 |
Rosetta Utilities
2014.35
|
|
Rosetta Utilities
2014.35
|
Functions | |
| RealOptionKey const | docking::ligand::harmonic_Calphas ("docking:ligand:harmonic_Calphas") |
| RealOptionKey const | docking::ligand::tether_ligand ("docking:ligand:tether_ligand") |
| RealVectorOptionKey const | docking::ligand::start_from ("docking:ligand:start_from") |
| StringOptionKey const | docking::ligand::option_file ("docking:ligand:option_file") |
| BooleanOptionKey const | docking::ligand::grid::grid ("docking:ligand:grid") |
| FileOptionKey const | docking::ligand::grid::grid_kin ("docking:ligand:grid:grid_kin") |
| FileOptionKey const | docking::ligand::grid::grid_map ("docking:ligand:grid:grid_map") |
| BooleanOptionKey const | DomainAssembly::DomainAssembly ("DomainAssembly") |
| BooleanOptionKey const | DomainAssembly::da_setup ("DomainAssembly:da_setup") |
| FileOptionKey const | DomainAssembly::da_setup_option_file ("DomainAssembly:da_setup_option_file") |
| FileOptionKey const | DomainAssembly::da_setup_output_pdb ("DomainAssembly:da_setup_output_pdb") |
| FileOptionKey const | DomainAssembly::da_linker_file ("DomainAssembly:da_linker_file") |
| FileOptionKey const | DomainAssembly::da_require_buried ("DomainAssembly:da_require_buried") |
| FileOptionKey const | DomainAssembly::da_start_pdb ("DomainAssembly:da_start_pdb") |
| BooleanOptionKey const | DomainAssembly::run_fullatom ("DomainAssembly:run_fullatom") |
| BooleanOptionKey const | DomainAssembly::run_centroid ("DomainAssembly:run_centroid") |
| BooleanOptionKey const | DomainAssembly::run_centroid_abinitio ("DomainAssembly:run_centroid_abinitio") |
| IntegerOptionKey const | DomainAssembly::da_nruns ("DomainAssembly:da_nruns") |
| IntegerOptionKey const | DomainAssembly::da_start_pdb_num ("DomainAssembly:da_start_pdb_num") |
| FileOptionKey const | DomainAssembly::da_linker_file_rna ("DomainAssembly:da_linker_file_rna") |
| StringOptionKey const | DomainAssembly::residues_repack_only ("DomainAssembly:residues_repack_only") |
| FileOptionKey const | DomainAssembly::da_eval_pose_map ("DomainAssembly:da_eval_pose_map") |
| BooleanOptionKey const | edensity::edensity ("edensity") |
| BooleanOptionKey const | edensity::debug ("edensity:debug") |
| StringOptionKey const | edensity::mapfile ("edensity:mapfile") |
| RealOptionKey const | edensity::mapreso ("edensity:mapreso") |
| RealOptionKey const | edensity::grid_spacing ("edensity:grid_spacing") |
| RealOptionKey const | edensity::centroid_density_mass ("edensity:centroid_density_mass") |
| IntegerOptionKey const | edensity::sliding_window ("edensity:sliding_window") |
| BooleanOptionKey const | edensity::cryoem_scatterers ("edensity:cryoem_scatterers") |
| RealOptionKey const | edensity::force_apix ("edensity:force_apix") |
| RealOptionKey const | edensity::fastdens_wt ("edensity:fastdens_wt") |
| RealVectorOptionKey const | edensity::fastdens_params ("edensity:fastdens_params") |
| BooleanOptionKey const | edensity::legacy_fastdens_score ("edensity:legacy_fastdens_score") |
| RealOptionKey const | edensity::sliding_window_wt ("edensity:sliding_window_wt") |
| BooleanOptionKey const | edensity::score_sliding_window_context ("edensity:score_sliding_window_context") |
| RealOptionKey const | edensity::whole_structure_ca_wt ("edensity:whole_structure_ca_wt") |
| RealOptionKey const | edensity::whole_structure_allatom_wt ("edensity:whole_structure_allatom_wt") |
| BooleanOptionKey const | edensity::debug_derivatives ("edensity:debug_derivatives") |
| StringOptionKey const | edensity::realign ("edensity:realign") |
| StringOptionKey const | edensity::membrane_axis ("edensity:membrane_axis") |
| RealOptionKey const | edensity::atom_mask ("edensity:atom_mask") |
| RealOptionKey const | edensity::atom_mask_min ("edensity:atom_mask_min") |
| RealOptionKey const | edensity::ca_mask ("edensity:ca_mask") |
| BooleanOptionKey const | edensity::score_symm_complex ("edensity:score_symm_complex") |
| RealOptionKey const | edensity::sc_scaling ("edensity:sc_scaling") |
| IntegerOptionKey const | edensity::n_kbins ("edensity:n_kbins") |
| BooleanOptionKey const | edensity::unmask_bb ("edensity:unmask_bb") |
| 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 | 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::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 | fast_loops::fast_loops ("fast_loops") |
| RealOptionKey const | fast_loops::window_accept_ratio ("fast_loops:window_accept_ratio") |
| IntegerOptionKey const | fast_loops::nr_scored_sampling_passes ("fast_loops:nr_scored_sampling_passes") |
| IntegerOptionKey const | fast_loops::nr_scored_fragments ("fast_loops:nr_scored_fragments") |
| IntegerOptionKey const | fast_loops::min_breakout_good_loops ("fast_loops:min_breakout_good_loops") |
