- s -

• s() : utility::py::Value
• s2d() : utility::subset_mapping
• safe_output() : basic::Tracer
• same_dimensions() : numeric::MathMatrix< T >
• same_type_as_me() : numeric::interpolation::spline::CompoundInterpolator , numeric::interpolation::spline::Interpolator , numeric::interpolation::spline::SimpleInterpolator
• sample() : numeric::random::DistributionSampler< T >
• samples() : numeric::random::WeightedReservoirSampler< T >
• sampLoc() : numeric::fourier::SO3coeffs
• sanity_check() : numeric::geometry::hashing::xyzStripeHash , numeric::geometry::hashing::xyzStripeHashWithMeta< T >
• save_constraints() : app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO
• save_cur_as_pdb() : app.pyrosetta_toolkit.modules.SQLPDB.PDB_database
• save_neighbors() : app.pyrosetta_toolkit.modules.calibur.calibur
• save_params() : app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO
• save_PDB() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• save_possible_simple_key() : yaml.scanner.Scanner
• save_random_num_neighbors() : app.pyrosetta_toolkit.modules.calibur.calibur
• save_session() : app.pyrosetta_toolkit.window_main.IO.SessionIO.SessionIO
• save_settings() : app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager
• save_whole_db_as_db() : app.pyrosetta_toolkit.modules.SQLPDB.PDB_database
• saveAS() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• saveDefaults() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• saveDesign() : app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow
• saveState() : numeric::random::mt19937_RG , numeric::random::RandomGenerator , numeric::random::standard_RG , numeric::random::uniform_RG
• saveToWD() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• scalar() : utility::options::OptionKey , utility::options::ScalarOptionKey , utility::options::VectorOptionKey
• ScalarOption() : utility::options::ScalarOption
• ScalarOption_T_() : utility::options::ScalarOption_T_< K, T >
• ScalarOptionKey() : utility::options::ScalarOptionKey
• scaled_add() : numeric::sphericalVector< typename > , numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• scaled_assign() : numeric::sphericalVector< typename > , numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• scaled_sub() : numeric::sphericalVector< typename > , numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• scan() : numeric::expression_parser::ArithmeticScanner
• scan_anchor() : yaml.scanner.Scanner
• scan_block_scalar() : yaml.scanner.Scanner
• scan_block_scalar_breaks() : yaml.scanner.Scanner
• scan_block_scalar_ignored_line() : yaml.scanner.Scanner
• scan_block_scalar_indentation() : yaml.scanner.Scanner
• scan_block_scalar_indicators() : yaml.scanner.Scanner
• scan_directive() : yaml.scanner.Scanner
• scan_directive_ignored_line() : yaml.scanner.Scanner
• scan_directive_name() : yaml.scanner.Scanner
• scan_flow_scalar() : yaml.scanner.Scanner
• scan_identifier() : numeric::expression_parser::ArithmeticScanner
• scan_literal() : numeric::expression_parser::ArithmeticScanner
• scan_tag() : yaml.scanner.Scanner
• scan_tag_directive_handle() : yaml.scanner.Scanner
• scan_tag_directive_prefix() : yaml.scanner.Scanner
• scan_tag_directive_value() : yaml.scanner.Scanner
• scan_to_next_token() : yaml.scanner.Scanner
• scan_yaml_directive_number() : yaml.scanner.Scanner
• scan_yaml_directive_value() : yaml.scanner.Scanner
• Schema() : basic::database::schema_generator::Schema
• score() : FragmentAssemblyMover , numeric::RocPoint
• score_loops() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• score_types_for_method() : test.T850_SubClassing.MyNewCI1B_Creator
• ScoreAnalyticEtableBenchmark() : ScoreAnalyticEtableBenchmark
• ScoreBenchmark() : ScoreBenchmark
• ScoreEachBenchmark() : ScoreEachBenchmark
• ScoreFragInfo() : ScoreFragInfo
• ScoreFragmentSetMover() : ScoreFragmentSetMover
• scorefxn() : ExtractATD
• scoreOption() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• scrub() : app.pyrosetta_toolkit.modules.SQLPDB.PDB_database
• SCWRL() : app.pyrosetta_toolkit.modules.protocols.MinimizationProtocols.MinimizationProtocols
• seek_beg() : utility::io::icstream , utility::io::irstream , utility::io::izstream
• seekoff() : boost_adaptbx::python::streambuf
• seekoff_without_calling_python() : boost_adaptbx::python::streambuf
• seekpos() : boost_adaptbx::python::streambuf
• select_pose_then_launch_fixpdb() : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• select_working_set() : Solver , Solver_NU
• self_pure_test_virtual_p() : utility::py::OverloadTest
• self_pure_test_virtual_ref() : utility::py::OverloadTest
• self_test_virtual_p() : utility::py::OverloadTest
• self_test_virtual_ref() : utility::py::OverloadTest
