- s -

• s : basic::options::OptionKeys::in::file
• s1 : basic::options::OptionKeys::stepwise
• s2 : basic::options::OptionKeys::stepwise
• sample_beta : basic::options::OptionKeys::stepwise::protein
• sample_both_sugar_base_rotamer : basic::options::OptionKeys::stepwise::rna
• sample_omega_at_pre_prolines : basic::options::OptionKeys::loops
• sample_ONLY_multiple_virtual_sugar : basic::options::OptionKeys::stepwise::rna
• sample_over_loops : basic::options::OptionKeys::remodel::staged_sampling
• sample_res : basic::options::OptionKeys::full_model
• sample_weight_file : basic::options::OptionKeys::lh
• sample_zero_probs_at : basic::options::OptionKeys::antibody::design
• sampler_allow_syn_pyrimidine : basic::options::OptionKeys::stepwise::rna
• sampler_assert_no_virt_sugar_sampling : basic::options::OptionKeys::stepwise::rna
• sampler_cluster_rmsd : basic::options::OptionKeys::stepwise::rna
• sampler_extra_beta_rotamer : basic::options::OptionKeys::stepwise::rna
• sampler_extra_chi_rotamer : basic::options::OptionKeys::stepwise::rna
• sampler_extra_epsilon_rotamer : basic::options::OptionKeys::stepwise::rna
• sampler_include_torsion_value_in_tag : basic::options::OptionKeys::stepwise::rna
• sampler_max_centroid_distance : basic::options::OptionKeys::stepwise::rna
• sampler_native_rmsd_screen : basic::options::OptionKeys::stepwise::rna
• sampler_native_screen_rmsd_cutoff : basic::options::OptionKeys::stepwise::rna
• sampler_num_pose_kept : basic::options::OptionKeys::stepwise::rna
• sampler_perform_o2prime_pack : basic::options::OptionKeys::stepwise::rna
• sampler_perform_phosphate_pack : basic::options::OptionKeys::stepwise::rna
• sampler_try_sugar_instantiation : basic::options::OptionKeys::stepwise::rna
• sampling : basic::options::OptionKeys::canonical_sampling::sampling
• sampling_prob : basic::options::OptionKeys::rigid
• sandbox : basic::options::OptionKeys::lh
• sanitize : basic::options::OptionKeys::cm::sanitize
• sasa : basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::sasa
• sasa_burial_cutoff : basic::options::OptionKeys::bunsat_calc2
• sasa_calculator_probe_radius : basic::options::OptionKeys::pose_metrics
• SASAfilter : basic::options::OptionKeys::chemically_conjugated_docking
• save_all_pdbs : basic::options::OptionKeys::pepspec
• save_loops_only : basic::options::OptionKeys::canonical_sampling::sampling
• save_low_pdbs : basic::options::OptionKeys::pepspec
• save_top : basic::options::OptionKeys::remodel
• saxs : basic::options::OptionKeys::score::saxs
• sc : basic::options::OptionKeys::canonical_sampling::probabilities
• sc_bb : basic::options::OptionKeys::orbitals
• sc_cst_maxdist : basic::options::OptionKeys::relax
• sc_min : basic::options::OptionKeys::antibody , basic::options::OptionKeys::casp , basic::options::OptionKeys::docking
• sc_min_only : basic::options::OptionKeys::ddg
• sc_min_res : basic::options::OptionKeys::docking
• sc_only : basic::options::OptionKeys::hotspot
• sc_prob_perturbcurrent : basic::options::OptionKeys::canonical_sampling::probabilities
• sc_prob_uniform : basic::options::OptionKeys::canonical_sampling::probabilities
• sc_prob_withinrot : basic::options::OptionKeys::canonical_sampling::probabilities
• sc_sc_bump_cutoff : basic::options::OptionKeys::enzdes
• sc_scaling : basic::options::OptionKeys::edensity , basic::options::OptionKeys::patterson
• sc_stats : basic::options::OptionKeys::orbitals
• scaffold_active_site_residues : basic::options::OptionKeys::match
• scaffold_active_site_residues_for_geomcsts : basic::options::OptionKeys::match
• scale_d : basic::options::OptionKeys::optimization
• scale_normalmode_dampen : basic::options::OptionKeys::optimization