| IntegerOptionKey const | fast_loops::min_breakout_fast_loops ("fast_loops:min_breakout_fast_loops") |
| IntegerOptionKey const | fast_loops::min_good_loops ("fast_loops:min_good_loops") |
| IntegerOptionKey const | fast_loops::min_fast_loops ("fast_loops:min_fast_loops") |
| RealOptionKey const | fast_loops::vdw_delta ("fast_loops:vdw_delta") |
| IntegerOptionKey const | fast_loops::give_up ("fast_loops:give_up") |
| RealOptionKey const | fast_loops::chainbreak_max ("fast_loops:chainbreak_max") |
| FileOptionKey const | fast_loops::fragsample_score ("fast_loops:fragsample_score") |
| FileOptionKey const | fast_loops::fragsample_patch ("fast_loops:fragsample_patch") |
| FileOptionKey const | fast_loops::overwrite_filter_scorefxn ("fast_loops:overwrite_filter_scorefxn") |
| FileOptionKey const | fast_loops::patch_filter_scorefxn ("fast_loops:patch_filter_scorefxn") |
| FileOptionKey const | fast_loops::filter_cst_file ("fast_loops:filter_cst_file") |
| RealOptionKey const | fast_loops::filter_cst_weight ("fast_loops:filter_cst_weight") |
| FileOptionKey const | fast_loops::fast_relax_sequence_file ("fast_loops:fast_relax_sequence_file") |
| BooleanOptionKey const | fingerprint::fingerprint ("fingerprint") |
| RealOptionKey const | fingerprint::atom_radius_scale ("fingerprint:atom_radius_scale") |
| RealOptionKey const | fingerprint::atom_radius_buffer ("fingerprint:atom_radius_buffer") |
| BooleanOptionKey const | fingerprint::include_hydrogens ("fingerprint:include_hydrogens") |
| BooleanOptionKey const | fingerprint::square_score ("fingerprint:square_score") |
| IntegerOptionKey const | fingerprint::set_origin ("fingerprint:set_origin") |
| IntegerOptionKey const | fingerprint::origin_res_num ("fingerprint:origin_res_num") |
| BooleanOptionKey const | flexpack::flexpack ("flexpack") |
| BooleanOptionKey const | flexpack::annealer::annealer ("flexpack:annealer") |
| RealOptionKey const | flexpack::annealer::inner_iteration_scale ("flexpack:annealer:inner_iteration_scale") |
| RealOptionKey const | flexpack::annealer::outer_iteration_scale ("flexpack:annealer:outer_iteration_scale") |
| RealOptionKey const | flexpack::annealer::fixbb_substitutions_scale ("flexpack:annealer:fixbb_substitutions_scale") |
| RealOptionKey const | flexpack::annealer::pure_movebb_substitutions_scale ("flexpack:annealer:pure_movebb_substitutions_scale") |
| RealOptionKey const | flexpack::annealer::rotsub_movebb_substitutions_scale ("flexpack:annealer:rotsub_movebb_substitutions_scale") |
| BooleanOptionKey const | flexPepDocking::flexPepDocking ("flexPepDocking") |
| StringOptionKey const | flexPepDocking::params_file ("flexPepDocking:params_file") |
| IntegerOptionKey const | flexPepDocking::peptide_anchor ("flexPepDocking:peptide_anchor") |
| StringOptionKey const | flexPepDocking::receptor_chain ("flexPepDocking:receptor_chain") |
| StringOptionKey const | flexPepDocking::peptide_chain ("flexPepDocking:peptide_chain") |
| BooleanOptionKey const | flexPepDocking::pep_fold_only ("flexPepDocking:pep_fold_only") |
| BooleanOptionKey const | flexPepDocking::lowres_abinitio ("flexPepDocking:lowres_abinitio") |
| BooleanOptionKey const | flexPepDocking::lowres_preoptimize ("flexPepDocking:lowres_preoptimize") |
| BooleanOptionKey const | flexPepDocking::flexPepDockingMinimizeOnly ("flexPepDocking:flexPepDockingMinimizeOnly") |
| BooleanOptionKey const | flexPepDocking::extend_peptide ("flexPepDocking:extend_peptide") |
| BooleanOptionKey const | flexPepDocking::pep_refine ("flexPepDocking:pep_refine") |
| BooleanOptionKey const | flexPepDocking::rbMCM ("flexPepDocking:rbMCM") |
| BooleanOptionKey const | flexPepDocking::torsionsMCM ("flexPepDocking:torsionsMCM") |
| BooleanOptionKey const | flexPepDocking::peptide_loop_model ("flexPepDocking:peptide_loop_model") |
| BooleanOptionKey const | flexPepDocking::backrub_peptide ("flexPepDocking:backrub_peptide") |
| BooleanOptionKey const | flexPepDocking::boost_fa_atr ("flexPepDocking:boost_fa_atr") |
| BooleanOptionKey const | flexPepDocking::ramp_fa_rep ("flexPepDocking:ramp_fa_rep") |
| BooleanOptionKey const | flexPepDocking::ramp_rama ("flexPepDocking:ramp_rama") |
| BooleanOptionKey const | flexPepDocking::flexpep_score_only ("flexPepDocking:flexpep_score_only") |
| FileOptionKey const | flexPepDocking::ref_startstruct ("flexPepDocking:ref_startstruct") |
| BooleanOptionKey const | flexPepDocking::use_cen_score ("flexPepDocking:use_cen_score") |
| BooleanOptionKey const | flexPepDocking::design_peptide ("flexPepDocking:design_peptide") |
| IntegerOptionKey const | flexPepDocking::rep_ramp_cycles ("flexPepDocking:rep_ramp_cycles") |
| IntegerOptionKey const | flexPepDocking::mcm_cycles ("flexPepDocking:mcm_cycles") |
| RealOptionKey const | flexPepDocking::random_phi_psi_preturbation ("flexPepDocking:random_phi_psi_preturbation") |
