor_dis") |
| BooleanOptionKey const | corrections::score::score12prime ("corrections:score:score12prime") |
| RealOptionKey const | corrections::score::hbond_energy_shift ("corrections:score:hbond_energy_shift") |
| RealOptionKey const | corrections::score::hb_sp2_BAH180_rise ("corrections:score:hb_sp2_BAH180_rise") |
| RealOptionKey const | corrections::score::hb_sp2_outer_width ("corrections:score:hb_sp2_outer_width") |
| BooleanOptionKey const | corrections::score::hb_sp2_chipen ("corrections:score:hb_sp2_chipen") |
| BooleanOptionKey const | corrections::score::hbond_measure_sp3acc_BAH_from_hvy ("corrections:score:hbond_measure_sp3acc_BAH_from_hvy") |
| BooleanOptionKey const | corrections::score::hb_fade_energy ("corrections:score:hb_fade_energy") |
| BooleanOptionKey const | corrections::score::use_bicubic_interpolation ("corrections:score:use_bicubic_interpolation") |
| BooleanOptionKey const | corrections::score::dun_normsd ("corrections:score:dun_normsd") |
| BooleanOptionKey const | corrections::score::dun_entropy_correction ("corrections:score:dun_entropy_correction") |
| BooleanOptionKey const | corrections::chemical::chemical ("corrections:chemical") |
| BooleanOptionKey const | corrections::chemical::icoor_05_2009 ("corrections:chemical:icoor_05_2009") |
| BooleanOptionKey const | corrections::chemical::parse_charge ("corrections:chemical:parse_charge") |
| BooleanOptionKey const | corrections::chemical::expand_st_chi2sampling ("corrections:chemical:expand_st_chi2sampling") |
| BooleanOptionKey const | mistakes::mistakes ("mistakes") |
| BooleanOptionKey const | mistakes::restore_pre_talaris_2013_behavior ("mistakes:restore_pre_talaris_2013_behavior") |
| BooleanOptionKey const | mistakes::chemical::chemical ("mistakes:chemical") |
| BooleanOptionKey const | mistakes::chemical::pre_talaris2013_geometries ("mistakes:chemical:pre_talaris2013_geometries") |
| BooleanOptionKey const | willmatch::willmatch ("willmatch") |
| RealOptionKey const | willmatch::arg_dun_th ("willmatch:arg_dun_th") |
| RealOptionKey const | willmatch::asp_dun_th ("willmatch:asp_dun_th") |
| RealOptionKey const | willmatch::glu_dun_th ("willmatch:glu_dun_th") |
| RealOptionKey const | willmatch::lys_dun_th ("willmatch:lys_dun_th") |
| BooleanOptionKey const | willmatch::usecache ("willmatch:usecache") |
| StringVectorOptionKey const | willmatch::write_reduced_matchset ("willmatch:write_reduced_matchset") |
| RealOptionKey const | willmatch::interface_size ("willmatch:interface_size") |
| RealOptionKey const | willmatch::max_dis_any ("willmatch:max_dis_any") |
| RealOptionKey const | willmatch::max_dis_all ("willmatch:max_dis_all") |
| RealOptionKey const | willmatch::max_dis_hb ("willmatch:max_dis_hb") |
| RealOptionKey const | willmatch::min_dis_hb ("willmatch:min_dis_hb") |
| RealOptionKey const | willmatch::max_dis_hb_colinear ("willmatch:max_dis_hb_colinear") |
| RealOptionKey const | willmatch::max_dis_metal ("willmatch:max_dis_metal") |
| RealOptionKey const | willmatch::max_ang_metal ("willmatch:max_ang_metal") |
| RealOptionKey const | willmatch::clash_dis ("willmatch:clash_dis") |
| RealOptionKey const | willmatch::c2_linker_dist ("willmatch:c2_linker_dist") |
| RealOptionKey const | willmatch::identical_match_dis ("willmatch:identical_match_dis") |
| RealOptionKey const | willmatch::chi1_increment ("willmatch:chi1_increment") |
| RealOptionKey const | willmatch::chi2_increment ("willmatch:chi2_increment") |
| RealOptionKey const | willmatch::c2_symm_increment ("willmatch:c2_symm_increment") |
| RealOptionKey const | willmatch::cb_sasa_thresh ("willmatch:cb_sasa_thresh") |
| BooleanOptionKey const | willmatch::design_interface ("willmatch:design_interface") |
| FileOptionKey const | willmatch::chilist ("willmatch:chilist") |
| FileOptionKey const | willmatch::fixed_res ("willmatch:fixed_res") |
| FileOptionKey const | willmatch::native1 ("willmatch:native1") |
| FileOptionKey const | willmatch::native2 ("willmatch:native2") |
| FileOptionKey const | willmatch::exclude_res1 ("willmatch:exclude_res1") |
| FileOptionKey const | willmatch::exclude_res2 ("willmatch:exclude_res2") |
| FileOptionKey const | willmatch::taglist ("willmatch:taglist") |
| IntegerVectorOptionKey const | willmatch::residues ("willmatch:residues") |
| BooleanOptionKey const | willmatch::symmetry_d2 ("willmatch:symmetry_d2") |
| BooleanOptionKey const | willmatch::symmetry_c2_dock ("willmatch:symmetry_c2_dock") |
| IntegerVectorOptionKey const | willmatch::splitwork ("willmatch:splitwork") |
| BooleanOptionKey const | willmatch::exclude_ala ("willmatch:exclude_ala") |
| RealOptionKey const | willmatch::match_overlap_dis ("willmatch:match_overlap_dis") |
| RealOptionKey const | willmatch::match_overlap_ang ("willmatch:match_overlap_ang") |
| IntegerVectorOptionKey const | willmatch::forbid_residues ("willmatch:forbid_residues") |
| RealVectorOptionKey const | willmatch::poi ("willmatch:poi") |
| RealOptionKey const | willmatch::poidis ("willmatch:poidis") |