• Semantic_actions() : utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• send() : utility::signals::LinkUnit , utility::signals::SignalHub< ResultType, Signal >
• send_char_to_node() : utility::SimulateMPI
• send_colors() : src.PyMolLink.PyMOLMover
• send_double_to_node() : utility::SimulateMPI
• send_doubles_to_node() : utility::SimulateMPI
• send_energy() : src.PyMolLink.PyMOLMover
• send_foldtree() : src.PyMolLink.PyMOLMover
• send_hbonds() : src.PyMolLink.PyMOLMover
• send_integer_to_node() : utility::SimulateMPI
• send_integers_to_node() : utility::SimulateMPI
• send_message() : src.PyMolLink.PySocketClient
• send_movemap() : src.PyMolLink.PyMOLMover
• send_point() : src.PyMolLink.PyMOLMover
• send_polars() : src.PyMolLink.PyMOLMover
• send_signal() : utility::signals::SignalHub< ResultType, Signal > , utility::signals::TokenHub< ResultType, Signal >
• send_ss() : src.PyMolLink.PyMOLMover
• send_string_to_node() : utility::SimulateMPI
• send_structure() : src.PyMolLink.PyMOLMover
• send_to_master() : utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >
• SendEPose() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• SendNewPose() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• SendPose() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• serialize() : numeric::interpolation::spline::CompoundInterpolator , numeric::interpolation::spline::Interpolator , numeric::interpolation::spline::SimpleInterpolator , yaml.serializer.Serializer
• serialize_node() : yaml.serializer.Serializer
• session() : utility::sql_database::session
• set() : basic::datacache::DataCache< Data > , basic::datacache::HierarchicalDataMap , basic::MetricValue< T > , basic::Report , basic::Reporter , numeric::IntervalSet< typename >
• set_abstract() : utility::tag::XMLSchemaElement
• set_accessed() : utility::options::Option
• set_all_flags() : numeric::ClusteringTreeNode
• set_alternative_search_paths() : utility::io::izstream
• set_basic_options() : app.pyrosetta_toolkit.modules.SQLPDB.SQLPDB
• set_chain_no() : PhProtocol
• set_char_msg() : utility::SimulateMPIMessage
• set_chunk_size() : utility::sql_database::session
• set_cl_value() : utility::options::Option , utility::options::ScalarOption , utility::options::VectorOption
• set_constraints_weight() : app.surface_docking.movers.FullAtomRelax
• set_db_mode() : utility::sql_database::session
• set_db_name() : utility::sql_database::session
• set_db_partition() : utility::sql_database::session
• set_default() : PhProtocol
• set_default_final_stream() : basic::Tracer
• set_diagonal() : numeric::xyzMatrix< typename > , ObjexxFCL::FArray2< typename >
• set_dimension() : numeric::MultiDimensionalHistogram
• set_dimension_sizes() : utility::FixedSizeLexicographicalIterator< S > , utility::LexicographicalIterator
• set_double_msg() : utility::SimulateMPIMessage
• set_doubles_msg() : utility::SimulateMPIMessage
• set_expression() : numeric::expression_parser::UnaryExpression
• set_fa_elec() : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager
• set_file_contents() : utility::io::FileContentsMap , utility::tag::XMLErrorHandler
• set_file_name() : PhProtocol
• set_filepath() : app.pyrosetta_toolkit.modules.ScoreAnalysis.ScoreAnalysis
• set_first_expression() : numeric::expression_parser::BinaryExpression
• set_gene() : app.pyrosetta_toolkit.modules.Structure.CDR
• set_head() : utility::in_place_list< T >
• set_identity() : numeric::HomogeneousTransform< T >
• set_identity_rotation() : numeric::HomogeneousTransform< T >
• set_identity_transform() : numeric::HomogeneousTransform< T >
• set_indent() : basic::Emitter
• set_index() : utility::libsvm::Svm_node_rosetta , utility::SimulateMPIMessage
• set_integer_msg() : utility::SimulateMPIMessage
• set_integers_msg() : utility::SimulateMPIMessage
• set_interpolator() : numeric::interpolation::Histogram< typename, typename >
• set_ios_hook() : basic::Tracer
• set_keep_input_scores() : MyScoreMover
• set_lb_function() : numeric::interpolation::spline::Interpolator
• set_Loop_for_region() : app.pyrosetta_toolkit.modules.Region.Region
• set_lower() : numeric::geometry::BoundingBox< typename >
• set_matrix_A() : basic::svd::SVD_Solver
• set_max_angle() : app.surface_docking.movers.CentroidRelax , app.surface_docking.movers.FullAtomRelax
• set_mc() : app.surface_docking.movers.FullAtomRelax
• set_minimize_sidechains() : app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper
• set_mm_std() : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager
• set_model_group() : utility::tag::XMLSchemaComplexType
• set_modelID() : app.pyrosetta_toolkit.modules.SQLPDB.SQLPDB
• set_movemap() : app.surface_docking.movers.FullAtomRelax
