Here is a list of all namespace members with links to the namespace documentation for each member:

- s -

• s : basic::options::OptionKeys::in::file , docking , in::file , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_common
• S : pyrosetta.distributed.cluster.base , pyrosetta.distributed.cluster.converters , pyrosetta.distributed.cluster.multiprocessing
• s1 : basic::options::OptionKeys::stepwise , stepwise
• s2 : basic::options::OptionKeys::stepwise , stepwise
• SA : amino_acids
• saccharide_sequence : basic::options::OptionKeys::carbohydrates , carbohydrates
• safe_duration_cast() : safe_duration_cast
• safe_float_conversion() : safe_duration_cast
• safe_strerror() : detail
• safely_check_map_for_key_and_insert_if_absent() : utility::thread
• safely_create_load_once_object_by_OP() : utility::thread
• safely_create_singleton() : utility::thread
• safely_determine_whether_singleton_exists() : utility::thread
• safely_prepare_statement() : basic::database
• safely_read_from_database() : basic::database
• safely_write_to_database() : basic::database
• same_ignoring_spaces() : utility
• sample_all_chi : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sample_around : basic::options::OptionKeys::sample_around , sample_around
• sample_beta : basic::options::OptionKeys::stepwise::protein , stepwise::protein
• sample_both_sugar_base_rotamer : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sample_cis_pro_frequency : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• sample_dna_interface() : demo.D110_DNA_interface
• sample_docking() : demo.D100_Docking
• sample_folding() : demo.D060_Folding
• sample_high_energy_conformers : basic::options::OptionKeys::rings , rings
• sample_jump : basic::options::OptionKeys::recces::base_pair , recces::base_pair
• sample_ligand_interface() : demo.D120_Ligand_interface
• sample_omega_at_pre_prolines : basic::options::OptionKeys::loops , loops
• sample_ONLY_multiple_virtual_sugar : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sample_over_loops : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• sample_pcs : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• sample_refinement() : demo.D070_Refinement
• sample_res : basic::options::OptionKeys::full_model , full_model
• sample_residues : basic::options::OptionKeys::recces::thermal_sampling , recces::thermal_sampling
• sample_single_loop_modeling() : demo.D080_Loop_modeling
• sample_sugar_res : basic::options::OptionKeys::full_model::rna , full_model::rna
• sample_weight_file : basic::options::OptionKeys::lh , lh
• sample_zero_probs_at() : antibody::design , basic::options::OptionKeys::antibody::design
• sampler_allow_syn_pyrimidine : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_assert_no_virt_sugar_sampling : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_extra_beta_rotamer : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_extra_chi_rotamer : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_extra_epsilon_rotamer : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_include_torsion_value_in_tag : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_max_centroid_distance : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_num_pose_kept : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_perform_phosphate_pack : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampler_silent_file : basic::options::OptionKeys::stepwise , stepwise
• sampler_try_sugar_instantiation : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• sampling : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• sampling_increment : local
• sampling_moves : run_backbone
• sampling_prob : basic::options::OptionKeys::rigid , rigid
• sampling_range : local
• sandbox : basic::options::OptionKeys::lh , lh
• sanitize : basic::options::OptionKeys::cm::sanitize , cm::sanitize
• sasa() : AnchoredDesign::filters , basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::sasa , mh::filter , sasa
• sasa_bur_cutoff : bur_nodon_tyr
• sasa_burial_cutoff : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• sasa_calculator_probe_radius : basic::options::OptionKeys::pose_metrics , pose_metrics
• sasa_score : extract_by_sidechain_sasa_score
• SASAfilter : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• save_all_pdbs : basic::options::OptionKeys::pepspec , pepspec
• SAVE_ARCHIVE : basic
• save_crash_report() : utility
• save_crash_report_to_console() : utility
• save_crash_report_to_file() : utility
• save_data : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• save_jump_histogram : basic::options::OptionKeys::rna::denovo::out , rna::denovo::out
• save_loops_only : basic::options::OptionKeys::canonical_sampling::sampling , canonical_sampling::sampling
• save_low_pdbs : basic::options::OptionKeys::pepspec , pepspec
• save_project() : ui::task
• save_score_terms : basic::options::OptionKeys::recces , recces
• save_sequences : basic::options::OptionKeys::coupled_moves , coupled_moves
• save_structures : basic::options::OptionKeys::coupled_moves , coupled_moves
• save_times : basic::options::OptionKeys::out , out
• save_top : basic::options::OptionKeys::remodel , remodel
• savend : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , kmeans_common
• saxs : basic::options::OptionKeys::score::saxs
• SAXS : basic
• saxs() : score::saxs
• SBin6D : numeric::geometry::hashing
• sbisect() : numeric::kinematic_closure
• sbyte : ObjexxFCL
• sc : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• sc_branch_rotamers : basic::options::OptionKeys::packing , packing
• sc_cst_maxdist : basic::options::OptionKeys::relax , relax
• sc_min() : antibody , basic::options::OptionKeys::antibody , basic::options::OptionKeys::casp , basic::options::OptionKeys::docking , casp , docking
• sc_min_only : basic::options::OptionKeys::ddg , ddg
• sc_min_res : basic::options::OptionKeys::docking , docking
• sc_only : basic::options::OptionKeys::hotspot , hotspot
• sc_prob() : backrub , basic::options::OptionKeys::backrub
• sc_prob_perturbcurrent : basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• sc_prob_uniform() : backrub , basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• sc_prob_withinrot() : backrub , basic::options::OptionKeys::backrub , basic::options::OptionKeys::canonical_sampling::probabilities , canonical_sampling::probabilities
• sc_sc_bump_cutoff : basic::options::OptionKeys::enzdes , enzdes
• sc_scaling : basic::options::OptionKeys::edensity , basic::options::OptionKeys::patterson , edensity , patterson
• sc_stats : basic::options::OptionKeys::orbitals , orbitals
• scaffold_active_site_residues : basic::options::OptionKeys::match , match
• scaffold_active_site_residues_for_geomcsts : basic::options::OptionKeys::match , match
• scaffold_epitope_residue_range : find_position_matches_using_inverse_rotamers
• scaffold_loop : basic::options::OptionKeys::AnchoredPDBCreator
• scaffold_pdb : basic::options::OptionKeys::AnchoredPDBCreator
• scalar_multiply() : PyMOL-Rosetta-relay-client , PyMOL-RosettaServer , pyrosetta.PyMOLRosettaServer
• scalar_product() : numeric
• scale : spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• scale_axes() : PyMOL-Rosetta-relay-client , PyMOL-RosettaServer , pyrosetta.PyMOLRosettaServer
• scale_d : basic::options::OptionKeys::optimization , optimization
• scale_normalmode_dampen : basic::options::OptionKeys::optimization , optimization
• scale_rb : basic::options::OptionKeys::optimization , optimization
• scale_rbangle : basic::options::OptionKeys::optimization , optimization
