- a -

• a() : ObjexxFCL::FArray1< typename > , ObjexxFCL::FArray1A< typename > , ObjexxFCL::FArray1D< typename > , ObjexxFCL::FArray1P< typename > , ObjexxFCL::FArray2< typename > , ObjexxFCL::FArray2A< typename > , ObjexxFCL::FArray2D< typename > , ObjexxFCL::FArray2P< typename > , ObjexxFCL::FArray3< typename > , ObjexxFCL::FArray3A< typename > , ObjexxFCL::FArray3D< typename > , ObjexxFCL::FArray3P< typename > , ObjexxFCL::FArray4< typename > , ObjexxFCL::FArray4A< typename > , ObjexxFCL::FArray4D< typename > , ObjexxFCL::FArray4P< typename > , ObjexxFCL::FArray5< typename > , ObjexxFCL::FArray5A< typename > , ObjexxFCL::FArray5D< typename > , ObjexxFCL::FArray5P< typename > , ObjexxFCL::FArray6< typename > , ObjexxFCL::FArray6A< typename > , ObjexxFCL::FArray6D< typename > , ObjexxFCL::FArray6P< typename > , ObjexxFCL::KeyFArray1D< typename > , ObjexxFCL::KeyFArray2D< typename > , ObjexxFCL::KeyFArray3D< typename > , ObjexxFCL::KeyFArray4D< typename > , ObjexxFCL::KeyFArray5D< typename > , ObjexxFCL::KeyFArray6D< typename >
• A1() : A1
• A2() : A2
• A3() : A3
• A4() : A4
• abs_source() : BuildBindings.ModuleBuilder
• absolute() : utility::file::FileName , utility::file::PathName
• AbsoluteValueExpression() : numeric::expression_parser::AbsoluteValueExpression
• accept() : myMC
• activate() : utility::Bound< typename > , utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::options::Option , utility::options::ScalarOption , utility::options::ScalarOption_T_< K, T > , utility::options::VariantOption< O > , utility::options::VectorOption , utility::options::VectorOption_T_< K, T >
• activated_index() : utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C >
• active() : ObjexxFCL::CArray< typename > , ObjexxFCL::CArrayP< typename > , ObjexxFCL::FArray< typename > , utility::Bound< typename > , 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::options::Option , utility::options::ScalarOption_T_< K, T > , utility::options::VariantOption< O > , utility::options::VectorOption_T_< K, T >
• active_variables() : numeric::expression_parser::BinaryExpression , numeric::expression_parser::Expression , numeric::expression_parser::ITEExpression , numeric::expression_parser::LiteralExpression , numeric::expression_parser::MaxExpression , numeric::expression_parser::MetaMaxExpression , numeric::expression_parser::MetaMinExpression , numeric::expression_parser::MinExpression , numeric::expression_parser::UnaryExpression , numeric::expression_parser::VariableExpression
• acyclic() : ObjexxFCL::Observer
• add() : basic::datacache::ConstDataMap , basic::datacache::DataMap
• Add() : basic::sampling::orientations::QuatSet
• add() : binder::Context , Histogram , numeric::geometry::BoundingBox< typename > , utility::factory::Factory< typename > , utility::json_spirit::Config_map< String > , utility::json_spirit::Config_vector< String > , 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::options::OptionCollection
• add_already_defined_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_atom() : sidechain_cst_3.Residue
• add_attribute() : utility::tag::XMLSchemaComplexType , utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_attributes() : utility::tag::XMLSchemaComplexType , utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_back() : utility::vectorL< SSize, T, A >
• add_black_listed_file() : utility::Inline_File_Provider
• add_boundary_function() : numeric::interpolation::spline::SplineGenerator
• add_built_in_options() : utility::options::OptionCollection
• add_column() : app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable , basic::database::insert_statement_generator::InsertGenerator , basic::database::schema_generator::PrimaryKey , basic::database::schema_generator::Schema
• add_constraint() : basic::database::schema_generator::Schema
• add_constructor() : yaml.constructor.BaseConstructor
• add_decl() : binder::IncludeSet
• add_default_resource_locator() : basic::resource_manager::LazyResourceManager
• add_diagonal() : numeric::xyzMatrix< typename >