• set_mpi_rank() : utility::SimulateMPI
• set_mutation_info() : app.pyrosetta_toolkit.modules.definitions.restype_definitions.definitions
• set_new_final_stream() : basic::Tracer
• set_next_correspondence() : utility::subset_mapping
• set_nmoves() : app.surface_docking.movers.CentroidRelax , app.surface_docking.movers.FullAtomRelax
• set_nread_limit_for_file() : utility::io::FileContentsMap
• set_open_mode() : basic::resource_manager::locator::FileListResourceLocator , basic::resource_manager::locator::FileSystemResourceLocator
• set_option_value_cl() : utility::options::OptionCollection
• set_option_value_file() : utility::options::OptionCollection
• set_options_menus() : app.pyrosetta_toolkit.window_main.frames.QuickProtocolsFrame.QuickProtocolsFrame
• set_orbitals() : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager
• set_output_DIR() : app.pyrosetta_toolkit.modules.SQLPDB.PDB_database
• set_output_occupancy_1() : app.pyrosetta_toolkit.modules.SQLPDB.PDB_database
• set_params() : app.surface_docking.movers.FullAtomRelax , numeric::interpolation::Histogram< typename, typename >
• set_parent() : basic::datacache::HierarchicalDataMap
• set_pdb_map() : app.pyrosetta_toolkit.modules.PythonPDB.PythonPDB
• set_pdbID() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceInfo , app.pyrosetta_toolkit.modules.SQLPDB.SQLPDB
• set_PDBLIST() : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• set_pdbpath() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceInfo
• set_pH_neighbor_pack() : PhProtocol
• set_pH_prepack() : PhProtocol
• set_pH_relax() : PhProtocol
• set_pka_all() : PhProtocol
• set_pka_rad() : PhProtocol
• set_point() : numeric::HomogeneousTransform< T >
• set_position_from_index() : utility::FixedSizeLexicographicalIterator< S > , utility::LexicographicalIterator
• set_postgres_schema_search_path() : utility::sql_database::DatabaseSessionManager
• set_pq_schema() : utility::sql_database::session
• set_prop() : app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager
• set_PyExitCallBack() : utility::py::PyExitCallback
• set_python_instance_state() : yaml.constructor.Constructor
• set_quote_options() : utility::tag::Tag
• set_reference_energies() : supercharge
• set_region() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceInfo
• set_repack_connection() : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMover
• set_repack_connection_and_insert() : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMover
• set_res_no() : PhProtocol
• set_resfile() : supercharge
• set_resfile_AvNAPSA() : supercharge
• set_residue_info() : app.pyrosetta_toolkit.modules.definitions.restype_definitions.definitions
• set_residue_of_interest() : app.pyrosetta_toolkit.window_main.IO.GUIInput.GUIInput
• set_rotamer_prot_stats() : PhProtocol
• set_scorefunction() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• set_scorefxn() : app.surface_docking.movers.FullAtomRelax , ScoreEachBenchmark
• set_second_expression() : numeric::expression_parser::BinaryExpression
• set_seed() : numeric::random::RandomGenerator
• set_sequence() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceInfo
• set_show_accessed_options_flag() : utility::options::OptionCollection
• set_show_unused_options_flag() : utility::options::OptionCollection
• set_skip_scoring() : MyScoreMover
• set_source_size() : utility::subset_mapping
• set_string() : fmt::internal::MakeValue< Char >
• set_string_msg() : utility::SimulateMPIMessage
• set_structID() : app.pyrosetta_toolkit.modules.SQLPDB.SQLPDB
• set_style() : app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable
• set_subelements_pick_one() : utility::tag::XMLSchemaComplexTypeGenerator
• set_subelements_pick_one_optional() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_subelements_pick_one_or_none() : utility::tag::XMLSchemaComplexTypeGenerator
• set_subelements_pick_one_required() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_subelements_repeatable() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_subelements_single_appearance_optional() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_subelements_single_appearance_required() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_subelements_single_appearance_required_and_ordered() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• set_surface() : supercharge
• set_tail() : utility::in_place_list< T >
• set_temperature() : app.pyrosetta_toolkit.window_main.IO.GUIOutput.GUIOutput
• set_throw_on_double_registration() : basic::resource_manager::FallbackConfigurationFactory , basic::resource_manager::ResourceLoaderFactory , basic::resource_manager::ResourceLocatorFactory , basic::resource_manager::ResourceOptionsFactory
