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Rosetta Utilities
2014.16.56682
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Rosetta Utilities
2014.16.56682
|
Functions | |
| FileOptionKey const | DomainAssembly::da_eval_pose_map ("DomainAssembly:da_eval_pose_map") |
| BooleanOptionKey const | remodel::remodel ("remodel") |
| BooleanOptionKey const | remodel::help ("remodel:help") |
| BooleanOptionKey const | remodel::autopilot ("remodel:autopilot") |
| FileOptionKey const | remodel::blueprint ("remodel:blueprint") |
| FileOptionKey const | remodel::cstfile ("remodel:cstfile") |
| IntegerOptionKey const | remodel::cstfilter ("remodel:cstfilter") |
| StringOptionKey const | remodel::cen_sfxn ("remodel:cen_sfxn") |
| BooleanOptionKey const | remodel::check_scored_centroid ("remodel:check_scored_centroid") |
| IntegerOptionKey const | remodel::num_trajectory ("remodel:num_trajectory") |
| IntegerOptionKey const | remodel::save_top ("remodel:save_top") |
| BooleanOptionKey const | remodel::swap_refine_confirm_protocols ("remodel:swap_refine_confirm_protocols") |
| IntegerOptionKey const | remodel::num_frag_moves ("remodel:num_frag_moves") |
| BooleanOptionKey const | remodel::bypass_fragments ("remodel:bypass_fragments") |
| BooleanOptionKey const | remodel::use_same_length_fragments ("remodel:use_same_length_fragments") |
| BooleanOptionKey const | remodel::enable_ligand_aa ("remodel:enable_ligand_aa") |
| BooleanOptionKey const | remodel::no_jumps ("remodel:no_jumps") |
| BooleanOptionKey const | remodel::backrub ("remodel:backrub") |
| BooleanOptionKey const | remodel::use_blueprint_sequence ("remodel:use_blueprint_sequence ") |
| BooleanOptionKey const | remodel::randomize_equivalent_fragments ("remodel:randomize_equivalent_fragments ") |
| BooleanOptionKey const | remodel::quick_and_dirty ("remodel:quick_and_dirty ") |
| BooleanOptionKey const | remodel::checkpoint ("remodel:checkpoint ") |
| BooleanOptionKey const | remodel::use_ccd_refine ("remodel:use_ccd_refine ") |
| BooleanOptionKey const | remodel::use_pose_relax ("remodel:use_pose_relax ") |
| BooleanOptionKey const | remodel::use_cart_relax ("remodel:use_cart_relax ") |
| BooleanOptionKey const | remodel::free_relax ("remodel:free_relax ") |
| BooleanOptionKey const | remodel::use_dssp_assignment ("remodel:use_dssp_assignment") |
| BooleanOptionKey const | remodel::keep_jumps_in_minimizer ("remodel:keep_jumps_in_minimizer ") |
| FileOptionKey const | remodel::output_fragfiles ("remodel:output_fragfiles") |
| FileOptionKey const | remodel::read_fragfile ("remodel:read_fragfile") |
| StringOptionKey const | remodel::generic_aa ("remodel:generic_aa") |
| RealOptionKey const | remodel::cluster_radius ("remodel:cluster_radius") |
| BooleanOptionKey const | remodel::use_clusters ("remodel:use_clusters") |
| BooleanOptionKey const | remodel::run_confirmation ("remodel:run_confirmation") |
| BooleanOptionKey const | remodel::cluster_on_entire_pose ("remodel:cluster_on_entire_pose") |
| IntegerOptionKey const | remodel::collect_clustered_top ("remodel:collect_clustered_top") |
| IntegerOptionKey const | remodel::dr_cycles ("remodel:dr_cycles") |
| IntegerOptionKey const | remodel::two_chain_tree ("remodel:two_chain_tree") |
| IntegerOptionKey const | remodel::repeat_structure ("remodel:repeat_structure") |
| IntegerOptionKey const | remodel::lh_ex_limit ("remodel:lh_ex_limit") |
| StringVectorOptionKey const | remodel::lh_filter_string ("remodel:lh_filter_string") |
| IntegerOptionKey const | remodel::lh_cbreak_selection ("remodel:lh_cbreak_selection") |
| BooleanOptionKey const | remodel::lh_closure_filter ("remodel:lh_closure_filter") |
| BooleanOptionKey const | remodel::cen_minimize ("remodel:cen_minimize") |
| IntegerOptionKey const | remodel::core_cutoff ("remodel:core_cutoff") |
| IntegerOptionKey const | remodel::boundary_cutoff ("remodel:boundary_cutoff") |
| BooleanOptionKey const | remodel::resclass_by_sasa ("remodel:resclass_by_sasa") |
| RealOptionKey const | remodel::helical_rise ("remodel:helical_rise") |
| RealOptionKey const | remodel::helical_radius ("remodel:helical_radius") |
| RealOptionKey const | remodel::helical_omega ("remodel:helical_omega") |
| RealOptionKey const | remodel::COM_sd ("remodel:COM_sd") |
| RealOptionKey const | remodel::COM_tolerance ("remodel:COM_tolerance") |
| BooleanOptionKey const | remodel::staged_sampling::staged_sampling ("remodel:staged_sampling") |
| FileOptionKey const | remodel::staged_sampling::residues_to_sample ("remodel:staged_sampling:residues_to_sample") |
| StringOptionKey const | remodel::staged_sampling::starting_sequence ("remodel:staged_sampling:starting_sequence") |
| FileOptionKey const | remodel::staged_sampling::starting_pdb ("remodel:staged_sampling:starting_pdb") |
| BooleanOptionKey const | remodel::staged_sampling::require_frags_match_blueprint ("remodel:staged_sampling:require_frags_match_blueprint") |
| BooleanOptionKey const | remodel::staged_sampling::start_w_ideal_helices ("remodel:staged_sampling:start_w_ideal_helices") |
| BooleanOptionKey const | remodel::staged_sampling::sample_over_loops ("remodel:staged_sampling:sample_over_loops") |
| BooleanOptionKey const | remodel::staged_sampling::small_moves ("remodel:staged_sampling:small_moves") |
| BooleanOptionKey const | remodel::staged_sampling::fa_relax_moves ("remodel:staged_sampling:fa_relax_moves") |
| BooleanOptionKey const | remodel::domainFusion::domainFusion ("remodel:domainFusion") |
| FileOptionKey const | remodel::domainFusion::insert_segment_from_pdb ("remodel:domainFusion:insert_segment_from_pdb") |
| RealOptionKey const | remodel::vdw ("remodel:vdw") |
| RealOptionKey const | remodel::rama ("remodel:rama") |
| RealOptionKey const | remodel::cbeta ("remodel:cbeta") |
| RealOptionKey const | remodel::cenpack ("remodel:cenpack") |
| RealOptionKey const | remodel::rg_local ("remodel:rg_local") |
| RealOptionKey const | remodel::hb_lrbb ("remodel:hb_lrbb") |
| RealOptionKey const | remodel::hb_srbb ("remodel:hb_srbb") |
| RealOptionKey const | remodel::rg ("remodel:rg") |
| RealOptionKey const | remodel::rsigma ("remodel:rsigma") |
| RealOptionKey const | remodel::ss_pair ("remodel:ss_pair") |
| BooleanOptionKey const | remodel::build_disulf ("remodel:build_disulf") |
| IntegerOptionKey const | remodel::max_disulf_allowed ("remodel:max_disulf_allowed") |
| RealOptionKey const | remodel::match_rt_limit ("remodel:match_rt_limit") |
| IntegerVectorOptionKey const | remodel::disulf_landing_range ("remodel:disulf_landing_range") |
| BooleanOptionKey const | remodel::design::design ("remodel:design") |
