|
Rosetta
|
Namespaces | |
| matdes | |
| matdes::design | |
| matdes::mutalyze | |
| mc | |
| mean_field | |
| mh | |
| mh::score | |
| mh::path | |
| mh::harvest | |
| mh::match | |
| mh::dump | |
| mh::filter | |
| magnesium | |
| magnesium::montecarlo | |
| motifs | |
| ms | |
| ms::checkpoint | |
Functions | |
| IntegerOptionKey const | matdes::design::grid_nsamp_radius ("matdes:design:grid_nsamp_radius") |
| RealOptionKey const | matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus") |
| BooleanOptionKey const | matdes::mutalyze::mutalyze ("matdes:mutalyze") |
| BooleanOptionKey const | matdes::mutalyze::calc_rot_boltz ("matdes:mutalyze:calc_rot_boltz") |
| BooleanOptionKey const | matdes::mutalyze::ala_scan ("matdes:mutalyze:ala_scan") |
| BooleanOptionKey const | matdes::mutalyze::revert_scan ("matdes:mutalyze:revert_scan") |
| BooleanOptionKey const | matdes::mutalyze::min_rb ("matdes:mutalyze:min_rb") |
| BooleanOptionKey const | mc::mc ("mc") |
| BooleanOptionKey const | mc::log_scores_in_MC ("mc:log_scores_in_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 | mean_field::mean_field ("mean_field") |
| FileVectorOptionKey const | mean_field::bb_list ("mean_field:bb_list") |
| FileOptionKey const | mean_field::dump_transfac ("mean_field:dump_transfac") |
| FileOptionKey const | mean_field::spec_profile ("mean_field:spec_profile") |
| FileOptionKey const | mean_field::bb_boltz_probs ("mean_field:bb_boltz_probs") |
| RealOptionKey const | mean_field::rot_norm_weight ("mean_field:rot_norm_weight") |
| RealOptionKey const | mean_field::bb_average_weight ("mean_field:bb_average_weight") |
| FileOptionKey const | mean_field::rf_peptide ("mean_field:rf_peptide") |
| BooleanOptionKey const | mean_field::include_all_aa ("mean_field:include_all_aa") |
| BooleanOptionKey const | mean_field::ga_pack_detect_interface ("mean_field:ga_pack_detect_interface") |
| BooleanOptionKey const | mean_field::biased_dist_all_gen ("mean_field:biased_dist_all_gen") |
| BooleanOptionKey const | mh::mh ("mh") |
| StringOptionKey const | mh::motif_out_file ("mh:motif_out_file") |
| FileVectorOptionKey const | mh::harvest_motifs ("mh:harvest_motifs") |
| FileVectorOptionKey const | mh::print_motifs ("mh:print_motifs") |
| FileVectorOptionKey const | mh::remove_duplicates ("mh:remove_duplicates") |
| FileVectorOptionKey const | mh::dump_motif_pdbs ("mh:dump_motif_pdbs") |
| FileVectorOptionKey const | mh::merge_motifs ("mh:merge_motifs") |
| FileVectorOptionKey const | mh::merge_scores ("mh:merge_scores") |
| BooleanOptionKey const | mh::merge_motifs_one_per_bin ("mh:merge_motifs_one_per_bin") |
| BooleanOptionKey const | mh::gen_reverse_motifs_on_load ("mh:gen_reverse_motifs_on_load") |
| FileVectorOptionKey const | mh::dump_input_pdb ("mh:dump_input_pdb") |
| FileVectorOptionKey const | mh::score_pdbs ("mh:score_pdbs") |
| FileVectorOptionKey const | mh::sequence_recovery ("mh:sequence_recovery") |
| FileVectorOptionKey const | mh::explicit_motif_score ("mh:explicit_motif_score") |
| FileVectorOptionKey const | mh::harvest_scores ("mh:harvest_scores") |
| FileOptionKey const | mh::print_scores ("mh:print_scores") |
| FileVectorOptionKey const | mh::dump_matching_motifs ("mh:dump_matching_motifs") |
