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

- t -

• t : protocols::hybridization::TMalign
• T_ : core::scoring::ResidualDipolarCoupling , protocols::toolbox::InteratomicVarianceMatrix
• t_ang_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::RNA_AnalyticLoopCloser
• T_bins : core::scoring::dna::DirectReadoutPotential
• T_ndx : protocols::moves::ReplicaExchangeMC
• t_predicate_func : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• T_rev : protocols::moves::ReplicaExchangeMC
• T_SURFACE : protocols::pockets::PocketGrid
• T_tag : protocols::moves::ReplicaExchangeMC
• TAB_DIR : protocols::sparta::Sparta::SpartaLib
• table_ : core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllEnergyContainer , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::DenseEnergyContainer
• table_size_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• TableLookupEtableEnergy() : core::scoring::etable::TableLookupEtableEnergy
• TableLookupEvaluator() : core::scoring::etable::TableLookupEvaluator
• tables_ : core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedEnergyContainer
• taboo_map_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• taboo_map_max_capacity_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• taboo_master_map_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• TabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• tabulate() : core::scoring::saxs::FormFactor , core::scoring::saxs::FormFactorManager
• Tag : core::conformation::signals::ConnectionEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory , protocols::filters::FilterFactory , protocols::jd2::parser::FragmentReader , protocols::moves::MoverFactory , protocols::protein_interface_design::DockDesignFilterFactory , protocols::qsar::scoring_grid::GridFactory
• tag : core::conformation::signals::ConnectionEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::optimization::EItem , protocols::qsar::qsarOptData , protocols::swa::rna::pose_data_struct2 , protocols::swa::rna::FB_Pose_Data , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::AlignEvaluator , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::OptEPositionData , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer
• tag_ : protocols::optimize_weights::OptEPositionData , protocols::pockets::PocketGrid , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer , core::fragment::CacheWrapper< T, XCacheUnit > , core::scoring::methods::BBDepCartBondedParameters , core::scoring::packstat::MultiProbePoseAccumulator , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::evaluation::AlignEvaluator , protocols::optimize_weights::SingleStructureData
• tag_activity_selection_ : protocols::qsar::qsarOptFunc
• tag_along_chains : protocols::ligand_docking::Rotate_info
• tag_along_jumps : protocols::ligand_docking::Rotate_info
• tag_along_jumps_ : protocols::ligand_docking::Translate
• tag_along_residues : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Ligand_info
• tag_format_string() : protocols::outputter::SilentFileOutputter
• tag_format_string_ : protocols::outputter::SilentFileOutputter
• tag_idx_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• TAG_IN_FILE : protocols::jd2::archive::ArchiveBase
• tag_is_done_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::rna::RNA_DeNovoProtocol
• tag_list : protocols::cluster::GatherPosesMover
• tag_map_ : protocols::frag_picker::QuotaDebug , protocols::frag_picker::quota::QuotaSelector
• tag_output_list_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• tag_prefix_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• tag_residues_ : protocols::features::DatabaseJobInputter
• tag_structures_ : protocols::features::DatabaseJobInputter
• tag_time() : protocols::simple_moves::DumpPdb
• tag_to_source_map_ONE_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• tag_to_source_map_TWO_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• TagList : protocols::toolbox::KClusterData
• TagPtr : protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::jd2::parser::FragmentReader , protocols::match::MatcherMover , protocols::moves::DsspMover , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::protein_interface_design::DockDesignFilterFactory , protocols::qsar::scoring_grid::GridFactory , protocols::simple_filters::HolesFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperation , core::pack::task::operation::TaskOperationFactory , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfacePacker , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential
• Tags : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• tags() : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• tags_ : core::import_pose::pose_stream::SilentFilePoseInputStream , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::frag_picker::QuotaDebug , protocols::frag_picker::quota::QuotaSelector , protocols::inputter::SilentFileInputter , protocols::toolbox::KClusterData
• TailsScoreMover() : protocols::simple_moves::TailsScoreMover