| BooleanOptionKey const | remodel::design::no_design ("remodel:design:no_design ") |
| BooleanOptionKey const | remodel::design::design_all ("remodel:design:design_all") |
| BooleanOptionKey const | remodel::design::allow_rare_aro_chi ("remodel:design:allow_rare_aro_chi") |
| BooleanOptionKey const | remodel::design::silent ("remodel:design:silent") |
| BooleanOptionKey const | remodel::design::skip_partial ("remodel:design:skip_partial") |
| BooleanOptionKey const | remodel::design::design_neighbors ("remodel:design:design_neighbors") |
| BooleanOptionKey const | remodel::design::find_neighbors ("remodel:design:find_neighbors") |
| BooleanOptionKey const | remodel::rank_by_bsasa ("remodel:rank_by_bsasa") |
| BooleanOptionKey const | remodel::RemodelLoopMover::RemodelLoopMover ("remodel:RemodelLoopMover") |
| RealOptionKey const | remodel::RemodelLoopMover::max_linear_chainbreak ("remodel:RemodelLoopMover:max_linear_chainbreak") |
| BooleanOptionKey const | remodel::RemodelLoopMover::randomize_loops ("remodel:RemodelLoopMover:randomize_loops") |
| BooleanOptionKey const | remodel::RemodelLoopMover::use_loop_hash ("remodel:RemodelLoopMover:use_loop_hash") |
| IntegerOptionKey const | remodel::RemodelLoopMover::allowed_closure_attempts ("remodel:RemodelLoopMover:allowed_closure_attempts") |
| IntegerOptionKey const | remodel::RemodelLoopMover::loophash_cycles ("remodel:RemodelLoopMover:loophash_cycles") |
| IntegerOptionKey const | remodel::RemodelLoopMover::simultaneous_cycles ("remodel:RemodelLoopMover:simultaneous_cycles") |
| IntegerOptionKey const | remodel::RemodelLoopMover::independent_cycles ("remodel:RemodelLoopMover:independent_cycles") |
| IntegerOptionKey const | remodel::RemodelLoopMover::boost_closure_cycles ("remodel:RemodelLoopMover:boost_closure_cycles") |
| BooleanOptionKey const | remodel::RemodelLoopMover::force_cutting_N ("remodel:RemodelLoopMover:force_cutting_N") |
| BooleanOptionKey const | remodel::RemodelLoopMover::bypass_closure ("remodel:RemodelLoopMover:bypass_closure") |
| BooleanOptionKey const | remodel::RemodelLoopMover::cyclic_peptide ("remodel:RemodelLoopMover:cyclic_peptide") |
| RealOptionKey const | remodel::RemodelLoopMover::temperature ("remodel:RemodelLoopMover:temperature") |
| IntegerOptionKey const | remodel::RemodelLoopMover::max_chews ("remodel:RemodelLoopMover:max_chews") |
| 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 | symmetry::symmetry ("symmetry") |
| StringOptionKey const | symmetry::symmetry_definition ("symmetry:symmetry_definition") |
| RealOptionKey const | symmetry::reweight_symm_interactions ("symmetry:reweight_symm_interactions") |
| BooleanOptionKey const | symmetry::initialize_rigid_body_dofs ("symmetry:initialize_rigid_body_dofs") |
| BooleanOptionKey const | symmetry::detect_bonds ("symmetry:detect_bonds") |
| RealVectorOptionKey const | symmetry::perturb_rigid_body_dofs ("symmetry:perturb_rigid_body_dofs") |
| BooleanOptionKey const | symmetry::symmetric_rmsd ("symmetry:symmetric_rmsd") |
| 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 | 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 | canonical_sampling::canonical_sampling ("canonical_sampling") |
| BooleanOptionKey const | canonical_sampling::probabilities::probabilities ("canonical_sampling:probabilities") |
| RealOptionKey const | canonical_sampling::probabilities::sc ("canonical_sampling:probabilities:sc") |
| RealOptionKey const | canonical_sampling::probabilities::localbb ("canonical_sampling:probabilities:localbb") |
| RealOptionKey const | canonical_sampling::probabilities::sc_prob_uniform ("canonical_sampling:probabilities:sc_prob_uniform") |
| RealOptionKey const | canonical_sampling::probabilities::sc_prob_withinrot ("canonical_sampling:probabilities:sc_prob_withinrot") |
| RealOptionKey const | canonical_sampling::probabilities::sc_prob_perturbcurrent ("canonical_sampling:probabilities:sc_prob_perturbcurrent") |
| BooleanOptionKey const | canonical_sampling::probabilities::MPI_sync_pools ("canonical_sampling:probabilities:MPI_sync_pools") |
| BooleanOptionKey const | canonical_sampling::probabilities::MPI_bcast ("canonical_sampling:probabilities:MPI_bcast") |
| BooleanOptionKey const | canonical_sampling::probabilities::fast_sc_moves ("canonical_sampling:probabilities:fast_sc_moves") |
| RealOptionKey const | canonical_sampling::probabilities::fast_sc_moves_ntrials ("canonical_sampling:probabilities:fast_sc_moves_ntrials") |
| BooleanOptionKey const | canonical_sampling::probabilities::no_jd2_output ("canonical_sampling:probabilities:no_jd2_output") |
| BooleanOptionKey const | canonical_sampling::probabilities::use_hierarchical_clustering ("canonical_sampling:probabilities:use_hierarchical_clustering") |
| IntegerOptionKey const | canonical_sampling::probabilities::hierarchical_max_cache_size ("canonical_sampling:probabilities:hierarchical_max_cache_size") |
| RealOptionKey const | canonical_sampling::probabilities::backrub ("canonical_sampling:probabilities:backrub") |
| RealOptionKey const | canonical_sampling::probabilities::conrot ("canonical_sampling:probabilities:conrot") |
| BooleanOptionKey const | canonical_sampling::sampling::sampling ("canonical_sampling:sampling") |
| BooleanOptionKey const | canonical_sampling::sampling::no_detailed_balance ("canonical_sampling:sampling:no_detailed_balance") |
| IntegerOptionKey const | canonical_sampling::sampling::ntrials ("canonical_sampling:sampling:ntrials") |
| RealOptionKey const | canonical_sampling::sampling::mc_kt ("canonical_sampling:sampling:mc_kt") |
| IntegerOptionKey const | canonical_sampling::sampling::interval_pose_dump ("canonical_sampling:sampling:interval_pose_dump") |
| IntegerOptionKey const | canonical_sampling::sampling::interval_data_dump ("canonical_sampling:sampling:interval_data_dump") |
| BooleanOptionKey const | canonical_sampling::sampling::output_only_cluster_transitions ("canonical_sampling:sampling:output_only_cluster_transitions") |
| RealOptionKey const | canonical_sampling::sampling::transition_threshold ("canonical_sampling:sampling:transition_threshold") |
| IntegerOptionKey const | canonical_sampling::sampling::max_files_per_dir ("canonical_sampling:sampling:max_files_per_dir") |
| BooleanOptionKey const | canonical_sampling::sampling::save_loops_only ("canonical_sampling:sampling:save_loops_only") |
| BooleanOptionKey const | canonical_sampling::sampling::dump_loops_only ("canonical_sampling:sampling:dump_loops_only") |
| BooleanOptionKey const | canonical_sampling::out::out ("canonical_sampling:out") |
| FileOptionKey const | canonical_sampling::out::new_structures ("canonical_sampling:out:new_structures") |