• set_token_type() : numeric::expression_parser::SimpleToken
• set_transaction_mode() : utility::sql_database::session
• set_transform() : numeric::HomogeneousTransform< T >
• set_ub_function() : numeric::interpolation::spline::Interpolator
• set_unit() : numeric::MathMatrix< T >
• set_upper() : numeric::geometry::BoundingBox< typename >
• set_value() : numeric::expression_parser::LiteralExpression , numeric::expression_parser::VariableExpression , utility::libsvm::Svm_node_rosetta
• set_vector_b() : basic::svd::SVD_Solver
• set_visited() : numeric::ClusteringTreeNode
• set_weight() : numeric::random::WeightedSampler
• set_xaxis_rotation_deg() : numeric::HomogeneousTransform< T >
• set_xaxis_rotation_rad() : numeric::HomogeneousTransform< T >
• set_yaxis_rotation_deg() : numeric::HomogeneousTransform< T >
• set_yaxis_rotation_rad() : numeric::HomogeneousTransform< T >
• set_zaxis_rotation_deg() : numeric::HomogeneousTransform< T >
• set_zaxis_rotation_rad() : numeric::HomogeneousTransform< T >
• set_zero() : numeric::MathMatrix< T >
• SetandUpdateListsF() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• SetandUpdateListsP() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• setChain() : loadPDB.PDBres
• setChainLabel() : loadPDB.chainType
• setDefaults() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• setFrag() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• setName() : utility::tag::Tag
• setOption() : utility::tag::Tag
• setOptions() : utility::tag::Tag
• setPrintId() : loadPDB.PDBres
• setProt() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• setSeed() : numeric::random::mt19937_RG , numeric::random::standard_RG , numeric::random::uniform_RG
• setTk() : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow , app.pyrosetta_toolkit.window_main.menu.Menus , app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow , app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager , app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager
• setTypes() : app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow
• setUp() : app.pyrosetta_toolkit.modules.prettytable.prettytable_test.BuildEquivelanceTest , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.CityDataTest , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.FloatFormatBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.FloatFormatTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.HrulesAllBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.HrulesNoneBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.IntegerFormatBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.NoBorderBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.NoHeaderBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.PresetBasicTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.SlicingTests , app.pyrosetta_toolkit.modules.prettytable.prettytable_test.SortingTests , DatabaseIOBenchmark , DesignBenchmark , DockingBenchmark< dock, TScale > , FastRelaxPerformanceBenchmark
• setup() : HPatchByChainNPDCalculator
• setUp() : InteractionGraphPerformanceBenchmark
• setup() : LigandDockBench
• setUp() : LigandDockBenchmark , LigandDockScriptBenchmark , MinimizerBenchmark< sft, TScale >
• setup() : NBuriedUnsatsCalcultor
• setUp() : OptionCollectionBenchmark , PDB_IOBenchmark , PerformanceBenchmark , ResidueTypeBenchmark , ScoreAnalyticEtableBenchmark , ScoreBenchmark , ScoreEachBenchmark , ShearMoverBenchmark , SmallMoverBenchmark
• setup() : src.utility.PythonPyExitCallback
• setUp() : XMLParseBenchmark
• setup() : zinc1_homodimer_design , zinc2_homodimer_design
• setup_filter_clashes() : zinc2_homodimer_setup
• setup_filter_stats() : DougsDockDesignMinimizeMagicMover
• setup_for_denseig() : InteractionGraphPerformanceBenchmark
• setup_for_linmemig() : InteractionGraphPerformanceBenchmark
• setup_for_mmstd() : FastRelaxPerformanceBenchmark , InteractionGraphPerformanceBenchmark
• setup_for_pdig() : InteractionGraphPerformanceBenchmark
• setup_for_sc12he() : FastRelaxPerformanceBenchmark , InteractionGraphPerformanceBenchmark
• setup_for_sc12sp2() : FastRelaxPerformanceBenchmark , InteractionGraphPerformanceBenchmark
• setup_for_score12() : FastRelaxPerformanceBenchmark , InteractionGraphPerformanceBenchmark
• setup_for_sp2hecart() : FastRelaxPerformanceBenchmark , InteractionGraphPerformanceBenchmark
• setup_grafted_monomer() : zinc2_homodimer_setup
• setup_homodimer() : zinc2_homodimer_setup
• setup_metalsite() : zinc1_homodimer_design , zinc2_homodimer_design
• setup_metalsite_constraints() : zinc1_homodimer_design
• setup_metalsites() : zinc2_homodimer_setup
• setup_movemap_bb_chi() : zinc1_homodimer_design
• setup_mover_and_run() : app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• setup_movers() : zinc1_homodimer_design
