Here is a list of all class members with links to the classes they belong to:

- a -

• a : _S2 , A1 , Atom , Base , basic::sampling::orientations::Triple , Bond , Data1 , ObjexxFCL::FArray1< T > , ObjexxFCL::FArray1A< T > , ObjexxFCL::FArray1D< T > , ObjexxFCL::FArray1P< T > , ObjexxFCL::FArray2< T > , ObjexxFCL::FArray2A< T > , ObjexxFCL::FArray2D< T > , ObjexxFCL::FArray2P< T > , ObjexxFCL::FArray3< T > , ObjexxFCL::FArray3A< T > , ObjexxFCL::FArray3D< T > , ObjexxFCL::FArray3P< T > , ObjexxFCL::FArray4< T > , ObjexxFCL::FArray4A< T > , ObjexxFCL::FArray4D< T > , ObjexxFCL::FArray4P< T > , ObjexxFCL::FArray5< T > , ObjexxFCL::FArray5A< T > , ObjexxFCL::FArray5D< T > , ObjexxFCL::FArray5P< T > , ObjexxFCL::FArray6< T > , ObjexxFCL::FArray6A< T > , ObjexxFCL::FArray6D< T > , ObjexxFCL::FArray6P< T > , ObjexxFCL::KeyFArray1D< T > , ObjexxFCL::KeyFArray2D< T > , ObjexxFCL::KeyFArray3D< T > , ObjexxFCL::KeyFArray4D< T > , ObjexxFCL::KeyFArray5D< T > , ObjexxFCL::KeyFArray6D< T > , outer::inner , POD4 , POD6 , S
• A() : Spacegroup
• A1() : A1
• a1_ : CoupledFunc
• A2() : A2 , PyCallBack_A2
• a2_ : CoupledFunc
• A3() : A3 , PyCallBack_A3
• A3BHbsCreatorMover() : A3BHbsCreatorMover
• A3BHbsDockDesignMinimizeMover() : A3BHbsDockDesignMinimizeMover
• A3BPeptideBuilder() : A3BPeptideBuilder
• A4() : A4 , PyCallBack_A4
• a_ : numeric::linear_algebra::EllipseParameters , Spacegroup
• a_double : Access
• a_float : testers::test_my_struct
• A_is_decomp_ : basic::svd::SVD_Solver
• A_is_set_ : basic::svd::SVD_Solver
• a_string : testers::test_my_struct
• a_vector : testers::test_my_struct
• aa : myspace::DataStruct , myspace::InputData
• aa1 : Hit , MatchLig
• aa2 : Hit , MatchLig
• aa2_dump_ : myspace::DataClass
• aa_ : ScoreFragInfo
• aas : Link
• ab_dock_chains() : protocols::antibody::design::AntibodyDesignMoverGenerator
• ab_dock_chains_ : protocols::antibody::design::AntibodyDesignMoverGenerator
• ab_info_ : myspace::GraftTester , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::task_operations::AddFrameworkProfilesOperation
• abbinding() : abbinding
• ABGEO() : JDmover
• abinitio_ : TryScoreFilter
• AbInitio_MPI() : AbInitio_MPI
• abort() : job_manager.CommandRunner , pyrosetta.distributed.cluster.logging_listeners.SocketListener , ui::network::Bowman , ui::network::BowmanThread
• abort_ : TCDock
• abort_button : job_manager.StatusWindow
• abort_network_operation() : ui::task::NetworkCall , ui::task::Node , ui::task::Updater
• abrelax_ : AbInitio_MPI
• abrelax_checkpoints_ : protocols::abinitio::JumpSpecificAbrelax
• abs_value : detail::int_writer< OutputIt, Char, UInt >
• AbsFunc() : AbsFunc
• absolute() : utility::file::FileName , utility::file::PathName
• AbsoluteValueExpression() : numeric::expression_parser::AbsoluteValueExpression
• absrms_to_orig_subsubs() : PoseWrap
• abv_motif_string_ : apps::pilot::frankdt::Motif
• acc_geom_check() : BuriedUnsatPolarsFinder
• accept() : myMC
• accept_ : myMC
• accept_and_report() : myspace::Scheduler
• acceptor_atoms_ : HBondedPairIterator
• acceptor_orbitals_ : HBondedPairIterator
• accessed_options_ : utility::tag::Tag
• accesses_jobinputter_in_apply() : AssignClusterToolMover
• accum : WorkDat
• accumulator() : detail::accumulator
• action_output_open() : ui::task::TaskView
• action_output_save_as() : ui::task::TaskView
• actions_ : utility::json_spirit::Json_grammer< Value_type, Iter_type >
• activate() : utility::Bound< T > , 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 : CST , DCST , ObjexxFCL::CArray< T > , ObjexxFCL::CArrayP< T > , ObjexxFCL::FArray< T > , utility::Bound< T > , 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_ : utility::Bound< T >
• active_set : Solver
• active_size : Solver
• 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
• adapt_threshold : pyrosetta.distributed.cluster.core.PyRosettaCluster
• add() : basic::citation_manager::CitationCollectionList , basic::datacache::ConstDataMap , basic::datacache::DataMap
• Add() : basic::sampling::orientations::QuatSet
• add() : binder::Context , numeric::geometry::BoundingBox< T > , numeric::sphericalVector< T > , numeric::xyzTriple< T > , numeric::xyzVector< T > , pyrosetta.bindings.pose.ResidueLabelAccessor , pyrosetta.distributed.viewer.core.Viewer , SetOfClusters , Tensor , ui::task::Node , utility::factory::Factory< P > , 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_already_defined_subelement_w_alt_element_name() : utility::tag::XMLSchemaSimpleSubelementList
• add_apcs_local() : PoseWrap