| BooleanOptionKey const | rdc::rdc ("rdc") |
| BooleanOptionKey const | rdc::correct_NH_length ("rdc:correct_NH_length") |
| BooleanOptionKey const | rdc::reduced_couplings ("rdc:reduced_couplings") |
| FileOptionKey const | rdc::weights ("rdc:weights") |
| RealOptionKey const | rdc::iterate_weights ("rdc:iterate_weights") |
| FileOptionKey const | rdc::segment_file ("rdc:segment_file") |
| StringOptionKey const | rdc::segment_scoring_mode ("rdc:segment_scoring_mode") |
| RealOptionKey const | rdc::total_weight ("rdc:total_weight") |
| RealOptionKey const | rdc::tensor_weight ("rdc:tensor_weight") |
| FileOptionKey const | rdc::print_rdc_values ("rdc:print_rdc_values") |
| RealOptionKey const | rdc::iterate_tol ("rdc:iterate_tol") |
| BooleanOptionKey const | rdc::iterate_reset ("rdc:iterate_reset") |
| FileOptionKey const | rdc::dump_weight_trajectory ("rdc:dump_weight_trajectory") |
| RealVectorOptionKey const | rdc::fix_normAzz ("rdc:fix_normAzz") |
| FileOptionKey const | rdc::select_residues_file ("rdc:select_residues_file") |
| StringOptionKey const | rdc::fit_method ("rdc:fit_method") |
| RealVectorOptionKey const | rdc::fixDa ("rdc:fixDa") |
| RealVectorOptionKey const | rdc::fixR ("rdc:fixR") |
| IntegerOptionKey const | rdc::nlsrepeat ("rdc:nlsrepeat") |
| BooleanOptionKey const | csa::csa ("csa") |
| BooleanOptionKey const | csa::useZ ("csa:useZ") |
| BooleanOptionKey const | dc::dc ("dc") |
| BooleanOptionKey const | dc::useZ ("dc:useZ") |
| BooleanOptionKey const | antibody::antibody ("antibody") |
| StringOptionKey const | antibody::numbering_scheme ("antibody:numbering_scheme") |
| StringOptionKey const | antibody::cdr_definition ("antibody:cdr_definition") |
| BooleanOptionKey const | antibody::graft_l1 ("antibody:graft_l1") |
| StringOptionKey const | antibody::l1_template ("antibody:l1_template") |
| BooleanOptionKey const | antibody::graft_l2 ("antibody:graft_l2") |
| StringOptionKey const | antibody::l2_template ("antibody:l2_template") |
| BooleanOptionKey const | antibody::graft_l3 ("antibody:graft_l3") |
| StringOptionKey const | antibody::l3_template ("antibody:l3_template") |
| BooleanOptionKey const | antibody::graft_h1 ("antibody:graft_h1") |
| StringOptionKey const | antibody::h1_template ("antibody:h1_template") |
| BooleanOptionKey const | antibody::graft_h2 ("antibody:graft_h2") |
| StringOptionKey const | antibody::h2_template ("antibody:h2_template") |
| BooleanOptionKey const | antibody::graft_h3 ("antibody:graft_h3") |
| StringOptionKey const | antibody::h3_template ("antibody:h3_template") |
| BooleanOptionKey const | antibody::h3_no_stem_graft ("antibody:h3_no_stem_graft") |
| BooleanOptionKey const | antibody::packonly_after_graft ("antibody:packonly_after_graft") |
| BooleanOptionKey const | antibody::stem_optimize ("antibody:stem_optimize") |
| IntegerOptionKey const | antibody::stem_optimize_size ("antibody:stem_optimize_size") |
| StringOptionKey const | antibody::preprocessing_script_version ("antibody:preprocessing_script_version") |
| BooleanOptionKey const | antibody::model_h3 ("antibody:model_h3") |
| BooleanOptionKey const | antibody::snugfit ("antibody:snugfit") |
| BooleanOptionKey const | antibody::refine_h3 ("antibody:refine_h3") |
| BooleanOptionKey const | antibody::h3_filter ("antibody:h3_filter") |
| RealOptionKey const | antibody::h3_filter_tolerance ("antibody:h3_filter_tolerance") |
| BooleanOptionKey const | antibody::cter_insert ("antibody:cter_insert") |
| BooleanOptionKey const | antibody::flank_residue_min ("antibody:flank_residue_min") |
| BooleanOptionKey const | antibody::sc_min ("antibody:sc_min") |
| BooleanOptionKey const | antibody::rt_min ("antibody:rt_min") |
| BooleanOptionKey const | antibody::bad_nter ("antibody:bad_nter") |
| BooleanOptionKey const | antibody::extend_h3_before_modeling ("antibody:extend_h3_before_modeling") |
| BooleanOptionKey const | antibody::idealize_h3_stems_before_modeling ("antibody:idealize_h3_stems_before_modeling") |
| StringOptionKey const | antibody::remodel ("antibody:remodel") |
| StringOptionKey const | antibody::refine ("antibody:refine") |
| StringOptionKey const | antibody::centroid_refine ("antibody:centroid_refine") |
| BooleanOptionKey const | antibody::constrain_cter ("antibody:constrain_cter") |
| BooleanOptionKey const | antibody::constrain_vlvh_qq ("antibody:constrain_vlvh_qq") |
| BooleanOptionKey const | antibody::snug_loops ("antibody:snug_loops") |
| FileOptionKey const | antibody::input_fv ("antibody:input_fv") |
| BooleanOptionKey const | antibody::camelid ("antibody:camelid") |
| BooleanOptionKey const | antibody::camelid_constraints ("antibody:camelid_constraints") |
| BooleanOptionKey const | antibody::design::design ("antibody:design") |
| StringOptionKey const | antibody::design::instructions ("antibody:design:instructions") |
| StringOptionKey const | antibody::design::antibody_database ("antibody:design:antibody_database") |
| StringVectorOptionKey const | antibody::design::design_cdrs ("antibody:design:design_cdrs") |
| BooleanOptionKey const | antibody::design::do_graft_design ("antibody:design:do_graft_design") |
| BooleanOptionKey const | antibody::design::do_post_graft_design_modeling ("antibody:design:do_post_graft_design_modeling") |
| BooleanOptionKey const | antibody::design::do_sequence_design ("antibody:design:do_sequence_design") |
| BooleanOptionKey const | antibody::design::do_post_design_modeling ("antibody:design:do_post_design_modeling") |
| IntegerOptionKey const | antibody::design::graft_rounds ("antibody:design:graft_rounds") |
| IntegerOptionKey const | antibody::design::top_graft_designs ("antibody:design:top_graft_designs") |
| BooleanOptionKey const | antibody::design::initial_perturb ("antibody:design:initial_perturb") |
| BooleanOptionKey const | antibody::design::use_deterministic ("antibody:design:use_deterministic") |
| BooleanOptionKey const | antibody::design::dump_post_graft_designs ("antibody:design:dump_post_graft_designs") |
| RealOptionKey const | antibody::design::interface_dis ("antibody:design:interface_dis") |
| RealOptionKey const | antibody::design::neighbor_dis ("antibody:design:neighbor_dis") |
| BooleanOptionKey const | antibody::design::dock_post_graft ("antibody:design:dock_post_graft") |
| BooleanOptionKey const | antibody::design::pack_post_graft ("antibody:design:pack_post_graft") |
| BooleanOptionKey const | antibody::design::rb_min_post_graft ("antibody:design:rb_min_post_graft") |
| BooleanOptionKey const | antibody::design::design_post_graft ("antibody:design:design_post_graft") |