| BooleanOptionKey const | mh::score_across_chains_only ("mh:score_across_chains_only") |
| BooleanOptionKey const | mh::normalize_score_ncontact ("mh:normalize_score_ncontact") |
| IntegerOptionKey const | mh::harvest_motifs_min_hh_ends ("mh:harvest_motifs_min_hh_ends") |
| BooleanOptionKey const | mh::ignore_io_errors ("mh:ignore_io_errors") |
| RealOptionKey const | mh::motif_match_radius ("mh:motif_match_radius") |
| RealVectorOptionKey const | mh::merge_similar_motifs ("mh:merge_similar_motifs") |
| BooleanOptionKey const | mh::score::score ("mh:score") |
| RealOptionKey const | mh::score::background_weight ("mh:score:background_weight") |
| RealOptionKey const | mh::score::ca_cb_clash_weight ("mh:score:ca_cb_clash_weight") |
| BooleanOptionKey const | mh::score::noloops ("mh:score:noloops") |
| BooleanOptionKey const | mh::score::nosheets ("mh:score:nosheets") |
| BooleanOptionKey const | mh::score::nohelix ("mh:score:nohelix") |
| BooleanOptionKey const | mh::score::spread_ss_element ("mh:score:spread_ss_element") |
| RealOptionKey const | mh::score::min_cover_fraction ("mh:score:min_cover_fraction") |
| RealOptionKey const | mh::score::strand_pair_weight ("mh:score:strand_pair_weight") |
| RealOptionKey const | mh::score::anti_polar_weight ("mh:score:anti_polar_weight") |
| RealOptionKey const | mh::score::min_contact_pairs ("mh:score:min_contact_pairs") |
| RealOptionKey const | mh::score::max_contact_pairs ("mh:score:max_contact_pairs") |
| RealOptionKey const | mh::score::max_cb_dis ("mh:score:max_cb_dis") |
| RealOptionKey const | mh::score::coverage_pow ("mh:score:coverage_pow") |
| BooleanOptionKey const | mh::score::use_ss1 ("mh:score:use_ss1") |
| BooleanOptionKey const | mh::score::use_ss2 ("mh:score:use_ss2") |
| BooleanOptionKey const | mh::score::use_aa1 ("mh:score:use_aa1") |
| BooleanOptionKey const | mh::score::use_aa2 ("mh:score:use_aa2") |
| BooleanOptionKey const | mh::score::use_log ("mh:score:use_log") |
| BooleanOptionKey const | mh::path::path ("mh:path") |
| StringVectorOptionKey const | mh::path::biounit ("mh:path:biounit") |
| StringVectorOptionKey const | mh::path::biounit_ideal ("mh:path:biounit_ideal") |
| StringVectorOptionKey const | mh::path::pdb ("mh:path:pdb") |
| StringVectorOptionKey const | mh::path::motifs ("mh:path:motifs") |
| StringVectorOptionKey const | mh::path::motifs_SC_SC ("mh:path:motifs_SC_SC") |
| StringVectorOptionKey const | mh::path::motifs_SC_BB ("mh:path:motifs_SC_BB") |
| StringVectorOptionKey const | mh::path::motifs_BB_BB ("mh:path:motifs_BB_BB") |
| StringVectorOptionKey const | mh::path::motifs_BB_PH ("mh:path:motifs_BB_PH") |
| StringVectorOptionKey const | mh::path::motifs_BB_PO ("mh:path:motifs_BB_PO") |
| StringVectorOptionKey const | mh::path::motifs_PH_PO ("mh:path:motifs_PH_PO") |
| StringVectorOptionKey const | mh::path::scores ("mh:path:scores") |
| StringVectorOptionKey const | mh::path::scores_SC_SC ("mh:path:scores_SC_SC") |
| StringVectorOptionKey const | mh::path::scores_SC_BB ("mh:path:scores_SC_BB") |
| StringVectorOptionKey const | mh::path::scores_BB_BB ("mh:path:scores_BB_BB") |
| StringVectorOptionKey const | mh::path::scores_BB_PH ("mh:path:scores_BB_PH") |