| RealOptionKey const | flexPepDocking::smove_angle_range ("flexPepDocking:smove_angle_range") |
| BooleanOptionKey const | flexPepDocking::min_receptor_bb ("flexPepDocking:min_receptor_bb") |
| RealOptionKey const | flexPepDocking::random_trans_start ("flexPepDocking:random_trans_start") |
| RealOptionKey const | flexPepDocking::random_rot_start ("flexPepDocking:random_rot_start") |
| BooleanOptionKey const | flexPepDocking::flexpep_prepack ("flexPepDocking:flexpep_prepack") |
| BooleanOptionKey const | flexPepDocking::flexpep_noprepack1 ("flexPepDocking:flexpep_noprepack1") |
| BooleanOptionKey const | flexPepDocking::flexpep_noprepack2 ("flexPepDocking:flexpep_noprepack2") |
| RealOptionKey const | flexPepDocking::score_filter ("flexPepDocking:score_filter") |
| IntegerOptionKey const | flexPepDocking::hb_filter ("flexPepDocking:hb_filter") |
| IntegerOptionKey const | flexPepDocking::hotspot_filter ("flexPepDocking:hotspot_filter") |
| StringOptionKey const | flexPepDocking::frag5 ("flexPepDocking:frag5") |
| RealOptionKey const | flexPepDocking::frag9_weight ("flexPepDocking:frag9_weight") |
| RealOptionKey const | flexPepDocking::frag5_weight ("flexPepDocking:frag5_weight") |
| RealOptionKey const | flexPepDocking::frag3_weight ("flexPepDocking:frag3_weight") |
| BooleanOptionKey const | flexPepDocking::pSer2Asp_centroid ("flexPepDocking:pSer2Asp_centroid") |
| BooleanOptionKey const | flexPepDocking::pSer2Glu_centroid ("flexPepDocking:pSer2Glu_centroid") |
| BooleanOptionKey const | flexPepDocking::dumpPDB_abinitio ("flexPepDocking:dumpPDB_abinitio") |
| BooleanOptionKey const | flexPepDocking::dumpPDB_lowres ("flexPepDocking:dumpPDB_lowres") |
| BooleanOptionKey const | flexPepDocking::dumpPDB_hires ("flexPepDocking:dumpPDB_hires") |
| BooleanOptionKey const | FloppyTail::FloppyTail ("FloppyTail") |
| IntegerOptionKey const | FloppyTail::flexible_start_resnum ("FloppyTail:flexible_start_resnum") |
| IntegerOptionKey const | FloppyTail::flexible_stop_resnum ("FloppyTail:flexible_stop_resnum") |
| StringOptionKey const | FloppyTail::flexible_chain ("FloppyTail:flexible_chain") |
| RealOptionKey const | FloppyTail::shear_on ("FloppyTail:shear_on") |
| BooleanOptionKey const | FloppyTail::pair_off ("FloppyTail:pair_off") |
| BooleanOptionKey const | FloppyTail::publication ("FloppyTail:publication") |
| BooleanOptionKey const | FloppyTail::C_root ("FloppyTail:C_root") |
| BooleanOptionKey const | FloppyTail::force_linear_fold_tree ("FloppyTail:force_linear_fold_tree") |
| BooleanOptionKey const | FloppyTail::debug ("FloppyTail:debug") |
| StringOptionKey const | FloppyTail::cen_weights ("FloppyTail:cen_weights") |
| BooleanOptionKey const | FloppyTail::perturb_show ("FloppyTail:perturb_show") |
| IntegerOptionKey const | FloppyTail::perturb_cycles ("FloppyTail:perturb_cycles") |
| RealOptionKey const | FloppyTail::perturb_temp ("FloppyTail:perturb_temp") |
| IntegerOptionKey const | FloppyTail::refine_cycles ("FloppyTail:refine_cycles") |
| RealOptionKey const | FloppyTail::refine_temp ("FloppyTail:refine_temp") |
| IntegerOptionKey const | FloppyTail::refine_repack_cycles ("FloppyTail:refine_repack_cycles") |
| BooleanOptionKey const | FloppyTail::short_tail::short_tail ("FloppyTail:short_tail") |
| RealOptionKey const | FloppyTail::short_tail::short_tail_fraction ("FloppyTail:short_tail:short_tail_fraction") |
| RealOptionKey const | FloppyTail::short_tail::short_tail_off ("FloppyTail:short_tail:short_tail_off") |
| BooleanOptionKey const | flxbb::flxbb ("flxbb") |
| BooleanOptionKey const | flxbb::view ("flxbb:view") |
| IntegerOptionKey const | flxbb::ncycle ("flxbb:ncycle") |
| RealOptionKey const | flxbb::constraints_sheet ("flxbb:constraints_sheet") |
| BooleanOptionKey const | flxbb::constraints_sheet_include_cacb_pseudotorsion ("flxbb:constraints_sheet_include_cacb_pseudotorsion") |
| RealOptionKey const | flxbb::constraints_NtoC ("flxbb:constraints_NtoC") |
| IntegerOptionKey const | flxbb::filter_trial ("flxbb:filter_trial") |
| StringOptionKey const | flxbb::filter_type ("flxbb:filter_type") |
| FileOptionKey const | flxbb::blueprint ("flxbb:blueprint") |
| BooleanOptionKey const | flxbb::movemap_from_blueprint ("flxbb:movemap_from_blueprint") |
| StringOptionKey const | flxbb::layer::layer ("flxbb:layer") |
| BooleanOptionKey const | fold_and_dock::fold_and_dock ("fold_and_dock") |
| BooleanOptionKey const | fold_and_dock::move_anchor_points ("fold_and_dock:move_anchor_points") |
| BooleanOptionKey const | fold_and_dock::set_anchor_at_closest_point ("fold_and_dock:set_anchor_at_closest_point") |
| BooleanOptionKey const | fold_and_dock::rotate_anchor_to_x ("fold_and_dock:rotate_anchor_to_x") |
| RealOptionKey const | fold_and_dock::trans_mag_smooth ("fold_and_dock:trans_mag_smooth") |
