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Rosetta
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Functions | |
| BooleanOptionKey const | stepwise::output_cluster_size ("stepwise:output_cluster_size") |
| BooleanOptionKey const | stepwise::lores ("stepwise:lores") |
| BooleanOptionKey const | stepwise::verbose_sampler ("stepwise:verbose_sampler") |
| BooleanOptionKey const | stepwise::pack_protein_side_chains ("stepwise:pack_protein_side_chains") |
| IntegerVectorOptionKey const | stepwise::definitely_virtualize ("stepwise:definitely_virtualize") |
| BooleanOptionKey const | stepwise::force_moving_res_for_erraser ("stepwise:force_moving_res_for_erraser") |
| BooleanOptionKey const | stepwise::boltzmann_choice_post_enumerated_minimize ("stepwise:boltzmann_choice_post_enumerated_minimize") |
| 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::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::skip_bulge_frequency ("stepwise:monte_carlo:skip_bulge_frequency") |
| 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_proposal_density_factor ("stepwise:monte_carlo:add_proposal_density_factor") |
| RealOptionKey const | stepwise::monte_carlo::add_delete_frequency ("stepwise:monte_carlo:add_delete_frequency") |
| RealOptionKey const | stepwise::monte_carlo::docking_frequency ("stepwise:monte_carlo:docking_frequency") |
| RealOptionKey const | stepwise::monte_carlo::submotif_frequency ("stepwise:monte_carlo:submotif_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") |
| BooleanOptionKey const | stepwise::monte_carlo::recover_low ("stepwise:monte_carlo:recover_low") |
| BooleanOptionKey const | stepwise::monte_carlo::use_precomputed_library ("stepwise:monte_carlo:use_precomputed_library") |
| BooleanOptionKey const | stepwise::monte_carlo::allow_submotif_split ("stepwise:monte_carlo:allow_submotif_split") |
| BooleanOptionKey const | stepwise::monte_carlo::force_submotif_without_intervening_bulge ("stepwise:monte_carlo:force_submotif_without_intervening_bulge") |
| BooleanOptionKey const | stepwise::monte_carlo::use_first_jump_for_submotif ("stepwise:monte_carlo:use_first_jump_for_submotif") |
| StringVectorOptionKey const | stepwise::monte_carlo::exclude_submotifs ("stepwise:monte_carlo:exclude_submotifs") |
| RealOptionKey const | stepwise::monte_carlo::vary_loop_length_frequency ("stepwise:monte_carlo:vary_loop_length_frequency") |
| BooleanOptionKey const | stepwise::monte_carlo::designing_with_noncanonicals ("stepwise:monte_carlo:designing_with_noncanonicals") |
| IntegerOptionKey const | stepwise::monte_carlo::checkpointing_frequency ("stepwise:monte_carlo:checkpointing_frequency") |
| BooleanOptionKey const | stepwise::monte_carlo::continue_until_none_missing ("stepwise:monte_carlo:continue_until_none_missing") |
| FileVectorOptionKey const | stepwise::monte_carlo::full_model_constraints ("stepwise:monte_carlo:full_model_constraints") |
| BooleanOptionKey const | stepwise::monte_carlo::csa::csa ("stepwise:monte_carlo:csa") |
| IntegerOptionKey const | stepwise::monte_carlo::csa::csa_bank_size ("stepwise:monte_carlo:csa:csa_bank_size") |
| RealOptionKey const | stepwise::monte_carlo::csa::csa_rmsd ("stepwise:monte_carlo:csa:csa_rmsd") |
| BooleanOptionKey const | stepwise::monte_carlo::csa::csa_output_rounds ("stepwise:monte_carlo:csa:csa_output_rounds") |
| BooleanOptionKey const | stepwise::monte_carlo::csa::annealing ("stepwise:monte_carlo:csa:annealing") |
| BooleanOptionKey const | stepwise::polar_hydrogens::polar_hydrogens ("stepwise:polar_hydrogens") |
| BooleanOptionKey const | stepwise::polar_hydrogens::vary_polar_hydrogen_geometry ("stepwise:polar_hydrogens:vary_polar_hydrogen_geometry") |
| RealOptionKey const | stepwise::polar_hydrogens::bond_angle_sd_polar_hydrogen ("stepwise:polar_hydrogens:bond_angle_sd_polar_hydrogen") |