• setup_output_tag() : zinc1_homodimer_design
• setup_pert_foldtree() : DougsDockDesignMinimizeMagicMover
• setup_Pmls() : numeric::fourier::SHT
• setup_protocol() : app.pyrosetta_toolkit.modules.protocols.FloppyTailProtocol.FloppyTailProtocol
• setup_real() : ObjexxFCL::FArray1D< typename > , ObjexxFCL::FArray2D< typename > , ObjexxFCL::FArray3D< typename > , ObjexxFCL::FArray4D< typename > , ObjexxFCL::FArray5D< typename > , ObjexxFCL::FArray6D< typename > , ObjexxFCL::KeyFArray1D< typename > , ObjexxFCL::KeyFArray2D< typename > , ObjexxFCL::KeyFArray3D< typename > , ObjexxFCL::KeyFArray4D< typename > , ObjexxFCL::KeyFArray5D< typename > , ObjexxFCL::KeyFArray6D< typename >
• setup_rollmoving() : zinc1_homodimer_design
• setup_scorefunctions() : zinc1_homodimer_design
• setup_taskfactory() : zinc1_homodimer_design
• setup_taskfactory_scorefunction_movers() : zinc2_homodimer_design
• setup_Weights() : numeric::fourier::SHT
• setup_Wig() : numeric::fourier::SHT
• SetupAdjacencyVector() : utility::graph::RingDetection< Graph >
• setupPackDesign() : app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignProtocols
• setWD() : app.pyrosetta_toolkit.window_modules.scorefunction.ScoreFxnControl.ScoreFxnControl
• SetWrapper() : ObjexxFCL::SetWrapper< typename >
• shared_from_this() : basic::datacache::CacheableString , basic::datacache::CacheableStringFloatMap , basic::datacache::CacheableStringMap , basic::datacache::DiagnosticData , basic::datacache::WriteableCacheableData , basic::datacache::WriteableCacheableMap
• sharm_invTransform() : numeric::fourier::SHT
• sharm_transform() : numeric::fourier::SHT
• ShearMoverBenchmark() : ShearMoverBenchmark
• shell() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.IterableIPShell
• shift_set() : ObjexxFCL::FArray< typename >
• shoInfo() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• shoProt() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• short_description() : utility::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• short_max() : numeric::geometry::hashing::xyzStripeHash , numeric::geometry::hashing::xyzStripeHashWithMeta< T >
• short_min() : numeric::geometry::hashing::xyzStripeHash , numeric::geometry::hashing::xyzStripeHashWithMeta< T >
• short_of() : ObjexxFCL::Fstring
• shortd() : utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• shorter() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• shorter_or_equal() : numeric::xyzTriple< typename > , numeric::xyzVector< typename >
• shoShearControl() : app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• shoTk() : app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMoverWindow , app.pyrosetta_toolkit.window_main.menu.Menus , app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow , app.pyrosetta_toolkit.window_modules.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager.ligand_ncaa_ptm_manager , app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager , app.pyrosetta_toolkit.window_modules.protocol_builder.ProtocolBuilder.MainProtocols
• shouldVisitTemplateInstantiations() : BinderVisitor
• show() : basic::resource_manager::JobOptions , basic::resource_manager::LazyResourceManager , basic::resource_manager::locator::DatabaseResourceLocator , basic::resource_manager::locator::FileListResourceLocator , basic::resource_manager::locator::FileSystemResourceLocator , basic::resource_manager::locator::NullResourceLocator , basic::resource_manager::ResourceConfiguration , basic::resource_manager::ResourceLocator , basic::resource_manager::ResourceManager , basic::resource_manager::ResourceOptions , numeric::HomogeneousTransform< T > , numeric::kdtree::HyperRectangle , numeric::kdtree::KDPoint , numeric::kdtree::KDPointList , numeric::Polynomial_1d , numeric::xyzMatrix< typename > , numeric::xyzVector< typename > , utility::excn::EXCN_Base , utility::excn::EXCN_Msg_Exception , utility::EXCN_utility_exit , utility::Show
• show_accessed_options() : utility::options::OptionCollection
• show_all() : utility::options::OptionCollection
• show_all_hier() : utility::options::OptionCollection
• show_contents() : utility::Inline_File_Provider
• show_energies() : app.pyrosetta_toolkit.window_main.frames.SimpleAnalysisFrame.SimpleAnalysisFrame
• show_fullcontrol_window() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_fxpdb_window() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_graftmover_window() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_gui() : app.pyrosetta_toolkit.pyrosetta_toolkit.main_window
• show_help() : utility::options::OptionCollection
• show_help_hier() : utility::options::OptionCollection