| StringVectorOptionKey const | mh::path::scores_BB_PO ("mh:path:scores_BB_PO") |
| StringVectorOptionKey const | mh::path::scores_PH_PO ("mh:path:scores_PH_PO") |
| StringVectorOptionKey const | mh::path::scores_frags ("mh:path:scores_frags") |
| BooleanOptionKey const | mh::harvest::harvest ("mh:harvest") |
| RealOptionKey const | mh::harvest::hash_cart_resl ("mh:harvest:hash_cart_resl") |
| RealOptionKey const | mh::harvest::hash_angle_resl ("mh:harvest:hash_angle_resl") |
| RealOptionKey const | mh::harvest::smoothing_factor ("mh:harvest:smoothing_factor") |
| BooleanOptionKey const | mh::harvest::idealize ("mh:harvest:idealize") |
| BooleanOptionKey const | mh::harvest::dump ("mh:harvest:dump") |
| RealOptionKey const | mh::harvest::min_bin_val ("mh:harvest:min_bin_val") |
| BooleanOptionKey const | mh::harvest::sep_aa ("mh:harvest:sep_aa") |
| BooleanOptionKey const | mh::harvest::sep_aa1 ("mh:harvest:sep_aa1") |
| BooleanOptionKey const | mh::harvest::sep_aa2 ("mh:harvest:sep_aa2") |
| BooleanOptionKey const | mh::harvest::sep_ss ("mh:harvest:sep_ss") |
| BooleanOptionKey const | mh::harvest::sep_dssp ("mh:harvest:sep_dssp") |
| RealVectorOptionKey const | mh::harvest::sep_lj ("mh:harvest:sep_lj") |
| RealVectorOptionKey const | mh::harvest::sep_hb ("mh:harvest:sep_hb") |
| RealVectorOptionKey const | mh::harvest::sep_nbrs ("mh:harvest:sep_nbrs") |
| RealVectorOptionKey const | mh::harvest::sep_bfac ("mh:harvest:sep_bfac") |
| RealVectorOptionKey const | mh::harvest::sep_dist ("mh:harvest:sep_dist") |
| BooleanOptionKey const | mh::harvest::weight_by_energy ("mh:harvest:weight_by_energy") |
| RealOptionKey const | mh::harvest::max_rmsd ("mh:harvest:max_rmsd") |
| IntegerOptionKey const | mh::harvest::max_res ("mh:harvest:max_res") |
| BooleanOptionKey const | mh::harvest::agg_with_max ("mh:harvest:agg_with_max") |
| RealOptionKey const | mh::harvest::multiplier ("mh:harvest:multiplier") |
| BooleanOptionKey const | mh::match::match ("mh:match") |
| BooleanOptionKey const | mh::match::interface_only ("mh:match:interface_only") |
| BooleanOptionKey const | mh::match::ss ("mh:match:ss") |
| BooleanOptionKey const | mh::match::ss1 ("mh:match:ss1") |
| BooleanOptionKey const | mh::match::ss2 ("mh:match:ss2") |
| BooleanOptionKey const | mh::match::aa ("mh:match:aa") |
| BooleanOptionKey const | mh::match::aa1 ("mh:match:aa1") |
| BooleanOptionKey const | mh::match::aa2 ("mh:match:aa2") |
| BooleanOptionKey const | mh::dump::dump ("mh:dump") |
| IntegerOptionKey const | mh::dump::limit_per_pair ("mh:dump:limit_per_pair") |
| IntegerOptionKey const | mh::dump::max_per_res ("mh:dump:max_per_res") |
| RealOptionKey const | mh::dump::max_ca_dis ("mh:dump:max_ca_dis") |
| RealOptionKey const | mh::dump::max_rms ("mh:dump:max_rms") |
| RealOptionKey const | mh::dump::resfile_min_pair_score ("mh:dump:resfile_min_pair_score") |
| RealOptionKey const | mh::dump::resfile_min_tot_score ("mh:dump:resfile_min_tot_score") |
| BooleanOptionKey const | mh::dump::resfile_dump ("mh:dump:resfile_dump") |
| BooleanOptionKey const | mh::dump::symmetric_motifs ("mh:dump:symmetric_motifs") |
| BooleanOptionKey const | mh::filter::filter ("mh:filter") |