| RealOptionKey const | stepwise::polar_hydrogens::bond_torsion_sd_polar_hydrogen ("stepwise:polar_hydrogens:bond_torsion_sd_polar_hydrogen") |
| BooleanOptionKey const | stepwise::polar_hydrogens::fix_lengths ("stepwise:polar_hydrogens:fix_lengths") |
| BooleanOptionKey const | stepwise::polar_hydrogens::fix_angles ("stepwise:polar_hydrogens:fix_angles") |
| BooleanOptionKey const | stepwise::polar_hydrogens::fix_torsions ("stepwise:polar_hydrogens:fix_torsions") |
| BooleanOptionKey const | stepwise::polar_hydrogens::disallow_pack_polar_hydrogens ("stepwise:polar_hydrogens:disallow_pack_polar_hydrogens") |
| BooleanOptionKey const | stepwise::polar_hydrogens::disallow_vary_geometry_proton_chi ("stepwise:polar_hydrogens:disallow_vary_geometry_proton_chi") |
| BooleanOptionKey const | stepwise::rna::rna ("stepwise:rna") |
| IntegerOptionKey const | stepwise::rna::sampler_num_pose_kept ("stepwise:rna:sampler_num_pose_kept") |
| RealOptionKey const | stepwise::rna::native_edensity_score_cutoff ("stepwise:rna:native_edensity_score_cutoff") |
| BooleanOptionKey const | stepwise::rna::o2prime_legacy_mode ("stepwise:rna:o2prime_legacy_mode") |
| BooleanOptionKey const | stepwise::rna::allow_virtual_o2prime_hydrogens ("stepwise:rna:allow_virtual_o2prime_hydrogens") |
| BooleanOptionKey const | stepwise::rna::sampler_perform_phosphate_pack ("stepwise:rna:sampler_perform_phosphate_pack") |
| BooleanOptionKey const | stepwise::rna::force_phosphate_instantiation ("stepwise:rna:force_phosphate_instantiation") |
| 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::sample_all_chi ("stepwise:rna:sample_all_chi") |
| 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::VDW_rep_optimize_memory_usage ("stepwise:rna:VDW_rep_optimize_memory_usage") |
| 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::minimize_and_score_native_pose ("stepwise:rna:minimize_and_score_native_pose") |
| BooleanOptionKey const | stepwise::rna::rm_virt_phosphate ("stepwise:rna:rm_virt_phosphate") |
| StringVectorOptionKey const | stepwise::rna::VDW_rep_screen_info ("stepwise:rna:VDW_rep_screen_info") |
| 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_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::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") |
| 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") |
| 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::tether_jump ("stepwise:rna:tether_jump") |
| BooleanOptionKey const | stepwise::rna::turn_off_rna_chem_map_during_optimize ("stepwise:rna:turn_off_rna_chem_map_during_optimize") |
| BooleanOptionKey const | stepwise::protein::protein ("stepwise:protein") |
| BooleanOptionKey const | stepwise::protein::global_optimize ("stepwise:protein:global_optimize") |
| BooleanOptionKey const | stepwise::protein::disable_sampling_of_loop_takeoff ("stepwise:protein:disable_sampling_of_loop_takeoff") |
| BooleanOptionKey const | stepwise::protein::sample_beta ("stepwise:protein:sample_beta") |
| BooleanOptionKey const | stepwise::protein::ghost_loops ("stepwise:protein:ghost_loops") |
| BooleanOptionKey const | stepwise::protein::centroid_screen ("stepwise:protein:centroid_screen") |
| RealOptionKey const | stepwise::protein::centroid_score_diff_cut ("stepwise:protein:centroid_score_diff_cut") |
| 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") |
| 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") |
| StringOptionKey const | stepwise::protein::disulfide_file ("stepwise:protein:disulfide_file") |
| BooleanOptionKey const | full_model::full_model ("full_model") |
| StringOptionKey const | full_model::global_seq_file ("full_model:global_seq_file") |
| ResidueChainVectorOptionKey const | full_model::cutpoint_open ("full_model:cutpoint_open") |
| ResidueChainVectorOptionKey const | full_model::cutpoint_closed ("full_model:cutpoint_closed") |