• 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_author() : basic::citation_manager::UnpublishedModuleInfo
• add_back() : utility::vectorL< L, T, A >
• add_black_listed_file() : utility::Inline_File_Provider
• add_boundary_function() : numeric::interpolation::spline::SplineGenerator
• add_buffer() : numeric::linear_algebra::EllipseParameters
• add_built_in_options() : utility::options::OptionCollection
• add_child() : SphereNode , utility::tag::XMLSchemaRepeatableCTNode
• add_citation() : basic::citation_manager::CitationCollection , basic::citation_manager::CitationManager
• add_citations() : basic::citation_manager::CitationManager
• add_co_author() : basic::citation_manager::Citation
• add_column() : basic::database::insert_statement_generator::InsertGenerator , basic::database::schema_generator::PrimaryKey , basic::database::schema_generator::Schema
• add_compare : detail::bigint
• add_constraint() : basic::database::schema_generator::Schema
• add_constraints() : protocols::abinitio::JumpSpecificAbrelax
• add_coordinate_constraints_to_pose() : MinTestMover
• add_decl() : binder::IncludeSet
• add_delimiter_spaces : formatting_range< Char, Enable > , formatting_tuple< Char, Enable >
• add_detached_scores_protocol() : pyrosetta.tests.distributed.cluster.test_smoke.ScoresTest
• add_diagonal() : numeric::xyzMatrix< T >
• add_distmax() : protocols::moves::SimpleCstMover
• add_distmin() : protocols::moves::SimpleCstMover
• add_domain() : DomainFinder
• add_edge() : utility::graph::Digraph , utility::graph::Graph , utility::graph::LowMemGraph< _LMNode, _LMEdge > , utility::graph::Node , utility::graph::UEVertex< V, E > , utility::graph::UpperEdgeGraph< V, E >
• add_edge_common() : utility::graph::UEVertex< V, E >
• add_edits() : utility::options::OptionCollection
• add_error() : utility::tag::XMLValidationOutput
• add_errors() : utility::tag::XMLValidationOutput
• add_evaluation() : protocols::abinitio::JumpSpecificAbrelax
• add_file() : ui::task::Task
• add_file_provider_hook() : utility::Inline_File_Provider
• add_first() : utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• add_flat_noise() : SimulateCryoMover
• add_float() : testers::test_my_struct
• add_floating_sc_csts() : PoseWrap
• add_footer() : zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• add_foreign_key() : basic::database::schema_generator::Schema
• add_frag_mover() : HECTAllMover , HECTMover
• add_function() : numeric::expression_parser::ArithmeticScanner
• add_functor() : ui::task::FunctorASyncSequence , ui::task::FunctorSequence
• add_gap_constraints_to_pose() : apps::pilot::SampleSecondaryStructureAlignmentMover
• add_gaussian_noise() : SimulateCryoMover
• add_group_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_hbond_and_omega_constraints_starting_at_seqpos() : A3BHbsCreatorMover
• add_header() : zlib_stream::basic_zip_ostream< Elem, Tr, ElemA, ByteT, ByteAT >
• add_if_missing() : utility::thread::MutableCache< K, V >
• add_include() : binder::IncludeSet
• add_incoming_edge() : utility::graph::DirectedNode
• add_index() : basic::database::schema_generator::Schema
• add_initial_constraints() : HemeBindingMover
• add_input_file() : utility::Inline_File_Provider
• add_insertion_operator() : binder::Context
• add_interface() : InterfaceHitDatabase
• add_job() : ui::task::Task
• 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_membrane_again() : TestQuickRelaxMover
• add_msg() : utility::excn::Exception
• add_mutant() : mutant_modeler.MutantModeler
• add_neighbor() : SphereNode
• add_node() : utility::graph::Digraph
• add_on_binder_for_namespaces() : binder::Config
• add_on_binder_for_namespaces_ : binder::Config
• add_on_binders() : binder::Config
• add_on_binders_ : binder::Config
• 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_outgoing_edge() : utility::graph::DirectedNode
• add_page() : job_manager.DatabaseWindow
• add_parent() : SphereNode
• add_perlin_noise() : SimulateCryoMover
• add_perturber() : Perturbers1 , Perturbers2
• add_prepostfix_space : formatting_range< Char, Enable > , formatting_tuple< Char, Enable >
• add_primary_author() : basic::citation_manager::Citation
• add_range() : numeric::interpolation::spline::CompoundInterpolator
• add_relevant() : utility::options::OptionCollection
• add_relevant_includes() : binder::Binder , binder::ClassBinder , binder::EnumBinder , binder::FunctionBinder
• add_relevant_includes_cached : binder::IncludeSet
• add_required_name_attribute() : utility::tag::XMLSchemaComplexTypeGenerator