• scale_theta : basic::options::OptionKeys::optimization , optimization
• scan : basic::options::OptionKeys::magnesium , magnesium
• scan_chi() : beta_sc_scan
• scan_contact() : myspace
• scan_Evalue() : myspace
• scanning() : demo.D090_Ala_scan
• scanning_analysis() : demo.D090_Ala_scan
• scattach_res_files : basic::options::OptionKeys::smhybrid , smhybrid
• scientific_Fstring_of() : ObjexxFCL
• scientific_string_of() : ObjexxFCL
• scipy() : numeric::kinematic_closure
• scmin_cartesian : basic::options::OptionKeys::optimization , optimization
• scmin_nonideal : basic::options::OptionKeys::optimization , optimization
• scmove : basic::options::OptionKeys::rot_anl , rot_anl
• score() : AnchoredDesign::filters , basic::options::OptionKeys::AnchoredDesign::filters , basic::options::OptionKeys::corrections::score , basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::score , basic::options::OptionKeys::nmr::score , basic::options::OptionKeys::out::path , basic::options::OptionKeys::rigid , basic::options::OptionKeys::score
• SCORE : basic
• score() : corrections::score , create_a3b_hbs , erraser_single_res_analysis , legacy_score_vs_rmsd , mh::filter , mh::score , nmr::score , out::path , rigid , score , test.G100_Functions_Input , test.G205_Module_RegionalScoring , test.Workshop4test , test.Workshop8test , torsion_scoring
• score12prime : basic::options::OptionKeys::corrections::score , corrections::score
• score2 : test.Workshop4test
• score3 : test.Workshop4test
• score_across_chains_only : basic::options::OptionKeys::mh , mh
• score_analysis : test.G204_Module_ScoreAnalysis
• SCORE_BEGIN_NOTIFY : basic
• score_between_opposite_terminal_segments : basic::options::OptionKeys::legacy_sewing , basic::options::OptionKeys::sewing , legacy_sewing , sewing
• score_cut : basic::options::OptionKeys::magnesium , magnesium
• score_cut_fl : basic::options::OptionKeys::boinc , boinc
• score_cut_pct : basic::options::OptionKeys::boinc , boinc
• score_cut_PDB : basic::options::OptionKeys::magnesium , magnesium
• score_cut_smart_throttle : basic::options::OptionKeys::boinc , boinc
• score_cutoff : basic::options::OptionKeys::ddg , ddg
• score_diff_cut : basic::options::OptionKeys::cluster , basic::options::OptionKeys::stepwise::protein , cluster , stepwise::protein
• SCORE_DOT : basic
• SCORE_END_NOTIFY : basic
• score_ensemble() : evaluate_beta_mutants
• score_exclude_res : basic::options::OptionKeys::evaluation , evaluation
• score_file : SewAssembler
• score_file_name : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• score_filter : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• score_filter_cutoff : basic::options::OptionKeys::loops , loops
• SCORE_FINALIZE : basic
• score_function : basic::options::OptionKeys::dna::specificity , dna::specificity
• score_functions : run_backbone
• score_fxn : beta_nonlocal , beta_sc_scan , evaluate_beta_mutants , lactamize , oop_scan , orn_macrocycle , test_nu_angles , test_terpenes , torsion_scoring
• score_fxn_ : create_a3b_hbs
• score_fxn_cart_ : create_a3b_hbs
• SCORE_LONG_RANGE_ENERGIES : basic
• score_mem_path : basic::options::OptionKeys::ligand_evolution , ligand_evolution
• SCORE_NEIGHBOR_ENERGIES : basic
• SCORE_ONEBODY_ENERGIES : basic
• score_only : basic::options::OptionKeys::carbohydrates::glycopeptide_docking , basic::options::OptionKeys::out::file , basic::options::OptionKeys::run , carbohydrates::glycopeptide_docking , out::file , run
• score_output_silent : basic::options::OptionKeys::frags , frags
• score_pdbs : basic::options::OptionKeys::mh , mh
• score_pose_cutpoint_variants : basic::options::OptionKeys::score , score
• SCORE_SETUP : basic
• score_sliding_window_context : basic::options::OptionKeys::edensity , edensity
• score_sscore_maxloop : basic::options::OptionKeys::evaluation , evaluation
• score_sscore_short_helix : basic::options::OptionKeys::evaluation , evaluation
• score_symm_complex : basic::options::OptionKeys::edensity , edensity
• score_threshold : metapatch
• score_type : basic::options::OptionKeys::blivens , blivens
• score_types : test.T200_Scoring
• score_with_ligand_wts_function : basic::options::OptionKeys::motifs , motifs
• score_with_rmsd : basic::options::OptionKeys::evaluation , evaluation
• scorecut : basic::options::OptionKeys::out , out
• scored_frag_cycles : basic::options::OptionKeys::loops , loops
• scored_hydrogen_sampling : basic::options::OptionKeys::magnesium , magnesium
• scorefile : basic::options::OptionKeys::out::file , extract_by_sidechain_sasa_score , out::file
• scorefile_format : basic::options::OptionKeys::out::file , out::file
• scorefilter : basic::options::OptionKeys::chemically_conjugated_docking , chemically_conjugated_docking
• scorefxn : basic::options::OptionKeys::DisulfideInsertion , DisulfideInsertion , docking , oop_conformations , pna , PyMOL_demo , test.G101_Functions_Output , test.G205_Module_RegionalScoring , test.T150_PyMOL_Integration , test.T200_Scoring , test.T201_Scoring_pre_talaris , test.T250_Constraints , test.T400_Refinement , test.T500_Packing , test.T660_LoopBuilding , test.T800_ClassicRelax , test.T880_Other , test.Workshop3test , test.Workshop5test , test.Workshop6test , test.Workshop7test , vancomycin
• scorefxn0 : basic::options::OptionKeys::trRosetta , trRosetta
• scorefxn1 : basic::options::OptionKeys::trRosetta , trRosetta
• scorefxn2 : basic::options::OptionKeys::trRosetta , test.Workshop3test , trRosetta
• scorefxn3 : basic::options::OptionKeys::trRosetta , trRosetta
• scorefxn_fullatom : basic::options::OptionKeys::trRosetta , trRosetta
• scorefxn_high : demo.D060_Folding , docking , loops , loops_kic , test.T650_LoopsKIC , test.Workshop7test
• scorefxn_high_min : docking
• scorefxn_low : demo.D060_Folding , docking , loops , loops_kic , test.T650_LoopsKIC , test.Workshop7test
• scorefxn_no_hbond : oop_conformations
• scoremethod : b3a_distro
• ScorePoint : ui::viewers
• scores : basic::options::OptionKeys::mh::path , demo.D060_Folding , legacy_score_vs_rmsd , mh::path , score_vs_rmsd , score_vs_time
• scores_BB_BB : basic::options::OptionKeys::mh::path , mh::path
• scores_BB_PH : basic::options::OptionKeys::mh::path , mh::path
• scores_BB_PO : basic::options::OptionKeys::mh::path , mh::path
• scores_frags : basic::options::OptionKeys::mh::path , mh::path
• scores_PH_PO : basic::options::OptionKeys::mh::path , mh::path
• scores_SC_BB : basic::options::OptionKeys::mh::path , mh::path
• scores_SC_SC : basic::options::OptionKeys::mh::path , mh::path
• ScoreTypesRegistry : pyrosetta
• scoring : basic::options::OptionKeys::frags::scoring , basic::options::OptionKeys::mp::scoring , frags::scoring , mp::scoring
• scoring_mode : metapatch
• scpn() : numeric::kinematic_closure::radians , numeric::kinematic_closure
• scratch : basic::options::OptionKeys::out::path , out::path
• screening_job_file : basic::options::OptionKeys::in::file , in::file
• screening_list : basic::options::OptionKeys::in::file , in::file
• script : basic::options::OptionKeys::relax , relax
• script_max_accept : basic::options::OptionKeys::relax , relax
• script_vars : basic::options::OptionKeys::parser , parser
• sdf2mdl() : pyrosetta.toolbox.load_ligand
• sdf_directory_path : basic::options::OptionKeys::motifs , motifs
• se_choice_opt : utility::tag
• se_choice_req : utility::tag
• se_cutoff : sequence_recovery
• se_none : utility::tag
• se_ordered_sets : utility::tag
• se_repeatable : utility::tag
• se_single_opt : utility::tag
• se_single_req : utility::tag
• se_single_req_ordered : utility::tag
• sec() : numeric