| BooleanOptionKey const | willmatch::homodimer ("willmatch:homodimer") |
| RealOptionKey const | willmatch::fa_dun_thresh ("willmatch:fa_dun_thresh") |
| 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") |
| RealOptionKey const | holes::cav_shrink ("holes:cav_shrink") |
| StringOptionKey const | holes::minimize ("holes:minimize") |
| BooleanOptionKey const | holes::debug ("holes:debug") |
| 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") |
| RealOptionKey const | packstat::max_cav_ball_radius ("packstat:max_cav_ball_radius") |
| BooleanOptionKey const | crossmatch::crossmatch ("crossmatch") |
| StringVectorOptionKey const | crossmatch::write_reduced_matchset ("crossmatch:write_reduced_matchset") |
| IntegerOptionKey const | crossmatch::interface_size ("crossmatch:interface_size") |
| RealOptionKey const | crossmatch::max_dis_any ("crossmatch:max_dis_any") |
| RealOptionKey const | crossmatch::max_dis_all ("crossmatch:max_dis_all") |
| RealOptionKey const | crossmatch::max_dis_metal ("crossmatch:max_dis_metal") |
| RealOptionKey const | crossmatch::clash_dis ("crossmatch:clash_dis") |
| RealOptionKey const | crossmatch::identical_match_dis ("crossmatch:identical_match_dis") |
| BooleanOptionKey const | smhybrid::smhybrid ("smhybrid") |
| BooleanOptionKey const | smhybrid::add_cavities ("smhybrid:add_cavities") |
| BooleanOptionKey const | smhybrid::abinitio_design ("smhybrid:abinitio_design") |
| BooleanOptionKey const | smhybrid::fa_refine ("smhybrid:fa_refine") |
| BooleanOptionKey const | smhybrid::virtual_nterm ("smhybrid:virtual_nterm") |
| BooleanOptionKey const | smhybrid::debug ("smhybrid:debug") |
| BooleanOptionKey const | smhybrid::refine ("smhybrid:refine") |
| BooleanOptionKey const | smhybrid::filter ("smhybrid:filter") |
| BooleanOptionKey const | smhybrid::floating_scs_rep ("smhybrid:floating_scs_rep") |
| BooleanOptionKey const | smhybrid::flxbb ("smhybrid:flxbb") |
| BooleanOptionKey const | smhybrid::centroid_all_val ("smhybrid:centroid_all_val") |
| BooleanOptionKey const | smhybrid::subsubs_attract ("smhybrid:subsubs_attract") |
| BooleanOptionKey const | smhybrid::linker_cst ("smhybrid:linker_cst") |
| BooleanOptionKey const | smhybrid::pseudosym ("smhybrid:pseudosym") |
| BooleanOptionKey const | smhybrid::design_linker ("smhybrid:design_linker") |
| BooleanOptionKey const | smhybrid::design ("smhybrid:design") |
| BooleanOptionKey const | smhybrid::restrict_design_to_interface ("smhybrid:restrict_design_to_interface") |
| BooleanOptionKey const | smhybrid::restrict_design_to_subsub_interface ("smhybrid:restrict_design_to_subsub_interface") |
| BooleanOptionKey const | smhybrid::design_hydrophobic ("smhybrid:design_hydrophobic") |
| BooleanOptionKey const | smhybrid::add_metal_at_0 ("smhybrid:add_metal_at_0") |
| IntegerOptionKey const | smhybrid::nres_mono ("smhybrid:nres_mono") |
| IntegerOptionKey const | smhybrid::abinitio_cycles ("smhybrid:abinitio_cycles") |
| IntegerOptionKey const | smhybrid::primary_subsubunit ("smhybrid:primary_subsubunit") |
| IntegerOptionKey const | smhybrid::minbb ("smhybrid:minbb") |
| IntegerOptionKey const | smhybrid::switch_concert_sub ("smhybrid:switch_concert_sub") |
| RealOptionKey const | smhybrid::temperature ("smhybrid:temperature") |
| BooleanOptionKey const | smhybrid::inter_subsub_cst ("smhybrid:inter_subsub_cst") |
| RealOptionKey const | smhybrid::rb_mag ("smhybrid:rb_mag") |
| StringOptionKey const | smhybrid::ss ("smhybrid:ss") |
| FileOptionKey const | smhybrid::symm_def_template ("smhybrid:symm_def_template") |
| FileOptionKey const | smhybrid::symm_def_template_reduced ("smhybrid:symm_def_template_reduced") |
| IntegerVectorOptionKey const | smhybrid::attach_as_sc ("smhybrid:attach_as_sc") |
| IntegerVectorOptionKey const | smhybrid::attach_as_sc_sub ("smhybrid:attach_as_sc_sub") |
| IntegerVectorOptionKey const | smhybrid::inversion_subs ("smhybrid:inversion_subs") |
| BooleanVectorOptionKey const | smhybrid::chainbreaks ("smhybrid:chainbreaks") |
| StringVectorOptionKey const | smhybrid::design_res_files ("smhybrid:design_res_files") |
| StringVectorOptionKey const | smhybrid::fixed_res_files ("smhybrid:fixed_res_files") |
| StringVectorOptionKey const | smhybrid::frag_res_files ("smhybrid:frag_res_files") |
| StringVectorOptionKey const | smhybrid::scattach_res_files ("smhybrid:scattach_res_files") |
| StringVectorOptionKey const | smhybrid::rep_edge_files ("smhybrid:rep_edge_files") |
| StringVectorOptionKey const | smhybrid::virtual_res_files ("smhybrid:virtual_res_files") |
| StringVectorOptionKey const | smhybrid::jumpcut_files ("smhybrid:jumpcut_files") |
| StringVectorOptionKey const | smhybrid::cst_sub_files ("smhybrid:cst_sub_files") |
| StringVectorOptionKey const | smhybrid::symm_file_tag ("smhybrid:symm_file_tag") |
| StringVectorOptionKey const | smhybrid::attach_atom ("smhybrid:attach_atom") |
| StringVectorOptionKey const | smhybrid::add_res_before ("smhybrid:add_res_before") |
| StringVectorOptionKey const | smhybrid::add_res_after ("smhybrid:add_res_after") |