• scale_rb : basic::options::OptionKeys::optimization
• scale_rbangle : basic::options::OptionKeys::optimization
• scale_theta : basic::options::OptionKeys::optimization
• scattach_res_files : basic::options::OptionKeys::smhybrid
• scmin_cartesian : basic::options::OptionKeys::optimization
• scmin_nonideal : basic::options::OptionKeys::optimization
• scmove : basic::options::OptionKeys::rot_anl
• score : basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::corrections::score , basic::options::OptionKeys::mh::score , basic::options::OptionKeys::out::path , basic::options::OptionKeys::rigid , basic::options::OptionKeys::score
• score12prime : basic::options::OptionKeys::corrections::score
• score_across_chains_only : basic::options::OptionKeys::mh
• score_cut_fl : basic::options::OptionKeys::boinc
• score_cut_pct : basic::options::OptionKeys::boinc
• score_cut_smart_throttle : basic::options::OptionKeys::boinc
• score_diff_cut : basic::options::OptionKeys::cluster , basic::options::OptionKeys::stepwise::protein
• score_exclude_res : basic::options::OptionKeys::evaluation
• score_filter : basic::options::OptionKeys::flexPepDocking
• score_filter_cutoff : basic::options::OptionKeys::loops
• score_function : basic::options::OptionKeys::dna::specificity
• score_only : basic::options::OptionKeys::out::file , basic::options::OptionKeys::run
• score_output_silent : basic::options::OptionKeys::frags
• score_pdbs : basic::options::OptionKeys::mh
• score_pose_cutpoint_variants : basic::options::OptionKeys::score
• score_sliding_window_context : basic::options::OptionKeys::edensity
• score_sscore_maxloop : basic::options::OptionKeys::evaluation
• score_sscore_short_helix : basic::options::OptionKeys::evaluation
• score_symm_complex : basic::options::OptionKeys::edensity
• score_tol : basic::options::OptionKeys::rot_anl
• score_type : basic::options::OptionKeys::blivens
• score_with_rmsd : basic::options::OptionKeys::evaluation
• scorecut : basic::options::OptionKeys::out
• scored_frag_cycles : basic::options::OptionKeys::loops
• scorefile : basic::options::OptionKeys::out::file
• scorefilter : basic::options::OptionKeys::chemically_conjugated_docking
• scoring : basic::options::OptionKeys::frags::scoring
• scratch : basic::options::OptionKeys::out::path
• screening_job_file : basic::options::OptionKeys::in::file
• screening_list : basic::options::OptionKeys::in::file
• script : basic::options::OptionKeys::els , basic::options::OptionKeys::relax
• script_max_accept : basic::options::OptionKeys::relax
• script_vars : basic::options::OptionKeys::parser
• secmatch_Ecutoff : basic::options::OptionKeys::enzdes
• secondary_seqdep_refene_fname : basic::options::OptionKeys::score
• secondary_structure_file : basic::options::OptionKeys::DenovoProteinDesign
• seed_offset : basic::options::OptionKeys::run
• segment_file : basic::options::OptionKeys::rdc
• segment_scoring_mode : basic::options::OptionKeys::rdc
• select_best_loop_from : basic::options::OptionKeys::loops
• select_residues_file : basic::options::OptionKeys::rdc
• select_structures_from_database : basic::options::OptionKeys::in
• selecting_rule : basic::options::OptionKeys::frags::picking
• selecting_scorefxn : basic::options::OptionKeys::frags::picking
• semiex_water_burial_cutoff : basic::options::OptionKeys::pose_metrics
• sep_bb_ss : basic::options::OptionKeys::in::rdf
• SEP_score_scalling : basic::options::OptionKeys::abinitio
• sep_switch_accelerate : basic::options::OptionKeys::jumps
• separate_db_per_mpi_process : basic::options::OptionKeys::inout::dbms
• seq : basic::options::OptionKeys::in::file
• seq_align : basic::options::OptionKeys::pepspec