• show_inaccessed_user_options() : utility::options::OptionCollection
• show_IpythonWindow() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_ligand_ncaa_ptm_manager() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_option_help() : utility::options::OptionCollection
• show_option_help_hier() : utility::options::OptionCollection
• show_OptionsSystemManager() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_ResfileDesignWindow() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_RosettaProtocolBuilder() : app.pyrosetta_toolkit.window_main.menu.Menus
• show_sequence() : app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame
• show_stream() : numeric::HomogeneousTransform< T >
• show_table_text() : utility::options::OptionCollection
• show_table_Wiki() : utility::options::OptionCollection
• show_unused_options() : utility::options::OptionCollection
• show_user() : utility::options::OptionCollection
• show_variant_info() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow
• show_window() : app.pyrosetta_toolkit.window_modules.full_control.FullControlWindow.FullControlWindow , app.pyrosetta_toolkit.window_modules.insert_bfactor.InsertBFactor.InsertBFactor
• showBanner() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• showmanyc() : boost_adaptbx::python::streambuf
• showPrompt() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• showReturned() : app.pyrosetta_toolkit.window_modules.interactive_terminal.interactive_terminal.TkConsoleView
• shrink() : ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , utility::BitVector< B > , utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyMap< K, T > , utility::keys::SmallKeyVector< K, T > , utility::vectorL< SSize, T, A > , utility::vectorL< L, bool, A >
• SHT() : numeric::fourier::SHT
• signal_allowed() : utility::signals::BufferedSignalHub< ResultType, Signal > , utility::signals::SignalHub< ResultType, Signal >
• SignalHub() : utility::signals::SignalHub< ResultType, Signal >
• simple_element_naming_func_has_been_set() : utility::tag::XMLSchemaSimpleSubelementList
• SimpleExpressionCreator() : numeric::expression_parser::SimpleExpressionCreator
• SimpleInterpolator() : numeric::interpolation::spline::SimpleInterpolator
• SimpleToken() : numeric::expression_parser::SimpleToken
• simulate_mpi() : utility::SimulateMPI
• SimulateMPI() : utility::SimulateMPI
• SimulateMPIData() : utility::SimulateMPIData
• SimulateMPIMessage() : utility::SimulateMPIMessage
• sin_cos_tolerance() : numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• SingletonBase() : utility::SingletonBase< T >
• SixDCoordinateBinner() : numeric::geometry::hashing::SixDCoordinateBinner
• SixDOffsetTree() : numeric::geometry::hashing::SixDOffsetTree
• size() : basic::datacache::ConstDataMap , basic::datacache::DataCache< Data > , basic::datacache::DataMap , fmt::BasicStringRef< Char > , fmt::BasicWriter< Char > , fmt::Buffer< T > , fmt::File , fmt::FormatInt , fmt::internal::FormatBuf< Char > , numeric::ClusteringTreeNode , numeric::geometry::hashing::xyzStripeHash , numeric::kdtree::KDPoint , numeric::kdtree::KDPointList , numeric::kdtree::KDTree , numeric::MathMatrix< T > , numeric::MathVector< T > , numeric::random::WeightedSampler , ObjexxFCL::CArray< typename > , ObjexxFCL::CArrayP< typename > , ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , ObjexxFCL::Cstring , ObjexxFCL::FArray< typename > , ObjexxFCL::FArraySection< typename > , ObjexxFCL::Fstring , ObjexxFCL::IndexRange , utility::BitSet< B > , utility::BitVector< B > , utility::fixedsizearray0< T, S > , utility::fixedsizearray1< T, S > , utility::FixedSizeLexicographicalIterator< S > , utility::graph::HideVertexVisitor< Graph > , utility::heap , utility::in_place_list< T > , utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyLookup< K > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyMap< K, T > , utility::keys::SmallKeyVector< K, T > , utility::LexicographicalIterator , utility::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VariantOption< O > , utility::options::VectorOption_T_< K, T > , utility::OrderedTuple< T > , utility::signals::SignalHub< ResultType, Signal > , utility::tag::Tag
• size1() : ObjexxFCL::FArray1< typename > , ObjexxFCL::FArray1A< typename > , ObjexxFCL::FArray1D< typename > , ObjexxFCL::FArray1P< typename > , ObjexxFCL::FArray2< typename > , ObjexxFCL::FArray3< typename > , ObjexxFCL::FArray4< typename > , ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::KeyFArray1D< typename >
• size2() : ObjexxFCL::FArray2< typename > , ObjexxFCL::FArray2A< typename > , ObjexxFCL::FArray2D< typename > , ObjexxFCL::FArray2P< typename > , ObjexxFCL::FArray3< typename > , ObjexxFCL::FArray4< typename > , ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::KeyFArray2D< typename >