| ResidueChainVectorOptionKey const | full_model::cyclize ("full_model:cyclize") |
| ResidueChainVectorOptionKey const | full_model::twoprime ("full_model:twoprime") |
| ResidueChainVectorOptionKey const | full_model::fiveprime_cap ("full_model:fiveprime_cap") |
| StringVectorOptionKey const | full_model::other_poses ("full_model:other_poses") |
| ResidueChainVectorOptionKey const | full_model::jump_res ("full_model:jump_res") |
| ResidueChainVectorOptionKey const | full_model::disulfide_res ("full_model:disulfide_res") |
| ResidueChainVectorOptionKey const | full_model::extra_min_res ("full_model:extra_min_res") |
| ResidueChainVectorOptionKey const | full_model::extra_min_jump_res ("full_model:extra_min_jump_res") |
| ResidueChainVectorOptionKey const | full_model::root_res ("full_model:root_res") |
| ResidueChainVectorOptionKey const | full_model::virtual_sugar_res ("full_model:virtual_sugar_res") |
| ResidueChainVectorOptionKey const | full_model::virtual_res ("full_model:virtual_res") |
| ResidueChainVectorOptionKey const | full_model::sample_res ("full_model:sample_res") |
| ResidueChainVectorOptionKey const | full_model::calc_rms_res ("full_model:calc_rms_res") |
| ResidueChainVectorOptionKey const | full_model::working_res ("full_model:working_res") |
| BooleanOptionKey const | full_model::motif_mode ("full_model:motif_mode") |
| BooleanOptionKey const | full_model::allow_jump_in_numbering ("full_model:allow_jump_in_numbering") |
| BooleanOptionKey const | full_model::rna::rna ("full_model:rna") |
| ResidueChainVectorOptionKey const | full_model::rna::terminal_res ("full_model:rna:terminal_res") |
| ResidueChainVectorOptionKey const | full_model::rna::block_stack_above_res ("full_model:rna:block_stack_above_res") |
| ResidueChainVectorOptionKey const | full_model::rna::block_stack_below_res ("full_model:rna:block_stack_below_res") |
| ResidueChainVectorOptionKey const | full_model::rna::force_syn_chi_res_list ("full_model:rna:force_syn_chi_res_list") |
| ResidueChainVectorOptionKey const | full_model::rna::force_anti_chi_res_list ("full_model:rna:force_anti_chi_res_list") |
| ResidueChainVectorOptionKey const | full_model::rna::force_north_sugar_list ("full_model:rna:force_north_sugar_list") |
| ResidueChainVectorOptionKey const | full_model::rna::force_south_sugar_list ("full_model:rna:force_south_sugar_list") |
| ResidueChainVectorOptionKey const | full_model::rna::bulge_res ("full_model:rna:bulge_res") |
| ResidueChainVectorOptionKey const | full_model::rna::sample_sugar_res ("full_model:rna:sample_sugar_res") |
| StringOptionKey const | recces::seq1 ("recces:seq1") |
| StringOptionKey const | recces::seq2 ("recces:seq2") |
| IntegerOptionKey const | recces::n_cycle ("recces:n_cycle") |
| RealOptionKey const | recces::a_form_range ("recces:a_form_range") |
| BooleanOptionKey const | recces::dump_pdb ("recces:dump_pdb") |
| BooleanOptionKey const | recces::dump_silent ("recces:dump_silent") |
| BooleanOptionKey const | recces::out_torsions ("recces:out_torsions") |
| RealVectorOptionKey const | recces::temps ("recces:temps") |
| RealVectorOptionKey const | recces::st_weights ("recces:st_weights") |
| BooleanOptionKey const | recces::save_score_terms ("recces:save_score_terms") |
| StringOptionKey const | recces::out_prefix ("recces:out_prefix") |
| IntegerOptionKey const | recces::dump_freq ("recces:dump_freq") |
| IntegerOptionKey const | recces::n_intermediate_dump ("recces:n_intermediate_dump") |
| BooleanOptionKey const | recces::output_min_pose ("recces:output_min_pose") |
| BooleanOptionKey const | recces::accept_no_op_moves ("recces:accept_no_op_moves") |
| RealOptionKey const | recces::histogram_min ("recces:histogram_min") |
| RealOptionKey const | recces::histogram_max ("recces:histogram_max") |