• seq_score : basic::options::OptionKeys::cm
• seq_sep_stages : basic::options::OptionKeys::fold_cst
• seqdep_refene_fname : basic::options::OptionKeys::score
• seqsep : basic::options::OptionKeys::mh::filter
• seqsim_E : basic::options::OptionKeys::frags
• seqsim_H : basic::options::OptionKeys::frags
• seqsim_L : basic::options::OptionKeys::frags
• sequence : basic::options::OptionKeys::relax
• sequence_file : basic::options::OptionKeys::relax
• sequence_recovery : basic::options::OptionKeys::mh
• sequence_separation : basic::options::OptionKeys::rigid
• sequential : basic::options::OptionKeys::casp
• series : basic::options::OptionKeys::run
• server_port : basic::options::OptionKeys::rbe
• server_url : basic::options::OptionKeys::rbe
• set_anchor_at_closest_point : basic::options::OptionKeys::fold_and_dock
• set_atom_properties : basic::options::OptionKeys::chemical
• set_origin : basic::options::OptionKeys::fingerprint
• set_pddf_filter : basic::options::OptionKeys::filters
• set_saxs_filter : basic::options::OptionKeys::filters
• set_weights : basic::options::OptionKeys::score
• setup : basic::options::OptionKeys::broker
• sewing : basic::options::OptionKeys::sewing
• sf : basic::options::OptionKeys::out
• share_data : basic::options::OptionKeys::ms
• shear_moves : basic::options::OptionKeys::docking::ligand
• shear_on : basic::options::OptionKeys::FloppyTail
• sheet_edge_pred : basic::options::OptionKeys::abinitio
• sheets : basic::options::OptionKeys::jumps
• shift_sog_func : basic::options::OptionKeys::james
• short_frag_cycles : basic::options::OptionKeys::loops
• short_loop_len : basic::options::OptionKeys::abinitio::star
• short_range_seqsep : basic::options::OptionKeys::rigid
• short_tail : basic::options::OptionKeys::FloppyTail::short_tail
• short_tail_fraction : basic::options::OptionKeys::FloppyTail::short_tail
• short_tail_off : basic::options::OptionKeys::FloppyTail::short_tail
• shorten_long_terminal_loop : basic::options::OptionKeys::loops
• shortest_wu : basic::options::OptionKeys::els
• shortrelax : basic::options::OptionKeys::loops
• show_accessed_options : basic::options::OptionKeys::out
• show_all_fixes : basic::options::OptionKeys::in
• show_extended : basic::options::OptionKeys::AnchoredDesign
• show_simulation_in_pymol : basic::options::OptionKeys::run
• show_time_on_cerr : basic
• SHRINK_FACTOR : basic
• shrink_pos_step : basic::options::OptionKeys::templates
• shrink_step : basic::options::OptionKeys::templates
• shuffle : basic::options::OptionKeys::run
• shuffle_nstruct : basic::options::OptionKeys::out
• shuffle_screening_jobs : basic::options::OptionKeys::in::file
• sicdock : basic::options::OptionKeys::sicdock
• sidechain_buried : basic::options::OptionKeys::score
• sidechain_exposed : basic::options::OptionKeys::score
• sidechain_only : basic::options::OptionKeys::pb_potential
• sigmoid_cs_A : basic::options::OptionKeys::frags
• sigmoid_cs_B : basic::options::OptionKeys::frags
• silent : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , basic::options::OptionKeys::remodel::design , basic::options::OptionKeys::resample , basic::options::OptionKeys::run , basic::options
• silent1 : basic::options::OptionKeys::stepwise
• silent2 : basic::options::OptionKeys::stepwise
• silent_comment_bound : basic::options::OptionKeys::out::file
• silent_decoytime : basic::options::OptionKeys::out::file
• silent_energy_cut : basic::options::OptionKeys::in::file
• silent_gz : basic::options::OptionKeys::out
• silent_input : basic::options::OptionKeys::run
• silent_list : basic::options::OptionKeys::in::file
• silent_optH : basic::options::OptionKeys::in::file
• silent_preserve_H : basic::options::OptionKeys::out::file