| StringVectorOptionKey const | smhybrid::add_ss_before ("smhybrid:add_ss_before") |
| StringVectorOptionKey const | smhybrid::add_ss_after ("smhybrid:add_ss_after") |
| StringVectorOptionKey const | smhybrid::add_atom_at_cen ("smhybrid:add_atom_at_cen") |
| StringVectorOptionKey const | smhybrid::attach_rsd ("smhybrid:attach_rsd") |
| BooleanOptionKey const | evolution::evolution ("evolution") |
| FileVectorOptionKey const | evolution::parentlist ("evolution:parentlist") |
| FileVectorOptionKey const | evolution::childlist ("evolution:childlist") |
| StringOptionKey const | evolution::action ("evolution:action") |
| RealOptionKey const | evolution::rms_threshold ("evolution:rms_threshold") |
| RealOptionKey const | evolution::rms_topmargin ("evolution:rms_topmargin") |
| StringOptionKey const | evolution::targetdir ("evolution:targetdir") |
| RealOptionKey const | evolution::padding_score_filter ("evolution:padding_score_filter") |
| RealOptionKey const | evolution::padding_stage2_filter ("evolution:padding_stage2_filter") |
| BooleanOptionKey const | cluster::cluster ("cluster") |
| BooleanOptionKey const | cluster::lite ("cluster:lite") |
| RealOptionKey const | cluster::input_score_filter ("cluster:input_score_filter") |
| RealOptionKey const | cluster::output_score_filter ("cluster:output_score_filter") |
| IntegerVectorOptionKey const | cluster::exclude_res ("cluster:exclude_res") |
| RealOptionKey const | cluster::thinout_factor ("cluster:thinout_factor") |
| IntegerOptionKey const | cluster::max_cluster_seeds ("cluster:max_cluster_seeds") |
| RealOptionKey const | cluster::radius ("cluster:radius") |
| IntegerOptionKey const | cluster::limit_cluster_size ("cluster:limit_cluster_size") |
| RealOptionKey const | cluster::limit_cluster_size_percent ("cluster:limit_cluster_size_percent") |
| RealOptionKey const | cluster::random_limit_cluster_size_percent ("cluster:random_limit_cluster_size_percent") |
| IntegerOptionKey const | cluster::limit_clusters ("cluster:limit_clusters") |
| IntegerOptionKey const | cluster::limit_total_structures ("cluster:limit_total_structures") |
| IntegerOptionKey const | cluster::max_total_cluster ("cluster:max_total_cluster") |
| BooleanOptionKey const | cluster::gdtmm ("cluster:gdtmm") |
| BooleanOptionKey const | cluster::sort_groups_by_energy ("cluster:sort_groups_by_energy") |
| BooleanOptionKey const | cluster::sort_groups_by_size ("cluster:sort_groups_by_size") |
| BooleanOptionKey const | cluster::remove_singletons ("cluster:remove_singletons") |
| BooleanOptionKey const | cluster::export_only_low ("cluster:export_only_low") |
| BooleanOptionKey const | cluster::remove_highest_energy_member ("cluster:remove_highest_energy_member") |
| BooleanOptionKey const | cluster::idealize_final_structures ("cluster:idealize_final_structures") |
| IntegerOptionKey const | cluster::limit_dist_matrix ("cluster:limit_dist_matrix") |
| BooleanOptionKey const | cluster::make_ensemble_cst ("cluster:make_ensemble_cst") |
| BooleanOptionKey const | cluster::hotspot_hash ("cluster:hotspot_hash") |
| BooleanOptionKey const | cluster::loops ("cluster:loops") |
| RealOptionKey const | cluster::population_weight ("cluster:population_weight") |
| StringOptionKey const | cluster::template_scores ("cluster:template_scores") |
| IntegerOptionKey const | cluster::K_level ("cluster:K_level") |
| RealVectorOptionKey const | cluster::K_radius ("cluster:K_radius") |
| IntegerVectorOptionKey const | cluster::K_n_cluster ("cluster:K_n_cluster") |
| StringVectorOptionKey const | cluster::K_style ("cluster:K_style") |
| RealOptionKey const | cluster::K_threshold ("cluster:K_threshold") |
| IntegerOptionKey const | cluster::K_n_sub ("cluster:K_n_sub") |
| IntegerOptionKey const | cluster::K_deque_size ("cluster:K_deque_size") |
| IntegerOptionKey const | cluster::K_deque_level ("cluster:K_deque_level") |
| BooleanOptionKey const | cluster::K_redundant ("cluster:K_redundant") |
| BooleanOptionKey const | cluster::K_not_fit_xyz ("cluster:K_not_fit_xyz") |
| BooleanOptionKey const | cluster::K_save_headers ("cluster:K_save_headers") |
| RealOptionKey const | cluster::score_diff_cut ("cluster:score_diff_cut") |
| BooleanOptionKey const | cluster::auto_tune ("cluster:auto_tune") |
| BooleanOptionKey const | rescore::rescore ("rescore") |
| BooleanOptionKey const | rescore::pose_metrics ("rescore:pose_metrics") |
| BooleanOptionKey const | rescore::assign_ss ("rescore:assign_ss") |
| BooleanOptionKey const | rescore::skip ("rescore:skip") |
| BooleanOptionKey const | rescore::verbose ("rescore:verbose") |
| StringOptionKey const | rescore::msms_analysis ("rescore:msms_analysis") |
| BooleanOptionKey const | mc::mc ("mc") |
| StringOptionKey const | mc::hierarchical_pool ("mc:hierarchical_pool") |
| FileOptionKey const | mc::read_structures_into_pool ("mc:read_structures_into_pool") |
| IntegerOptionKey const | mc::convergence_check_frequency ("mc:convergence_check_frequency") |
| FileOptionKey const | mc::known_structures ("mc:known_structures") |