| RealOptionKey const | recces::histogram_spacing ("recces:histogram_spacing") |
| BooleanOptionKey const | recces::base_pair::base_pair ("recces:base_pair") |
| RealOptionKey const | recces::base_pair::rmsd_cutoff ("recces:base_pair:rmsd_cutoff") |
| RealOptionKey const | recces::base_pair::translation_mag ("recces:base_pair:translation_mag") |
| RealOptionKey const | recces::base_pair::rotation_mag ("recces:base_pair:rotation_mag") |
| BooleanOptionKey const | recces::base_pair::recces ("recces:base_pair:recces") |
| BooleanOptionKey const | recces::base_pair::block_stack ("recces:base_pair:block_stack") |
| BooleanOptionKey const | recces::base_pair::sample_jump ("recces:base_pair:sample_jump") |
| BooleanOptionKey const | recces::thermal_sampling::thermal_sampling ("recces:thermal_sampling") |
| IntegerVectorOptionKey const | recces::thermal_sampling::sample_residues ("recces:thermal_sampling:sample_residues") |
| IntegerVectorOptionKey const | recces::thermal_sampling::free_residues ("recces:thermal_sampling:free_residues") |
| IntegerVectorOptionKey const | recces::thermal_sampling::loop_residues ("recces:thermal_sampling:loop_residues") |
| RealOptionKey const | recces::thermal_sampling::angle_range_bb ("recces:thermal_sampling:angle_range_bb") |
| RealOptionKey const | recces::thermal_sampling::angle_range_free_bb ("recces:thermal_sampling:angle_range_free_bb") |
| RealOptionKey const | recces::thermal_sampling::angle_range_chi ("recces:thermal_sampling:angle_range_chi") |
| RealOptionKey const | recces::thermal_sampling::angle_range_free_chi ("recces:thermal_sampling:angle_range_free_chi") |
| RealOptionKey const | recces::thermal_sampling::chi_stdev ("recces:thermal_sampling:chi_stdev") |
| RealOptionKey const | recces::thermal_sampling::bb_stdev ("recces:thermal_sampling:bb_stdev") |
| RealOptionKey const | recces::thermal_sampling::standard_bb_stdev ("recces:thermal_sampling:standard_bb_stdev") |
| BooleanOptionKey const | recces::thermal_sampling::setup_base_pair_constraints ("recces:thermal_sampling:setup_base_pair_constraints") |
| 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 | TailSegment::TailSegment ("TailSegment") |
| IntegerOptionKey const | TailSegment::refine_cycles ("TailSegment:refine_cycles") |
| IntegerOptionKey const | TailSegment::refine_repack_cycles ("TailSegment:refine_repack_cycles") |
| BooleanOptionKey const | templates::templates ("templates") |
| FileOptionKey const | templates::config ("templates:config") |
| BooleanOptionKey const | templates::fix_aligned_residues ("templates:fix_aligned_residues") |
| FileOptionKey const | templates::fix_frag_file ("templates:fix_frag_file") |
| IntegerOptionKey const | templates::fix_margin ("templates:fix_margin") |
| IntegerOptionKey const | templates::min_nr_large_frags ("templates:min_nr_large_frags") |
| IntegerOptionKey const | templates::min_nr_small_frags ("templates:min_nr_small_frags") |
| BooleanOptionKey const | templates::no_pick_fragments ("templates:no_pick_fragments") |
| IntegerOptionKey const | templates::nr_large_copies ("templates:nr_large_copies") |
| IntegerOptionKey const | templates::nr_small_copies ("templates:nr_small_copies") |
| BooleanOptionKey const | templates::pairings ("templates:pairings") |
| BooleanOptionKey const | templates::pick_multiple_sizes ("templates:pick_multiple_sizes") |
| BooleanOptionKey const | templates::strand_constraint ("templates:strand_constraint") |
| BooleanOptionKey const | templates::vary_frag_size ("templates:vary_frag_size") |
| BooleanOptionKey const | templates::no_culling ("templates:no_culling") |
| FileOptionKey const | templates::helix_pairings ("templates:helix_pairings") |
| FileOptionKey const | templates::prefix ("templates:prefix") |
| IntegerOptionKey const | templates::change_movemap ("templates:change_movemap") |