• silent_print_all_score_headers : basic::options::OptionKeys::out::file
• silent_read_through_errors : basic::options::OptionKeys::in::file
• silent_renumber : basic::options::OptionKeys::in::file
• silent_score_prefix : basic::options::OptionKeys::in::file
• silent_scores_wanted : basic::options::OptionKeys::in::file
• silent_select_random : basic::options::OptionKeys::in::file
• silent_select_range_len : basic::options::OptionKeys::in::file
• silent_select_range_mul : basic::options::OptionKeys::in::file
• silent_select_range_start : basic::options::OptionKeys::in::file
• silent_struct_type : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file
• simple_append_map : basic::options::OptionKeys::stepwise::rna
• simultaneous_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover
• single_chain : basic::options::OptionKeys::frags::nonlocal
• single_helix_rmsd_cutoff : basic::options::OptionKeys::sewing
• single_loop_ensemble_size : basic::options::OptionKeys::enzdes
• single_res_scoring : basic::options::OptionKeys::ddg
• singlenode : basic::options::OptionKeys::els
• skim_size : basic::options::OptionKeys::lh
• skip : basic::options::OptionKeys::rescore
• skip_1mers : basic::options::OptionKeys::loops
• skip_3mers : basic::options::OptionKeys::loops
• skip_9mers : basic::options::OptionKeys::loops
• skip_ccd_moves : basic::options::OptionKeys::loops
• skip_convergence_check : basic::options::OptionKeys::abinitio
• skip_coord_constraints : basic::options::OptionKeys::rna , basic::options::OptionKeys::stepwise::protein
• skip_deletions : basic::options::OptionKeys::stepwise::monte_carlo
• skip_failed_simulations : basic::options::OptionKeys::in::file
• skip_fragment_moves : basic::options::OptionKeys::RBSegmentRelax
• skip_hydrogens : basic::options::OptionKeys::score::saxs
• skip_minimize : basic::options::OptionKeys::stepwise::protein
• skip_o2prime_trials : basic::options::OptionKeys::rna
• skip_on_noviolation_in_stage1 : basic::options::OptionKeys::fold_cst
• skip_partial : basic::options::OptionKeys::remodel::design
• skip_rb_moves : basic::options::OptionKeys::RBSegmentRelax
• skip_redundant : basic::options::OptionKeys::constraints
• skip_redundant_width : basic::options::OptionKeys::constraints
• skip_relax : basic::options::OptionKeys::cp
• skip_sampling : basic::options::OptionKeys::stepwise::rna
• skip_seqshift_moves : basic::options::OptionKeys::RBSegmentRelax
• skip_set_reasonable_fold_tree : basic::options::OptionKeys::run
• skip_stage2 : basic::options::OptionKeys::cm::hybridize
• skip_stages : basic::options::OptionKeys::abinitio
• skipl : numeric::kinematic_closure
• slice_res1 : basic::options::OptionKeys::stepwise
• slice_res2 : basic::options::OptionKeys::stepwise
• slide_contact_frequency : basic::options::OptionKeys::fold_and_dock
• sliding_window : basic::options::OptionKeys::edensity
• sliding_window_wt : basic::options::OptionKeys::edensity
• small_cycles : basic::options::OptionKeys::rigid
• small_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize
• small_moves : basic::options::OptionKeys::remodel::staged_sampling
• smhybrid : basic::options::OptionKeys::smhybrid
• smooth_cycles_only : basic::options::OptionKeys::abinitio
• smooth_fa_elec : basic::options::OptionKeys::score
• smooth_move_frac : basic::options::OptionKeys::membrane
• smove_angle_range : basic::options::OptionKeys::flexPepDocking
• snug_loops : basic::options::OptionKeys::antibody
• snugfit : basic::options::OptionKeys::antibody
• soft_rep : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::docking::ligand
• soft_rep_design : basic::options::OptionKeys::packing