| IntegerOptionKey const | antibody::design::dock_rounds ("antibody:design:dock_rounds") |
| StringOptionKey const | antibody::design::ab_dock_chains ("antibody:design:ab_dock_chains") |
| StringOptionKey const | antibody::design::design_method ("antibody:design:design_method") |
| IntegerOptionKey const | antibody::design::design_rounds ("antibody:design:design_rounds") |
| StringOptionKey const | antibody::design::design_scorefxn ("antibody:design:design_scorefxn") |
| BooleanOptionKey const | antibody::design::benchmark_basic_design ("antibody:design:benchmark_basic_design") |
| BooleanOptionKey const | antibody::design::use_filters ("antibody:design:use_filters") |
| IntegerOptionKey const | antibody::design::stats_cutoff ("antibody:design:stats_cutoff") |
| IntegerOptionKey const | antibody::design::sample_zero_probs_at ("antibody:design:sample_zero_probs_at") |
| BooleanOptionKey const | antibody::design::conservative_h3_design ("antibody:design:conservative_h3_design") |
| BooleanOptionKey const | antibody::design::turn_conservation ("antibody:design:turn_conservation") |
| BooleanOptionKey const | antibody::design::extend_native_cdrs ("antibody:design:extend_native_cdrs") |
| 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 | threadsc::threadsc ("threadsc") |
| StringOptionKey const | threadsc::src_chain ("threadsc:src_chain") |
| StringOptionKey const | threadsc::trg_chain ("threadsc:trg_chain") |
| IntegerOptionKey const | threadsc::src_first_resid ("threadsc:src_first_resid") |
| IntegerOptionKey const | threadsc::trg_first_resid ("threadsc:trg_first_resid") |
| IntegerOptionKey const | threadsc::nres ("threadsc:nres") |
| IntegerOptionKey const | threadsc::trg_anchor ("threadsc:trg_anchor") |
| BooleanOptionKey const | cp::cp ("cp") |
| RealOptionKey const | cp::cutoff ("cp:cutoff") |
| StringOptionKey const | cp::minimizer ("cp:minimizer") |
| StringOptionKey const | cp::relax_sfxn ("cp:relax_sfxn") |
| StringOptionKey const | cp::pack_sfxn ("cp:pack_sfxn") |
| RealOptionKey const | cp::minimizer_tol ("cp:minimizer_tol") |
| StringOptionKey const | cp::minimizer_score_fxn ("cp:minimizer_score_fxn") |
| StringOptionKey const | cp::output ("cp:output") |
| IntegerOptionKey const | cp::ncycles ("cp:ncycles") |
| IntegerOptionKey const | cp::max_failures ("cp:max_failures") |
| BooleanOptionKey const | cp::print_reports ("cp:print_reports") |
| StringOptionKey const | cp::vipReportFile ("cp:vipReportFile") |
| StringOptionKey const | cp::exclude_file ("cp:exclude_file") |
| StringOptionKey const | cp::relax_mover ("cp:relax_mover") |
| BooleanOptionKey const | cp::skip_relax ("cp:skip_relax") |
| BooleanOptionKey const | cp::local_relax ("cp:local_relax") |
| BooleanOptionKey const | cp::print_intermediate_pdbs ("cp:print_intermediate_pdbs") |
| BooleanOptionKey const | cp::use_unrelaxed_starting_points ("cp:use_unrelaxed_starting_points") |
| BooleanOptionKey const | cp::easy_vip_acceptance ("cp:easy_vip_acceptance") |
| BooleanOptionKey const | archive::archive ("archive") |
| BooleanOptionKey const | archive::reread_all_structures ("archive:reread_all_structures") |
| IntegerOptionKey const | archive::completion_notify_frequency ("archive:completion_notify_frequency") |
| BooleanOptionKey const | optimization::optimization ("optimization") |
| IntegerOptionKey const | optimization::default_max_cycles ("optimization:default_max_cycles") |
| RealOptionKey const | optimization::armijo_min_stepsize ("optimization:armijo_min_stepsize") |
| RealOptionKey const | optimization::scale_normalmode_dampen ("optimization:scale_normalmode_dampen") |
| IntegerOptionKey const | optimization::lbfgs_M ("optimization:lbfgs_M") |
| RealOptionKey const | optimization::scale_d ("optimization:scale_d") |
| RealOptionKey const | optimization::scale_theta ("optimization:scale_theta") |
| RealOptionKey const | optimization::scale_rb ("optimization:scale_rb") |
| RealOptionKey const | optimization::scale_rbangle ("optimization:scale_rbangle") |
| BooleanOptionKey const | optimization::scmin_nonideal ("optimization:scmin_nonideal") |
| BooleanOptionKey const | optimization::scmin_cartesian ("optimization:scmin_cartesian") |
| BooleanOptionKey const | optimization::nonideal ("optimization:nonideal") |
| BooleanOptionKey const | stepwise::stepwise ("stepwise") |
| StringVectorOptionKey const | stepwise::s1 ("stepwise:s1") |
| StringVectorOptionKey const | stepwise::s2 ("stepwise:s2") |
| StringVectorOptionKey const | stepwise::silent1 ("stepwise:silent1") |
| StringVectorOptionKey const | stepwise::silent2 ("stepwise:silent2") |
| StringVectorOptionKey const | stepwise::tags1 ("stepwise:tags1") |
| StringVectorOptionKey const | stepwise::tags2 ("stepwise:tags2") |
| IntegerVectorOptionKey const | stepwise::slice_res1 ("stepwise:slice_res1") |
| IntegerVectorOptionKey const | stepwise::slice_res2 ("stepwise:slice_res2") |
| IntegerVectorOptionKey const | stepwise::input_res1 ("stepwise:input_res1") |
| IntegerVectorOptionKey const | stepwise::input_res2 ("stepwise:input_res2") |
| BooleanOptionKey const | stepwise::backbone_only1 ("stepwise:backbone_only1") |
| BooleanOptionKey const | stepwise::backbone_only2 ("stepwise:backbone_only2") |
| IntegerVectorOptionKey const | stepwise::fixed_res ("stepwise:fixed_res") |
| IntegerVectorOptionKey const | stepwise::working_res ("stepwise:working_res") |
| BooleanOptionKey const | stepwise::test_encapsulation ("stepwise:test_encapsulation") |
| BooleanOptionKey const | stepwise::choose_random ("stepwise:choose_random") |
| IntegerOptionKey const | stepwise::num_random_samples ("stepwise:num_random_samples") |
| IntegerOptionKey const | stepwise::num_pose_minimize ("stepwise:num_pose_minimize") |
| StringOptionKey const | stepwise::align_pdb ("stepwise:align_pdb") |
| BooleanOptionKey const | stepwise::enumerate ("stepwise:enumerate") |
| BooleanOptionKey const | stepwise::preminimize ("stepwise:preminimize") |
| BooleanOptionKey const | stepwise::monte_carlo::monte_carlo ("stepwise:monte_carlo") |
| BooleanOptionKey const | stepwise::monte_carlo::verbose_scores ("stepwise:monte_carlo:verbose_scores") |
| BooleanOptionKey const | stepwise::monte_carlo::skip_deletions ("stepwise:monte_carlo:skip_deletions") |
| BooleanOptionKey const | stepwise::monte_carlo::erraser ("stepwise:monte_carlo:erraser") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_internal_hinge_moves ("stepwise:monte_carlo:allow_internal_hinge_moves") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_internal_local_moves ("stepwise:monte_carlo:allow_internal_local_moves") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_skip_bulge ("stepwise:monte_carlo:allow_skip_bulge") |