• secmatch_Ecutoff : basic::options::OptionKeys::enzdes , enzdes
• secondary_residue_selector : test.T020_Pose_Bindings
• secondary_seqdep_refene_fname : basic::options::OptionKeys::score , score
• SECONDARY_STRUCTURE_ENERGY : basic
• secondary_structure_file : basic::options::OptionKeys::DenovoProteinDesign , DenovoProteinDesign
• SECONDARY_STRUCTURE_HSPAIR_ENERGY : basic
• SECONDARY_STRUCTURE_SHEETS_FROM_DIMERS_ENERGY : basic
• SECONDARY_STRUCTURE_SSPAIR_ENERGY : basic
• secret : PyMOL-Rosetta-relay-client
• secstruct : basic::options::OptionKeys::mp , basic::options::OptionKeys::rna::denovo , local , mp , rna::denovo
• secstruct_file : basic::options::OptionKeys::rna::denovo , rna::denovo
• secstruct_general : basic::options::OptionKeys::rna::denovo , rna::denovo
• secstruct_general_file : basic::options::OptionKeys::rna::denovo , rna::denovo
• secstruct_legacy : basic::options::OptionKeys::rna::denovo , rna::denovo
• section_pattern : make_comparison
• seed_ensemble : basic::options::OptionKeys::jd2 , jd2
• seed_ensemble_weights : basic::options::OptionKeys::jd2 , jd2
• seed_ensemble_weights_file : basic::options::OptionKeys::jd2 , jd2
• seed_offset : basic::options::OptionKeys::run , run
• seeds : basic::options::OptionKeys::cm , cm
• seg_string : basic::options::OptionKeys::lh , lh
• segment_ends : SewAppend
• segment_file : basic::options::OptionKeys::rdc , rdc
• segment_file_generatorCOP : apps::pilot::frankdt
• segment_file_generatorOP : apps::pilot::frankdt
• segment_scoring_mode : basic::options::OptionKeys::rdc , rdc
• segment_starts : SewAppend
• select_area() : add_xyz_to_pose
• select_best_loop_from : basic::options::OptionKeys::loops , loops
• select_structures_from_database : basic::options::OptionKeys::in , in
• selecting_rule : basic::options::OptionKeys::frags::picking , frags::picking
• selecting_scorefxn : basic::options::OptionKeys::frags::picking , frags::picking
• semiex_water_burial_cutoff : basic::options::OptionKeys::pose_metrics , pose_metrics
• send_char_to_node() : utility
• send_data_to_head_node() : basic::mpi
• send_double_to_node() : utility
• send_doubles_to_node() : utility
• send_integer_to_node() : utility
• send_integers_to_node() : utility
• send_size_to_node() : utility
• send_sizes_to_node() : utility
• send_string_to_node() : utility
• sentinel_t : detail
• sep : basic::options::OptionKeys::sc , test.T900_distributed
• sep_aa : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_aa1 : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_aa2 : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_bb_ss : basic::options::OptionKeys::in::rdf , in::rdf
• sep_bfac : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_dist : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_dssp : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_hb : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_lj : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_nbrs : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_ss : basic::options::OptionKeys::mh::harvest , mh::harvest
• sep_switch_accelerate : basic::options::OptionKeys::jumps , jumps
• separate_db_per_mpi_process : basic::options::OptionKeys::inout::dbms , inout::dbms
• seq : basic::options::OptionKeys::in::file , beta_sc_scan , in::file , PyMOL_demo , test.T850_SubClassing
• seq1 : basic::options::OptionKeys::recces , recces
• seq2 : basic::options::OptionKeys::recces , recces
• seq_align : basic::options::OptionKeys::pepspec , pepspec
• seq_design_cdrs() : antibody::design , basic::options::OptionKeys::antibody::design
• seq_design_profile_samples() : antibody::design , basic::options::OptionKeys::antibody::design
• seq_design_stats_cutoff() : antibody::design , basic::options::OptionKeys::antibody::design
• seq_mover : test.Workshop5test
• seq_rebuild() : erraser_wrapper
• seq_rebuild_new() : erraser_wrapper
• seq_recov_filename : sequence_recovery
• seq_score : basic::options::OptionKeys::cm , cm
• seq_sep_stages : basic::options::OptionKeys::fold_cst , fold_cst
• seqdep_refene_fname : basic::options::OptionKeys::score , score
• seqmover : test.T400_Refinement
• seqsep : basic::options::OptionKeys::mh::filter , mh::filter , ncontact
• seqsep_tol : chrisk
• seqsim_E : basic::options::OptionKeys::frags , frags
• seqsim_H : basic::options::OptionKeys::frags , frags
• seqsim_L : basic::options::OptionKeys::frags , frags
• sequence : basic::options::OptionKeys::relax , basic::options::OptionKeys::rna::denovo , demo.D060_Folding , relax , rna::denovo
• SEQUENCE_COMPARISON : basic
• sequence_distance_minimum : test.T020_Pose_Bindings
• sequence_file : basic::options::OptionKeys::cyclic_peptide , basic::options::OptionKeys::helical_bundle_predict , basic::options::OptionKeys::relax , cyclic_peptide , helical_bundle_predict , relax
• sequence_match_position : usec
• sequence_match_sequence : usec
• sequence_recovery : basic::options::OptionKeys::mh , mh
• sequence_separation : basic::options::OptionKeys::rigid , rigid
• sequence_symmetric_annealer : basic::options::OptionKeys::packing , packing
• sequential : basic::options::OptionKeys::casp , casp , utility::keys
• sequential_mpi_job_distribution : basic::options::OptionKeys::jd2 , jd2
• serialize() : numeric
• server_base_url() : ui::task
• server_port : basic::options::OptionKeys::rbe , rbe
• server_url : basic::options::OptionKeys::rbe , rbe , ui::task
• SESSION : helpers
• sessionCOP : utility::sql_database
• sessionOP : utility::sql_database
• Set() : pyrosetta
• set_add_on_binder() : rosetta_binders
• set_add_on_binder_maybe_has_insertion_operator() : rosetta_binders
• set_anchor_at_closest_point : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• set_application_name() : utility
• set_atom_properties : basic::options::OptionKeys::chemical , chemical
• set_atomic_charge : basic::options::OptionKeys::chemical , chemical
• set_boolean_option() : basic::options
• set_boolean_vector_option() : basic::options
• set_cache_size() : basic::database
• set_cereal_pickleable() : pyrosetta.distributed.utility.pickle
• set_file_option() : basic::options
• set_file_vector_option() : basic::options
• set_integer_option() : basic::options
• set_integer_vector_option() : basic::options
• set_logging_handler : pyrosetta.tests.bindings.core.test_pose , pyrosetta.tests.distributed.test_concurrency , test.T121_core
• set_logging_sink() : pyrosetta.logging_support
• set_lores_weights : basic::options::OptionKeys::rna::denovo , rna::denovo
• set_main_exit_callback() : utility
• set_option() : basic::options
• set_options_string() : utility
• set_origin : basic::options::OptionKeys::fingerprint , fingerprint
• set_patch_atomic_charge : basic::options::OptionKeys::chemical , chemical
• set_path_option() : basic::options
• set_path_vector_option() : basic::options
• set_pdb_author : basic::options::OptionKeys::out::file , out::file
• set_pdb_viewer_path() : ui::config
• set_pddf_filter : basic::options::OptionKeys::filters , filters
• set_protein_esp_to_zero : basic::options::OptionKeys::fingerprint , fingerprint
• set_real_option() : basic::options
• set_real_vector_option() : basic::options
• set_saxs_filter : basic::options::OptionKeys::filters , filters
• set_segment : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• set_show_crash_report_on_console() : utility
• set_special_torsion_params : basic::options::OptionKeys::corrections::genpotential , corrections::genpotential
• set_spectrum() : PyMOL-Rosetta-relay-client , PyMOL-RosettaServer , pyrosetta.PyMOLRosettaServer