| RealOptionKey const | mc::max_rmsd_against_known_structures ("mc:max_rmsd_against_known_structures") |
| IntegerVectorOptionKey const | mc::excluded_residues_from_rmsd ("mc:excluded_residues_from_rmsd") |
| IntegerOptionKey const | mc::heat_convergence_check ("mc:heat_convergence_check") |
| BooleanOptionKey const | batch_relax::batch_relax ("batch_relax") |
| IntegerOptionKey const | batch_relax::batch_size ("batch_relax:batch_size") |
| BooleanOptionKey const | relax::relax ("relax") |
| BooleanOptionKey const | relax::fast ("relax:fast") |
| BooleanOptionKey const | relax::thorough ("relax:thorough") |
| BooleanOptionKey const | relax::membrane ("relax:membrane") |
| BooleanOptionKey const | relax::centroid_mode ("relax:centroid_mode") |
| IntegerOptionKey const | relax::default_repeats ("relax:default_repeats") |
| BooleanOptionKey const | relax::dualspace ("relax:dualspace") |
| BooleanOptionKey const | relax::ramady ("relax:ramady") |
| RealOptionKey const | relax::ramady_rms_limit ("relax:ramady_rms_limit") |
| RealOptionKey const | relax::ramady_cutoff ("relax:ramady_cutoff") |
| IntegerOptionKey const | relax::ramady_max_rebuild ("relax:ramady_max_rebuild") |
| BooleanOptionKey const | relax::ramady_force ("relax:ramady_force") |
| FileOptionKey const | relax::script ("relax:script") |
| IntegerOptionKey const | relax::script_max_accept ("relax:script_max_accept") |
| BooleanOptionKey const | relax::superimpose_to_native ("relax:superimpose_to_native") |
| FileOptionKey const | relax::superimpose_to_file ("relax:superimpose_to_file") |
| BooleanOptionKey const | relax::constrain_relax_to_native_coords ("relax:constrain_relax_to_native_coords") |
| BooleanOptionKey const | relax::constrain_relax_to_start_coords ("relax:constrain_relax_to_start_coords") |
| BooleanOptionKey const | relax::coord_constrain_sidechains ("relax:coord_constrain_sidechains") |
| RealOptionKey const | relax::sc_cst_maxdist ("relax:sc_cst_maxdist") |
| BooleanOptionKey const | relax::limit_aroma_chi2 ("relax:limit_aroma_chi2") |
| BooleanOptionKey const | relax::respect_resfile ("relax:respect_resfile") |
| BooleanOptionKey const | relax::bb_move ("relax:bb_move") |
| BooleanOptionKey const | relax::chi_move ("relax:chi_move") |
| BooleanOptionKey const | relax::jump_move ("relax:jump_move") |
| BooleanOptionKey const | relax::dna_move ("relax:dna_move") |
| BooleanOptionKey const | relax::fix_omega ("relax:fix_omega") |
| BooleanOptionKey const | relax::minimize_bond_lengths ("relax:minimize_bond_lengths") |
| BooleanOptionKey const | relax::minimize_bond_angles ("relax:minimize_bond_angles") |
| IntegerOptionKey const | relax::minimize_bondlength_subset ("relax:minimize_bondlength_subset") |
| IntegerOptionKey const | relax::minimize_bondangle_subset ("relax:minimize_bondangle_subset") |
| StringOptionKey const | relax::min_type ("relax:min_type") |
| BooleanOptionKey const | relax::cartesian ("relax:cartesian") |
| RealOptionKey const | relax::chainbreak_weight ("relax:chainbreak_weight") |
| RealOptionKey const | relax::linear_chainbreak_weight ("relax:linear_chainbreak_weight") |
| RealOptionKey const | relax::overlap_chainbreak_weight ("relax:overlap_chainbreak_weight") |
| BooleanOptionKey const | relax::classic ("relax:classic") |
| FileOptionKey const | relax::sequence_file ("relax:sequence_file") |
| BooleanOptionKey const | relax::quick ("relax:quick") |
| BooleanOptionKey const | relax::sequence ("relax:sequence") |
| IntegerOptionKey const | relax::minirelax_repeats ("relax:minirelax_repeats") |
| RealOptionKey const | relax::minirelax_sdev ("relax:minirelax_sdev") |
| BooleanOptionKey const | relax::wobblemoves ("relax:wobblemoves") |
| FileOptionKey const | relax::constrain_relax_segments ("relax:constrain_relax_segments") |
| RealOptionKey const | relax::coord_cst_width ("relax:coord_cst_width") |
| RealOptionKey const | relax::coord_cst_stdev ("relax:coord_cst_stdev") |
| BooleanOptionKey const | relax::ramp_constraints ("relax:ramp_constraints") |
| RealOptionKey const | relax::energycut ("relax:energycut") |
| BooleanOptionKey const | relax::mini ("relax:mini") |
| IntegerOptionKey const | relax::stage1_ramp_cycles ("relax:stage1_ramp_cycles") |
| IntegerOptionKey const | relax::stage1_ramp_inner_cycles ("relax:stage1_ramp_inner_cycles") |
| IntegerOptionKey const | relax::stage2_repack_period ("relax:stage2_repack_period") |
| IntegerOptionKey const | relax::stage2_cycles ("relax:stage2_cycles") |
| RealOptionKey const | relax::min_tolerance ("relax:min_tolerance") |
| IntegerOptionKey const | relax::stage3_cycles ("relax:stage3_cycles") |
| RealOptionKey const | relax::cycle_ratio ("relax:cycle_ratio") |
| RealOptionKey const | relax::filter_stage2_beginning ("relax:filter_stage2_beginning") |
| RealOptionKey const | relax::filter_stage2_quarter ("relax:filter_stage2_quarter") |
| RealOptionKey const | relax::filter_stage2_half ("relax:filter_stage2_half") |