| RealOptionKey const | stepwise::monte_carlo::from_scratch_frequency ("stepwise:monte_carlo:from_scratch_frequency") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_split_off ("stepwise:monte_carlo:allow_split_off") |
| IntegerOptionKey const | stepwise::monte_carlo::cycles ("stepwise:monte_carlo:cycles") |
| RealOptionKey const | stepwise::monte_carlo::temperature ("stepwise:monte_carlo:temperature") |
| RealOptionKey const | stepwise::monte_carlo::add_delete_frequency ("stepwise:monte_carlo:add_delete_frequency") |
| RealOptionKey const | stepwise::monte_carlo::intermolecular_frequency ("stepwise:monte_carlo:intermolecular_frequency") |
| RealOptionKey const | stepwise::monte_carlo::minimize_single_res_frequency ("stepwise:monte_carlo:minimize_single_res_frequency") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_variable_bond_geometry ("stepwise:monte_carlo:allow_variable_bond_geometry") |
| RealOptionKey const | stepwise::monte_carlo::switch_focus_frequency ("stepwise:monte_carlo:switch_focus_frequency") |
| RealOptionKey const | stepwise::monte_carlo::just_min_after_mutation_frequency ("stepwise:monte_carlo:just_min_after_mutation_frequency") |
| BooleanOptionKey const | stepwise::monte_carlo::local_redock_only ("stepwise:monte_carlo:local_redock_only") |
| BooleanOptionKey const | stepwise::monte_carlo::make_movie ("stepwise:monte_carlo:make_movie") |
| StringVectorOptionKey const | stepwise::move ("stepwise:move") |
| BooleanOptionKey const | stepwise::use_green_packer ("stepwise:use_green_packer") |
| BooleanOptionKey const | stepwise::rna::rna ("stepwise:rna") |
| IntegerOptionKey const | stepwise::rna::sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept") |
| BooleanOptionKey const | stepwise::rna::sampler_native_rmsd_screen ("stepwise:rna:sampler_native_rmsd_screen") |
| RealOptionKey const | stepwise::rna::sampler_native_screen_rmsd_cutoff ("stepwise:rna:sampler_native_screen_rmsd_cutoff") |
| RealOptionKey const | stepwise::rna::sampler_cluster_rmsd ("stepwise:rna:sampler_cluster_rmsd") |
| RealOptionKey const | stepwise::rna::native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff") |
| BooleanOptionKey const | stepwise::rna::sampler_perform_o2prime_pack ("stepwise:rna:sampler_perform_o2prime_pack") |
| BooleanOptionKey const | stepwise::rna::sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack") |
| BooleanOptionKey const | stepwise::rna::VERBOSE ("stepwise:rna:VERBOSE") |
| BooleanOptionKey const | stepwise::rna::distinguish_pucker ("stepwise:rna:distinguish_pucker") |
| BooleanOptionKey const | stepwise::rna::finer_sampling_at_chain_closure ("stepwise:rna:finer_sampling_at_chain_closure") |
| BooleanOptionKey const | stepwise::rna::PBP_clustering_at_chain_closure ("stepwise:rna:PBP_clustering_at_chain_closure") |
| BooleanOptionKey const | stepwise::rna::sampler_allow_syn_pyrimidine ("stepwise:rna:sampler_allow_syn_pyrimidine") |
| BooleanOptionKey const | stepwise::rna::sampler_extra_chi_rotamer ("stepwise:rna:sampler_extra_chi_rotamer") |
| BooleanOptionKey const | stepwise::rna::sampler_extra_beta_rotamer ("stepwise:rna:sampler_extra_beta_rotamer") |
| BooleanOptionKey const | stepwise::rna::sampler_extra_epsilon_rotamer ("stepwise:rna:sampler_extra_epsilon_rotamer") |
| BooleanOptionKey const | stepwise::rna::force_centroid_interaction ("stepwise:rna:force_centroid_interaction") |
| BooleanOptionKey const | stepwise::rna::virtual_sugar_legacy_mode ("stepwise:rna:virtual_sugar_legacy_mode") |
| BooleanOptionKey const | stepwise::rna::erraser ("stepwise:rna:erraser") |
| BooleanOptionKey const | stepwise::rna::centroid_screen ("stepwise:rna:centroid_screen") |
| BooleanOptionKey const | stepwise::rna::VDW_atr_rep_screen ("stepwise:rna:VDW_atr_rep_screen") |
| BooleanOptionKey const | stepwise::rna::skip_sampling ("stepwise:rna:skip_sampling") |
| BooleanOptionKey const | stepwise::rna::minimizer_perform_minimize ("stepwise:rna:minimizer_perform_minimize") |
| BooleanOptionKey const | stepwise::rna::minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose") |
| BooleanOptionKey const | stepwise::rna::rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate") |
| RealOptionKey const | stepwise::rna::VDW_rep_alignment_RMSD_CUTOFF ("stepwise:rna:VDW_rep_alignment_RMSD_CUTOFF") |
| StringVectorOptionKey const | stepwise::rna::VDW_rep_delete_matching_res ("stepwise:rna:VDW_rep_delete_matching_res") |
| RealOptionKey const | stepwise::rna::VDW_rep_screen_physical_pose_clash_dist_cutoff ("stepwise:rna:VDW_rep_screen_physical_pose_clash_dist_cutoff") |
| BooleanOptionKey const | stepwise::rna::integration_test ("stepwise:rna:integration_test") |
| BooleanOptionKey const | stepwise::rna::allow_bulge_at_chainbreak ("stepwise:rna:allow_bulge_at_chainbreak") |
| BooleanOptionKey const | stepwise::rna::parin_favorite_output ("stepwise:rna:parin_favorite_output") |
| BooleanOptionKey const | stepwise::rna::reinitialize_CCD_torsions ("stepwise:rna:reinitialize_CCD_torsions") |
| BooleanOptionKey const | stepwise::rna::sample_both_sugar_base_rotamer ("stepwise:rna:sample_both_sugar_base_rotamer") |
| BooleanOptionKey const | stepwise::rna::sampler_include_torsion_value_in_tag ("stepwise:rna:sampler_include_torsion_value_in_tag") |
| BooleanOptionKey const | stepwise::rna::sampler_assert_no_virt_sugar_sampling ("stepwise:rna:sampler_assert_no_virt_sugar_sampling") |
| BooleanOptionKey const | stepwise::rna::sampler_try_sugar_instantiation ("stepwise:rna:sampler_try_sugar_instantiation") |
| BooleanOptionKey const | stepwise::rna::do_not_sample_multiple_virtual_sugar ("stepwise:rna:do_not_sample_multiple_virtual_sugar") |
| BooleanOptionKey const | stepwise::rna::sample_ONLY_multiple_virtual_sugar ("stepwise:rna:sample_ONLY_multiple_virtual_sugar") |
| BooleanOptionKey const | stepwise::rna::allow_base_pair_only_centroid_screen ("stepwise:rna:allow_base_pair_only_centroid_screen") |
| BooleanOptionKey const | stepwise::rna::minimizer_output_before_o2prime_pack ("stepwise:rna:minimizer_output_before_o2prime_pack") |
| BooleanOptionKey const | stepwise::rna::minimizer_perform_o2prime_pack ("stepwise:rna:minimizer_perform_o2prime_pack") |
| BooleanOptionKey const | stepwise::rna::minimizer_rename_tag ("stepwise:rna:minimizer_rename_tag") |
| IntegerVectorOptionKey const | stepwise::rna::minimize_res ("stepwise:rna:minimize_res") |
| StringVectorOptionKey const | stepwise::rna::alignment_res ("stepwise:rna:alignment_res") |
| IntegerVectorOptionKey const | stepwise::rna::native_alignment_res ("stepwise:rna:native_alignment_res") |