• set_std_string_std_less_std_string_std_allocator_std_string_t : pyrosetta
• set_string_option() : basic::options
• set_string_vector_option() : basic::options
• set_surface_esp_to_zero : basic::options::OptionKeys::fingerprint , fingerprint
• set_tm_helical : basic::options::OptionKeys::relax::range , relax::range
• set_torsion_params : basic::options::OptionKeys::corrections::genpotential , corrections::genpotential
• set_up_movemap() : beta_sc_scan
• set_user_credentials() : ui::config
• set_weights : basic::options::OptionKeys::score , score
• setPoseExtraScore() : pyrosetta.bindings.warnings
• setup : basic::options::OptionKeys::broker , basic::options::OptionKeys::mp::setup , broker , mp::setup
• setup_base_pair_constraints : basic::options::OptionKeys::recces::thermal_sampling , recces::thermal_sampling
• setup_file_and_dir_names() : general_RNP_setup_script
• setup_hook() : execute , kic_runner , run_backbone , run_sidechain
• setup_job() : DRRAFTER
• SETUP_NBLIST : basic
• setup_next_round() : drrafter_rna
• setup_out_dir() : submit_jobs
• setup_package() : setup
• setup_packer() : myspace
• setup_pert_foldtree() : hbs_creator
• setup_source_directory_links() : build
• setup_tag2string() : basic
• setup_target_logger() : pyrosetta.distributed.cluster.logging_support
• setup_target_logging() : pyrosetta.distributed.cluster.logging_support
• setup_worker_logging() : pyrosetta.distributed.cluster.logging_support
• sewing : basic::options::OptionKeys::sewing , sewing
• sf : basic::options::OptionKeys::out , out , test.Workshop9test
• sf_new : test.T850_SubClassing , test.T860_SubClassing_EnergyMethods , test.T870_SubClassing_EnergyMethods2
• sformat_idxof() : numeric::random
• sfxn : test.T120_core , test.T150_core , test.T220_AtomAtomPairEnergies
• shap_dun10_dir : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_dun10_enable : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_dun10_smooth_level : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_dun10_use_minus_log_P_ignore_P : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_p_aa_pp : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_p_aa_pp_enable : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_p_aa_pp_smooth_level : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_rama_enable : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_rama_map : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_rama_nogridshift : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shap_rama_smooth_level : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shapovalov_lib : basic::options::OptionKeys::corrections::shapovalov_lib , corrections::shapovalov_lib
• shapovalov_lib_fixes_enable : basic::options::OptionKeys::corrections , corrections
• shared_style : styles.rama
• shear_mover : test.Workshop5test
• shear_moves : basic::options::OptionKeys::docking::ligand , docking::ligand , local
• shear_on : basic::options::OptionKeys::FloppyTail , basic::options::OptionKeys , FloppyTail
• shearmover : test.T400_Refinement
• shearmoves : demo.D070_Refinement
• sheets : basic::options::OptionKeys::jumps , jumps
• shell : app_runner , kic_runner
• shell_radius : basic::options::OptionKeys::mp::lipid_acc , mp::lipid_acc
• shit_stat_altpos : clean_pdb_keep_ligand
• shit_stat_insres : clean_pdb_keep_ligand
• shit_stat_misdns : clean_pdb_keep_ligand
• shit_stat_modres : clean_pdb_keep_ligand
• sho_cutoff : basic::options::OptionKeys::pose_metrics::shobuns , pose_metrics::shobuns
• shobuns : basic::options::OptionKeys::pose_metrics::shobuns , pose_metrics::shobuns
• short : options_will
• short_frag_cycles : basic::options::OptionKeys::loops , loops
• short_frag_filename : demo.D060_Folding
• short_frag_length : demo.D060_Folding
• short_inserts : demo.D060_Folding
• short_of() : ObjexxFCL
• short_residence_time_mode : basic::options::OptionKeys::hydrate , hydrate
• short_tail : basic::options::OptionKeys::FloppyTail::short_tail , FloppyTail::short_tail
• short_tail_fraction : basic::options::OptionKeys::FloppyTail::short_tail , basic::options::OptionKeys , FloppyTail::short_tail
• short_tail_off : basic::options::OptionKeys::FloppyTail::short_tail , basic::options::OptionKeys , FloppyTail::short_tail
• short_to_long : amino_acids
• shorten_long_terminal_loop : basic::options::OptionKeys::loops , loops
• shorter_interval_case() : detail::dragonbox
• show_accessed_options : basic::options::OptionKeys::out , out
• show_accessed_options_T() : utility::options
• show_all_fixes : basic::options::OptionKeys::in , in
• show_bb_table() : kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_bb_dependent_rotlib , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• show_crash_report_on_console_ : utility
• show_derivatives_check : basic::options::OptionKeys::hydrate , hydrate
• show_etable_contributions : basic::options::OptionKeys::score , score
• show_extended() : AnchoredDesign , basic::options::OptionKeys::AnchoredDesign
• show_info : basic::options::OptionKeys::nmr::pcs , basic::options::OptionKeys::nmr::pre , basic::options::OptionKeys::nmr::rdc , nmr::pcs , nmr::pre , nmr::rdc
• show_pre_filtered_water_rotamers_count : basic::options::OptionKeys::hydrate , hydrate
• show_pre_post_filter_water_rotamers : basic::options::OptionKeys::hydrate , hydrate
• show_residues_near_water : basic::options::OptionKeys::hydrate , hydrate
• show_rotamer_count : basic::options::OptionKeys::hydrate , hydrate
• show_simulation_in_pymol : basic::options::OptionKeys::run , run
• show_time() : basic
• show_time_on_cerr : basic
• show_unused_options : basic::options::OptionKeys::out , out
• show_unused_options_T() : utility::options
• show_virtual_residues : basic::options::OptionKeys::view , view
• SHRINK_FACTOR : basic
• shrink_pos_step : basic::options::OptionKeys::templates , templates
• shrink_step : basic::options::OptionKeys::templates , templates
• shuffle : basic::options::OptionKeys::run , run
• shuffle_nstruct : basic::options::OptionKeys::out , out
• shuffle_screening_jobs : basic::options::OptionKeys::in::file , in::file
• sicdock : basic::options::OptionKeys::sicdock , sicdock
• side_length : test.Workshop9test
• sidechain_buried : basic::options::OptionKeys::score , score
• sidechain_exposed : basic::options::OptionKeys::score , score
• sidechain_isopeptide_indices : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• sidechain_only : basic::options::OptionKeys::pb_potential , pb_potential
• SIDECHAINMCMOVER : basic
• SIDECHAINMOVER : basic
• sigma : erraser_analysis , spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib
• sigmoid_cs_A : basic::options::OptionKeys::frags , frags
• sigmoid_cs_B : basic::options::OptionKeys::frags , frags
• sign() : numeric::linear_algebra , numeric , ObjexxFCL
• sign_transfered() : numeric
• signal_handler() : utility
• significant_residues_for_motifs : basic::options::OptionKeys::motifs , motifs
• silent : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , basic::options::OptionKeys::resample , basic::options , in::file , out::file , resample
• silent1 : basic::options::OptionKeys::stepwise , stepwise
• silent2 : basic::options::OptionKeys::stepwise , stepwise
• silent_energy_cut : basic::options::OptionKeys::in::file , in::file
• SILENT_FILL_POSE : basic
• SILENT_FILL_STRUCT : basic
• silent_gz : basic::options::OptionKeys::out , out
• silent_list : basic::options::OptionKeys::in::file , in::file
• silent_output : basic::options::OptionKeys::cluster::energy_based_clustering , cluster::energy_based_clustering