• add_edits() : utility::options::OptionCollection
• add_file_provider_hook() : utility::Inline_File_Provider
• add_first() : utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• add_footer() : zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• add_foreign_key() : basic::database::schema_generator::Schema
• add_function() : numeric::expression_parser::ArithmeticScanner
• add_group_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_header() : zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• add_implicit_resolver() : yaml.resolver.BaseResolver
• add_include() : binder::IncludeSet
• add_indent() : yaml.scanner.Scanner
• add_index() : basic::database::schema_generator::Schema
• add_input_file() : utility::Inline_File_Provider
• add_insertion_operator() : binder::Context
• add_job_options() : basic::resource_manager::LazyResourceManager
• add_key() : 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 >
• add_known_value() : numeric::interpolation::spline::SplineGenerator
• add_msg() : utility::excn::EXCN_Msg_Exception
• add_multi_constructor() : yaml.constructor.BaseConstructor
• add_multi_representer() : yaml.representer.BaseRepresenter
• add_observer() : PosePyObserver
• add_on_binders() : binder::Config
• add_option() : app.pyrosetta_toolkit.window_modules.options_system.OptionSystemManager.OptionSystemManager , basic::resource_manager::JobOptions
• add_optional_name_attribute() : utility::tag::XMLSchemaComplexTypeGenerator
• add_ordered_subelement_set_as_optional() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_ordered_subelement_set_as_pick_one() : utility::tag::XMLSchemaComplexTypeGenerator
• add_ordered_subelement_set_as_pick_one_optional() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_ordered_subelement_set_as_pick_one_or_none() : utility::tag::XMLSchemaComplexTypeGenerator
• add_ordered_subelement_set_as_pick_one_required() : utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_ordered_subelement_set_as_repeatable() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_ordered_subelement_set_as_required() : utility::tag::XMLSchemaComplexTypeGenerator , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• add_path_resolver() : yaml.resolver.BaseResolver
• add_range() : numeric::interpolation::spline::CompoundInterpolator
• add_reference_residue() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceResults
• add_region() : app.pyrosetta_toolkit.modules.Region.Regions , app.pyrosetta_toolkit.window_main.frames.InputFrame.InputFrame
• add_relevant() : utility::options::OptionCollection
• add_relevant_includes() : binder::Binder , binder::ClassBinder , binder::EnumBinder , binder::FunctionBinder
• add_representer() : yaml.representer.BaseRepresenter
• add_required_name_attribute() : utility::tag::XMLSchemaComplexTypeGenerator
• add_residue() : app.pyrosetta_toolkit.modules.DesignBreakdown.SequenceResults , app.pyrosetta_toolkit.modules.Structure.CDR
• add_resource() : basic::resource_manager::ResourceManager
• add_resource_configuration() : basic::resource_manager::LazyResourceManager
• add_resource_locator() : basic::resource_manager::LazyResourceManager
• add_resource_options() : basic::resource_manager::LazyResourceManager
• add_resource_tag_by_job_tag() : basic::resource_manager::LazyResourceManager
• add_restriction() : utility::tag::XMLSchemaRestriction
• add_rms() : numeric::model_quality::RmsData
• add_row() : app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable , basic::database::insert_statement_generator::InsertGenerator
• add_simple_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_standard_functions() : numeric::expression_parser::ArithmeticScanner
• add_symbol() : numeric::CalculatorParser
• add_to_binded() : binder::Context
• add_to_current() : utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• add_to_current_designs_callback() : app.pyrosetta_toolkit.window_modules.design.ResfileDesignWindow.ResfileDesignWindow
• add_top_level_element() : utility::tag::XMLSchemaDefinition