| RealOptionKey const | fold_and_dock::rot_mag_smooth ("fold_and_dock:rot_mag_smooth") |
| RealOptionKey const | fold_and_dock::rb_rot_magnitude ("fold_and_dock:rb_rot_magnitude") |
| RealOptionKey const | fold_and_dock::rb_trans_magnitude ("fold_and_dock:rb_trans_magnitude") |
| IntegerOptionKey const | fold_and_dock::rigid_body_cycles ("fold_and_dock:rigid_body_cycles") |
| RealOptionKey const | fold_and_dock::move_anchor_frequency ("fold_and_dock:move_anchor_frequency") |
| RealOptionKey const | fold_and_dock::rigid_body_frequency ("fold_and_dock:rigid_body_frequency") |
| BooleanOptionKey const | fold_and_dock::rigid_body_disable_mc ("fold_and_dock:rigid_body_disable_mc") |
| RealOptionKey const | fold_and_dock::slide_contact_frequency ("fold_and_dock:slide_contact_frequency") |
| BooleanOptionKey const | fold_cst::fold_cst ("fold_cst") |
| RealOptionKey const | fold_cst::constraint_skip_rate ("fold_cst:constraint_skip_rate") |
| IntegerOptionKey const | fold_cst::violation_skip_basis ("fold_cst:violation_skip_basis") |
| IntegerOptionKey const | fold_cst::violation_skip_ignore ("fold_cst:violation_skip_ignore") |
| BooleanOptionKey const | fold_cst::keep_skipped_csts ("fold_cst:keep_skipped_csts") |
| BooleanOptionKey const | fold_cst::no_minimize ("fold_cst:no_minimize") |
| BooleanOptionKey const | fold_cst::force_minimize ("fold_cst:force_minimize") |
| RealVectorOptionKey const | fold_cst::seq_sep_stages ("fold_cst:seq_sep_stages") |
| IntegerOptionKey const | fold_cst::reramp_cst_cycles ("fold_cst:reramp_cst_cycles") |
| RealOptionKey const | fold_cst::reramp_start_cstweight ("fold_cst:reramp_start_cstweight") |
| IntegerOptionKey const | fold_cst::reramp_iterations ("fold_cst:reramp_iterations") |
| BooleanOptionKey const | fold_cst::skip_on_noviolation_in_stage1 ("fold_cst:skip_on_noviolation_in_stage1") |
| RealOptionKey const | fold_cst::stage1_ramp_cst_cycle_factor ("fold_cst:stage1_ramp_cst_cycle_factor") |
| RealOptionKey const | fold_cst::stage2_constraint_threshold ("fold_cst:stage2_constraint_threshold") |
| BooleanOptionKey const | fold_cst::ignore_sequence_seperation ("fold_cst:ignore_sequence_seperation") |
| BooleanOptionKey const | fold_cst::no_recover_low_at_constraint_switch ("fold_cst:no_recover_low_at_constraint_switch") |
| BooleanOptionKey const | fold_cst::ramp_coord_cst ("fold_cst:ramp_coord_cst") |
| BooleanOptionKey const | fold_from_loops::fold_from_loops ("fold_from_loops") |
| BooleanOptionKey const | fold_from_loops::native_ca_cst ("fold_from_loops:native_ca_cst") |
| FileOptionKey const | fold_from_loops::swap_loops ("fold_from_loops:swap_loops") |
| StringOptionKey const | fold_from_loops::checkpoint ("fold_from_loops:checkpoint") |
| RealOptionKey const | fold_from_loops::ca_csts_dev ("fold_from_loops:ca_csts_dev") |
| IntegerOptionKey const | fold_from_loops::add_relax_cycles ("fold_from_loops:add_relax_cycles") |
| IntegerOptionKey const | fold_from_loops::loop_mov_nterm ("fold_from_loops:loop_mov_nterm") |
| IntegerOptionKey const | fold_from_loops::loop_mov_cterm ("fold_from_loops:loop_mov_cterm") |
| RealOptionKey const | fold_from_loops::ca_rmsd_cutoff ("fold_from_loops:ca_rmsd_cutoff") |
| IntegerVectorOptionKey const | fold_from_loops::res_design_bs ("fold_from_loops:res_design_bs") |
| FileOptionKey const | fold_from_loops::clear_csts ("fold_from_loops:clear_csts") |
| BooleanOptionKey const | fold_from_loops::output_centroid ("fold_from_loops:output_centroid") |
| BooleanOptionKey const | fold_from_loops::add_cst_loop ("fold_from_loops:add_cst_loop") |
| BooleanOptionKey const | frags::frags ("frags") |
| BooleanOptionKey const | frags::filter_JC ("frags:filter_JC") |
| BooleanOptionKey const | frags::bounded_protocol ("frags:bounded_protocol") |
| BooleanOptionKey const | frags::keep_all_protocol ("frags:keep_all_protocol") |
| BooleanOptionKey const | frags::quota_protocol ("frags:quota_protocol") |
| BooleanOptionKey const | frags::nonlocal_pairs ("frags:nonlocal_pairs") |
| BooleanOptionKey const | frags::fragment_contacts ("frags:fragment_contacts") |
| BooleanOptionKey const | frags::p_value_selection ("frags:p_value_selection") |
| IntegerOptionKey const | frags::n_frags ("frags:n_frags") |
| FileOptionKey const | frags::allowed_pdb ("frags:allowed_pdb") |
| StringVectorOptionKey const | frags::ss_pred ("frags:ss_pred") |
| FileOptionKey const | frags::spine_x ("frags:spine_x") |
| FileOptionKey const | frags::depth ("frags:depth") |
| FileOptionKey const | frags::denied_pdb ("frags:denied_pdb") |
| IntegerVectorOptionKey const | frags::frag_sizes ("frags:frag_sizes") |
| BooleanOptionKey const | frags::write_ca_coordinates ("frags:write_ca_coordinates") |
| BooleanOptionKey const | frags::write_scores ("frags:write_scores") |
| BooleanOptionKey const | frags::annotate ("frags:annotate") |