• soft_wts : basic::options::OptionKeys::pepspec , basic::options::OptionKeys::score
• sog_cst_param : basic::options::OptionKeys::constraints
• sog_cutoff : basic::options::OptionKeys::james
• sog_upper_bound : basic::options::OptionKeys::constraints
• solvate : basic::options::OptionKeys::packing
• sort_groups_by_energy : basic::options::OptionKeys::cluster
• sort_groups_by_size : basic::options::OptionKeys::cluster
• span_files : basic::options::OptionKeys::membrane
• spanfile : basic::options::OptionKeys::in::file
• sparse_pdb_output : basic::options::OptionKeys::dna::design
• sparta_dir : basic::options::OptionKeys::evaluation
• special_rotweight : basic::options::OptionKeys::motifs
• specificity : basic::options::OptionKeys::dna::design::specificity , basic::options::OptionKeys::dna::specificity
• spin : basic::options::OptionKeys::docking
• spine_x : basic::options::OptionKeys::frags
• splitwork : basic::options::OptionKeys::willmatch
• spread : basic::options::OptionKeys::loops
• spread_ss_element : basic::options::OptionKeys::mh::score
• sqrt_pssm : basic::options::OptionKeys::optE
• square_score : basic::options::OptionKeys::fingerprint
• src_chain : basic::options::OptionKeys::threadsc
• src_first_resid : basic::options::OptionKeys::threadsc
• ss : basic::options::OptionKeys::cm::hybridize , basic::options::OptionKeys::smhybrid , basic::options::OptionKeys::ufv
• ss1 : basic::options::OptionKeys::mh::filter
• ss2 : basic::options::OptionKeys::mh::filter
• ss_pair : basic::options::OptionKeys::remodel
• ss_pred : basic::options::OptionKeys::frags
• ss_type : basic::options::OptionKeys::pepspec
• SSrbrelax : basic::options::OptionKeys::SSrbrelax
• stage1 : basic::options::OptionKeys::resample
• stage1_1_cycles : basic::options::OptionKeys::cm::hybridize
• stage1_2_cycles : basic::options::OptionKeys::cm::hybridize
• stage1_3_cycles : basic::options::OptionKeys::cm::hybridize
• stage1_4_cenrot_score : basic::options::OptionKeys::cm::hybridize
• stage1_4_cycles : basic::options::OptionKeys::cm::hybridize
• stage1_increase_cycles : basic::options::OptionKeys::cm::hybridize
• stage1_patch : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize
• stage1_probability : basic::options::OptionKeys::cm::hybridize
• stage1_ramp_cst_cycle_factor : basic::options::OptionKeys::fold_cst
• stage1_ramp_cycles : basic::options::OptionKeys::relax
• stage1_ramp_inner_cycles : basic::options::OptionKeys::relax
• stage1_weights : basic::options::OptionKeys::cm::hybridize
• stage2 : basic::options::OptionKeys::resample
• stage2_constraint_threshold : basic::options::OptionKeys::fold_cst
• stage2_cycles : basic::options::OptionKeys::relax
• stage2_increase_cycles : basic::options::OptionKeys::cm::hybridize
• stage2_patch : basic::options::OptionKeys::abinitio , basic::options::OptionKeys::cm::hybridize
• stage2_repack_period : basic::options::OptionKeys::relax
• stage2_temperature : basic::options::OptionKeys::cm::hybridize
• stage2_weights : basic::options::OptionKeys::cm::hybridize
• stage2min_increase_cycles : basic::options::OptionKeys::cm::hybridize
• stage3_cycles : basic::options::OptionKeys::relax
• stage3a_patch : basic::options::OptionKeys::abinitio
• stage3b_patch : basic::options::OptionKeys::abinitio
• stage4_patch : basic::options::OptionKeys::abinitio
• stage5_patch : basic::options::OptionKeys::abinitio
• staged_sampling : basic::options::OptionKeys::remodel::staged_sampling
• stages : basic::options::OptionKeys::rigid
• standard : basic::options
• star : basic::options::OptionKeys::abinitio::star
• start : basic::options::OptionKeys::cutoutdomain
• start_clock : basic
• start_from : basic::options::OptionKeys::docking::ligand