| IntegerVectorOptionKey const | stepwise::rna::rmsd_res ("stepwise:rna:rmsd_res") |
| IntegerVectorOptionKey const | stepwise::rna::missing_res ("stepwise:rna:missing_res") |
| IntegerVectorOptionKey const | stepwise::rna::missing_res2 ("stepwise:rna:missing_res2") |
| IntegerOptionKey const | stepwise::rna::job_queue_ID ("stepwise:rna:job_queue_ID") |
| BooleanOptionKey const | stepwise::rna::minimize_and_score_sugar ("stepwise:rna:minimize_and_score_sugar") |
| IntegerVectorOptionKey const | stepwise::rna::global_sample_res_list ("stepwise:rna:global_sample_res_list") |
| FileOptionKey const | stepwise::rna::filter_output_filename ("stepwise:rna:filter_output_filename") |
| BooleanOptionKey const | stepwise::rna::combine_long_loop_mode ("stepwise:rna:combine_long_loop_mode") |
| BooleanOptionKey const | stepwise::rna::combine_helical_silent_file ("stepwise:rna:combine_helical_silent_file") |
| BooleanOptionKey const | stepwise::rna::output_extra_RMSDs ("stepwise:rna:output_extra_RMSDs") |
| IntegerVectorOptionKey const | stepwise::rna::force_syn_chi_res_list ("stepwise:rna:force_syn_chi_res_list") |
| IntegerVectorOptionKey const | stepwise::rna::force_north_sugar_list ("stepwise:rna:force_north_sugar_list") |
| IntegerVectorOptionKey const | stepwise::rna::force_south_sugar_list ("stepwise:rna:force_south_sugar_list") |
| IntegerVectorOptionKey const | stepwise::rna::protonated_H1_adenosine_list ("stepwise:rna:protonated_H1_adenosine_list") |
| IntegerVectorOptionKey const | stepwise::rna::native_virtual_res ("stepwise:rna:native_virtual_res") |
| BooleanOptionKey const | stepwise::rna::simple_append_map ("stepwise:rna:simple_append_map") |
| BooleanOptionKey const | stepwise::rna::allow_fixed_res_at_moving_res ("stepwise:rna:allow_fixed_res_at_moving_res") |
| BooleanOptionKey const | stepwise::rna::force_user_defined_jumps ("stepwise:rna:force_user_defined_jumps") |
| StringVectorOptionKey const | stepwise::rna::jump_point_pairs ("stepwise:rna:jump_point_pairs") |
| IntegerVectorOptionKey const | stepwise::rna::terminal_res ("stepwise:rna:terminal_res") |
| BooleanOptionKey const | stepwise::rna::add_virt_root ("stepwise:rna:add_virt_root") |
| BooleanOptionKey const | stepwise::rna::floating_base ("stepwise:rna:floating_base") |
| IntegerOptionKey const | stepwise::rna::floating_base_anchor_res ("stepwise:rna:floating_base_anchor_res") |
| BooleanOptionKey const | stepwise::rna::allow_chain_boundary_jump_partner_right_at_fixed_BP ("stepwise:rna:allow_chain_boundary_jump_partner_right_at_fixed_BP") |
| IntegerVectorOptionKey const | stepwise::rna::bulge_res ("stepwise:rna:bulge_res") |
| BooleanOptionKey const | stepwise::rna::rebuild_bulge_mode ("stepwise:rna:rebuild_bulge_mode") |
| BooleanOptionKey const | stepwise::rna::virtual_sugar_keep_base_fixed ("stepwise:rna:virtual_sugar_keep_base_fixed") |
| BooleanOptionKey const | stepwise::rna::virtual_sugar_do_minimize ("stepwise:rna:virtual_sugar_do_minimize") |
| RealOptionKey const | stepwise::rna::sampler_max_centroid_distance ("stepwise:rna:sampler_max_centroid_distance") |
| BooleanOptionKey const | stepwise::rna::filter_user_alignment_res ("stepwise:rna:filter_user_alignment_res") |
| BooleanOptionKey const | stepwise::rna::output_pdb ("stepwise:rna:output_pdb") |
| BooleanOptionKey const | stepwise::rna::tether_jump ("stepwise:rna:tether_jump") |
| BooleanOptionKey const | stepwise::rna::unified_framework ("stepwise:rna:unified_framework") |
| BooleanOptionKey const | stepwise::protein::protein ("stepwise:protein") |
| BooleanOptionKey const | stepwise::protein::global_optimize ("stepwise:protein:global_optimize") |
| BooleanOptionKey const | stepwise::protein::disallow_backbone_sampling ("stepwise:protein:disallow_backbone_sampling") |
| BooleanOptionKey const | stepwise::protein::disable_sampling_of_loop_takeoff ("stepwise:protein:disable_sampling_of_loop_takeoff") |
| BooleanOptionKey const | stepwise::protein::dump ("stepwise:protein:dump") |
| BooleanOptionKey const | stepwise::protein::sample_beta ("stepwise:protein:sample_beta") |
| BooleanOptionKey const | stepwise::protein::ghost_loops ("stepwise:protein:ghost_loops") |
| BooleanOptionKey const | stepwise::protein::rescore_only ("stepwise:protein:rescore_only") |
| StringOptionKey const | stepwise::protein::min_type ("stepwise:protein:min_type") |
| RealOptionKey const | stepwise::protein::min_tolerance ("stepwise:protein:min_tolerance") |
| BooleanOptionKey const | stepwise::protein::centroid_screen ("stepwise:protein:centroid_screen") |
| RealOptionKey const | stepwise::protein::centroid_score_diff_cut ("stepwise:protein:centroid_score_diff_cut") |
| BooleanOptionKey const | stepwise::protein::skip_minimize ("stepwise:protein:skip_minimize") |
| StringOptionKey const | stepwise::protein::centroid_weights ("stepwise:protein:centroid_weights") |
| RealOptionKey const | stepwise::protein::score_diff_cut ("stepwise:protein:score_diff_cut") |
| BooleanOptionKey const | stepwise::protein::filter_native_big_bins ("stepwise:protein:filter_native_big_bins") |
| BooleanOptionKey const | stepwise::protein::cluster_by_all_atom_rmsd ("stepwise:protein:cluster_by_all_atom_rmsd") |
| BooleanOptionKey const | stepwise::protein::centroid_output ("stepwise:protein:centroid_output") |
| IntegerOptionKey const | stepwise::protein::n_sample ("stepwise:protein:n_sample") |
| IntegerOptionKey const | stepwise::protein::nstruct_centroid ("stepwise:protein:nstruct_centroid") |
| BooleanOptionKey const | stepwise::protein::ccd_close ("stepwise:protein:ccd_close") |
| IntegerVectorOptionKey const | stepwise::protein::bridge_res ("stepwise:protein:bridge_res") |
| RealOptionKey const | stepwise::protein::rmsd_screen ("stepwise:protein:rmsd_screen") |
| BooleanOptionKey const | stepwise::protein::cart_min ("stepwise:protein:cart_min") |
| BooleanOptionKey const | stepwise::protein::move_jumps_between_chains ("stepwise:protein:move_jumps_between_chains") |
| BooleanOptionKey const | stepwise::protein::use_packer_instead_of_rotamer_trials ("stepwise:protein:use_packer_instead_of_rotamer_trials") |
| BooleanOptionKey const | stepwise::protein::expand_loop_takeoff ("stepwise:protein:expand_loop_takeoff") |
| BooleanOptionKey const | stepwise::protein::skip_coord_constraints ("stepwise:protein:skip_coord_constraints") |
| BooleanOptionKey const | stepwise::protein::allow_virtual_side_chains ("stepwise:protein:allow_virtual_side_chains") |
| BooleanOptionKey const | stepwise::protein::protein_prepack ("stepwise:protein:protein_prepack") |