• add_resource() : basic::datacache::DataMap
• add_restriction() : utility::tag::XMLSchemaRestriction
• add_rms() : numeric::model_quality::RmsData
• add_rounds() : CartPerturber
• add_row() : basic::database::insert_statement_generator::InsertGenerator
• add_score_types() : CapriTotalEnergy
• add_senior_author() : basic::citation_manager::Citation
• add_simple_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_standard_functions() : numeric::expression_parser::ArithmeticScanner
• add_subelement() : utility::tag::XMLSchemaSimpleSubelementList
• add_sym_cst() : ConstraintConfig
• add_symbol() : numeric::CalculatorParser
• add_symmop() : pointGroupHit
• add_task() : ui::task::Project
• add_to_binded() : binder::Context
• add_to_C() : pseudoTrace
• add_to_current() : utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• add_to_current_ : protocols::antibody::task_operations::AddFrameworkProfilesOperation
• add_to_N() : pseudoTrace
• add_to_scorefile() : MPInterfaceStatistics
• add_top_level_element() : utility::tag::XMLSchemaDefinition
• add_value() : HeapContainer< T, Comparator > , numeric::random::ReservoirSampler< T >
• add_variable() : numeric::expression_parser::ArithmeticScanner , numeric::expression_parser::SimpleExpressionCreator
• add_warnings() : utility::tag::XMLValidationOutput
• add_weight() : numeric::random::WeightedSampler
• add_zinc_constraints() : ZincMinimize
• AddExpression() : numeric::expression_parser::AddExpression
• AddFrameworkProfilesOperation() : protocols::antibody::task_operations::AddFrameworkProfilesOperation
• additional_decoy_info : pyrosetta.toolbox.py_jobdistributor.PyJobDistributor
• addmem_ : TestQuickRelaxMover
• address_ : ui::task::NetworkCall
• addTag() : utility::tag::Tag
• addTrace() : pseudoTraceRecords
• adjacent_bbbb_check() : BuriedUnsatPolarsFinder
• advance_to() : basic_format_context< OutputIt, Char > , basic_format_parse_context< Char, ErrorHandler > , basic_printf_context< OutputIt, Char >
• AE1 : A< T >
• AE1_V0 : A< T >
• AE1_V1 : A< T >
• AE2_struct : A< T >
• AE3_class : A< T >
• AE3_not_binded : A< T >
• AE3_V0_not_binded : A< T >
• AE3_V1_not_binded : A< T >
• AE4_not_binded : A< T >
• AE5_not_binded : A< T >
• AE5_V0_not_binded : A< T >
• AE5_V1_not_binded : A< T >
• AE6_not_binded : A< T >
• affiliation() : basic::citation_manager::UnpublishedModuleAuthor
• affiliation_ : basic::citation_manager::UnpublishedModuleAuthor
• after_send() : utility::signals::PausableSignalHub< ReturnType, Signal > , utility::signals::SignalHub< ReturnType, Signal >
• age() : schema.Job
• AHD_and_dist_check() : BuriedUnsatPolarsFinder
• AHD_geom_eval_threshold : xtal_water_bunsat
• AHD_geom_eval_threshold_ : hbond_geom_strat
• AHdist_geom_eval_threshold : xtal_water_bunsat
• AHdist_geom_eval_threshold_ : hbond_geom_strat
• ala_interface() : HDdesignMover
• ala_interface_ : HDdesignMover
• algorithm : schema.Job
• algorithm_ : NativeEnsemble
• align : basic_format_specs< Char > , detail::bigint , numeric::xyzTransform< T >
• align_c() : Link
• align_chunk() : apps::pilot::AlignChunkMover
• align_chunk_ : apps::pilot::MultiTemplateAlignChunkMover
• align_clusters() : ClusterCycDisulf
• align_fast() : numeric::xyzTransform< T >
• align_info() : MatchAligner , MatchLig , Tet4HMatchAligner
• align_n() : Link
• align_option_ : apps::pilot::MultiTemplateAlignChunkMover
• align_orig_pose() : PoseWrap
• align_rot() : MatchAligner , Tet4HMatchAligner
• align_to_ss_only_ : apps::pilot::AlignChunkMover
• align_trial_counter_ : apps::pilot::AlignChunkMover
• AlignChunkMover() : apps::pilot::AlignChunkMover
• aligned_ : ThisApplication
• aligned_seq_ : ThisApplication
• alive : pyrosetta.tests.distributed.test_gil.HeartBeat
• all() : pyrosetta.bindings.pose.PoseScoreAccessor , pyrosetta.bindings.scores.core.PoseCacheAccessor , pyrosetta.bindings.scores.energies.EnergiesAccessor , pyrosetta.bindings.scores.extra_scores.ExtraFloatScoresDataAccessor , pyrosetta.bindings.scores.extra_scores.ExtraScoresAccessor , pyrosetta.bindings.scores.extra_scores.ExtraStringScoresDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeRealDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricCompositeStringDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueProbabilitiesDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueRealDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricPerResidueStringDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricRealDataAccessor , pyrosetta.bindings.scores.simple_metrics.SimpleMetricStringDataAccessor