• start_from_random_rb_conf : basic::options::OptionKeys::enzdes
• start_models_only : basic::options::OptionKeys::cm
• start_native : basic::options::OptionKeys::abinitio
• start_w_ideal_helices : basic::options::OptionKeys::remodel::staged_sampling
• starting_pdb : basic::options::OptionKeys::remodel::staged_sampling
• starting_refEs : basic::options::OptionKeys::optE
• starting_sequence : basic::options::OptionKeys::remodel::staged_sampling
• starting_template : basic::options::OptionKeys::cm::hybridize
• stats_cutoff : basic::options::OptionKeys::antibody::design
• status : basic::options::OptionKeys::run
• std_IO_exit_error_code : basic::options::OptionKeys::out
• steal_3mers : basic::options::OptionKeys::abinitio
• steal_9mers : basic::options::OptionKeys::abinitio
• steal_extra_residues : basic::options::OptionKeys::cm
• stealfrags : basic::options::OptionKeys::loops
• stealfrags_times : basic::options::OptionKeys::loops
• stem_optimize : basic::options::OptionKeys::antibody
• stem_optimize_size : basic::options::OptionKeys::antibody
• stepwise : basic::options::OptionKeys::stepwise
• strand_assembly : basic::options::OptionKeys::strand_assembly
• strand_constraint : basic::options::OptionKeys::templates
• strand_dist_cutoff : basic::options::OptionKeys::abinitio
• strand_movement_params : basic::options::OptionKeys::RBSegmentRelax
• strand_pair_weight : basic::options::OptionKeys::mh::score
• stretch_strand_dist_cutoff : basic::options::OptionKeys::abinitio
• strict_loops : basic::options::OptionKeys::loops
• struct_ids : basic::options::OptionKeys::in::dbms
• structural_similarity : basic::options::OptionKeys::evaluation
• subset_to_keep : basic::options::OptionKeys::docking::ligand
• subsubs_attract : basic::options::OptionKeys::smhybrid
• sucker_params : basic::options::OptionKeys::in::file
• suffix : basic::options::OptionKeys::out
• sulph_dist_cutoff : basic::options::OptionKeys::bunsat_calc2
• super_secret_fixed_interface_mode : basic::options::OptionKeys::AnchoredDesign::testing
• superimpose_native : basic::options::OptionKeys::loops
• superimpose_to_file : basic::options::OptionKeys::relax
• superimpose_to_native : basic::options::OptionKeys::relax
• suppress_checkpointing : basic::options::OptionKeys::ddg
• suppress_checkpoints : basic::options::OptionKeys::run
• suppress_zero_occ_pdb_output : basic::options::OptionKeys::out::file
• surface : basic::options::OptionKeys::flxbb::layer
• surface_accessibility : basic::options::OptionKeys::packstat
• surface_vectors : basic::options::OptionKeys::in::file
• svmmodel : basic::options::OptionKeys::ProQ
• swap_loops : basic::options::OptionKeys::fold_from_loops
• swap_refine_confirm_protocols : basic::options::OptionKeys::remodel
• switch_concert_sub : basic::options::OptionKeys::smhybrid
• switch_focus_frequency : basic::options::OptionKeys::stepwise::monte_carlo
• symE_bonus : basic::options::OptionKeys::score
• symE_units : basic::options::OptionKeys::score
• symfragrm : basic::options::OptionKeys::lh::symfragrm
• symm_def_template : basic::options::OptionKeys::smhybrid
• symm_def_template_reduced : basic::options::OptionKeys::smhybrid
• symm_file_tag : basic::options::OptionKeys::smhybrid
• symmetric_rmsd : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::symmetry
• symmetry : basic::options::OptionKeys::docking::symmetry , basic::options::OptionKeys::symmetry
• symmetry_c2_dock : basic::options::OptionKeys::willmatch
• symmetry_d2 : basic::options::OptionKeys::willmatch
• symmetry_definition : basic::options::OptionKeys::symmetry
• symmetry_residue : basic::options::OptionKeys::abinitio
• syn_G_potential_bonus : basic::options::OptionKeys::score