• silent_preserve_H : basic::options::OptionKeys::out::file , out::file
• silent_print_all_score_headers : basic::options::OptionKeys::out::file , out::file
• SILENT_READ_TAG_TEST : basic
• silent_read_through_errors : basic::options::OptionKeys::in::file , in::file
• silent_renumber : basic::options::OptionKeys::in::file , in::file
• silent_score_prefix : basic::options::OptionKeys::in::file , in::file
• silent_scores_wanted : basic::options::OptionKeys::in::file , in::file
• silent_select_random : basic::options::OptionKeys::in::file , in::file
• silent_select_range_len : basic::options::OptionKeys::in::file , in::file
• silent_select_range_mul : basic::options::OptionKeys::in::file , in::file
• silent_select_range_start : basic::options::OptionKeys::in::file , in::file
• SILENT_SET_POSE_COORDS : basic
• silent_struct_type : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , in::file , out::file
• sim_replace_obj : basic::options::OptionKeys::lh , lh
• SIMANNEALING : basic
• similarity_cut : basic::options::OptionKeys::cm , cm
• similarity_limit : basic::options::OptionKeys::cm , cm
• similarity_measure : basic::options::OptionKeys::lh , lh
• similarity_method : basic::options::OptionKeys::lh , lh
• similarity_reference : basic::options::OptionKeys::lh , lh
• similarity_tolerance : basic::options::OptionKeys::lh , lh
• simple_append_map : basic::options::OptionKeys::stepwise::rna , stepwise::rna
• simple_metrics : basic::options::OptionKeys::simple_metrics , simple_metrics
• simple_print : HelicalAssembly
• simple_relax : basic::options::OptionKeys::rna::denovo , rna::denovo
• SimpleCstMoverCOP : protocols::moves
• SimpleCstMoverOP : protocols::moves
• SimpleInterpolatorCOP : numeric::interpolation::spline
• SimpleInterpolatorOP : numeric::interpolation::spline
• SIMPLEINTGRAPH : basic
• SimpleTokenCOP : numeric::expression_parser
• SimpleTokenOP : numeric::expression_parser
• simplify_std_class_name() : binder
• simplify_std_class_name_raw() : binder
• simulate_mpi_message_type : utility
• SimulateMPIMessageCOP : utility
• SimulateMPIMessageOP : utility
• simultaneous_cycles : basic::options::OptionKeys::remodel::RemodelLoopMover , remodel::RemodelLoopMover
• sin_cos_range() : numeric
• sin_of() : numeric
• sinc() : numeric::statistics
• sincos() : numeric::kinematic_closure::radians , numeric::kinematic_closure
• SINFXN() : numeric::crick_equations
• single_away_rotamer : basic::options::OptionKeys::hydrate , hydrate
• single_chain : basic::options::OptionKeys::frags::nonlocal , frags::nonlocal
• single_glycan_color : basic::options::OptionKeys::view , view
• single_line_arrays : utility::json_spirit
• single_loop_ensemble_size : basic::options::OptionKeys::enzdes , enzdes
• singleton : test.T150_core
• sinh_taylor() : numeric::statistics
• SixDCoordinateBinnerCOP : numeric::geometry::hashing
• SixDCoordinateBinnerOP : numeric::geometry::hashing
• size : amino_acids
• Size : numeric::random , numeric
• size() : ObjexxFCL
• Size : platform
• size : subloop_histogram
• Size3 : numeric::geometry::hashing
• Size4 : numeric::geometry::hashing
• Size6 : numeric::geometry::hashing
• sized() : ObjexxFCL
• skim_size : basic::options::OptionKeys::lh , lh
• skip : basic::options::OptionKeys::rescore , kmeans_adaptive_kernel_density_bb_dependent_rotlib , kmeans_common , ObjexxFCL::format , rescore , score_vs_rmsd , utility::io
• skip_1mers : basic::options::OptionKeys::loops , loops
• skip_3mers : basic::options::OptionKeys::loops , loops
• skip_9mers : basic::options::OptionKeys::loops , loops
• skip_align : basic::options::OptionKeys::cluster , cluster
• skip_bulge_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• skip_ccd_moves : basic::options::OptionKeys::loops , loops
• skip_clash_check : drrafter_rna
• skip_classic_cart_setup : basic::options::OptionKeys::in , in
• skip_connect_info : basic::options::OptionKeys::inout , inout
• skip_convergence_check() : abinitio , basic::options::OptionKeys::abinitio
• skip_coord_constraints : basic::options::OptionKeys::rna::denovo::minimize , basic::options::OptionKeys::stepwise::protein , rna::denovo::minimize , stepwise::protein
• skip_deletions : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• skip_failed_simulations : basic::options::OptionKeys::in::file , in::file
• skip_filters : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• skip_fragment_moves : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• skip_initial_loop_build : basic::options::OptionKeys::loops , loops
• skip_loop_generation : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• skip_minimize : basic::options::OptionKeys::rna::erraser , basic::options::OptionKeys::stepwise , rna::erraser , stepwise
• skip_modeling : basic::options::OptionKeys::tcrmodel , tcrmodel
• skip_new_cart_setup : basic::options::OptionKeys::in , in
• skip_o2prime_trials : basic::options::OptionKeys::rna::denovo::minimize , rna::denovo::minimize
• skip_on_noviolation_in_stage1 : basic::options::OptionKeys::fold_cst , fold_cst
• skip_pack_and_min : basic::options::OptionKeys::PDB_diagnostic , PDB_diagnostic
• skip_partial : basic::options::OptionKeys::remodel::design , remodel::design
• skip_preminimize : basic::options::OptionKeys::stepwise , stepwise
• skip_rb_moves : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• skip_redundant : basic::options::OptionKeys::constraints , constraints
• skip_redundant_width : basic::options::OptionKeys::constraints , constraints
• skip_refinement : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• skip_relax : basic::options::OptionKeys::cp , basic::options::OptionKeys::relax::range , cp , relax::range
• skip_repack : basic::options::OptionKeys::partial_thread , partial_thread
• skip_seqshift_moves : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• skip_set_reasonable_fold_tree : basic::options::OptionKeys::run , run
• skip_sitegraft_repack : devel::metal_interface , local
• skip_stage2 : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• skip_stages() : abinitio , basic::options::OptionKeys::abinitio
• skip_zero_isc : basic::options::OptionKeys::peptide_deriver , peptide_deriver
• skipl : numeric::kinematic_closure
• skipping : binder
• slice_1base_indicies() : pyrosetta.bindings.utility
• slice_res1 : basic::options::OptionKeys::stepwise , stepwise
• slice_res2 : basic::options::OptionKeys::stepwise , stepwise
• slice_width : basic::options::OptionKeys::mp::lipid_acc , mp::lipid_acc
• sliced2orig_merge_back() : erraser_util
• slid : test.Workshop7test
• slide : test.Workshop7test
• slide_contact_frequency : basic::options::OptionKeys::fold_and_dock , fold_and_dock
• slide_criteria_type : make_symmdef_file_denovo
• slide_criteria_val : make_symmdef_file_denovo
• slide_glycan_into_contact : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• slide_into_contact : docking , test.T600_Docking
• slide_order : make_symmdef_file_denovo
• slide_threshold : basic::options::OptionKeys::mp::dock , mp::dock
• slide_type : make_symmdef_file_denovo
• SlideIntoContact : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• sliding_window : basic::options::OptionKeys::edensity , edensity
• sliding_window_wt : basic::options::OptionKeys::edensity , edensity
• slurp() : utility
• sm_prob() : backrub , basic::options::OptionKeys::backrub
• small_cycles : basic::options::OptionKeys::rigid , rigid
• small_division_by_pow10() : detail::dragonbox
• small_docking_moves : basic::options::OptionKeys::rna::denovo , rna::denovo
• small_frag_insertion_weight : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• small_frag_mover_stage1_weight : basic::options::OptionKeys::broker , broker