• All : utility::options::OptionCollection
• all_ : SphereSampler , utility::options::OptionCollection
• all_keys() : pyrosetta.bindings.scores.core.PoseCacheAccessor
• all_matches_below_threshold() : numeric::coordinate_fitting::FlatLookup< QueryType, EntryType, Real >
• all_messages_ : utility::SimulateMPIData
• all_pairs_shortest_paths() : utility::graph::Graph
• all_scores() : pyrosetta.bindings.scores.core.PoseCacheAccessor
• allBenchmarks() : PerformanceBenchmark
• AllCrmsd() : AllCrmsd
• allfrags : FragmentAssemblyMover
• allnodes_ : SphereSample
• alloc_ : basic_memory_buffer< T, SIZE, Allocator >
• allocate_assign_char_buffer() : utility::io::ozstream
• allocated() : utility::graph::NegSpaceElement< T >
• allocated_ : utility::graph::NegSpaceElement< T >
• Allocator : utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyMapTraits< K, T > , utility::keys::KeySetTraits< K > , utility::keys::KeyVector< K, T > , utility::keys::KeyVectorTraits< K > , utility::keys::SmallKeyMap< K, T > , utility::keys::SmallKeyVector< K, T > , utility::vector0< T, A > , utility::vector0< bool, A > , utility::vector1< T, A > , utility::vector1< bool, A > , utility::vectorL< L, T, A > , utility::vectorL< L, bool, A >
• allocator_type : utility::keys::ClassKeyMap< K, T, C > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyMapTraits< K, T > , utility::keys::KeySetTraits< K > , utility::keys::KeyVector< K, T > , utility::keys::KeyVectorTraits< K > , utility::keys::SmallKeyMap< K, T > , utility::keys::SmallKeyVector< K, T > , utility::vector0< T, A > , utility::vector0< bool, A > , utility::vector1< T, A > , utility::vector1< bool, A > , utility::vectorL< L, T, A > , utility::vectorL< L, bool, A >
• allow_de_ : zinc_stats::ZincStatisticGenerator
• allow_his_ : zinc_stats::ZincStatisticGenerator
• allow_null_ : basic::database::schema_generator::Column
• allow_reuse_address : pyrosetta.distributed.cluster.logging_listeners.SocketListener
• allow_syn_pyrimidine : erraser_option.erraser_option
• allowed_elements_ : MetalSiteFinderMover
• allowed_elements_list_ : MetalSiteFinderMover
• allowed_secstruct_ : zinc_stats::ZincStatisticGenerator
• AllowLoopEnd : StructureConfidence
• allowNonProtein_ : HBondReporter
• aln_chain_ : CalcIrms
• alpha : decision_function , Solver , Spacegroup , WorkDat
• alpha_ : Arch , Spacegroup , TCDock
• alpha_status : Solver
• alt : basic_format_specs< Char >
• alternative_search_paths_ : utility::io::izstream
• always_show_output : job_manager.StatusWindow
• am_ : PickBAB
• an_int : testers::test_my_struct
• analyze_and_filter() : UBQ_E2Mover , UBQ_GTPase_disulfide_Mover
• analyze_tree() : ThisApplication
• anchor : APDBCMover
• AnchorFinderMover() : AnchorFinderMover
• AndExpression() : numeric::expression_parser::AndExpression
• angle : latticeHit , numeric::BodyPosition< T > , numeric::Quaternion< T >
• angle1() : Arch
• angle1_ : Arch
• angle2() : Arch
• angle2_ : Arch
• angle_max_ : TestQuickRelaxMover
• angle_of : numeric::xyzTriple< T >
• angle_scorefxn_ : zinc1_homodimer_design
• angle_stdev_ : ZincMatchFilter
• angle_tolerance() : numeric::NumericTraits< double > , numeric::NumericTraits< float > , numeric::NumericTraits< long double >
• angle_weight_ : ZincMatchFilter
• ANGLE_WT : pseudoTrace
• angth : KRSQuery
• angular_distance_between() : numeric::EulerAngles< T >
• AnnealableGraphBaseOP : core::pack::annealer::FixbbSimAnnealer
• ansi_color_escape() : detail::ansi_color_escape< Char >
• AntibodyDesignMoverGenerator() : protocols::antibody::design::AntibodyDesignMoverGenerator
• AntibodyInfoRMLoader() : protocols::surface_docking::AntibodyInfoRMLoader
• AntibodyInfoRMOptions() : protocols::antibody::AntibodyInfoRMOptions
• any_type() : rosetta_binders::has_insertion_operator_implementation::any_type , utility::type_traits::has_insertion_operator_implementation::any_type
• any_vectors_ : utility::options::OptionCollection
• AnyOption() : utility::options::AnyOption< T >
• AnyOptionKey() : utility::options::AnyOptionKey
• Anys : utility::options::OptionCollection
• anys_ : utility::options::OptionCollection
• AnyVectorOption() : utility::options::AnyVectorOption< T >
• AnyVectorOptionKey() : utility::options::AnyVectorOptionKey
• AnyVectors : utility::options::OptionCollection
• APDBCMover() : APDBCMover
• apolar : fiberHit
• app : ui::task::Task::Job
• append() : basic_memory_buffer< T, SIZE, Allocator > , detail::buffer< T > , numeric::expression_parser::TokenSet , ObjexxFCL::ChunkVector< T > , SecondaryStructureChunk , utility::vectorL< L, T, A > , utility::vectorL< L, bool, A >