| IntegerOptionKey const | frags::nr_large_copies ("frags:nr_large_copies") |
| IntegerOptionKey const | frags::n_candidates ("frags:n_candidates") |
| BooleanOptionKey const | frags::write_rama_tables ("frags:write_rama_tables") |
| RealOptionKey const | frags::rama_C ("frags:rama_C") |
| RealOptionKey const | frags::rama_B ("frags:rama_B") |
| RealOptionKey const | frags::sigmoid_cs_A ("frags:sigmoid_cs_A") |
| RealOptionKey const | frags::sigmoid_cs_B ("frags:sigmoid_cs_B") |
| RealOptionKey const | frags::seqsim_H ("frags:seqsim_H") |
| RealOptionKey const | frags::seqsim_E ("frags:seqsim_E") |
| RealOptionKey const | frags::seqsim_L ("frags:seqsim_L") |
| RealOptionKey const | frags::rama_norm ("frags:rama_norm") |
| StringOptionKey const | frags::describe_fragments ("frags:describe_fragments") |
| RealOptionKey const | frags::picking_old_max_score ("frags:picking_old_max_score") |
| BooleanOptionKey const | frags::write_sequence_only ("frags:write_sequence_only") |
| BooleanOptionKey const | frags::output_silent ("frags:output_silent") |
| BooleanOptionKey const | frags::score_output_silent ("frags:score_output_silent") |
| BooleanOptionKey const | frags::scoring::scoring ("frags:scoring") |
| FileOptionKey const | frags::scoring::config ("frags:scoring:config") |
| StringOptionKey const | frags::scoring::profile_score ("frags:scoring:profile_score") |
| BooleanOptionKey const | frags::picking::picking ("frags:picking") |
| StringOptionKey const | frags::picking::selecting_rule ("frags:picking:selecting_rule") |
| StringOptionKey const | frags::picking::selecting_scorefxn ("frags:picking:selecting_scorefxn") |
| FileOptionKey const | frags::picking::quota_config_file ("frags:picking:quota_config_file") |
| IntegerVectorOptionKey const | frags::picking::query_pos ("frags:picking:query_pos") |
| BooleanOptionKey const | frags::nonlocal::nonlocal ("frags:nonlocal") |
| BooleanOptionKey const | frags::nonlocal::relax_input ("frags:nonlocal:relax_input") |
| BooleanOptionKey const | frags::nonlocal::relax_input_with_coordinate_constraints ("frags:nonlocal:relax_input_with_coordinate_constraints") |
| IntegerOptionKey const | frags::nonlocal::relax_frags_repeats ("frags:nonlocal:relax_frags_repeats") |
| BooleanOptionKey const | frags::nonlocal::single_chain ("frags:nonlocal:single_chain") |
| RealOptionKey const | frags::nonlocal::min_contacts_per_res ("frags:nonlocal:min_contacts_per_res") |
| RealOptionKey const | frags::nonlocal::max_ddg_score ("frags:nonlocal:max_ddg_score") |
| RealOptionKey const | frags::nonlocal::max_rmsd_after_relax ("frags:nonlocal:max_rmsd_after_relax") |
| BooleanOptionKey const | frags::nonlocal::output_frags_pdbs ("frags:nonlocal:output_frags_pdbs") |
| BooleanOptionKey const | frags::nonlocal::output_idealized ("frags:nonlocal:output_idealized") |
| BooleanOptionKey const | frags::nonlocal::output_silent ("frags:nonlocal:output_silent") |
| BooleanOptionKey const | frags::contacts::contacts ("frags:contacts") |
| IntegerOptionKey const | frags::contacts::min_seq_sep ("frags:contacts:min_seq_sep") |
| RealVectorOptionKey const | frags::contacts::dist_cutoffs ("frags:contacts:dist_cutoffs") |
| RealOptionKey const | frags::contacts::centroid_distance_scale_factor ("frags:contacts:centroid_distance_scale_factor") |
| StringVectorOptionKey const | frags::contacts::type ("frags:contacts:type") |
| IntegerOptionKey const | frags::contacts::neighbors ("frags:contacts:neighbors") |
| BooleanOptionKey const | frags::contacts::output_all ("frags:contacts:output_all") |
| BooleanOptionKey const | frags::ABEGO::ABEGO ("frags:ABEGO") |
| RealOptionKey const | frags::ABEGO::phi_psi_range_A ("frags:ABEGO:phi_psi_range_A") |
| BooleanOptionKey const | holes::holes ("holes") |
| FileOptionKey const | holes::dalphaball ("holes:dalphaball") |
| FileOptionKey const | holes::params ("holes:params") |
| IntegerOptionKey const | holes::h_mode ("holes:h_mode") |
| BooleanOptionKey const | holes::water ("holes:water") |
| BooleanOptionKey const | holes::make_pdb ("holes:make_pdb") |
| BooleanOptionKey const | holes::make_voids ("holes:make_voids") |
| BooleanOptionKey const | holes::atom_scores ("holes:atom_scores") |
| BooleanOptionKey const | holes::residue_scores ("holes:residue_scores") |
| StringOptionKey const | holes::minimize ("holes:minimize") |
| BooleanOptionKey const | holes::debug ("holes:debug") |
| BooleanOptionKey const | hotspot::hotspot ("hotspot") |
| BooleanOptionKey const | hotspot::allow_gly ("hotspot:allow_gly") |
| BooleanOptionKey const | hotspot::allow_proline ("hotspot:allow_proline") |
| BooleanOptionKey const | hotspot::benchmark ("hotspot:benchmark") |
| StringVectorOptionKey const | hotspot::residue ("hotspot:residue") |
| FileOptionKey const | hotspot::hashfile ("hotspot:hashfile") |