| BooleanOptionKey const | mh::filter::filter_harvest ("mh:filter:filter_harvest") |
| BooleanOptionKey const | mh::filter::filter_io ("mh:filter:filter_io") |
| StringOptionKey const | mh::filter::pdb ("mh:filter:pdb") |
| StringOptionKey const | mh::filter::lig ("mh:filter:lig") |
| StringOptionKey const | mh::filter::motif_type ("mh:filter:motif_type") |
| StringOptionKey const | mh::filter::restype1 ("mh:filter:restype1") |
| StringOptionKey const | mh::filter::restype2 ("mh:filter:restype2") |
| StringOptionKey const | mh::filter::restype ("mh:filter:restype") |
| StringOptionKey const | mh::filter::restype_one ("mh:filter:restype_one") |
| StringOptionKey const | mh::filter::not_restype ("mh:filter:not_restype") |
| StringOptionKey const | mh::filter::not_restype_one ("mh:filter:not_restype_one") |
| IntegerOptionKey const | mh::filter::seqsep ("mh:filter:seqsep") |
| IntegerOptionKey const | mh::filter::max_seqsep ("mh:filter:max_seqsep") |
| BooleanOptionKey const | mh::filter::no_hb_bb ("mh:filter:no_hb_bb") |
| RealOptionKey const | mh::filter::mindist2 ("mh:filter:mindist2") |
| RealOptionKey const | mh::filter::maxdist2 ("mh:filter:maxdist2") |
| StringOptionKey const | mh::filter::ss1 ("mh:filter:ss1") |
| StringOptionKey const | mh::filter::ss2 ("mh:filter:ss2") |
| StringOptionKey const | mh::filter::dssp1 ("mh:filter:dssp1") |
| StringOptionKey const | mh::filter::dssp2 ("mh:filter:dssp2") |
| StringOptionKey const | mh::filter::aa1 ("mh:filter:aa1") |
| StringOptionKey const | mh::filter::aa2 ("mh:filter:aa2") |
| RealOptionKey const | mh::filter::sasa ("mh:filter:sasa") |
| RealOptionKey const | mh::filter::faatr ("mh:filter:faatr") |
| RealOptionKey const | mh::filter::hb_sc ("mh:filter:hb_sc") |
| RealOptionKey const | mh::filter::hb_bb_sc ("mh:filter:hb_bb_sc") |
| RealOptionKey const | mh::filter::hb_bb ("mh:filter:hb_bb") |
| RealOptionKey const | mh::filter::occupancy ("mh:filter:occupancy") |
| RealOptionKey const | mh::filter::coorderr ("mh:filter:coorderr") |
| BooleanOptionKey const | mh::filter::uniformfrag ("mh:filter:uniformfrag") |
| RealOptionKey const | mh::filter::faatr_or_hbbb ("mh:filter:faatr_or_hbbb") |
| RealOptionKey const | mh::filter::faatr_or_hb ("mh:filter:faatr_or_hb") |
| BooleanOptionKey const | mh::filter::noloops ("mh:filter:noloops") |
| BooleanOptionKey const | mh::filter::oneloop ("mh:filter:oneloop") |
| BooleanOptionKey const | mh::filter::nodisulf ("mh:filter:nodisulf") |
| RealOptionKey const | mh::filter::score ("mh:filter:score") |
| BooleanOptionKey const | magnesium::magnesium ("magnesium") |
| BooleanOptionKey const | magnesium::scan ("magnesium:scan") |
| IntegerVectorOptionKey const | magnesium::mg_res ("magnesium:mg_res") |
| BooleanOptionKey const | magnesium::minimize_during_scoring ("magnesium:minimize_during_scoring") |
| ResidueChainVectorOptionKey const | magnesium::ligand_res ("magnesium:ligand_res") |
| IntegerVectorOptionKey const | magnesium::pose_ligand_res ("magnesium:pose_ligand_res") |
| BooleanOptionKey const | magnesium::lores_scan ("magnesium:lores_scan") |
| RealOptionKey const | magnesium::xyz_step ("magnesium:xyz_step") |
| RealOptionKey const | magnesium::score_cut ("magnesium:score_cut") |