| RealOptionKey const | relax::filter_stage2_end ("relax:filter_stage2_end") |
| BooleanOptionKey const | relax::centroid::centroid ("relax:centroid") |
| StringOptionKey const | relax::centroid::weights ("relax:centroid:weights") |
| BooleanOptionKey const | relax::centroid::ramp_vdw ("relax:centroid:ramp_vdw") |
| BooleanOptionKey const | relax::centroid::ramp_rama ("relax:centroid:ramp_rama") |
| StringOptionKey const | relax::centroid::parameters ("relax:centroid:parameters") |
| BooleanOptionKey const | relax::centroid::do_final_repack ("relax:centroid:do_final_repack") |
| BooleanOptionKey const | relax::centroid::increase_vdw_radii ("relax:centroid:increase_vdw_radii") |
| BooleanOptionKey const | enzdes::enzdes ("enzdes") |
| StringOptionKey const | enzdes::checkpoint ("enzdes:checkpoint") |
| BooleanOptionKey const | enzdes::enz_score ("enzdes:enz_score") |
| BooleanOptionKey const | enzdes::enz_repack ("enzdes:enz_repack") |
| BooleanOptionKey const | enzdes::cst_opt ("enzdes:cst_opt") |
| BooleanOptionKey const | enzdes::cst_predock ("enzdes:cst_predock") |
| RealOptionKey const | enzdes::trans_magnitude ("enzdes:trans_magnitude") |
| RealOptionKey const | enzdes::rot_magnitude ("enzdes:rot_magnitude") |
| RealOptionKey const | enzdes::dock_trials ("enzdes:dock_trials") |
| BooleanOptionKey const | enzdes::cst_min ("enzdes:cst_min") |
| BooleanOptionKey const | enzdes::cst_design ("enzdes:cst_design") |
| IntegerOptionKey const | enzdes::design_min_cycles ("enzdes:design_min_cycles") |
| BooleanOptionKey const | enzdes::make_consensus_mutations ("enzdes:make_consensus_mutations") |
| BooleanOptionKey const | enzdes::bb_min ("enzdes:bb_min") |
| RealOptionKey const | enzdes::bb_min_allowed_dev ("enzdes:bb_min_allowed_dev") |
| RealOptionKey const | enzdes::loop_bb_min_allowed_dev ("enzdes:loop_bb_min_allowed_dev") |
| RealOptionKey const | enzdes::minimize_ligand_torsions ("enzdes:minimize_ligand_torsions") |
| RealOptionKey const | enzdes::minimize_all_ligand_torsions ("enzdes:minimize_all_ligand_torsions") |
| BooleanOptionKey const | enzdes::chi_min ("enzdes:chi_min") |
| BooleanOptionKey const | enzdes::min_all_jumps ("enzdes:min_all_jumps") |
| BooleanOptionKey const | enzdes::cst_dock ("enzdes:cst_dock") |
| BooleanOptionKey const | enzdes::run_ligand_motifs ("enzdes:run_ligand_motifs") |
| BooleanOptionKey const | enzdes::enz_debug ("enzdes:enz_debug") |
| FileOptionKey const | enzdes::cstfile ("enzdes:cstfile") |
| FileOptionKey const | enzdes::enz_loops_file ("enzdes:enz_loops_file") |
| BooleanOptionKey const | enzdes::flexbb_protocol ("enzdes:flexbb_protocol") |
| BooleanOptionKey const | enzdes::remodel_protocol ("enzdes:remodel_protocol") |
| BooleanOptionKey const | enzdes::kic_loop_sampling ("enzdes:kic_loop_sampling") |
| StringOptionKey const | enzdes::dump_loop_samples ("enzdes:dump_loop_samples") |
| BooleanOptionKey const | enzdes::fix_catalytic_aa ("enzdes:fix_catalytic_aa") |
| IntegerOptionKey const | enzdes::additional_packing_ligand_rb_confs ("enzdes:additional_packing_ligand_rb_confs") |
| IntegerOptionKey const | enzdes::ex_catalytic_rot ("enzdes:ex_catalytic_rot") |
| IntegerOptionKey const | enzdes::single_loop_ensemble_size ("enzdes:single_loop_ensemble_size") |
| IntegerOptionKey const | enzdes::loop_generator_trials ("enzdes:loop_generator_trials") |
| BooleanOptionKey const | enzdes::no_catres_min_in_loopgen ("enzdes:no_catres_min_in_loopgen") |
| RealOptionKey const | enzdes::mc_kt_low ("enzdes:mc_kt_low") |
| RealOptionKey const | enzdes::mc_kt_high ("enzdes:mc_kt_high") |
| RealOptionKey const | enzdes::min_cacb_deviation ("enzdes:min_cacb_deviation") |
| RealOptionKey const | enzdes::max_bb_deviation ("enzdes:max_bb_deviation") |
| RealOptionKey const | enzdes::max_bb_deviation_from_startstruct ("enzdes:max_bb_deviation_from_startstruct") |
| IntegerOptionKey const | enzdes::flexbb_outstructs ("enzdes:flexbb_outstructs") |
| IntegerOptionKey const | enzdes::remodel_trials ("enzdes:remodel_trials") |
| BooleanOptionKey const | enzdes::remodel_secmatch ("enzdes:remodel_secmatch") |
| BooleanOptionKey const | enzdes::dump_inverse_rotamers ("enzdes:dump_inverse_rotamers") |
| RealOptionKey const | enzdes::remodel_aggressiveness ("enzdes:remodel_aggressiveness") |
| RealOptionKey const | enzdes::favor_native_res ("enzdes:favor_native_res") |
| BooleanOptionKey const | enzdes::detect_design_interface ("enzdes:detect_design_interface") |
| BooleanOptionKey const | enzdes::include_catres_in_interface_detection ("enzdes:include_catres_in_interface_detection") |
| BooleanOptionKey const | enzdes::arg_sweep_interface ("enzdes:arg_sweep_interface") |
| RealOptionKey const | enzdes::arg_sweep_cutoff ("enzdes:arg_sweep_cutoff") |
| RealOptionKey const | enzdes::cut1 ("enzdes:cut1") |
| RealOptionKey const | enzdes::cut2 ("enzdes:cut2") |
| RealOptionKey const | enzdes::cut3 ("enzdes:cut3") |
| RealOptionKey const | enzdes::cut4 ("enzdes:cut4") |
| RealOptionKey const | enzdes::lig_packer_weight ("enzdes:lig_packer_weight") |