| BooleanOptionKey const | stepwise::protein::protein_atr_rep_screen ("stepwise:protein:protein_atr_rep_screen") |
| BooleanOptionKey const | full_model::full_model ("full_model") |
| IntegerVectorOptionKey const | full_model::cutpoint_open ("full_model:cutpoint_open") |
| IntegerVectorOptionKey const | full_model::cutpoint_closed ("full_model:cutpoint_closed") |
| StringVectorOptionKey const | full_model::other_poses ("full_model:other_poses") |
| IntegerVectorOptionKey const | full_model::extra_min_res ("full_model:extra_min_res") |
| IntegerVectorOptionKey const | full_model::jump_res ("full_model:jump_res") |
| IntegerVectorOptionKey const | full_model::root_res ("full_model:root_res") |
| IntegerVectorOptionKey const | full_model::virtual_sugar_res ("full_model:virtual_sugar_res") |
| IntegerVectorOptionKey const | full_model::virtual_res ("full_model:virtual_res") |
| IntegerVectorOptionKey const | full_model::sample_res ("full_model:sample_res") |
| IntegerVectorOptionKey const | full_model::calc_rms_res ("full_model:calc_rms_res") |
| BooleanOptionKey const | ufv::ufv ("ufv") |
| IntegerOptionKey const | ufv::left ("ufv:left") |
| IntegerOptionKey const | ufv::right ("ufv:right") |
| StringOptionKey const | ufv::ss ("ufv:ss") |
| StringOptionKey const | ufv::aa_during_build ("ufv:aa_during_build") |
| StringOptionKey const | ufv::aa_during_design_refine ("ufv:aa_during_design_refine") |
| BooleanOptionKey const | ufv::keep_junction_torsions ("ufv:keep_junction_torsions") |
| FileOptionKey const | ufv::ufv_loops ("ufv:ufv_loops") |
| BooleanOptionKey const | ufv::use_fullmer ("ufv:use_fullmer") |
| StringOptionKey const | ufv::centroid_loop_mover ("ufv:centroid_loop_mover") |
| BooleanOptionKey const | ufv::no_neighborhood_design ("ufv:no_neighborhood_design") |
| IntegerOptionKey const | ufv::dr_cycles ("ufv:dr_cycles") |
| StringOptionKey const | ufv::centroid_sfx ("ufv:centroid_sfx") |
| StringOptionKey const | ufv::centroid_sfx_patch ("ufv:centroid_sfx_patch") |
| StringOptionKey const | ufv::fullatom_sfx ("ufv:fullatom_sfx") |
| StringOptionKey const | ufv::fullatom_sfx_patch ("ufv:fullatom_sfx_patch") |
| BooleanOptionKey const | ufv::insert::insert ("ufv:insert") |
| FileOptionKey const | ufv::insert::insert_pdb ("ufv:insert:insert_pdb") |
| FileOptionKey const | ufv::insert::attached_pdb ("ufv:insert:attached_pdb") |
| StringOptionKey const | ufv::insert::connection_scheme ("ufv:insert:connection_scheme") |
| BooleanOptionKey const | chrisk::chrisk ("chrisk") |
| BooleanOptionKey const | chrisk::hb_elec ("chrisk:hb_elec") |
| BooleanOptionKey const | rot_anl::rot_anl ("rot_anl") |
| StringOptionKey const | rot_anl::tag ("rot_anl:tag") |
| BooleanOptionKey const | rot_anl::premin ("rot_anl:premin") |
| BooleanOptionKey const | rot_anl::min ("rot_anl:min") |
| BooleanOptionKey const | rot_anl::diff_to_min ("rot_anl:diff_to_min") |
| BooleanOptionKey const | rot_anl::repack ("rot_anl:repack") |
| BooleanOptionKey const | rot_anl::rtmin ("rot_anl:rtmin") |
| BooleanOptionKey const | rot_anl::scmove ("rot_anl:scmove") |
| BooleanOptionKey const | rot_anl::design ("rot_anl:design") |
| RealOptionKey const | rot_anl::score_tol ("rot_anl:score_tol") |
| RealOptionKey const | rot_anl::rmsd_tol ("rot_anl:rmsd_tol") |
| BooleanOptionKey const | rot_anl::dump_pdb ("rot_anl:dump_pdb") |
| IntegerOptionKey const | rot_anl::nloop_scmove ("rot_anl:nloop_scmove") |
| BooleanOptionKey const | sewing::sewing ("sewing") |
| FileOptionKey const | sewing::query_structure_path ("sewing:query_structure_path") |
| IntegerOptionKey const | sewing::frag1_start ("sewing:frag1_start") |
| IntegerOptionKey const | sewing::frag1_end ("sewing:frag1_end") |
| IntegerOptionKey const | sewing::frag2_start ("sewing:frag2_start") |
| IntegerOptionKey const | sewing::frag2_end ("sewing:frag2_end") |
| IntegerOptionKey const | sewing::minimum_helix_contacts ("sewing:minimum_helix_contacts") |
| IntegerOptionKey const | sewing::helices_to_add ("sewing:helices_to_add") |
| RealOptionKey const | sewing::single_helix_rmsd_cutoff ("sewing:single_helix_rmsd_cutoff") |
| RealOptionKey const | sewing::helix_pair_rmsd_cutoff ("sewing:helix_pair_rmsd_cutoff") |
| FileOptionKey const | sewing::nat_ro_file ("sewing:nat_ro_file") |
| RealOptionKey const | sewing::helix_cap_dist_cutoff ("sewing:helix_cap_dist_cutoff") |
| RealOptionKey const | sewing::helix_contact_dist_cutoff ("sewing:helix_contact_dist_cutoff") |
| IntegerOptionKey const | sewing::min_helix_size ("sewing:min_helix_size") |
| BooleanOptionKey const | strand_assembly::strand_assembly ("strand_assembly") |
| IntegerOptionKey const | strand_assembly::min_num_strands_to_deal ("strand_assembly:min_num_strands_to_deal") |
| IntegerOptionKey const | strand_assembly::max_num_strands_to_deal ("strand_assembly:max_num_strands_to_deal") |
| BooleanOptionKey const | strand_assembly::extract_native_only ("strand_assembly:extract_native_only") |
| IntegerOptionKey const | strand_assembly::min_res_in_strand ("strand_assembly:min_res_in_strand") |
| IntegerOptionKey const | strand_assembly::max_res_in_strand ("strand_assembly:max_res_in_strand") |
| RealOptionKey const | strand_assembly::min_O_N_dis ("strand_assembly:min_O_N_dis") |
| RealOptionKey const | strand_assembly::max_O_N_dis ("strand_assembly:max_O_N_dis") |
| RealOptionKey const | strand_assembly::min_sheet_dis ("strand_assembly:min_sheet_dis") |
| RealOptionKey const | strand_assembly::max_sheet_dis ("strand_assembly:max_sheet_dis") |
| RealOptionKey const | strand_assembly::min_sheet_torsion ("strand_assembly:min_sheet_torsion") |
| RealOptionKey const | strand_assembly::max_sheet_torsion ("strand_assembly:max_sheet_torsion") |
| RealOptionKey const | strand_assembly::min_sheet_angle ("strand_assembly:min_sheet_angle") |
| RealOptionKey const | strand_assembly::max_sheet_angle ("strand_assembly:max_sheet_angle") |
| RealOptionKey const | strand_assembly::min_shortest_dis_sidechain_inter_sheet ("strand_assembly:min_shortest_dis_sidechain_inter_sheet") |
| BooleanOptionKey const | pepspec::pepspec ("pepspec") |
| StringOptionKey const | pepspec::soft_wts ("pepspec:soft_wts") |
| StringOptionKey const | pepspec::cen_wts ("pepspec:cen_wts") |
| BooleanOptionKey const | pepspec::binding_score ("pepspec:binding_score") |
| BooleanOptionKey const | pepspec::no_cen ("pepspec:no_cen") |
| BooleanOptionKey const | pepspec::no_cen_rottrials ("pepspec:no_cen_rottrials") |
| BooleanOptionKey const | pepspec::run_sequential ("pepspec:run_sequential") |
| IntegerOptionKey const | pepspec::pep_anchor ("pepspec:pep_anchor") |
| StringOptionKey const | pepspec::pep_chain ("pepspec:pep_chain") |