| RealOptionKey const | magnesium::score_cut_PDB ("magnesium:score_cut_PDB") |
| BooleanOptionKey const | magnesium::integration_test ("magnesium:integration_test") |
| BooleanOptionKey const | magnesium::tether_to_closest_res ("magnesium:tether_to_closest_res") |
| BooleanOptionKey const | magnesium::fixup ("magnesium:fixup") |
| BooleanOptionKey const | magnesium::pack_water_hydrogens ("magnesium:pack_water_hydrogens") |
| BooleanOptionKey const | magnesium::hydrate ("magnesium:hydrate") |
| BooleanOptionKey const | magnesium::monte_carlo ("magnesium:monte_carlo") |
| BooleanOptionKey const | magnesium::scored_hydrogen_sampling ("magnesium:scored_hydrogen_sampling") |
| BooleanOptionKey const | magnesium::all_hydration_frames ("magnesium:all_hydration_frames") |
| BooleanOptionKey const | magnesium::leave_other_waters ("magnesium:leave_other_waters") |
| BooleanOptionKey const | magnesium::minimize ("magnesium:minimize") |
| RealOptionKey const | magnesium::minimize_mg_coord_constraint_distance ("magnesium:minimize_mg_coord_constraint_distance") |
| BooleanOptionKey const | magnesium::montecarlo::montecarlo ("magnesium:montecarlo") |
| RealOptionKey const | magnesium::montecarlo::temperature ("magnesium:montecarlo:temperature") |
| IntegerOptionKey const | magnesium::montecarlo::cycles ("magnesium:montecarlo:cycles") |
| BooleanOptionKey const | magnesium::montecarlo::dump ("magnesium:montecarlo:dump") |
| RealOptionKey const | magnesium::montecarlo::add_delete_frequency ("magnesium:montecarlo:add_delete_frequency") |
| BooleanOptionKey const | motifs::motifs ("motifs") |
| RealOptionKey const | motifs::close_enough ("motifs:close_enough") |
| IntegerOptionKey const | motifs::max_depth ("motifs:max_depth") |
| BooleanOptionKey const | motifs::keep_motif_xtal_location ("motifs:keep_motif_xtal_location") |
| RealOptionKey const | motifs::pack_score_cutoff ("motifs:pack_score_cutoff") |
| RealOptionKey const | motifs::hb_score_cutoff ("motifs:hb_score_cutoff") |
| RealOptionKey const | motifs::water_score_cutoff ("motifs:water_score_cutoff") |
| RealOptionKey const | motifs::pack_min_threshold ("motifs:pack_min_threshold") |
| RealOptionKey const | motifs::pack_max_threshold ("motifs:pack_max_threshold") |
| RealOptionKey const | motifs::hbond_min_threshold ("motifs:hbond_min_threshold") |
| RealOptionKey const | motifs::hbond_max_threshold ("motifs:hbond_max_threshold") |
| RealOptionKey const | motifs::elec_min_threshold ("motifs:elec_min_threshold") |
| RealOptionKey const | motifs::elec_max_threshold ("motifs:elec_max_threshold") |
| RealOptionKey const | motifs::duplicate_dist_cutoff ("motifs:duplicate_dist_cutoff") |
| RealOptionKey const | motifs::duplicate_angle_cutoff ("motifs:duplicate_angle_cutoff") |
| StringOptionKey const | motifs::motif_output_directory ("motifs:motif_output_directory") |
| BooleanOptionKey const | motifs::eliminate_weak_motifs ("motifs:eliminate_weak_motifs") |
| RealOptionKey const | motifs::duplicate_motif_cutoff ("motifs:duplicate_motif_cutoff") |
| BooleanOptionKey const | motifs::preminimize_motif_pdbs ("motifs:preminimize_motif_pdbs") |
| BooleanOptionKey const | motifs::preminimize_motif_pdbs_sconly ("motifs:preminimize_motif_pdbs_sconly") |