| BooleanOptionKey const | templates::force_native_topology ("templates:force_native_topology") |
| RealOptionKey const | templates::topology_rank_cutoff ("templates:topology_rank_cutoff") |
| IntegerOptionKey const | templates::min_frag_size ("templates:min_frag_size") |
| IntegerOptionKey const | templates::max_shrink ("templates:max_shrink") |
| IntegerOptionKey const | templates::shrink_step ("templates:shrink_step") |
| IntegerOptionKey const | templates::shrink_pos_step ("templates:shrink_pos_step") |
| IntegerOptionKey const | templates::min_padding ("templates:min_padding") |
| IntegerOptionKey const | templates::min_align_pos ("templates:min_align_pos") |
| IntegerOptionKey const | templates::max_align_pos ("templates:max_align_pos") |
| BooleanOptionKey const | templates::cst::cst ("templates:cst") |
| IntegerOptionKey const | templates::cst::topN ("templates:cst:topN") |
| RealOptionKey const | templates::cst::wTopol ("templates:cst:wTopol") |
| RealOptionKey const | templates::cst::wExtern ("templates:cst:wExtern") |
| BooleanOptionKey const | templates::fragsteal::fragsteal ("templates:fragsteal") |
| IntegerOptionKey const | templates::fragsteal::topN ("templates:fragsteal:topN") |
| RealOptionKey const | templates::fragsteal::wTopol ("templates:fragsteal:wTopol") |
| RealOptionKey const | templates::fragsteal::wExtern ("templates:fragsteal:wExtern") |
| BooleanOptionKey const | trRosetta::trRosetta ("trRosetta") |
| FileOptionKey const | trRosetta::msa_file ("trRosetta:msa_file") |
| StringOptionKey const | trRosetta::write_constraints_to_file ("trRosetta:write_constraints_to_file") |
| BooleanOptionKey const | trRosetta::only_write_constraints ("trRosetta:only_write_constraints") |
| BooleanOptionKey const | trRosetta::use_distance_constraints ("trRosetta:use_distance_constraints") |
| BooleanOptionKey const | trRosetta::use_omega_constraints ("trRosetta:use_omega_constraints") |
| BooleanOptionKey const | trRosetta::use_theta_constraints ("trRosetta:use_theta_constraints") |
| BooleanOptionKey const | trRosetta::use_phi_constraints ("trRosetta:use_phi_constraints") |
| RealOptionKey const | trRosetta::distance_constraint_prob_cutoff ("trRosetta:distance_constraint_prob_cutoff") |
| RealOptionKey const | trRosetta::omega_constraint_prob_cutoff ("trRosetta:omega_constraint_prob_cutoff") |
| RealOptionKey const | trRosetta::theta_constraint_prob_cutoff ("trRosetta:theta_constraint_prob_cutoff") |
| RealOptionKey const | trRosetta::phi_constraint_prob_cutoff ("trRosetta:phi_constraint_prob_cutoff") |
| StringOptionKey const | trRosetta::backbone_randomization_mode ("trRosetta:backbone_randomization_mode") |
| StringOptionKey const | trRosetta::backbone_minimization_mode ("trRosetta:backbone_minimization_mode") |
| RealOptionKey const | trRosetta::cis_peptide_prob_non_prepro ("trRosetta:cis_peptide_prob_non_prepro") |
| RealOptionKey const | trRosetta::cis_peptide_prob_prepro ("trRosetta:cis_peptide_prob_prepro") |
| FileOptionKey const | trRosetta::scorefxn0 ("trRosetta:scorefxn0") |
| FileOptionKey const | trRosetta::scorefxn1 ("trRosetta:scorefxn1") |
| FileOptionKey const | trRosetta::scorefxn2 ("trRosetta:scorefxn2") |
| FileOptionKey const | trRosetta::scorefxn3 ("trRosetta:scorefxn3") |
| FileOptionKey const | trRosetta::scorefxn_fullatom ("trRosetta:scorefxn_fullatom") |
| BooleanOptionKey const | trRosetta::mutate_gly_to_ala ("trRosetta:mutate_gly_to_ala") |
| BooleanOptionKey const | trRosetta::fullatom_refinement ("trRosetta:fullatom_refinement") |
| RealOptionKey const | trRosetta::distance_constraint_weight ("trRosetta:distance_constraint_weight") |
| RealOptionKey const | trRosetta::phi_constraint_weight ("trRosetta:phi_constraint_weight") |
| RealOptionKey const | trRosetta::omega_constraint_weight ("trRosetta:omega_constraint_weight") |
1.9.1