| FileOptionKey const | hotspot::target ("hotspot:target") |
| IntegerOptionKey const | hotspot::target_res ("hotspot:target_res") |
| RealOptionKey const | hotspot::target_dist ("hotspot:target_dist") |
| FileOptionKey const | hotspot::density ("hotspot:density") |
| FileOptionKey const | hotspot::weighted_density ("hotspot:weighted_density") |
| FileOptionKey const | hotspot::rms_target ("hotspot:rms_target") |
| FileOptionKey const | hotspot::rms_hotspot ("hotspot:rms_hotspot") |
| IntegerOptionKey const | hotspot::rms_hotspot_res ("hotspot:rms_hotspot_res") |
| BooleanOptionKey const | hotspot::rescore ("hotspot:rescore") |
| RealOptionKey const | hotspot::threshold ("hotspot:threshold") |
| BooleanOptionKey const | hotspot::sc_only ("hotspot:sc_only") |
| BooleanOptionKey const | hotspot::fxnal_group ("hotspot:fxnal_group") |
| BooleanOptionKey const | hotspot::cluster ("hotspot:cluster") |
| BooleanOptionKey const | hotspot::colonyE ("hotspot:colonyE") |
| IntegerOptionKey const | hotspot::length ("hotspot:length") |
| BooleanOptionKey const | hotspot::envhb ("hotspot:envhb") |
| RealOptionKey const | hotspot::angle ("hotspot:angle") |
| IntegerOptionKey const | hotspot::angle_res ("hotspot:angle_res") |
| BooleanOptionKey const | indexed_structure_store::indexed_structure_store ("indexed_structure_store") |
| FileOptionKey const | indexed_structure_store::fragment_store ("indexed_structure_store:fragment_store") |
| BooleanOptionKey const | lh::lh ("lh") |
| IntegerVectorOptionKey const | lh::loopsizes ("lh:loopsizes") |
| IntegerOptionKey const | lh::num_partitions ("lh:num_partitions") |
| PathOptionKey const | lh::db_path ("lh:db_path") |
| BooleanOptionKey const | lh::exclude_homo ("lh:exclude_homo") |
| BooleanOptionKey const | lh::bss ("lh:bss") |
| StringOptionKey const | lh::refstruct ("lh:refstruct") |
| StringOptionKey const | lh::homo_file ("lh:homo_file") |
| RealVectorOptionKey const | lh::createdb_rms_cutoff ("lh:createdb_rms_cutoff") |
| RealOptionKey const | lh::min_bbrms ("lh:min_bbrms") |
| RealOptionKey const | lh::max_bbrms ("lh:max_bbrms") |
| RealOptionKey const | lh::min_rms ("lh:min_rms") |
| RealOptionKey const | lh::max_rms ("lh:max_rms") |
| BooleanOptionKey const | lh::filter_by_phipsi ("lh:filter_by_phipsi") |
| IntegerOptionKey const | lh::max_radius ("lh:max_radius") |
| IntegerOptionKey const | lh::max_struct ("lh:max_struct") |
| IntegerOptionKey const | lh::max_struct_per_radius ("lh:max_struct_per_radius") |
| RealOptionKey const | lh::grid_space_multiplier ("lh:grid_space_multiplier") |
| RealOptionKey const | lh::grid_angle_multiplier ("lh:grid_angle_multiplier") |
| IntegerOptionKey const | lh::skim_size ("lh:skim_size") |
| IntegerOptionKey const | lh::rounds ("lh:rounds") |
| StringOptionKey const | lh::jobname ("lh:jobname") |
| IntegerOptionKey const | lh::max_lib_size ("lh:max_lib_size") |
| IntegerOptionKey const | lh::max_emperor_lib_size ("lh:max_emperor_lib_size") |
| IntegerOptionKey const | lh::max_emperor_lib_round ("lh:max_emperor_lib_round") |
| IntegerOptionKey const | lh::library_expiry_time ("lh:library_expiry_time") |
| StringOptionKey const | lh::objective_function ("lh:objective_function") |
| IntegerOptionKey const | lh::expire_after_rounds ("lh:expire_after_rounds") |
| StringOptionKey const | lh::mpi_resume ("lh:mpi_resume") |
| StringOptionKey const | lh::mpi_feedback ("lh:mpi_feedback") |
| IntegerOptionKey const | lh::mpi_batch_relax_chunks ("lh:mpi_batch_relax_chunks") |
| IntegerOptionKey const | lh::mpi_batch_relax_absolute_max ("lh:mpi_batch_relax_absolute_max") |
| IntegerOptionKey const | lh::mpi_outbound_wu_buffer_size ("lh:mpi_outbound_wu_buffer_size") |
| IntegerOptionKey const | lh::mpi_loophash_split_size ("lh:mpi_loophash_split_size ") |
| RealOptionKey const | lh::mpi_metropolis_temp ("lh:mpi_metropolis_temp") |
| IntegerOptionKey const | lh::mpi_save_state_interval ("lh:mpi_save_state_interval") |
| BooleanOptionKey const | lh::mpi_master_save_score_only ("lh:mpi_master_save_score_only") |
| IntegerOptionKey const | lh::max_loophash_per_structure ("lh:max_loophash_per_structure") |
| RealOptionKey const | lh::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") |
| RealOptionKey const | lh::radius_size ("lh:radius_size") |
| BooleanOptionKey const | lh::fragpdb::fragpdb ("lh:fragpdb") |
| StringOptionKey const | lh::fragpdb::out_path ("lh:fragpdb:out_path") |
| IntegerVectorOptionKey const | lh::fragpdb::indexoffset ("lh:fragpdb:indexoffset") |
| StringVectorOptionKey const | lh::fragpdb::bin ("lh:fragpdb:bin") |
| BooleanOptionKey const | lh::symfragrm::symfragrm ("lh:symfragrm") |
| FileVectorOptionKey const | lh::symfragrm::pdblist ("lh:symfragrm:pdblist") |
| BooleanOptionKey const | loopfcst::loopfcst ("loopfcst") |