| BooleanOptionKey const | motifs::place_adduct_waters ("motifs:place_adduct_waters") |
| FileVectorOptionKey const | motifs::list_motifs ("motifs:list_motifs") |
| StringOptionKey const | motifs::motif_filename ("motifs:motif_filename") |
| StringOptionKey const | motifs::file_prefix ("motifs:file_prefix") |
| StringOptionKey const | motifs::build_residue_file ("motifs:build_residue_file") |
| StringOptionKey const | motifs::motif_flexible_loop_file ("motifs:motif_flexible_loop_file") |
| StringOptionKey const | motifs::residue_trim_file ("motifs:residue_trim_file") |
| StringOptionKey const | motifs::BPData ("motifs:BPData") |
| FileVectorOptionKey const | motifs::list_dnaconformers ("motifs:list_dnaconformers") |
| StringVectorOptionKey const | motifs::target_dna_defs ("motifs:target_dna_defs") |
| StringVectorOptionKey const | motifs::motif_build_defs ("motifs:motif_build_defs") |
| IntegerVectorOptionKey const | motifs::motif_build_positions ("motifs:motif_build_positions") |
| RealOptionKey const | motifs::r1 ("motifs:r1") |
| RealOptionKey const | motifs::r2 ("motifs:r2") |
| RealOptionKey const | motifs::z1 ("motifs:z1") |
| RealOptionKey const | motifs::z2 ("motifs:z2") |
| RealOptionKey const | motifs::dtest ("motifs:dtest") |
| IntegerOptionKey const | motifs::rotlevel ("motifs:rotlevel") |
| IntegerOptionKey const | motifs::num_repacks ("motifs:num_repacks") |
| BooleanOptionKey const | motifs::minimize ("motifs:minimize") |
| BooleanOptionKey const | motifs::minimize_dna ("motifs:minimize_dna") |
| BooleanOptionKey const | motifs::run_motifs ("motifs:run_motifs") |
| BooleanOptionKey const | motifs::expand_motifs ("motifs:expand_motifs") |
| BooleanOptionKey const | motifs::aromatic_motifs ("motifs:aromatic_motifs") |
| BooleanOptionKey const | motifs::dump_motifs ("motifs:dump_motifs") |
| BooleanOptionKey const | motifs::quick_and_dirty ("motifs:quick_and_dirty") |
| RealOptionKey const | motifs::special_rotweight ("motifs:special_rotweight") |
| StringOptionKey const | motifs::output_file ("motifs:output_file") |
| StringOptionKey const | motifs::data_file ("motifs:data_file") |
| StringOptionKey const | motifs::target_aa ("motifs:target_aa") |
| BooleanOptionKey const | motifs::flex_sugar ("motifs:flex_sugar") |
| BooleanOptionKey const | motifs::clear_bprots ("motifs:clear_bprots") |
| IntegerOptionKey const | motifs::rots2add ("motifs:rots2add") |
| BooleanOptionKey const | motifs::restrict_to_wt ("motifs:restrict_to_wt") |
| BooleanOptionKey const | motifs::rerun_motifsearch ("motifs:rerun_motifsearch") |
| BooleanOptionKey const | motifs::no_rotamer_bump ("motifs:no_rotamer_bump") |
| RealOptionKey const | motifs::ligand_motif_sphere ("motifs:ligand_motif_sphere") |
| BooleanOptionKey const | motifs::output_build_positions_only ("motifs:output_build_positions_only") |
| RealOptionKey const | motifs::specific_build_position ("motifs:specific_build_position") |
| BooleanOptionKey const | motifs::verbosity ("motifs:verbosity") |
| StringOptionKey const | motifs::params_directory_path ("motifs:params_directory_path") |
| StringOptionKey const | motifs::sdf_directory_path ("motifs:sdf_directory_path") |