• take_coordinates_from_pose() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• TalosSSSimilarity() : protocols::frag_picker::scores::TalosSSSimilarity
• targ_ang() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_ang_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base2_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base2_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_dih() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_dih_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_res() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_res_ : protocols::toolbox::match_enzdes_util::ResInteractions
• target : protocols::pockets::PCluster
• TARGET : protocols::pockets::PocketGrid
• target_ : protocols::noesy_assign::PeakCalibrator , protocols::simple_moves::MutateResidue
• target_accept_ratio() : protocols::abinitio::IterativeBase
• target_accept_ratio_ : protocols::abinitio::IterativeBase
• target_Ashifts_ : protocols::frag_picker::scores::AmbigCSScore
• target_Bshifts_ : protocols::frag_picker::scores::AmbigCSScore
• target_ca_dev_ : protocols::frag_picker::scores::PCS_FragDistance
• target_ca_dist_ : protocols::frag_picker::scores::PCS_FragDistance
• target_chain_ : protocols::seeded_abinitio::SeedFoldTree
• target_conformer() : protocols::motifs::MotifHit
• target_conformer_ : protocols::motifs::MotifHit
• target_conformers_map() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_conformers_map_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_distance_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover
• target_downstream_coords_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_downstream_res_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_end_ : protocols::simple_moves::SuperimposeMover
• target_geomcst_coords_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_geomcst_id_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_end_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_for_focused_build_point_begin_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_for_focused_build_point_end_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_positions() : protocols::motifs::BuildPosition , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_positions_ : protocols::motifs::BuildPosition , protocols::motifs::IRCollection , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_proximity_to_native_conformation_ : protocols::enzdes::EnzdesFlexibleRegion
• target_proximity_to_other_conformations_ : protocols::enzdes::EnzdesFlexibleRegion
• target_res() : protocols::pockets::PocketConstraint
• target_res_ : protocols::enzdes::RepackWithoutLigandFilter
• target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget
• target_residue_ : protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::ResidueBurialFilter
• target_residue_type_ : core::pack::task::ResidueLevelTask_
• target_residues() : protocols::enzdes::PackRotamersMoverPartGreedy
• target_residues_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::DesignRepackMover
• target_resnum_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover
• target_restype_index_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_restypes_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::TargetRotamerCoords
• target_sequence() : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::toolbox::task_operations::ThreadSequenceOperation
• target_sequence_ : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::hybridization::FoldTreeHybridize , protocols::toolbox::task_operations::ThreadSequenceOperation
• target_shifts_ : protocols::frag_picker::scores::CSScore
• target_sign_ : protocols::noesy_assign::PeakCalibrator
• target_start_ : protocols::simple_moves::SuperimposeMover
• target_stub : protocols::hotspot_hashing::ConstPattern
• target_total_residue() : protocols::abinitio::Templates
• target_type() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask
• target_values_ : protocols::noesy_assign::PeakCalibrator
• targeted_dna() : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• targeted_dna_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::motifs::MotifDnaPacker
• targetPocketHeuristicScore() : protocols::pockets::PocketGrid
• targetPocketHydrophobicProteinSurface() : protocols::pockets::PocketGrid
• targetPocketPolarProteinSurface() : protocols::pockets::PocketGrid
• targetPocketProteinSurface() : protocols::pockets::PocketGrid
• targetPocketSolventSurface() : protocols::pockets::PocketGrid
• targetPocketVolume() : protocols::pockets::PocketGrid
• TargetRotamerCoords() : protocols::match::downstream::TargetRotamerCoords
• targets_ : protocols::protein_interface_design::filters::DisulfideFilter
• TargetValues : protocols::noesy_assign::PeakCalibrator
• task : protocols::forge::remodel::WorkingRemodelSet , core::pack::rotamer_set::RotamerSets , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::forge::remodel::RemodelDesignMover , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• task_ : core::pack::rotamer_set::RotamerSets , protocols::analysis::InterfaceAnalyzerMover , protocols::docking::SidechainMinMover , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flexpack::FlexPacker , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::protein_interface_design::movers::RandomMutation , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::symmetric_docking::SymSidechainMinMover