| RealOptionKey const | loopfcst::coord_cst_weight ("loopfcst:coord_cst_weight") |
| BooleanOptionKey const | loopfcst::coord_cst_all_atom ("loopfcst:coord_cst_all_atom") |
| BooleanOptionKey const | loopfcst::use_general_protocol ("loopfcst:use_general_protocol") |
| FileOptionKey const | loopfcst::coord_cst_weight_array ("loopfcst:coord_cst_weight_array") |
| FileOptionKey const | loopfcst::dump_coord_cst_weight_array ("loopfcst:dump_coord_cst_weight_array") |
| BooleanOptionKey const | LoopModel::LoopModel ("LoopModel") |
| FileOptionKey const | LoopModel::input_pdb ("LoopModel:input_pdb") |
| BooleanOptionKey const | make_rot_lib::make_rot_lib ("make_rot_lib") |
| FileOptionKey const | make_rot_lib::options_file ("make_rot_lib:options_file") |
| IntegerVectorOptionKey const | make_rot_lib::two_fold_symetry_135_315 ("make_rot_lib:two_fold_symetry_135_315") |
| IntegerVectorOptionKey const | make_rot_lib::two_fold_symetry_0_180 ("make_rot_lib:two_fold_symetry_0_180") |
| IntegerVectorOptionKey const | make_rot_lib::three_fold_symetry_90_210_330 ("make_rot_lib:three_fold_symetry_90_210_330") |
| BooleanOptionKey const | match::match ("match") |
| StringOptionKey const | match::lig_name ("match:lig_name") |
| RealOptionKey const | match::bump_tolerance ("match:bump_tolerance") |
| FileOptionKey const | match::active_site_definition_by_residue ("match:active_site_definition_by_residue") |
| FileOptionKey const | match::active_site_definition_by_gridlig ("match:active_site_definition_by_gridlig") |
| FileOptionKey const | match::required_active_site_atom_names ("match:required_active_site_atom_names") |
| FileOptionKey const | match::grid_boundary ("match:grid_boundary") |
| FileOptionKey const | match::geometric_constraint_file ("match:geometric_constraint_file") |
| FileOptionKey const | match::scaffold_active_site_residues ("match:scaffold_active_site_residues") |
| FileOptionKey const | match::scaffold_active_site_residues_for_geomcsts ("match:scaffold_active_site_residues_for_geomcsts") |
| RealOptionKey const | match::euclid_bin_size ("match:euclid_bin_size") |
| RealOptionKey const | match::euler_bin_size ("match:euler_bin_size") |
| BooleanOptionKey const | match::consolidate_matches ("match:consolidate_matches") |
| IntegerOptionKey const | match::output_matches_per_group ("match:output_matches_per_group") |
| StringVectorOptionKey const | match::orientation_atoms ("match:orientation_atoms") |
| StringOptionKey const | match::output_format ("match:output_format") |
| StringOptionKey const | match::match_grouper ("match:match_grouper") |
| RealOptionKey const | match::grouper_downstream_rmsd ("match:grouper_downstream_rmsd") |
| BooleanOptionKey const | match::output_matchres_only ("match:output_matchres_only") |
| IntegerVectorOptionKey const | match::geom_csts_downstream_output ("match:geom_csts_downstream_output") |
| BooleanOptionKey const | match::filter_colliding_upstream_residues ("match:filter_colliding_upstream_residues") |
| RealOptionKey const | match::upstream_residue_collision_tolerance ("match:upstream_residue_collision_tolerance") |
| RealOptionKey const | match::upstream_residue_collision_score_cutoff ("match:upstream_residue_collision_score_cutoff") |
| RealOptionKey const | match::upstream_residue_collision_Wfa_atr ("match:upstream_residue_collision_Wfa_atr") |
| RealOptionKey const | match::upstream_residue_collision_Wfa_rep ("match:upstream_residue_collision_Wfa_rep") |
| RealOptionKey const | match::upstream_residue_collision_Wfa_sol ("match:upstream_residue_collision_Wfa_sol") |
| BooleanOptionKey const | match::filter_upstream_downstream_collisions ("match:filter_upstream_downstream_collisions") |
| RealOptionKey const | match::updown_collision_tolerance ("match:updown_collision_tolerance") |
| RealOptionKey const | match::updown_residue_collision_score_cutoff ("match:updown_residue_collision_score_cutoff") |
| RealOptionKey const | match::updown_residue_collision_Wfa_atr ("match:updown_residue_collision_Wfa_atr") |
| RealOptionKey const | match::updown_residue_collision_Wfa_rep ("match:updown_residue_collision_Wfa_rep") |
| RealOptionKey const | match::updown_residue_collision_Wfa_sol ("match:updown_residue_collision_Wfa_sol") |
| BooleanOptionKey const | match::define_match_by_single_downstream_positioning ("match:define_match_by_single_downstream_positioning") |
| IntegerOptionKey const | match::ligand_rotamer_index ("match:ligand_rotamer_index") |
| BooleanOptionKey const | match::enumerate_ligand_rotamers ("match:enumerate_ligand_rotamers") |
| BooleanOptionKey const | match::only_enumerate_non_match_redundant_ligand_rotamers ("match:only_enumerate_non_match_redundant_ligand_rotamers") |
| BooleanOptionKey const | match::dynamic_grid_refinement ("match:dynamic_grid_refinement") |