| StringOptionKey const | motifs::mol2_directory_path ("motifs:mol2_directory_path") |
| StringOptionKey const | motifs::mol2_file ("motifs:mol2_file") |
| StringOptionKey const | motifs::mol2_amino_acid ("motifs:mol2_amino_acid") |
| StringOptionKey const | motifs::params_custom_file_name ("motifs:params_custom_file_name") |
| StringOptionKey const | motifs::ligand_3_letter_code ("motifs:ligand_3_letter_code") |
| StringOptionKey const | motifs::ligand_1_letter_code ("motifs:ligand_1_letter_code") |
| StringOptionKey const | motifs::ligand_full_name ("motifs:ligand_full_name") |
| BooleanOptionKey const | motifs::write_param_to_pdb ("motifs:write_param_to_pdb") |
| RealOptionKey const | motifs::protein_discovery_locus ("motifs:protein_discovery_locus") |
| RealOptionKey const | motifs::fa_rep_cutoff ("motifs:fa_rep_cutoff") |
| RealOptionKey const | motifs::fa_atr_cutoff ("motifs:fa_atr_cutoff") |
| BooleanOptionKey const | motifs::output_ligand_pdb ("motifs:output_ligand_pdb") |
| BooleanOptionKey const | motifs::check_new_param_file ("motifs:check_new_param_file") |
| RealOptionKey const | motifs::ddg_cutoff ("motifs:ddg_cutoff") |
| IntegerOptionKey const | motifs::best_pdbs_to_keep ("motifs:best_pdbs_to_keep") |
| IntegerOptionKey const | motifs::resolution_scale_factor ("motifs:resolution_scale_factor") |
| RealOptionKey const | motifs::x_min_holes ("motifs:x_min_holes") |
| RealOptionKey const | motifs::x_max_holes ("motifs:x_max_holes") |
| RealOptionKey const | motifs::y_min_holes ("motifs:y_min_holes") |
| RealOptionKey const | motifs::y_max_holes ("motifs:y_max_holes") |
| RealOptionKey const | motifs::z_min_holes ("motifs:z_min_holes") |
| RealOptionKey const | motifs::z_max_holes ("motifs:z_max_holes") |
| BooleanOptionKey const | motifs::highresdocker_allow_minimization ("motifs:highresdocker_allow_minimization") |
| BooleanOptionKey const | motifs::highresdocker_allow_repacking ("motifs:highresdocker_allow_repacking") |
| BooleanOptionKey const | motifs::highresdocker_use_all_residues ("motifs:highresdocker_use_all_residues") |
| StringOptionKey const | motifs::ligand_motif_output_directory_name ("motifs:ligand_motif_output_directory_name") |
| StringOptionKey const | motifs::ligand_motif_output_file_name ("motifs:ligand_motif_output_file_name") |
| BooleanOptionKey const | motifs::output_motifs_as_pdb ("motifs:output_motifs_as_pdb") |
| BooleanOptionKey const | motifs::output_motifs ("motifs:output_motifs") |
| BooleanOptionKey const | ms::ms ("ms") |
| IntegerOptionKey const | ms::pop_from_ss ("ms:pop_from_ss") |
| IntegerOptionKey const | ms::pop_size ("ms:pop_size") |
| IntegerOptionKey const | ms::generations ("ms:generations") |
| IntegerOptionKey const | ms::num_packs ("ms:num_packs") |
| IntegerOptionKey const | ms::numresults ("ms:numresults") |
| RealOptionKey const | ms::anchor_offset ("ms:anchor_offset") |
| RealOptionKey const | ms::Boltz_temp ("ms:Boltz_temp") |
| RealOptionKey const | ms::mutate_rate ("ms:mutate_rate") |
| RealOptionKey const | ms::fraction_by_recombination ("ms:fraction_by_recombination") |
| BooleanOptionKey const | ms::checkpoint::checkpoint ("ms:checkpoint") |
| StringOptionKey const | ms::checkpoint::prefix ("ms:checkpoint:prefix") |
1.9.1