| IntegerOptionKey const | pepspec::n_peptides ("pepspec:n_peptides") |
| IntegerOptionKey const | pepspec::n_build_loop ("pepspec:n_build_loop") |
| IntegerOptionKey const | pepspec::n_cgrelax_loop ("pepspec:n_cgrelax_loop") |
| IntegerOptionKey const | pepspec::n_dock_loop ("pepspec:n_dock_loop") |
| RealOptionKey const | pepspec::interface_cutoff ("pepspec:interface_cutoff") |
| BooleanOptionKey const | pepspec::use_input_bb ("pepspec:use_input_bb") |
| BooleanOptionKey const | pepspec::remove_input_bb ("pepspec:remove_input_bb") |
| StringOptionKey const | pepspec::homol_csts ("pepspec:homol_csts") |
| RealOptionKey const | pepspec::p_homol_csts ("pepspec:p_homol_csts") |
| StringOptionKey const | pepspec::frag_file ("pepspec:frag_file") |
| BooleanOptionKey const | pepspec::gen_pep_bb_sequential ("pepspec:gen_pep_bb_sequential") |
| StringOptionKey const | pepspec::input_seq ("pepspec:input_seq") |
| StringOptionKey const | pepspec::ss_type ("pepspec:ss_type") |
| BooleanOptionKey const | pepspec::upweight_interface ("pepspec:upweight_interface") |
| BooleanOptionKey const | pepspec::calc_sasa ("pepspec:calc_sasa") |
| BooleanOptionKey const | pepspec::diversify_pep_seqs ("pepspec:diversify_pep_seqs") |
| IntegerOptionKey const | pepspec::diversify_lvl ("pepspec:diversify_lvl") |
| BooleanOptionKey const | pepspec::dump_cg_bb ("pepspec:dump_cg_bb") |
| BooleanOptionKey const | pepspec::save_low_pdbs ("pepspec:save_low_pdbs") |
| BooleanOptionKey const | pepspec::save_all_pdbs ("pepspec:save_all_pdbs") |
| BooleanOptionKey const | pepspec::no_design ("pepspec:no_design") |
| StringOptionKey const | pepspec::pdb_list ("pepspec:pdb_list") |
| StringOptionKey const | pepspec::ref_pdb_list ("pepspec:ref_pdb_list") |
| BooleanOptionKey const | pepspec::add_buffer_res ("pepspec:add_buffer_res") |
| StringOptionKey const | pepspec::cg_res_type ("pepspec:cg_res_type") |
| IntegerOptionKey const | pepspec::native_pep_anchor ("pepspec:native_pep_anchor") |
| StringOptionKey const | pepspec::native_pep_chain ("pepspec:native_pep_chain") |
| BooleanOptionKey const | pepspec::native_align ("pepspec:native_align") |
| BooleanOptionKey const | pepspec::rmsd_analysis ("pepspec:rmsd_analysis") |
| BooleanOptionKey const | pepspec::phipsi_analysis ("pepspec:phipsi_analysis") |
| StringOptionKey const | pepspec::anchor_type ("pepspec:anchor_type") |
| BooleanOptionKey const | pepspec::no_prepack_prot ("pepspec:no_prepack_prot") |
| BooleanOptionKey const | pepspec::prep_use_ref_rotamers ("pepspec:prep_use_ref_rotamers") |
| IntegerOptionKey const | pepspec::n_prepend ("pepspec:n_prepend") |
| IntegerOptionKey const | pepspec::n_append ("pepspec:n_append") |
| RealOptionKey const | pepspec::clash_cutoff ("pepspec:clash_cutoff") |
| RealOptionKey const | pepspec::n_anchor_dock_std_devs ("pepspec:n_anchor_dock_std_devs") |
| RealOptionKey const | pepspec::prep_trans_std_dev ("pepspec:prep_trans_std_dev") |
| RealOptionKey const | pepspec::prep_rot_std_dev ("pepspec:prep_rot_std_dev") |
| BooleanOptionKey const | pepspec::seq_align ("pepspec:seq_align") |
| StringOptionKey const | pepspec::prep_align_prot_to ("pepspec:prep_align_prot_to") |
| BooleanOptionKey const | sicdock::sicdock ("sicdock") |
| RealOptionKey const | sicdock::clash_dis ("sicdock:clash_dis") |
| RealOptionKey const | sicdock::contact_dis ("sicdock:contact_dis") |
| RealOptionKey const | sicdock::hash_2D_vs_3D ("sicdock:hash_2D_vs_3D") |
| RealOptionKey const | sicdock::term_min_expose ("sicdock:term_min_expose") |
| RealOptionKey const | sicdock::term_max_angle ("sicdock:term_max_angle") |
| 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::merge_motifs_one_per_bin ("mh:merge_motifs_one_per_bin") |
| BooleanOptionKey const | mh::generate_reverse_motifs ("mh:generate_reverse_motifs") |
| FileVectorOptionKey const | mh::dump_input_pdb ("mh:dump_input_pdb") |
| FileVectorOptionKey const | mh::score_pdbs ("mh:score_pdbs") |
| 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::sequence_recovery ("mh:sequence_recovery") |
| FileVectorOptionKey const | mh::explicit_motif_score ("mh:explicit_motif_score") |
| 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") |
| BooleanOptionKey const | mh::normalize_score_ncontact ("mh:normalize_score_ncontact") |
| 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") |
| 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::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::occupancy ("mh:filter:occupancy") |
| 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 | orbitals::orbitals ("orbitals") |
| BooleanOptionKey const | orbitals::Hpol ("orbitals:Hpol") |
| BooleanOptionKey const | orbitals::Haro ("orbitals:Haro") |
| BooleanOptionKey const | orbitals::bb_stats ("orbitals:bb_stats") |
| BooleanOptionKey const | orbitals::sc_stats ("orbitals:sc_stats") |
| BooleanOptionKey const | orbitals::orb_orb_stats ("orbitals:orb_orb_stats") |
| BooleanOptionKey const | orbitals::sc_bb ("orbitals:sc_bb") |
| BooleanOptionKey const | cutoutdomain::cutoutdomain ("cutoutdomain") |
| IntegerOptionKey const | cutoutdomain::start ("cutoutdomain:start") |
| IntegerOptionKey const | cutoutdomain::end ("cutoutdomain:end") |
| BooleanOptionKey const | carbohydrates::carbohydrates ("carbohydrates") |
| BooleanOptionKey const | carbohydrates::lock_rings ("carbohydrates:lock_rings") |
| BooleanOptionKey const | dwkulp::dwkulp ("dwkulp") |
| StringOptionKey const | dwkulp::forcePolyAAfragments ("dwkulp:forcePolyAAfragments") |
| 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 | gpu::gpu ("gpu") |
| IntegerOptionKey const | gpu::device ("gpu:device") |
| IntegerOptionKey const | gpu::threads ("gpu:threads") |
| 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") |
| BooleanOptionKey const | pb_potential::calcenergy ("pb_potential:calcenergy") |
| BooleanOptionKey const | bunsat_calc2::bunsat_calc2 ("bunsat_calc2") |
| BooleanOptionKey const | bunsat_calc2::layered_sasa ("bunsat_calc2:layered_sasa") |
| BooleanOptionKey const | bunsat_calc2::generous_hbonds ("bunsat_calc2:generous_hbonds") |
| RealOptionKey const | bunsat_calc2::sasa_burial_cutoff ("bunsat_calc2:sasa_burial_cutoff") |
| RealOptionKey const | bunsat_calc2::AHD_cutoff ("bunsat_calc2:AHD_cutoff") |
| RealOptionKey const | bunsat_calc2::dist_cutoff ("bunsat_calc2:dist_cutoff") |
| RealOptionKey const | bunsat_calc2::hxl_dist_cutoff ("bunsat_calc2:hxl_dist_cutoff") |
| RealOptionKey const | bunsat_calc2::sulph_dist_cutoff ("bunsat_calc2:sulph_dist_cutoff") |
| RealOptionKey const | bunsat_calc2::metal_dist_cutoff ("bunsat_calc2:metal_dist_cutoff") |
1.8.7