• small_mover : test.Workshop5test
• small_moves : basic::options::OptionKeys::remodel::staged_sampling , local , remodel::staged_sampling
• small_tor_mover : pna
• small_vector0 : utility
• small_vector1 : utility
• smallest_ring_size() : utility::graph
• smallmover : test.T400_Refinement
• smallmoves : demo.D070_Refinement
• smart_annealer : basic::options::OptionKeys::packing , packing
• smart_annealer_cutoff : basic::options::OptionKeys::packing , packing
• smart_annealer_disable_during_quench : basic::options::OptionKeys::packing , packing
• smart_annealer_model : basic::options::OptionKeys::packing , packing
• smart_annealer_pick_again : basic::options::OptionKeys::packing , packing
• smart_int : execute , run_backbone , run_sidechain
• SmartSEWINGTesterCOP : apps::pilot::frankdt
• SmartSEWINGTesterOP : apps::pilot::frankdt
• smhybrid : basic::options::OptionKeys::smhybrid , smhybrid
• smiles_file : basic::options::OptionKeys::ligand_evolution , ligand_evolution
• smooth_cycles_only() : abinitio , basic::options::OptionKeys::abinitio
• smooth_fa_elec : basic::options::OptionKeys::score , score
• smooth_move_frac : basic::options::OptionKeys::membrane , membrane
• smoothing_factor : basic::options::OptionKeys::mh::harvest , mh::harvest
• smove_angle_range : basic::options::OptionKeys::flexPepDocking , flexPepDocking
• smpi_char : utility
• smpi_double : utility
• smpi_doubles : utility
• smpi_integer : utility
• smpi_integers : utility
• smpi_size : utility
• smpi_sizes : utility
• smpi_string : utility
• snprintf_float() : detail
• snprintf_float< double >() : detail
• snprintf_float< long double >() : detail
• snug_loops() : antibody , basic::options::OptionKeys::antibody
• snugfit() : antibody , basic::options::OptionKeys::antibody
• soft_clash : basic::options::OptionKeys::carbohydrates::clash_check , carbohydrates::clash_check
• soft_design : basic::options::OptionKeys::msd
• soft_rep : basic::options::OptionKeys::dna::specificity , basic::options::OptionKeys::docking::ligand , dna::specificity , docking::ligand
• soft_rep_design : basic::options::OptionKeys::packing , packing
• soft_wts : basic::options::OptionKeys::pepspec , basic::options::OptionKeys::score , pepspec , score
• sog_cst_param : basic::options::OptionKeys::constraints , constraints
• sog_upper_bound : basic::options::OptionKeys::constraints , constraints
• solid_capstyle : subloop_histogram
• solutions : closure_error , explosion_error
• solv : test.T220_AtomAtomPairEnergies
• solv_total : test.T220_AtomAtomPairEnergies
• solv_unsat_calc : byres_data
• solvate : byres_data
• solve_sturm() : numeric::kinematic_closure
• solvent_exposure : basic::options::OptionKeys::solvent_exposure , solvent_exposure
• SolverType : numeric::kinematic_closure
• some_storage : test.T860_SubClassing_EnergyMethods
• sort_groups_by_energy : basic::options::OptionKeys::cluster , cluster
• sort_groups_by_size : basic::options::OptionKeys::cluster , cluster
• SORT_POOL : basic
• sort_PoseWithScore() : protocols::abinitio
• source_structure_residues : pyrosetta.tests.protocols.indexed_structure_store.data
• source_suffix : conf
• sources : pilot_app_settings
• SPACE() : ObjexxFCL::format
• space() : ObjexxFCL::format
• SPACE() : ObjexxFCL
• space() : ObjexxFCL , sign
• space_fill_cutoff_differential_score_sub : basic::options::OptionKeys::motifs , motifs
• space_fill_cutoff_score : basic::options::OptionKeys::motifs , motifs
• space_fill_cutoff_score_sub : basic::options::OptionKeys::motifs , motifs
• spacing : basic::options::OptionKeys::mp::visualize , mp::visualize
• span1 : basic::options::OptionKeys::mp::setup , mp::setup
• span2 : basic::options::OptionKeys::mp::setup , mp::setup
• spanfile : basic::options::OptionKeys::in::file , in::file
• spanfiles : basic::options::OptionKeys::mp::setup , mp::setup
• spanning : basic::options::OptionKeys::mp , mp
• spans_from_structure : basic::options::OptionKeys::mp::setup , mp::setup
• sparse_pdb_output : basic::options::OptionKeys::dna::design , dna::design
• sparta_dir : basic::options::OptionKeys::evaluation , evaluation
• spearman_r() : numeric::statistics
• spec_profile : basic::options::OptionKeys::mean_field , mean_field
• special_rotweight : basic::options::OptionKeys::motifs , motifs
• species : basic::options::OptionKeys::enzymes , enzymes
• specific_build_position : basic::options::OptionKeys::motifs , motifs
• specificity : basic::options::OptionKeys::dna::design::specificity , basic::options::OptionKeys::dna::specificity , dna::design::specificity , dna::specificity
• spherical_to_xyz() : numeric
• spherical_wave : basic::options::OptionKeys::relax::range , relax::range
• spin : basic::options::OptionKeys::docking , docking , test.T600_Docking
• spine_x : basic::options::OptionKeys::frags , frags
• spinlabel : basic::options::OptionKeys::nmr::spinlabel , nmr::spinlabel
• spline_from_file() : numeric::interpolation
• spline_from_stream() : numeric::interpolation
• spline_interpolate() : numeric::interpolation::spline
• spline_second_derivative() : numeric::interpolation::spline
• SplineFromStreamMode : numeric::interpolation
• split() : binder , utility
• split_by_newlines() : utility
• split_in_two() : binder
• split_socket_address() : pyrosetta.distributed.cluster.logging_filters
• split_to_list() : utility
• split_to_set() : utility
• split_unfolded_energies_atom_type : basic::options::OptionKeys::unfolded_state , unfolded_state
• split_unfolded_energies_file : basic::options::OptionKeys::unfolded_state , unfolded_state
• split_whitespace() : utility
• splitwork : basic::options::OptionKeys::willmatch , willmatch
• spread : basic::options::OptionKeys::loops , loops
• spread_ss_element : basic::options::OptionKeys::mh::score , mh::score
• sq_vec_distance() : numeric::kdtree
• sql : test.G203_Module_SQLPDB
• sqlite_url : job_manager
• sqr() : numeric::interpolation::spline , numeric::statistics
• sqrt_2pi : numeric::constants::d , numeric::constants::f , numeric::constants::ld , numeric::constants::r
• sqrt_pssm : basic::options::OptionKeys::optE , optE
• square() : numeric , ObjexxFCL , test.Workshop9test
• square_planar_metal_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_planar_metal_positions : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_planar_metal_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_pyramidal_metal_constraints_energy_filter_multiplier : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_pyramidal_metal_positions : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_pyramidal_metal_sidechain_distance_filter_multiplier : basic::options::OptionKeys::cyclic_peptide , cyclic_peptide
• square_score : basic::options::OptionKeys::fingerprint , fingerprint
• SquarerootExpressionCOP : numeric::expression_parser
• SquarerootExpressionOP : numeric::expression_parser
• SRange : ObjexxFCL
• src_chain : basic::options::OptionKeys::threadsc , threadsc
• src_first_resid : basic::options::OptionKeys::threadsc , threadsc
• srlz : basic::options::OptionKeys::in::file , basic::options::OptionKeys::out::file , in::file , out::file
• srlz_override : basic::options::OptionKeys::in::file , in::file
• ss : basic::options::OptionKeys::mh::match , basic::options::OptionKeys::ufv , challenge , mh::match
• SS() : ObjexxFCL::format
• ss() : ufv
• ss1 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match , mh::filter , mh::match
• ss2 : basic::options::OptionKeys::mh::filter , basic::options::OptionKeys::mh::match , mh::filter , mh::match