• append_Aform_residue() : dsRNA_grow
• append_common_tag_subelements() : FixbbJobQueen
• append_component() : enumerate_junctions.Design
• append_job_tag_subelements() : FixbbJobQueen
• append_particle() : utility::tag::XMLSchemaModelGroup
• append_particles() : utility::tag::XMLSchemaModelGroup
• append_symmops() : pointGroupHit
• append_to_density() : SimulateCryoMover
• append_to_fragment_store() : pyrosetta.protocols.h5_fragment_store_provider.H5PyFragmentStoreProvider
• append_vec() : testers::test_my_struct
• AppendDataBytes() : GetURLHandler
• Application() : protocols::abinitio::Application
• ApplicationContext() : protocols::abinitio::ApplicationContext
• apply() : A3BHbsCreatorMover , A3BHbsDockDesignMinimizeMover , A3BPeptideBuilder , abbinding , AbInitio_MPI , AnchorFinderMover , APDBCMover , apps::pilot::AlignChunkMover , apps::pilot::CustomFragmentMover , apps::pilot::CustomStarTreeMover , apps::pilot::HelixMover , apps::pilot::MultiTemplateAlignChunkMover , apps::pilot::SampleSecondaryStructureAlignmentMover , AssignClusterToolMover , B3AADihedralGrabber , BacksideHbondFinderMover , BBG_Cyclic_Mover , BBMover , Benchmark , BondedRNA_Mover , BreadthMover , BUNS_Output , BuriedUnsatPolarsFinder , CalcCdrRms , CalcIrms , CalcsTestMover , CartPerturber , CartRefineWrapperMover , CaToAllAtom , CenRelaxMover , CenRotCanonicalMover , CenRotDockingMover , CenRotRBRelaxMover , CenRotRelaxMover , CenRotSidechainMover , ChallengeMover , ChiMover , ClearPoseHeader , CloseContactWithResidue , ClosureMover , CollectCoordinates , ColorByLipidType , complex_interface_optimize , compute_Irmsd , ComputeProfileMover , ComputeSAXSSpectrum , ConcertedTorsionMover , ConstraintMinimizer , ConstraintStatsMover , ConstraintToolMover , CountContact , CovalentPeptidomimeticCreator , CovalentPeptidomimeticDockDesign , CrystCluster , CrystDesign , CrystFFTDock , CrystHbondsReporter , CrystRelax , CustomMover , CycBBMover , DeleteSegments , Designer , DesignGlycansProtocol , DetectSymmetry , DockGlycansProtocol , DougsDockDesignMinimizeMagicMover , dsRNA_grow , DuboisChiMover , DummyMover , ElecDensMinPackMinMover , EnvToolMover , ExemplarMover , ExposedStrandMover , ExtractATD , FaSolReporter , FastThreadingMover , FindOptimalHydrophobicThk , FitMover , FloatScMonteCarlo , FloatScRandomChi , FloatScRotMover , FloppyTailMover , Foldptn , FoldTreeOutputter , ForgetMover , FragmentBasedDesign , generate_hbond_geometry , GlycanClashCheckMover , GlycomutagenesisProtocol , GraftDesignCDRs , GunnTest , hackLAMMover , HBondReporter , HbondZinc , HbondZincBackbone , HbsCreatorMover , HbsDesignMover , HDdesignMover , HDmakerMover , HECTMover , HelicalPdbGeneratorMover , HemaggTrimer , HemeBindingMover , HemeReplace , Hit , HolesTrainingDataMover , HotspotPlacementMover , IAMover , IdentifyCDRClusters , InjectorMover , InteractionDistMinimizer , InterfaceDDGMover , InterfaceFeaturesTests , InterfaceStrandFinderMover , InverseRotlibDumpMover , JDmover , JDtestmover , khSandbox2 , KHSandbox , khSandbox , LDConverterMover , LigandDockingHbondsReporter , LigandRepackMinimizeProtocol , LigChiMover , LoadMembraneMover , LocalRmsd , LoopHash_Analyze , LoopHashRelax_Sampler , MakeCanonicalHelix , MakeSegmentFileMPI , MembraneDockingxMover , MembraneMinMover , MembraneRelaxMover , MembraneSampleMover , MembraneSfxnMover , MembraneTransformMover , MembraneViewMover , MetalSiteFinderMover , MikeLinkerMover , MinCenrotMover , Minimize , MinPackMinMover , MinTestMover , MinToolMover , MirrorSymmTest , MotifDock , MotifScanMover , MoveThenFixH , MoveThenFixHMin , MPDomainAssembly , MPFindInterfaceTestMover , MPFoldingMover , MPframeworkTest1Mover , MPframeworkTestMover , MPInterfaceStatistics , MPScoreFunctionFingerprintMover , mtransferase , MyApp , MyMover , MyProtocol , MyRotMover , MyScoreMover , MySlideMover , myspace::Evaluator , myspace::GraftTester , MyTransMover , NativeEnsemble , NCMinimize , numeric::BodyPosition< T > , numeric::Quaternion< T > , OopDesignMover , OutputCenrotIntCoord , OutputMover , Packing_energies , PackingAngle , PairDistance , PBPotentialMover , PepMinMover , PeptiodMovieMover , PeptoidDesignMover , PeptoidDihedralGrabber , PeptoidRotamerRecoverer , PerturbStruct , PhDocking , PhProtocol , PickBAB , PrintFeatures , PrintPDDF , PrintSequenceMover , Protocol_MolecularDynamics , protocols::abinitio::ComputeTotalDistCst , protocols::abinitio::PcaEvaluator , protocols::abinitio::ShowViolation , protocols::abinitio::Stage1Sampler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::task_operations::AddFrameworkProfilesOperation , protocols::moves::FragCaptureMover , protocols::moves::SimpleCstMover , pyrosetta.bindings.scores.base.PoseCacheAccessorBase , pyrosetta.distributed.tasks.rosetta_scripts.MultioutputRosettaScriptsTask , pyrosetta.distributed.tasks.rosetta_scripts.SingleoutputRosettaScriptsTask , pyrosetta.distributed.viewer.modules.setBackgroundColor , pyrosetta.distributed.viewer.modules.setDisulfides , pyrosetta.distributed.viewer.modules.setHydrogenBonds , pyrosetta.distributed.viewer.modules.setHydrogens , pyrosetta.distributed.viewer.modules.setStyle , pyrosetta.distributed.viewer.modules.setSurface , pyrosetta.distributed.viewer.modules.setZoom , pyrosetta.distributed.viewer.modules.setZoomTo , RamaTestMover , RDCScoreMover , RDCToolMover , RDF_Mover , RelaxCDRsMover , RepackCenrotMover , RepackMinCenrotMover , RescoreCenrot , RescorePDDF , RescoreSAXS , RMSByResStatistics , RmsfMover , RNA_ScoreMover , RosettaHolesMover , RotateSAXS , run_score_hotspot , run_score_patchdock_hotspot , SampleTiltProtocol , Sasa , sasa_qdMover , ScMinMover , ScoreFunctionFingerprintMover , ScoreMover , ScTrials , SeqBBTorSRFD , SetupHotspotMover , SetupMover , SilentProlineFixMover , SimpleBBMover , SimulateCryoMover , SmoothFragRepackMover , SpartaSuperDeviationMover , SSM_energies , StatefulMover , StepwiseTorsionMover , SuperDeviationMover , SwapElementsMover1 , SwapElementsMover2 , SymFixbbMover , SymRBMover , test.T850_SubClassing.My_New_Mover , test.Workshop9_my_shapes.PhiNByXDegreesMover , TestJD2Mover , TestMMOP , TestQuickRelaxMover , TNM , TorsionVectorMover , TriazoleCreator , TrizaolamerDockDesignMinimizeMover , UBQ_E2Mover , UBQ_GTPase_disulfide_Mover , ViewMembraneProteinMover , XMLprinterMover , xtal_water_bunsat , ZF_PatchupMover , zinc1_homodimer_design , zinc1_homodimer_setup , zinc2_homodimer_design , zinc2_homodimer_setup , zinc_helix_cap , ZincMatchFilter , ZincMinimize , ZincSiteEvaluator
• apply_bb_csts() : ConstraintConfig
• apply_cen_csts() : ConstraintConfig
• apply_csts() : ConstraintConfig
• apply_dcsts() : ConstraintConfig
• apply_fa_csts() : ConstraintConfig
• apply_linking_constraints() : protocols::jd2::RECONMPIJobDistributor
• apply_parsed_protocol() : protocols::jd2::RECONMPIJobDistributor
• apply_transform() : apps::pilot::AlignChunkMover
• approx_lever_distance() : numeric::xyzTransform< T >
• AppSettings() : AppSettings
• arch() : TCDock
• arch_ : TCDock
• ArchI32() : ArchI32
• ArchI52() : ArchI52
• ArchI53() : ArchI53
• ArchO32() : ArchO32
• ArchO42() : ArchO42
• ArchO43() : ArchO43
• ArchP4_42() : ArchP4_42
• ArchP4g_42d() : ArchP4g_42d
• ArchP4m_42d() : ArchP4m_42d
• ArchP6_32() : ArchP6_32
• ArchP6m_32d() : ArchP6m_32d
• ArchT32() : ArchT32
• ArchT33() : ArchT33
• area() : test.Workshop9_my_shapes.MyCircle , test.Workshop9_my_shapes.MyShape , test.Workshop9_my_shapes.MySquare
• arg() : basic_format_context< OutputIt, Char > , basic_printf_context< OutputIt, Char >
• Arg : utility::factory::Factory< P >
• arg_ : detail::arg_converter< T, Context > , detail::char_converter< Context >
• arg_converter() : detail::arg_converter< T, Context >
• arg_data() : detail::arg_data< T, Char, NUM_ARGS, NUM_NAMED_ARGS > , detail::arg_data< T, Char, NUM_ARGS, 0 >
• arg_FArray : ObjexxFCL::FArray1< T > , ObjexxFCL::FArray1A< T > , ObjexxFCL::FArray1D< T > , ObjexxFCL::FArray2< T > , ObjexxFCL::FArray2A< T > , ObjexxFCL::FArray2D< T > , ObjexxFCL::FArray3< T > , ObjexxFCL::FArray3A< T > , ObjexxFCL::FArray3D< T > , ObjexxFCL::FArray4< T > , ObjexxFCL::FArray4A< T > , ObjexxFCL::FArray4D< T > , ObjexxFCL::FArray5< T > , ObjexxFCL::FArray5A< T > , ObjexxFCL::FArray5D< T > , ObjexxFCL::FArray6< T > , ObjexxFCL::FArray6A< T > , ObjexxFCL::FArray6D< T >
• arg_formatter() : detail::arg_formatter< OutputIt, Char >
• arg_formatter_base() : detail::arg_formatter_base< OutputIt, Char, ErrorHandler >
• arg_id() : basic_format_context< OutputIt, Char > , detail::format_part< Char >::replacement , detail::id_adapter< Handler, Char >
• arg_id_end : detail::format_part< Char >
• arg_index : detail::format_part< Char >::value
• arg_join() : arg_join< It, Sentinel, Char >
• arg_ref() : detail::arg_ref< Char >
• arg_ref_type : detail::dynamic_specs_handler< ParseContext > , formatter< std::chrono::duration< Rep, Period >, Char >
• arg_type_ : detail::numeric_specs_checker< ErrorHandler >