| BooleanOptionKey const | enzdes::no_unconstrained_repack ("enzdes:no_unconstrained_repack") |
| RealOptionKey const | enzdes::secmatch_Ecutoff ("enzdes:secmatch_Ecutoff") |
| FileOptionKey const | enzdes::change_lig ("enzdes:change_lig") |
| StringOptionKey const | enzdes::process_ligrot_separately ("enzdes:process_ligrot_separately") |
| BooleanOptionKey const | enzdes::start_from_random_rb_conf ("enzdes:start_from_random_rb_conf") |
| RealOptionKey const | enzdes::bb_bump_cutoff ("enzdes:bb_bump_cutoff") |
| RealOptionKey const | enzdes::sc_sc_bump_cutoff ("enzdes:sc_sc_bump_cutoff") |
| BooleanOptionKey const | enzdes::no_packstat_calculation ("enzdes:no_packstat_calculation") |
| StringOptionKey const | enzdes::compare_native ("enzdes:compare_native") |
| BooleanOptionKey const | enzdes::final_repack_without_ligand ("enzdes:final_repack_without_ligand") |
| BooleanOptionKey const | enzdes::dump_final_repack_without_ligand_pdb ("enzdes:dump_final_repack_without_ligand_pdb") |
| BooleanOptionKey const | enzdes::parser_read_cloud_pdb ("enzdes:parser_read_cloud_pdb") |
| BooleanOptionKey const | sasa::sasa ("sasa") |
| StringOptionKey const | sasa::method ("sasa:method") |
| BooleanOptionKey const | sasa::include_hydrogens_explicitly ("sasa:include_hydrogens_explicitly") |
| RealOptionKey const | sasa::probe_radius ("sasa:probe_radius") |
| BooleanOptionKey const | sasa::include_probe_radius_in_atom_radii ("sasa:include_probe_radius_in_atom_radii") |
| BooleanOptionKey const | sasa::include_only_C_S_in_hsasa ("sasa:include_only_C_S_in_hsasa") |
| BooleanOptionKey const | sasa::exclude_polar_atoms_by_charge_in_hsasa ("sasa:exclude_polar_atoms_by_charge_in_hsasa") |
| RealOptionKey const | sasa::polar_charge_cutoff ("sasa:polar_charge_cutoff") |
| StringOptionKey const | sasa::implicit_hydrogen_radii_set ("sasa:implicit_hydrogen_radii_set") |
| StringOptionKey const | sasa::explicit_hydrogen_radii_set ("sasa:explicit_hydrogen_radii_set") |
| BooleanOptionKey const | packing::packing ("packing") |
| BooleanOptionKey const | packing::repack_only ("packing:repack_only") |
| BooleanOptionKey const | packing::prevent_repacking ("packing:prevent_repacking") |
| RealOptionKey const | packing::cenrot_cutoff ("packing:cenrot_cutoff") |
| BooleanOptionKey const | packing::ignore_ligand_chi ("packing:ignore_ligand_chi") |
| IntegerOptionKey const | packing::ndruns ("packing:ndruns") |
| BooleanOptionKey const | packing::soft_rep_design ("packing:soft_rep_design") |
| BooleanOptionKey const | packing::use_electrostatic_repulsion ("packing:use_electrostatic_repulsion") |
| BooleanOptionKey const | packing::dump_rotamer_sets ("packing:dump_rotamer_sets") |
| RealOptionKey const | packing::dunbrack_prob_buried ("packing:dunbrack_prob_buried") |
| RealOptionKey const | packing::dunbrack_prob_nonburied ("packing:dunbrack_prob_nonburied") |
| RealOptionKey const | packing::dunbrack_prob_nonburied_semirotameric ("packing:dunbrack_prob_nonburied_semirotameric") |
| BooleanOptionKey const | packing::no_optH ("packing:no_optH") |
| BooleanOptionKey const | packing::optH_MCA ("packing:optH_MCA") |
| BooleanOptionKey const | packing::pack_missing_sidechains ("packing:pack_missing_sidechains") |
| BooleanOptionKey const | packing::preserve_c_beta ("packing:preserve_c_beta") |
| BooleanOptionKey const | packing::flip_HNQ ("packing:flip_HNQ") |
| IntegerVectorOptionKey const | packing::fix_his_tautomer ("packing:fix_his_tautomer") |
| BooleanOptionKey const | packing::print_pymol_selection ("packing:print_pymol_selection") |
| BooleanOptionKey const | packing::ex1::ex1 ("packing:ex1") |
| IntegerOptionKey const | packing::ex1::level ("packing:ex1:level") |
| BooleanOptionKey const | packing::ex1::operate ("packing:ex1:operate") |
| BooleanOptionKey const | packing::ex2::ex2 ("packing:ex2") |
| IntegerOptionKey const | packing::ex2::level ("packing:ex2:level") |
| BooleanOptionKey const | packing::ex2::operate ("packing:ex2:operate") |
| BooleanOptionKey const | packing::ex3::ex3 ("packing:ex3") |
| IntegerOptionKey const | packing::ex3::level ("packing:ex3:level") |
| BooleanOptionKey const | packing::ex3::operate ("packing:ex3:operate") |
| BooleanOptionKey const | packing::ex4::ex4 ("packing:ex4") |
| IntegerOptionKey const | packing::ex4::level ("packing:ex4:level") |
| BooleanOptionKey const | packing::ex4::operate ("packing:ex4:operate") |
| BooleanOptionKey const | packing::ex1aro::ex1aro ("packing:ex1aro") |
| IntegerOptionKey const | packing::ex1aro::level ("packing:ex1aro:level") |
| BooleanOptionKey const | packing::ex2aro::ex2aro ("packing:ex2aro") |
| IntegerOptionKey const | packing::ex2aro::level ("packing:ex2aro:level") |
| BooleanOptionKey const | packing::ex1aro_exposed::ex1aro_exposed ("packing:ex1aro_exposed") |
| IntegerOptionKey const | packing::ex1aro_exposed::level ("packing:ex1aro_exposed:level") |
| BooleanOptionKey const | packing::ex2aro_exposed::ex2aro_exposed ("packing:ex2aro_exposed") |
| IntegerOptionKey const | packing::ex2aro_exposed::level ("packing:ex2aro_exposed:level") |