| BooleanOptionKey const | match::build_round1_hits_twice ("match:build_round1_hits_twice") |
| BooleanOptionKey const | matdes::matdes ("matdes") |
| IntegerOptionKey const | matdes::num_subs_building_block ("matdes:num_subs_building_block") |
| IntegerOptionKey const | matdes::num_subs_total ("matdes:num_subs_total") |
| StringOptionKey const | matdes::pdbID ("matdes:pdbID") |
| StringOptionKey const | matdes::prefix ("matdes:prefix") |
| RealVectorOptionKey const | matdes::radial_disp ("matdes:radial_disp") |
| RealVectorOptionKey const | matdes::angle ("matdes:angle") |
| StringOptionKey const | matdes::tag ("matdes:tag") |
| BooleanOptionKey const | matdes::dock::dock ("matdes:dock") |
| RealOptionKey const | matdes::dock::neg_r ("matdes:dock:neg_r") |
| BooleanOptionKey const | matdes::dock::dump_pdb ("matdes:dock:dump_pdb") |
| BooleanOptionKey const | matdes::dock::dump_chainA_only ("matdes:dock:dump_chainA_only") |
| BooleanOptionKey const | matdes::design::design ("matdes:design") |
| RealOptionKey const | matdes::design::contact_dist ("matdes:design:contact_dist") |
| RealOptionKey const | matdes::design::grid_size_angle ("matdes:design:grid_size_angle") |
| RealOptionKey const | matdes::design::grid_size_radius ("matdes:design:grid_size_radius") |
| IntegerOptionKey const | matdes::design::grid_nsamp_angle ("matdes:design:grid_nsamp_angle") |
| IntegerOptionKey const | matdes::design::grid_nsamp_radius ("matdes:design:grid_nsamp_radius") |
| RealOptionKey const | matdes::design::fav_nat_bonus ("matdes:design:fav_nat_bonus") |
| 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 | 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::dump_motif_pdbs ("mh:dump_motif_pdbs") |
| FileVectorOptionKey const | mh::merge_motifs ("mh:merge_motifs") |
| BooleanOptionKey const | mh::generate_reverse_motifs ("mh:generate_reverse_motifs") |
| FileVectorOptionKey const | mh::dump_input_pdb ("mh:dump_input_pdb") |
| FileVectorOptionKey const | mh::xform_score_data ("mh:xform_score_data") |
| FileVectorOptionKey const | mh::xform_score_data_ee ("mh:xform_score_data_ee") |
| FileVectorOptionKey const | mh::xform_score_data_eh ("mh:xform_score_data_eh") |
| FileVectorOptionKey const | mh::xform_score_data_he ("mh:xform_score_data_he") |
| FileVectorOptionKey const | mh::xform_score_data_hh ("mh:xform_score_data_hh") |
| FileVectorOptionKey const | mh::xform_score_data_sspair ("mh:xform_score_data_sspair") |
| FileVectorOptionKey const | mh::input_motifs ("mh:input_motifs") |
| 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") |
| RealOptionKey const | mh::dump_matching_motifs_cutoff ("mh:dump_matching_motifs_cutoff") |
| BooleanOptionKey const | mh::score_across_chains_only ("mh:score_across_chains_only") |
| IntegerOptionKey const | mh::dump_motif_pdbs_min_counts ("mh:dump_motif_pdbs_min_counts") |
| RealOptionKey const | mh::hash_cart_size ("mh:hash_cart_size") |
| RealOptionKey const | mh::hash_cart_resl ("mh:hash_cart_resl") |
| RealOptionKey const | mh::hash_angle_resl ("mh:hash_angle_resl") |
| IntegerOptionKey const | mh::harvest_motifs_min_hh_ends ("mh:harvest_motifs_min_hh_ends") |
| IntegerOptionKey const | mh::harvest_scores_min_count ("mh:harvest_scores_min_count") |
| 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") |
| BooleanOptionKey const | mh::score::noloops ("mh:score:noloops") |
| RealOptionKey const | mh::score::strand_pair_weight ("mh:score:strand_pair_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") |
| 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::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") |
| 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::coorderr ("mh:filter:coorderr") |
| 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") |
| 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 | 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") |
| IntegerOptionKey const | ms::checkpoint::interval ("ms:checkpoint:interval") |
| BooleanOptionKey const | ms::checkpoint::gz ("ms:checkpoint:gz") |
| BooleanOptionKey const | ms::checkpoint::rename ("ms:checkpoint:rename") |
| 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::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::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 | parser::parser ("parser") |
| StringOptionKey const | parser::protocol ("parser:protocol") |
| StringVectorOptionKey const | parser::script_vars ("parser:script_vars") |
| BooleanOptionKey const | parser::view ("parser:view") |
| StringOptionKey const | parser::patchdock ("parser:patchdock") |
| IntegerVectorOptionKey const | parser::patchdock_random_entry ("parser:patchdock_random_entry") |
| 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::epsilon ("pb_potential:epsilon") |
| IntegerOptionKey const | pb_potential::apbs_debug ("pb_potential:apbs_debug") |
1.8.7