• ss_pair : basic::options::OptionKeys::remodel , remodel
• ss_pred : basic::options::OptionKeys::frags , frags
• ss_type : basic::options::OptionKeys::pepspec , pepspec
• SSize : numeric , ObjexxFCL , platform
• SSrbrelax : basic::options::OptionKeys::SSrbrelax , SSrbrelax
• st_weights : basic::options::OptionKeys::recces , recces
• stack_elec_sigmoidal_die : basic::options::OptionKeys::score , score
• stacklevel : rosetta
• stage1 : basic::options::OptionKeys::resample
• STAGE1 : basic
• stage1() : resample
• stage1_1_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_2_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_3_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_4_cenrot_score : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_4_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_increase_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_patch() : abinitio , basic::options::OptionKeys::abinitio
• stage1_perturb_glycan_com_rot_mag : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage1_perturb_glycan_com_trans_mag : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage1_probability : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage1_ramp_cst_cycle_factor : basic::options::OptionKeys::fold_cst , fold_cst
• stage1_ramp_cycles : basic::options::OptionKeys::relax , relax
• stage1_ramp_inner_cycles : basic::options::OptionKeys::relax , relax
• stage1_rotate_glycan_about_com : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage1_torsion_uniform_pert_mag : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage2 : basic::options::OptionKeys::resample
• STAGE2 : basic
• stage2() : resample
• stage2_constraint_threshold : basic::options::OptionKeys::fold_cst , fold_cst
• stage2_cycles : basic::options::OptionKeys::relax , relax
• stage2_increase_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage2_patch() : abinitio , basic::options::OptionKeys::abinitio
• stage2_repack_period : basic::options::OptionKeys::relax , relax
• stage2_rot_mag : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage2_temperature : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• stage2_trans_mag : basic::options::OptionKeys::carbohydrates::glycan_dock , carbohydrates::glycan_dock
• stage2min_increase_cycles : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• STAGE3 : basic
• stage3_cycles : basic::options::OptionKeys::relax , relax
• stage3a_patch() : abinitio , basic::options::OptionKeys::abinitio
• stage3b_patch() : abinitio , basic::options::OptionKeys::abinitio
• STAGE4 : basic
• stage4_patch() : abinitio , basic::options::OptionKeys::abinitio
• STAGE5 : basic
• stage5_patch() : abinitio , basic::options::OptionKeys::abinitio
• staged_constraints : basic::options::OptionKeys::rna::denovo , rna::denovo
• staged_sampling : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• stages : basic::options::OptionKeys::rigid , rigid
• standard : basic::options
• standard_bb_stdev : basic::options::OptionKeys::recces::thermal_sampling , recces::thermal_sampling
• standard_name() : binder
• standard_name_raw() : binder
• standard_packer_task() : pyrosetta
• standard_task_factory() : pyrosetta
• star() : abinitio::star , basic::options::OptionKeys::abinitio::star , ObjexxFCL
• start : basic::options::OptionKeys::cutoutdomain , cutoutdomain , test.Workshop5test
• start_clock : basic
• start_cys : ss_loop_builder
• start_file() : basic::options
• start_files() : basic::options
• start_from : basic::options::OptionKeys::docking::ligand , docking::ligand
• start_from_random_rb_conf : basic::options::OptionKeys::enzdes , enzdes
• start_min_score : erraser_single_res_analysis
• start_models_only : basic::options::OptionKeys::cm , cm
• start_native() : abinitio , basic::options::OptionKeys::abinitio
• start_res : indel
• START_rna_validate_data : erraser_analysis
• start_rosetta_server() : PyMOL-Rosetta-relay-client , PyMOL-RosettaServer , pyrosetta.PyMOLRosettaServer
• start_time : rna_rosetta_ready_set , rna_rosetta_to_pdb
• start_udp_server() : pyrosetta.network.rosetta_udp_to_tcp_bridge
• start_udp_to_tcp_bridge_daemon() : pyrosetta.network.rosetta_udp_to_tcp_bridge
• start_w_ideal_helices : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• start_weight : rpb
• starting_model : basic::options::OptionKeys::legacy_sewing , legacy_sewing
• starting_non_canonical : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• starting_p : docking , loops , loops_kic , test.T600_Docking , test.T650_LoopsKIC
• starting_p_centroid : docking , loops , loops_kic , test.T650_LoopsKIC
• starting_pdb : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling , SewAppend , SewAssembler
• starting_pose : test.Workshop7test
• starting_refEs : basic::options::OptionKeys::optE , optE
• starting_sequence : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• starting_template : basic::options::OptionKeys::cm::hybridize , cm::hybridize
• StartRosettaThread() : nacl_rosetta
• startswith() : utility
• std_dev() : numeric::statistics
• std_dev_with_provided_mean() : numeric::statistics
• std_exit_wrapper() : utility::options
• std_IO_exit_error_code : basic::options::OptionKeys::out , out
• stdev() : myspace
• stdout : build
• stdout_is_tty() : utility
• steal_3mers() : abinitio , basic::options::OptionKeys::abinitio
• steal_9mers() : abinitio , basic::options::OptionKeys::abinitio
• steal_extra_residues : basic::options::OptionKeys::cm , cm
• stealfrags : basic::options::OptionKeys::loops , loops
• stealfrags_times : basic::options::OptionKeys::loops , loops
• steepness : basic::options::OptionKeys::mp , mp
• stem_optimize() : antibody , basic::options::OptionKeys::antibody
• stem_optimize_size() : antibody , basic::options::OptionKeys::antibody
• step : test_mm_lj
• steps : correlation_time
• stepwise : basic::options::OptionKeys::stepwise , stepwise
• steric_fusion_scanCOP : apps::pilot::frankdt
• steric_fusion_scanOP : apps::pilot::frankdt
• store_name : basic::options::OptionKeys::indexed_structure_store , indexed_structure_store
• store_segment_motif_match() : apps::pilot::frankdt
• str : auto-DRRAFTER_setup , auto-DRRAFTER_setup_next_round , combine_pdbs , DRRAFTER , drrafter_rna , enumerate_junctions , finalize_models , find_lowest_scoring_relaxed_struct , general_RNP_setup_script , get_final_ddG_scores , get_lowest_scoring_relaxed_models , pyrosetta.distributed.cluster.config , pyrosetta.distributed.cluster , pyrosetta.distributed.cluster.worker_plugins , pyrosetta.tests.distributed.cluster.print_discovered_test_cases , pyrosetta.tests.distributed.test_dask , relax_starting_structure , setup_for_complex_scoring_general
• str_dn() : ObjexxFCL
• str_dncase() : ObjexxFCL
• str_to_packed() : pyrosetta.distributed.packed_pose.core
• str_to_pose() : pyrosetta.distributed.packed_pose.core
• str_type : utility::json_spirit
• str_up() : ObjexxFCL
• str_upcase() : ObjexxFCL
• strand_assembly : basic::options::OptionKeys::strand_assembly , strand_assembly
• strand_constraint : basic::options::OptionKeys::templates , templates
• strand_movement_params : basic::options::OptionKeys::RBSegmentRelax , RBSegmentRelax
• strand_pair_weight : basic::options::OptionKeys::mh::score , mh::score
• StrategyFiltered : zlib_stream
• StrategyHuffmanOnly : zlib_stream
• strftime() : detail
• strict_loops : basic::options::OptionKeys::loops , loops
• strict_ss_changes : local
• stride : basic::options::OptionKeys::dump_trajectory , dump_trajectory
• string2float() : utility
• string2int() : utility
• string2Real() : utility