• add_value() : numeric::random::ReservoirSampler< T >
• add_variable() : numeric::expression_parser::ArithmeticScanner , numeric::expression_parser::SimpleExpressionCreator
• add_weight() : numeric::random::WeightedSampler
• addCentroid() : loadPDB.PDBres
• addCentroids() : loadPDB.Protein , loadPDB.ProteinChain
• AddExpression() : numeric::expression_parser::AddExpression
• addscCentroid() : loadPDB.PDBres
• addTag() : utility::tag::Tag
• after_send() : utility::signals::PausableSignalHub< ResultType, Signal > , utility::signals::SignalHub< ResultType, Signal >
• ala_interface() : HDdesignMover
• align() : fmt::AlignSpec , fmt::TypeSpec< TYPE > , numeric::xyzTransform< typename >
• align_fast() : numeric::xyzTransform< typename >
• AlignSpec() : fmt::AlignSpec
• AlignTypeSpec() : fmt::AlignTypeSpec< TYPE >
• all_matches_below_threshold() : numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >
• all_tracers() : basic::TracerManager
• allBenchmarks() : PerformanceBenchmark
• allocate_assign_char_buffer() : utility::io::ozstream
• analyze_and_filter() : UBQ_E2Mover , UBQ_GTPase_disulfide_Mover , UBQ_GTPaseMover
• analyze_scalar() : yaml.emitter.Emitter
• analyze_vip() : app.pyrosetta_toolkit.modules.protocols.AnalysisProtocols.AnalysisProtocols
• anchor_node() : yaml.serializer.Serializer
• AnchorFinderMover() : AnchorFinderMover
• AndExpression() : numeric::expression_parser::AndExpression
• angle() : numeric::BodyPosition< typename > , numeric::Quaternion< typename >
• angle_tolerance() : numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• angular_distance_between() : numeric::EulerAngles< typename >
• any_type() : rosetta_binders::has_insertion_operator_implementation::any_type
• AnyOption() : utility::options::AnyOption< T >
• AnyOptionKey() : utility::options::AnyOptionKey
• AnyVectorOption() : utility::options::AnyVectorOption< T >
• AnyVectorOptionKey() : utility::options::AnyVectorOptionKey
• APDBCMover() : APDBCMover
• append() : fmt::Buffer< T > , numeric::expression_parser::TokenSet , ObjexxFCL::ChunkVector< typename > , utility::vectorL< SSize, T, A >
• append_float_length() : fmt::BasicWriter< Char >
• append_particle() : utility::tag::XMLSchemaModelGroup
• append_particles() : utility::tag::XMLSchemaModelGroup
• apply() : AnchorFinderMover , APDBCMover , app.pyrosetta_toolkit.modules.protocols.AnalysisProtocols.VIP_Wrapper , app.pyrosetta_toolkit.modules.protocols.DesignProtocols.DesignWrapper , app.pyrosetta_toolkit.modules.protocols.DockingProtocols.LowResWrapper , app.pyrosetta_toolkit.modules.protocols.GraftingProtocols.GraftMover , app.pyrosetta_toolkit.window_modules.vicinity_options.vicinity_window.vicinityrelaxwindow , app.surface_docking.movers.Abinitio , app.surface_docking.movers.CentroidRelax , app.surface_docking.movers.FullAtomRelax , CaToAllAtom , CoupledMovesProtocol , DougsDockDesignMinimizeMagicMover , DummyMover , ExemplarMover , ExposedStrandMover , ExtractATD , FitMover , HbsDesignMover , HDdesignMover , HDmakerMover , IAMover , IdentifyCDRClusters , LigandDockBench , LigandRepackMinimizeProtocol , Minimize , MyScoreMover , NCMinimize , numeric::BodyPosition< typename > , numeric::Quaternion< typename > , OopDesignMover , PackingAngle , PeptoidDesignMover , PhProtocol , RmsfMover , src.protocols.jd2.RosettaScriptWrapper , src.PyMolLink.PyMOLMover , supercharge , test.T850_SubClassing.My_New_Mover , test.Workshop9_my_shapes.PhiNByXDegreesMover , UBQ_E2Mover , UBQ_GTPase_disulfide_Mover , UBQ_GTPaseMover , ViewMembraneProteinMover , zinc1_homodimer_design , zinc1_homodimer_setup , zinc2_homodimer_design , zinc2_homodimer_setup
• apply_map() : loadPDB.Protein , loadPDB.ProteinChain
• apply_to_failure() : src.protocols.jd2.RosettaScriptWrapper
• applyConstraints() : app.surface_docking.movers.FullAtomRelax
• approx_lever_distance() : numeric::xyzTransform< typename >
• are_sequences_for_regions_same_length() : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• are_sequences_same_length() : app.pyrosetta_toolkit.modules.DesignBreakdown.DesignBreakdown