• args() : basic_format_context< OutputIt, Char > , detail::arg_data< T, Char, NUM_ARGS, NUM_NAMED_ARGS > , detail::arg_data< T, Char, NUM_ARGS, 0 > , detail::default_arg_formatter< OutputIt, Char >
• args_ : basic_format_args< Context > , basic_format_context< OutputIt, Char > , basic_printf_context< OutputIt, Char > , detail::arg_data< T, Char, NUM_ARGS, NUM_NAMED_ARGS > , detail::arg_data< T, Char, NUM_ARGS, 0 >
• Argument() : ui::network::Argument
• argv_copy_ : utility::options::OptionCollection
• ArithmeticASTFactor() : numeric::expression_parser::ArithmeticASTFactor
• ArithmeticASTRestAndClause() : numeric::expression_parser::ArithmeticASTRestAndClause
• ArithmeticASTRestExpression() : numeric::expression_parser::ArithmeticASTRestExpression
• ArithmeticASTRestOrClause() : numeric::expression_parser::ArithmeticASTRestOrClause
• ArithmeticASTRestTerm() : numeric::expression_parser::ArithmeticASTRestTerm
• ArithmeticASTValue() : numeric::expression_parser::ArithmeticASTValue
• ArithmeticScanner() : numeric::expression_parser::ArithmeticScanner
• array() : utility::graph::NegSpaceElement< T >
• Array : utility::json_spirit::Value_impl< Config >
• Array0() : utility::graph::Array0< T >
• array_ : ObjexxFCL::CArray< T > , ObjexxFCL::CArrayP< T > , ObjexxFCL::Chunk< T > , ObjexxFCL::FArray1< T > , ObjexxFCL::FArray1A< T > , ObjexxFCL::FArray1D< T > , ObjexxFCL::FArray1P< T > , ObjexxFCL::FArray2< T > , ObjexxFCL::FArray2A< T > , ObjexxFCL::FArray2D< T > , ObjexxFCL::FArray2P< T > , ObjexxFCL::FArray3< T > , ObjexxFCL::FArray3A< T > , ObjexxFCL::FArray3D< T > , ObjexxFCL::FArray3P< T > , ObjexxFCL::FArray4< T > , ObjexxFCL::FArray4A< T > , ObjexxFCL::FArray4D< T > , ObjexxFCL::FArray4P< T > , ObjexxFCL::FArray5< T > , ObjexxFCL::FArray5A< T > , ObjexxFCL::FArray5D< T > , ObjexxFCL::FArray5P< T > , ObjexxFCL::FArray6< T > , ObjexxFCL::FArray6A< T > , ObjexxFCL::FArray6D< T > , ObjexxFCL::FArray6P< T > , ObjexxFCL::FArray< T > , ObjexxFCL::FArraySection< T > , ObjexxFCL::KeyFArray1D< T > , ObjexxFCL::KeyFArray2D< T > , ObjexxFCL::KeyFArray3D< T > , ObjexxFCL::KeyFArray4D< T > , ObjexxFCL::KeyFArray5D< T > , ObjexxFCL::KeyFArray6D< T > , utility::fixedsizearray0< T, S > , utility::fixedsizearray1< T, S > , utility::graph::Array0< T > , utility::graph::ArrayPoolElement< T > , utility::graph::NegSpaceElement< T > , utility::json_spirit::Json_grammer< Value_type, Iter_type >::definition< ScannerT >
• array_blocks_ : utility::graph::ArrayPool< T >
• array_size() : ObjexxFCL::FArray< T > , utility::graph::ArrayPool< T >
• array_size_ : ObjexxFCL::FArray1< T > , ObjexxFCL::FArray1A< T > , ObjexxFCL::FArray1D< T > , ObjexxFCL::FArray1P< T > , ObjexxFCL::FArray2< T > , ObjexxFCL::FArray2A< T > , ObjexxFCL::FArray2D< T > , ObjexxFCL::FArray2P< T > , ObjexxFCL::FArray3< T > , ObjexxFCL::FArray3A< T > , ObjexxFCL::FArray3D< T > , ObjexxFCL::FArray3P< T > , ObjexxFCL::FArray4< T > , ObjexxFCL::FArray4A< T > , ObjexxFCL::FArray4D< T > , ObjexxFCL::FArray4P< T > , ObjexxFCL::FArray5< T > , ObjexxFCL::FArray5A< T > , ObjexxFCL::FArray5D< T > , ObjexxFCL::FArray5P< T > , ObjexxFCL::FArray6< T > , ObjexxFCL::FArray6A< T > , ObjexxFCL::FArray6D< T > , ObjexxFCL::FArray6P< T > , ObjexxFCL::FArray< T > , ObjexxFCL::KeyFArray1D< T > , ObjexxFCL::KeyFArray2D< T > , ObjexxFCL::KeyFArray3D< T > , ObjexxFCL::KeyFArray4D< T > , ObjexxFCL::KeyFArray5D< T > , ObjexxFCL::KeyFArray6D< T > , utility::graph::ArrayPool< T >
• array_size_bounded() : ObjexxFCL::FArray< T >
• array_size_unbounded() : ObjexxFCL::FArray< T >
• Array_type : utility::json_spirit::Config_map< String > , utility::json_spirit::Config_vector< String > , utility::json_spirit::Generator< Value_type, Ostream_type > , utility::json_spirit::Semantic_actions< Value_type, Iter_type >
• ArrayPool() : utility::graph::ArrayPool< T > , utility::graph::ArrayPoolElement< T >
• ArrayPoolElement() : utility::graph::ArrayPoolElement< T >
• article_title() : basic::citation_manager::Citation
• article_title_ : basic::citation_manager::Citation
• as_string() : fiberHit , pointGroupHit
• asR() : numeric::urs_Quat
• assert_in() : basic::Emitter
• assert_unique_keys() : pyrosetta.bindings.scores.core.PoseCacheAccessor
• assert_valid_position() : numeric::MathVector< T >
• assign() : detail::bigint , detail::fp , numeric::sphericalVector< T > , numeric::xyzTriple< T > , numeric::xyzVector< T > , ObjexxFCL::CArray< T > , ObjexxFCL::CArrayP< T > , ObjexxFCL::Chunk< T > , ObjexxFCL::ChunkVector< T > , 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_ownership() : ui::task::Project