• string2Size() : utility
• string2uint() : utility
• string_contains_gt_lt_or_ampersand() : utility::tag
• string_of() : ObjexxFCL
• STRING_OPTION : utility::options
• string_split() : utility
• string_split_multi_delim() : utility
• string_split_simple() : utility
• string_to_sha1() : utility
• string_vector_from_char_vector() : utility
• STRING_VECTOR_OPTION : utility::options
• stringafteroption() : basic::options
• StringOption : basic::options
• StringOptionKey : basic::options
• StringResourceStreamCOP : basic::resource_manager::locator
• StringResourceStreamOP : basic::resource_manager::locator
• stringstream_add_on_binder() : rosetta_binders
• StringVectorOption : basic::options
• StringVectorOptionKey : basic::options
• strip() : ObjexxFCL , utility
• strip_whitespace() : ObjexxFCL
• stripped() : ObjexxFCL
• stripped_whitespace() : ObjexxFCL
• StrongReal : utility
• StrongSize : utility
• struct_ids : basic::options::OptionKeys::in::dbms , in::dbms
• structural_similarity : basic::options::OptionKeys::evaluation , evaluation
• structured_array_broadcast_rmsd() : pyrosetta.numeric.alignment.rmsd_calc
• structured_array_to_basic() : pyrosetta.utility.array
• structured_array_unaligned_broadcast_rmsd() : pyrosetta.numeric.alignment.rmsd_calc
• stub_constraint_strength : scaffold_matcher
• stublist_filename : basic::options::OptionKeys
• style : correlation_time , score_vs_rmsd , styles.blue , styles.green , styles.rainbow , styles.rama , styles.red
• sub_matrix_filename : sequence_recovery
• subangstrom() : average_rmsds
• subdir_project_template : update_ui_project
• subfraction_size : BundlePairRmsdCalculator
• Subject : ObjexxFCL
• SubjectMulti : ObjexxFCL
• SubjectSingle : ObjexxFCL
• subjob_pattern : average_rmsds
• subjobs : average_rmsds
• submit_jobs() : submit_jobs
• submotif_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• subprocess_call() : erraser_util
• subprocess_out() : erraser_util
• subprojects : pilot_app_settings
• subset_mappingCOP : utility
• subset_mappingOP : utility
• subset_to_keep : basic::options::OptionKeys::docking::ligand , docking::ligand
• substitute_esc_chars() : utility::json_spirit
• substrate_type : basic::options::OptionKeys::carbohydrates::glycopeptide_docking , carbohydrates::glycopeptide_docking
• subsubs_attract : basic::options::OptionKeys::smhybrid , smhybrid
• subsystem_size : make_symmdef_file_denovo
• subtract() : numeric
• subtract_degree_angles() : basic
• subtract_radian_angles() : basic
• SUBTRACT_SYMBOL : numeric::expression_parser
• SubtractExpressionCOP : numeric::expression_parser
• SubtractExpressionOP : numeric::expression_parser
• subunits : make_symmdef_file_denovo
• success : loops_kic , test.T650_LoopsKIC
• sucker_params : basic::options::OptionKeys::in::file , in::file
• suffix : basic::options::OptionKeys::out , out
• sugardonor_residue : basic::options::OptionKeys::carbohydrates::glycopeptide_docking , carbohydrates::glycopeptide_docking
• suite1 : erraser_analysis
• suite2 : erraser_analysis
• suite_outlier1 : erraser_analysis
• suite_outlier2 : erraser_analysis
• suiteness_bonus : basic::options::OptionKeys::score::rna , score::rna
• sulph_dist_cutoff : basic::options::OptionKeys::bunsat_calc2 , bunsat_calc2
• sum() : numeric
• sum_of_square_differences() : numeric::linear_algebra
• sumP : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• super_secret_fixed_interface_mode() : AnchoredDesign::testing , basic::options::OptionKeys::AnchoredDesign::testing
• superimpose_coordinate_array() : pyrosetta.numeric.alignment.rmsd_calc
• superimpose_native : basic::options::OptionKeys::loops , loops
• superimpose_over_all : basic::options::OptionKeys::stepwise , stepwise
• superimpose_structured_array() : pyrosetta.numeric.alignment.rmsd_calc
• superimpose_to_file : basic::options::OptionKeys::relax , relax
• superimpose_to_native : basic::options::OptionKeys::relax , relax , score_app
• suppress_bp_constraint : basic::options::OptionKeys::rna::denovo , rna::denovo
• suppress_checkpointing : basic::options::OptionKeys::ddg , ddg
• suppress_checkpoints : basic::options::OptionKeys::run , run
• suppress_zero_occ_pdb_output : basic::options::OptionKeys::out::file , out::file
• surf : kmeans_adaptive_kernel_density_bb_dependent_rotlib
• surface_accessibility : basic::options::OptionKeys::packstat , packstat
• surface_atom_cutoff : local
• surface_residue : local
• surface_residue_cutoff : local
• surface_vectors : basic::options::OptionKeys::in::file , in::file
• surfaceAA : basic::options::OptionKeys::remodel , remodel
• surfacedesign : surface_app
• surfacescan : surface_app
• surfacescore : surface_app
• SVD_SolverCOP : basic::svd
• SVD_SolverOP : basic::svd
• svdcmp() : numeric::linear_algebra
• Svm_node_rosettaOP : utility::libsvm
• Svm_rosettaCOP : utility::libsvm
• Svm_rosettaOP : utility::libsvm
• svmmodel : basic::options::OptionKeys::ProQ , ProQ
• SW() : ObjexxFCL::format
• sw_high : test.Workshop8test
• sw_low : test.Workshop8test
• SWA_rebuild_erraser() : erraser_wrapper
• SWA_rebuild_erraser_async() : erraser_wrapper
• SWA_rebuild_erraser_multiproc() : erraser_wrapper
• SWA_rebuild_erraser_postproc() : erraser_wrapper
• swap() : ObjexxFCL , utility::keys , utility
• swap4_aligned() : utility
• swap_loops : basic::options::OptionKeys::fold_from_loops , fold_from_loops
• swap_no_notify() : ObjexxFCL
• swap_refine_confirm_protocols : basic::options::OptionKeys::remodel , remodel
• switch : test.Workshop4test
• switch2 : test.Workshop4test
• switch_concert_sub : basic::options::OptionKeys::smhybrid , smhybrid
• switch_focus_frequency : basic::options::OptionKeys::stepwise::monte_carlo , stepwise::monte_carlo
• switch_low : test.Workshop7test
• sym_move : basic::options::OptionKeys::remodel::staged_sampling , remodel::staged_sampling
• SymDock_fa_rep_max : basic::options::OptionKeys::docking , docking
• SymDock_fa_sol_max : basic::options::OptionKeys::docking , docking
• SymDock_lowres_filter : basic::options::OptionKeys::docking , docking
• SymDock_reduce_motif_dock_weights : basic::options::OptionKeys::docking , docking
• symE_bonus : basic::options::OptionKeys::score , score
• symE_units : basic::options::OptionKeys::score , score
• symfragrm : basic::options::OptionKeys::lh::symfragrm , lh::symfragrm
• symlink() : build
• symlink_tree() : build
• symm_def_template : basic::options::OptionKeys::smhybrid , smhybrid
• symm_def_template_reduced : basic::options::OptionKeys::smhybrid , smhybrid
• symm_file_tag : basic::options::OptionKeys::smhybrid , smhybrid
• symm_hack_arity : basic::options::OptionKeys::rna::denovo , rna::denovo
• symm_type_name : make_symmdef_file_denovo
• symmetric_gly_tables : basic::options::OptionKeys::score , score
• symmetric_motifs : basic::options::OptionKeys::mh::dump , mh::dump
• symmetric_rmsd : basic::options::OptionKeys::evaluation , basic::options::OptionKeys::symmetry , evaluation , symmetry
• symmetrize_output : basic::options::OptionKeys::make_mainchain_potential , make_mainchain_potential
• symmetry : basic::options::OptionKeys::symmetry , symmetry
• symmetry_c2_dock : basic::options::OptionKeys::willmatch , willmatch
• symmetry_d2 : basic::options::OptionKeys::willmatch , willmatch
• symmetry_definition : basic::options::OptionKeys::symmetry , symmetry
• symmetry_residue() : abinitio , basic::options::OptionKeys::abinitio
• syn_anti_check() : erraser_analysis , erraser_single_res_analysis
• syn_G_potential_bonus : basic::options::OptionKeys::score::rna , score::rna
• sys_sleep() : utility