• size3() : ObjexxFCL::FArray3< typename > , ObjexxFCL::FArray3A< typename > , ObjexxFCL::FArray3D< typename > , ObjexxFCL::FArray3P< typename > , ObjexxFCL::FArray4< typename > , ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::KeyFArray3D< typename >
• size4() : ObjexxFCL::FArray4< typename > , ObjexxFCL::FArray4A< typename > , ObjexxFCL::FArray4D< typename > , ObjexxFCL::FArray4P< typename > , ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::KeyFArray4D< typename >
• size5() : ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray5A< typename > , ObjexxFCL::FArray5D< typename > , ObjexxFCL::FArray5P< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::KeyFArray5D< typename >
• size6() : ObjexxFCL::FArray6< typename > , ObjexxFCL::FArray6A< typename > , ObjexxFCL::FArray6D< typename > , ObjexxFCL::FArray6P< typename > , ObjexxFCL::KeyFArray6D< typename >
• size_bounded() : ObjexxFCL::FArray< typename >
• size_constraint_string() : utility::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• size_dynamic() : ObjexxFCL::DynamicIndexRange
• size_of() : ObjexxFCL::FArray< typename >
• size_set() : ObjexxFCL::FArray< typename >
• size_unbounded() : ObjexxFCL::FArray< typename >
• Skip() : ObjexxFCL::format::Skip
• skipping_requested() : binder::Binder
• SmallKeyMap() : utility::keys::SmallKeyMap< K, T >
• SmallKeyVector() : utility::keys::SmallKeyVector< K, T >
• SmallMoverBenchmark() : SmallMoverBenchmark
• so3_correlate() : numeric::fourier::SHT
• SO3coeffs() : numeric::fourier::SO3coeffs
• so3CombineCoef() : numeric::fourier::SHT
• Solve() : Solver , Solver_NU
• Solver() : Solver
• Solver_NU() : Solver_NU
• sort() : utility::keys::ClassKeyVector< K, T, C >
• sort_binders() : binder::Context
• sorted_values() : numeric::kdtree::KDPointList
• source_id_is_mapped() : utility::subset_mapping
• source_size() : utility::subset_mapping
• space() : utility::json_spirit::Generator< Value_type, Ostream_type >
• space_prefixed() : utility::options::OptionCollection
• spec() : fmt::internal::BasicArgFormatter< Impl, Char >
• specified_check() : utility::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• specified_report() : utility::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• sph_standardize() : numeric::fourier::SHT
• sphericalVector() : numeric::sphericalVector< typename >
• SplineGenerator() : numeric::interpolation::spline::SplineGenerator
• split_axis() : numeric::kdtree::KDNode
• split_region_and_fix_sequences() : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• sqr() : numeric::interpolation::spline::BicubicSpline , numeric::interpolation::spline::CubicSpline
• square() : numeric::xyzTriple< typename > , numeric::xyzVector< typename > , ObjexxFCL::CArray< typename > , ObjexxFCL::CArrayP< typename > , ObjexxFCL::ChunkVector< typename > , ObjexxFCL::FArray2< typename >
• square_norm() : numeric::MathVector< T >
• SquarerootExpression() : numeric::expression_parser::SquarerootExpression
• src() : utility::SimulateMPIMessage
• stale_possible_simple_keys() : yaml.scanner.Scanner
• standard_RG() : numeric::random::standard_RG
• standard_width() : ObjexxFCL::TypeTraits< T > , ObjexxFCL::TypeTraits< double > , ObjexxFCL::TypeTraits< float > , ObjexxFCL::TypeTraits< int > , ObjexxFCL::TypeTraits< long double > , ObjexxFCL::TypeTraits< long int > , ObjexxFCL::TypeTraits< short int > , ObjexxFCL::TypeTraits< unsigned int > , ObjexxFCL::TypeTraits< unsigned long int > , ObjexxFCL::TypeTraits< unsigned short int >
• standardise_filename() : utility::Inline_File_Provider
• Star() : ObjexxFCL::Star
• start() : numeric::MultiDimensionalHistogram , utility::json_spirit::Json_grammer< Value_type, Iter_type >::definition< ScannerT >
• start_decoy() : pyrosetta.PyJobDistributor , src.PyJobDistributor
• start_doc() : basic::Emitter , basic::JsonEmitter , basic::YamlEmitter
• start_list() : basic::Emitter
• start_map() : basic::Emitter
• start_raw() : basic::Emitter , basic::JsonEmitter , basic::YamlEmitter
• states() : numeric::fourier::kiss_fftnd_state
• StaticIndexRange() : ObjexxFCL::StaticIndexRange
• status() : numeric::RocPoint
• step_size() : numeric::interpolation::Histogram< typename, typename >
• str() : basic::datacache::CacheableString , fmt::BasicWriter< Char > , fmt::FormatInt , fmt::StrFormatSpec< Char >
• stream() : basic::resource_manager::locator::FileStream , basic::resource_manager::locator::NullStream , basic::resource_manager::locator::StringResourceStream , basic::resource_manager::ResourceStream , utility::io::icstream , utility::io::irstream , utility::io::izstream , utility::io::ocstream , utility::io::orstream , utility::io::ozstream