• assign_pow10() : detail::bigint
• assign_ss_ : MyScoreMover
• assign_value_of() : ObjexxFCL::Dimension , ObjexxFCL::StaticIndexRange
• AssignClusterToolMover() : AssignClusterToolMover
• assigned_frags : FragmentAssemblyMover
• assigned_frags_ : FragMonteCarlo
• assignment : numeric::CalculatorParser
• Assignments_ : numeric::VoxelGrid< T >
• ast_context : BinderVisitor
• ast_string() : numeric::expression_parser::ASTPrinter
• ASTPrinter() : numeric::expression_parser::ASTPrinter
• at() : numeric::VoxelArray< _Float, _Value > , numeric::xyzTriple< T > , utility::keys::ClassKeyVector< K, T, C > , utility::keys::KeyVector< K, T > , utility::keys::SmallKeyVector< K, T > , utility::small_vectorL< T, L, BUFFER_SIZE > , utility::vectorL< L, T, A > , utility::vectorL< L, bool, A >
• at_end() : utility::FixedSizeLexicographicalIterator< S > , utility::LexicographicalIterator
• atm1 : DCST
• atm2 : DCST
• Atom() : Atom
• atom() : SameResidueTypeConstraint
• atom_hydrophobic_ : MyAtom
• atom_i() : DistancePrediction
• atom_i_ : DistancePrediction
• atom_ids_ : SameResidueTypeConstraint
• atom_j() : DistancePrediction
• atom_j_ : DistancePrediction
• atom_map_ : apps::pilot::AlignChunkMover
• atom_name() : DistanceMatrix , pep_coord_cst
• atom_name_ : DistanceMatrix
• atom_sasa_ : xtal_water_bunsat
• atom_sasa_cutoff_ : BacksideHbondFinderMover
• atom_scores() : RosettaHolesMover
• atom_scores_ : RosettaHolesMover
• atom_type_name() : RDF_Mover
• atom_vdw_ : CustomMover
• atomic_interaction_cutoff() : CapriTotalEnergy , CapriTwoBodyEnergy , test.T870_SubClassing_EnergyMethods2.CD2B_Method , test.T870_SubClassing_EnergyMethods2.CI2B_Method , test.Workshop9_my_shapes.CI2BScoreMethod
• atomID : HECTMover
• AtomID : SwapElementsMover1 , SwapElementsMover2
• atomID : UBQ_E2Mover
• atomid_is_contacting_crystallographic_water() : xtal_water_bunsat
• atomID_tot : HECTMover , UBQ_E2Mover
• atomIDs : HECTMover , UBQ_E2Mover , UBQ_GTPase_disulfide_Mover
• atomno() : numeric::geometry::hashing::Ball
• atomno_ : numeric::geometry::hashing::Ball
• AtomNumFilter() : AtomNumFilter
• atoms_ : sidechain_cst_3.Residue
• atoms_to_constrain_ : HemeBindingMover
• atr() : GridWeights
• atr_ : GridWeights
• atr_mult_ : DockGlycansProtocol
• attach() : ObjexxFCL::CArrayP< T > , ObjexxFCL::FArray1A< T > , ObjexxFCL::FArray1P< T > , ObjexxFCL::FArray2A< T > , ObjexxFCL::FArray2P< T > , ObjexxFCL::FArray3A< T > , ObjexxFCL::FArray3P< T > , ObjexxFCL::FArray4A< T > , ObjexxFCL::FArray4P< T > , ObjexxFCL::FArray5A< T > , ObjexxFCL::FArray5P< T > , ObjexxFCL::FArray6A< T > , ObjexxFCL::FArray6P< T > , ObjexxFCL::FArray< T > , PoseWrap
• attach_as_sc_ : PoseWrap
• attach_atom_ : PoseWrap
• attach_rsd_ : PoseWrap
• attach_to_region_ : PoseWrap
• attach_valid() : enumerate_junctions.Design
• attached_scattach_res_ : PoseWrap
• attached_scattach_res_name_ : PoseWrap
• attempt_pyrimidine_flip : erraser_option.erraser_option
• attribute_w_default() : utility::tag::XMLSchemaAttribute
• attributes : utility::tag::XMLSchemaSimpleSubelementList::ElementSummary
• attributes_ : utility::tag::XMLSchemaComplexType , utility::tag::XMLSchemaComplexTypeGeneratorImpl
• author_name() : basic::citation_manager::UnpublishedModuleAuthor
• author_name_ : basic::citation_manager::UnpublishedModuleAuthor
• AuthorNames() : basic::citation_manager::AuthorNames
• authors_ : basic::citation_manager::UnpublishedModuleInfo
• auto_cut : ElecDensMinPackMinReporter
• auto_increment() : basic::database::schema_generator::Column
• auto_increment_ : basic::database::schema_generator::Column
• auto_increment_base() : basic::database::schema_generator::Column
• auto_increment_base_ : basic::database::schema_generator::Column
• AutoKey() : utility::keys::AutoKey< O, S, C > , utility::keys::Key
• av_dev_RDCs_ : RDCToolMover
• available_resource_loaders() : basic::resource_manager::ResourceLoaderFactory
• average_RDCs_ : RDCToolMover
• axes : pointGroupHit
• axis : HelixHit , MatchAlignInfo , numeric::BodyPosition< T >
• Axis : numeric::BodyPosition< T > , numeric::Quaternion< T >
• axis() : numeric::Quaternion< T > , pointGroupHit , SphereNode
• axis1() : Arch
• axis1_ : Arch
• axis2() : Arch
• axis2_ : Arch
• axis_ : SphereNode
• axis_range() : numeric::interpolation::InterpolatedPotential< N >
• axis_ranges_ : numeric::interpolation::InterpolatedPotential< N >
• axismap_ : TCDock
• AxisRotationSampler() : numeric::AxisRotationSampler
• axs : Hit , KRSQuery