• area() : test.Workshop9_my_shapes.MyCircle , test.Workshop9_my_shapes.MyShape , test.Workshop9_my_shapes.MySquare
• ArgFormatter() : fmt::internal::ArgFormatter< Char >
• ArgList() : fmt::ArgList
• args() : fmt::internal::FormatterBase
• ArgType() : fmt::internal::ArgType
• ArithmeticASTRestExpression() : numeric::expression_parser::ArithmeticASTRestExpression
• ArithmeticASTRestTerm() : numeric::expression_parser::ArithmeticASTRestTerm
• ArithmeticASTValue() : numeric::expression_parser::ArithmeticASTValue
• ArithmeticScanner() : numeric::expression_parser::ArithmeticScanner
• array_size() : ObjexxFCL::FArray< typename >
• array_size_bounded() : ObjexxFCL::FArray< typename >
• array_size_unbounded() : ObjexxFCL::FArray< typename >
• ascend_resolver() : yaml.resolver.BaseResolver
• asR() : numeric::urs_Quat
• assert_in() : basic::Emitter
• assert_valid_position() : numeric::MathVector< T >
• assign() : numeric::sphericalVector< typename > , numeric::xyzTriple< typename > , numeric::xyzVector< typename > , ObjexxFCL::CArray< typename > , ObjexxFCL::CArrayP< typename > , ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< typename > , ObjexxFCL::DynamicIndexRange , ObjexxFCL::format::Bite< T > , ObjexxFCL::IndexRange , ObjexxFCL::StaticIndexRange , utility::file::FileName , utility::file::PathName , 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 >
• assign_data() : utility::OrderedTuple< T >
• assign_IA_mover() : IAMover
• assign_if() : ObjexxFCL::Dimension
• assign_if_bigger() : ObjexxFCL::Dimension
• assign_if_bigger_nic() : ObjexxFCL::Dimension
• assign_if_half() : ObjexxFCL::Dimension
• assign_if_half_nic() : ObjexxFCL::Dimension
• assign_if_nic() : ObjexxFCL::Dimension
• assign_Key() : utility::keys::AutoKey< O, S, C > , utility::keys::Key , utility::keys::UserKey< O, S, C >
• assign_no_notify() : ObjexxFCL::DynamicIndexRange
• assign_value_of() : ObjexxFCL::Dimension , ObjexxFCL::StaticIndexRange
• ast_string() : numeric::expression_parser::ASTPrinter
• ASTPrinter() : numeric::expression_parser::ASTPrinter
• at() : numeric::xyzTriple< typename > , numeric::xyzVector< typename > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyVector< K, T > , utility::vectorL< SSize, T, A > , utility::vectorL< L, bool, A >
• at_end() : utility::FixedSizeLexicographicalIterator< S > , utility::LexicographicalIterator
• atomic_interaction_cutoff() : test.T870_SubClassing_EnergyMethods2.CD2B_Method , test.T870_SubClassing_EnergyMethods2.CI2B_Method , test.Workshop9_my_shapes.CI2BScoreMethod
• atomno() : numeric::geometry::hashing::Ball
• attach() : ObjexxFCL::CArrayP< typename > , ObjexxFCL::FArray1A< typename > , ObjexxFCL::FArray1P< typename > , ObjexxFCL::FArray2A< typename > , ObjexxFCL::FArray2P< typename > , ObjexxFCL::FArray3A< typename > , ObjexxFCL::FArray3P< typename > , ObjexxFCL::FArray4A< typename > , ObjexxFCL::FArray4P< typename > , ObjexxFCL::FArray5A< typename > , ObjexxFCL::FArray5P< typename > , ObjexxFCL::FArray6A< typename > , ObjexxFCL::FArray6P< typename > , ObjexxFCL::FArray< typename >
• attachDomains() : app.pyrosetta_toolkit.modules.Structure.protein_info
• attribute_w_default() : utility::tag::XMLSchemaAttribute
• auto_change_keep_observer_history() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• auto_change_observer() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• auto_change_send_observer_energies() : app.pyrosetta_toolkit.window_modules.pymol_integration.PyMOL.AdvancedPyMOL
• auto_increment() : basic::database::schema_generator::Column
• auto_increment_base() : basic::database::schema_generator::Column
• auto_set_decoys() : app.pyrosetta_toolkit.window_main.IO.GUIOutput.GUIOutput
• auto_set_write() : app.pyrosetta_toolkit.window_main.IO.GUIOutput.GUIOutput
• AutoKey() : utility::keys::AutoKey< O, S, C >
• available_resource_loaders() : basic::resource_manager::ResourceLoaderFactory
• AvNAPSA_values() : supercharge
• axis() : numeric::BodyPosition< typename > , numeric::Quaternion< typename >