| BooleanOptionKey const | packing::exdna::exdna ("packing:exdna") |
| IntegerOptionKey const | packing::exdna::level ("packing:exdna:level") |
| IntegerOptionKey const | packing::extrachi_cutoff ("packing:extrachi_cutoff") |
| FileVectorOptionKey const | packing::resfile ("packing:resfile") |
| RealOptionKey const | packing::outeriterations_scaling ("packing:outeriterations_scaling") |
| RealOptionKey const | packing::inneriterations_scaling ("packing:inneriterations_scaling") |
| BooleanOptionKey const | packing::explicit_h2o ("packing:explicit_h2o") |
| StringVectorOptionKey const | packing::adducts ("packing:adducts") |
| BooleanOptionKey const | packing::solvate ("packing:solvate") |
| BooleanOptionKey const | packing::use_input_sc ("packing:use_input_sc") |
| FileVectorOptionKey const | packing::unboundrot ("packing:unboundrot") |
| RealOptionKey const | packing::max_rotbump_energy ("packing:max_rotbump_energy") |
| BooleanOptionKey const | packing::lazy_ig ("packing:lazy_ig") |
| BooleanOptionKey const | packing::double_lazy_ig ("packing:double_lazy_ig") |
| IntegerOptionKey const | packing::double_lazy_ig_mem_limit ("packing:double_lazy_ig_mem_limit") |
| IntegerOptionKey const | packing::linmem_ig ("packing:linmem_ig") |
| IntegerOptionKey const | packing::multi_cool_annealer ("packing:multi_cool_annealer") |
| RealVectorOptionKey const | packing::minpack_temp_schedule ("packing:minpack_temp_schedule") |
| IntegerOptionKey const | packing::minpack_inner_iteration_scale ("packing:minpack_inner_iteration_scale") |
| BooleanOptionKey const | packing::minpack_disable_bumpcheck ("packing:minpack_disable_bumpcheck") |
| BooleanOptionKey const | phil::phil ("phil") |
| IntegerOptionKey const | phil::nloop ("phil:nloop") |
| StringOptionKey const | phil::vall_file ("phil:vall_file") |
| StringOptionKey const | phil::align_file ("phil:align_file") |
| BooleanOptionKey const | wum::wum ("wum") |
| IntegerOptionKey const | wum::n_slaves_per_master ("wum:n_slaves_per_master") |
| IntegerOptionKey const | wum::n_masters ("wum:n_masters") |
| IntegerOptionKey const | wum::memory_limit ("wum:memory_limit") |
| StringOptionKey const | wum::extra_scorefxn ("wum:extra_scorefxn") |
| FileOptionKey const | wum::extra_scorefxn_ref_structure ("wum:extra_scorefxn_ref_structure") |
| IntegerOptionKey const | wum::extra_scorefxn_relax ("wum:extra_scorefxn_relax") |
| RealOptionKey const | wum::trim_proportion ("wum:trim_proportion") |
| BooleanOptionKey const | els::els ("els") |
| IntegerOptionKey const | els::master_wu_per_send ("els:master_wu_per_send") |
| StringOptionKey const | els::vars ("els:vars") |
| FileOptionKey const | els::script ("els:script") |
| IntegerOptionKey const | els::num_traj ("els:num_traj") |
| IntegerOptionKey const | els::traj_per_master ("els:traj_per_master") |
| IntegerOptionKey const | els::shortest_wu ("els:shortest_wu") |
| BooleanOptionKey const | els::pool ("els:pool") |
| BooleanOptionKey const | els::singlenode ("els:singlenode") |
| BooleanOptionKey const | lh::lh ("lh") |
| StringOptionKey const | lh::db_prefix ("lh:db_prefix") |
| 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::rms_limit ("lh:rms_limit") |
| 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") |
| 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 | rbe::rbe ("rbe") |
| StringOptionKey const | rbe::server_url ("rbe:server_url") |
| StringOptionKey const | rbe::server_port ("rbe:server_port") |
| RealOptionKey const | rbe::poll_frequency ("rbe:poll_frequency") |
| BooleanOptionKey const | blivens::blivens ("blivens") |
| BooleanOptionKey const | blivens::disulfide_scorer::disulfide_scorer ("blivens:disulfide_scorer") |
| RealOptionKey const | blivens::disulfide_scorer::nds_prob ("blivens:disulfide_scorer:nds_prob") |
| RealOptionKey const | blivens::disulfide_scorer::cys_prob ("blivens:disulfide_scorer:cys_prob") |
| StringOptionKey const | blivens::score_type ("blivens:score_type") |
| BooleanOptionKey const | krassk::krassk ("krassk") |
| IntegerOptionKey const | krassk::left_tail ("krassk:left_tail") |
| IntegerOptionKey const | krassk::right_tail ("krassk:right_tail") |
| BooleanOptionKey const | krassk::tail_mode ("krassk:tail_mode") |
| IntegerOptionKey const | krassk::tail_mode_name ("krassk:tail_mode_name") |
| StringOptionKey const | krassk::tail_output_file_name ("krassk:tail_output_file_name") |
| BooleanOptionKey const | rotamerdump::rotamerdump ("rotamerdump") |
| BooleanOptionKey const | rotamerdump::xyz ("rotamerdump:xyz") |
| BooleanOptionKey const | rotamerdump::one_body ("rotamerdump:one_body") |
| BooleanOptionKey const | rotamerdump::two_body ("rotamerdump:two_body") |
| BooleanOptionKey const | rotamerdump::annealer ("rotamerdump:annealer") |
| BooleanOptionKey const | robert::robert ("robert") |
| StringOptionKey const | robert::pairdata_input_pdb_list ("robert:pairdata_input_pdb_list") |
| RealOptionKey const | robert::pcs_maxsub_filter ("robert:pcs_maxsub_filter") |