• Stream_reader() : utility::json_spirit::Stream_reader< Istream_type, Value_type >
• Stream_reader_thrower() : utility::json_spirit::Stream_reader_thrower< Istream_type, Value_type >
• stream_setup() : utility::options::RealOption , utility::options::RealVectorOption , utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• streambuf() : boost_adaptbx::python::streambuf
• streambuf_capsule() : boost_adaptbx::python::streambuf_capsule
• StrFormatSpec() : fmt::StrFormatSpec< Char >
• strict() : utility::Bound< typename >
• Strict() : utility::Bound< typename >
• strict_lower() : utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• strict_upper() : utility::options::ScalarOption_T_< K, T > , utility::options::VectorOption_T_< K, T >
• string_msg() : utility::SimulateMPIMessage
• string_of() : ObjexxFCL::Fstring
• StringOption() : utility::options::StringOption
• StringOptionKey() : utility::options::StringOptionKey
• StringResourceStream() : basic::resource_manager::locator::StringResourceStream
• StringVectorOption() : utility::options::StringVectorOption
• StringVectorOptionKey() : utility::options::StringVectorOptionKey
• strip() : ObjexxFCL::Fstring
• strip_whitespace() : ObjexxFCL::Fstring
• stripped() : ObjexxFCL::Fstring
• stripped_whitespace() : ObjexxFCL::Fstring , utility::keys::KeyLookup< K >
• subelement_behavior() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• subset_mapping() : utility::subset_mapping
• substate() : numeric::fourier::kiss_dct_state , numeric::fourier::kiss_fftr_state , numeric::fourier::kiss_fftsplit_state
• substitution_group() : utility::tag::XMLSchemaElement
• subtract_diagonal() : numeric::xyzMatrix< typename >
• SubtractExpression() : numeric::expression_parser::SubtractExpression
• suffix() : utility::options::OptionCollection
• sum() : numeric::MathVector< T >
• sum_radius() : numeric::geometry::hashing::SixDOffsetTree
• super_mute() : basic::Tracer
• super_mute_() : basic::Tracer
• super_twiddles() : numeric::fourier::kiss_dct_state , numeric::fourier::kiss_fftr_state
• supercharge() : supercharge
• svbksb() : basic::svd::SVD_Solver
• SVC_Q() : SVC_Q
• SVD_Solver() : basic::svd::SVD_Solver
• svdcmp() : basic::svd::SVD_Solver
• Svm_node_rosetta() : utility::libsvm::Svm_node_rosetta
• Svm_rosetta() : utility::libsvm::Svm_rosetta
• SVR_Q() : SVR_Q
• swap() : numeric::Quaternion< typename > , ObjexxFCL::CArray< typename > , ObjexxFCL::CArrayP< typename > , ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , ObjexxFCL::Cstring , ObjexxFCL::Dimension , ObjexxFCL::DynamicIndexRange , ObjexxFCL::FArray1D< typename > , ObjexxFCL::FArray2D< typename > , ObjexxFCL::FArray3D< typename > , ObjexxFCL::FArray4D< typename > , ObjexxFCL::FArray5D< typename > , ObjexxFCL::FArray6D< typename > , ObjexxFCL::IndexRange , ObjexxFCL::KeyFArray1D< typename > , ObjexxFCL::KeyFArray2D< typename > , ObjexxFCL::KeyFArray3D< typename > , ObjexxFCL::KeyFArray4D< typename > , ObjexxFCL::KeyFArray5D< typename > , ObjexxFCL::KeyFArray6D< typename > , ObjexxFCL::StaticIndexRange , utility::BitSet< B > , utility::BitVector< B > , utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyMap< K, T > , utility::keys::SmallKeyVector< K, T > , utility::vectorL< SSize, T, A > , utility::vectorL< L, bool, A >
• swap1DB() : ObjexxFCL::FArray1< typename >
• swap2DB() : ObjexxFCL::FArray2< typename >
• swap3DB() : ObjexxFCL::FArray3< typename >
• swap4DB() : ObjexxFCL::FArray4< typename >
• swap5DB() : ObjexxFCL::FArray5< typename >
• swap6DB() : ObjexxFCL::FArray6< typename >
• swap_cols() : numeric::MathMatrix< T >
• swap_index() : Cache , Kernel , ONE_CLASS_Q , QMatrix , Solver , SVC_Q , SVR_Q
• swap_no_notify() : ObjexxFCL::Dimension , ObjexxFCL::DynamicIndexRange
• swap_rows() : numeric::MathMatrix< T >
• swapB() : ObjexxFCL::FArray< typename >
• switch_off_orbitals() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• switch_on_orbitals() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• switch_to_fa_elec() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• switch_to_fa_pair() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• switch_to_paapp() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• switch_to_rama() : app.pyrosetta_toolkit.modules.RegionalScoring.RegionalScoring
• sym_repack_minimize() : HDdesignMover
• symhash64() : numeric::xyzTransform< typename >
• symmetric() : ObjexxFCL::FArray2< typename >
• sync() : basic::basic_otstream< CharT, Traits >::basic_tstringbuf< _CharT, _Traits > , boost_adaptbx::python::streambuf , utility::io::mpi_stream::basic_mpi_streambuf< Elem, Tr, ElemA, ByteT, ByteAT > , zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >
• SystemError() : fmt::SystemError