| RealOptionKey const | robert::pcs_maxsub_rmsd ("robert:pcs_maxsub_rmsd") |
| BooleanOptionKey const | robert::pcs_dump_cluster ("robert:pcs_dump_cluster") |
| RealOptionKey const | robert::pcs_cluster_coverage ("robert:pcs_cluster_coverage") |
| BooleanOptionKey const | robert::pcs_cluster_lowscoring ("robert:pcs_cluster_lowscoring") |
| BooleanOptionKey const | cmiles::cmiles ("cmiles") |
| BooleanOptionKey const | cmiles::kcluster::kcluster ("cmiles:kcluster") |
| IntegerOptionKey const | cmiles::kcluster::num_clusters ("cmiles:kcluster:num_clusters") |
| BooleanOptionKey const | cmiles::jumping::jumping ("cmiles:jumping") |
| IntegerOptionKey const | cmiles::jumping::resi ("cmiles:jumping:resi") |
| IntegerOptionKey const | cmiles::jumping::resj ("cmiles:jumping:resj") |
| BooleanOptionKey const | james::james ("james") |
| IntegerOptionKey const | james::min_seqsep ("james:min_seqsep") |
| StringVectorOptionKey const | james::atom_names ("james:atom_names") |
| RealVectorOptionKey const | james::dist_thresholds ("james:dist_thresholds") |
| RealVectorOptionKey const | james::torsion_thresholds ("james:torsion_thresholds") |
| RealOptionKey const | james::sog_cutoff ("james:sog_cutoff") |
| BooleanOptionKey const | james::shift_sog_func ("james:shift_sog_func") |
| StringOptionKey const | james::min_type ("james:min_type") |
| RealOptionKey const | james::min_tol ("james:min_tol") |
| BooleanOptionKey const | james::debug ("james:debug") |
| RealOptionKey const | james::real ("james:real") |
| IntegerOptionKey const | james::n_designs ("james:n_designs") |
| BooleanOptionKey const | james::awesome_mode ("james:awesome_mode") |
| IntegerOptionKey const | james::n_clusters ("james:n_clusters") |
| BooleanOptionKey const | james::thread_unaligned ("james:thread_unaligned") |
| BooleanOptionKey const | membrane::membrane ("membrane") |
| FileVectorOptionKey const | membrane::lipid_acc_files ("membrane:lipid_acc_files") |
| FileVectorOptionKey const | membrane::span_files ("membrane:span_files") |
| FileVectorOptionKey const | membrane::embed_files ("membrane:embed_files") |
| BooleanOptionKey const | membrane::include_lips ("membrane:include_lips") |
| IntegerOptionKey const | membrane::normal_cycles ("membrane:normal_cycles") |
| RealOptionKey const | membrane::normal_mag ("membrane:normal_mag") |
| RealOptionKey const | membrane::center_mag ("membrane:center_mag") |
| RealOptionKey const | membrane::smooth_move_frac ("membrane:smooth_move_frac") |
| BooleanOptionKey const | membrane::no_interpolate_Mpair ("membrane:no_interpolate_Mpair") |
| BooleanOptionKey const | membrane::Menv_penalties ("membrane:Menv_penalties") |
| BooleanOptionKey const | membrane::Membed_init ("membrane:Membed_init") |
| BooleanOptionKey const | membrane::Fa_Membed_update ("membrane:Fa_Membed_update") |
| BooleanOptionKey const | membrane::center_search ("membrane:center_search") |
| BooleanOptionKey const | membrane::normal_search ("membrane:normal_search") |
| IntegerOptionKey const | membrane::center_max_delta ("membrane:center_max_delta") |
| IntegerOptionKey const | membrane::normal_start_angle ("membrane:normal_start_angle") |
| IntegerOptionKey const | membrane::normal_delta_angle ("membrane:normal_delta_angle") |
| IntegerOptionKey const | membrane::normal_max_angle ("membrane:normal_max_angle") |
| BooleanOptionKey const | membrane::debug ("membrane:debug") |
| BooleanOptionKey const | membrane::fixed_membrane ("membrane:fixed_membrane") |
| RealVectorOptionKey const | membrane::membrane_center ("membrane:membrane_center") |
| RealVectorOptionKey const | membrane::membrane_normal ("membrane:membrane_normal") |
| BooleanOptionKey const | membrane::view ("membrane:view") |
| BooleanOptionKey const | membrane::Mhbond_depth ("membrane:Mhbond_depth") |
| RealOptionKey const | membrane::thickness ("membrane:thickness") |
| BooleanOptionKey const | casp::casp ("casp") |
| StringOptionKey const | casp::decoy ("casp:decoy") |
| StringOptionKey const | casp::wt ("casp:wt") |
| StringOptionKey const | casp::rots ("casp:rots") |
| RealOptionKey const | casp::opt_radius ("casp:opt_radius") |
| BooleanOptionKey const | casp::repack ("casp:repack") |
| BooleanOptionKey const | casp::sc_min ("casp:sc_min") |
| BooleanOptionKey const | casp::sequential ("casp:sequential") |
| RealOptionKey const | casp::num_iterations ("casp:num_iterations") |
| StringOptionKey const | casp::weight_file ("casp:weight_file") |
| StringOptionKey const | casp::refine_res ("casp:refine_res") |
| BooleanOptionKey const | pose_metrics::pose_metrics ("pose_metrics") |
| RealOptionKey const | pose_metrics::atomic_burial_cutoff ("pose_metrics:atomic_burial_cutoff") |
| RealOptionKey const | pose_metrics::sasa_calculator_probe_radius ("pose_metrics:sasa_calculator_probe_radius") |
| RealOptionKey const | pose_metrics::interface_cutoff ("pose_metrics:interface_cutoff") |
| IntegerOptionKey const | pose_metrics::min_sequence_separation ("pose_metrics:min_sequence_separation") |
1.8.7