• task_factory : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::backrub::BackrubSidechainMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• task_factory_ : protocols::anchored_design::AnchorMoversData , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::features::ReportToDB , protocols::features::RotamerRecoveryFeatures , protocols::floppy_tail::FloppyTailMover , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::optimize_weights::IterativeOptEDriver , protocols::outputter::ResFileOutputter , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::relax::RelaxProtocolBase , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::RotamerDump::RotamerDumpMover , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• task_factory_set() : protocols::protein_interface_design::filters::Torsion
• task_factory_set_ : protocols::protein_interface_design::filters::Torsion
• task_initialized() : protocols::simple_moves::sidechain_moves::SidechainMover
• task_initialized_ : protocols::simple_moves::sidechain_moves::SidechainMover
• task_invalidated_ : protocols::simple_filters::PackerNeighborGraphFilter
• task_is_valid() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover
• task_layers_ : protocols::flxbb::LayerDesignOperation
• task_mode() : core::pack::task::ResidueLevelTask_
• task_op_ : protocols::match::TaskOperationMPM
• task_operation_creator_map_ : core::pack::task::operation::TaskOperationFactory
• task_operations_ : protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::flxbb::CombinedTaskOperation
• task_scaling_ : protocols::simple_moves::GenericMonteCarloMover
• task_string() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• TaskAwareCsts() : protocols::protein_interface_design::movers::TaskAwareCsts
• TaskAwareMinMover() : protocols::simple_moves::TaskAwareMinMover
• TaskFactory : protocols::simple_moves::GreenPacker , core::pack::task::TaskFactory
• TaskFactoryCOP : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• TaskFactoryOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker
• TaskLayer : protocols::flxbb::LayerDesignOperation
• TaskLayers : protocols::flxbb::LayerDesignOperation
• TaskOperation : core::pack::task::operation::ReplicateTask , core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface , core::pack::task::TaskFactory , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::SeqprofConsensusOperation
• TaskOperationCOP : core::pack::task::TaskFactory
• TaskOperationCreatorMap : core::pack::task::operation::TaskOperationFactory
• TaskOperationFactory() : core::pack::task::operation::TaskOperationFactory
• TaskOperationLoader() : protocols::jd2::parser::TaskOperationLoader
• TaskOperationMPM() : protocols::match::TaskOperationMPM
• TaskOperationOP : protocols::flxbb::CombinedTaskOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::SeqprofConsensusOperation , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::ReplicateTask , core::pack::task::operation::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::RestrictToInterface , core::pack::task::TaskFactory , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::AddLigandMotifRotamers , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation
• TaskOperationOPs : core::pack::task::operation::TaskOperationFactory
• TaskOperationRegistrator() : core::pack::task::operation::TaskOperationRegistrator< T >
• TaskOperationSP : core::pack::task::TaskFactory
• Tau() : core::scoring::FACTSPotential
• Tau_ : core::scoring::FACTSPotential
• TCacheUnit : core::fragment::CacheWrapper< T, XCacheUnit >
• TCacheUnitAP : core::fragment::CacheWrapper< T, XCacheUnit >
• TCacheUnitOP : core::fragment::CacheWrapper< T, XCacheUnit >
• tccw : core::scoring::packstat::Circle
• tcw : core::scoring::packstat::Circle
• tear_down() : protocols::nonlocal::StarTreeBuilder , protocols::nonlocal::TreeBuilder
• tear_down_kinematics() : protocols::star::StarAbinitio
• tell_neighbors_to_prep_for_relaxation() : core::pack::interaction_graph::FASTERNode
• temp : core::scoring::APBSConfig::R_PARAM , core::pose::UnrecognizedAtomRecord , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::simple_moves::TorsionDOFMover
• temp1() : core::scoring::AtomNeighbor
• temp1_ : core::scoring::AtomNeighbor
• temp2() : core::scoring::AtomNeighbor
• temp2_ : core::scoring::AtomNeighbor
• temp3() : core::scoring::AtomNeighbor
• temp3_ : core::scoring::AtomNeighbor
• temp4() : core::scoring::AtomNeighbor
• temp4_ : core::scoring::AtomNeighbor
• temp_ : core::pose::UnrecognizedAtomRecord , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::TorsionDOFMover
• temp_coord_for_evaluation_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• temp_coords_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• temp_EMap_ : core::scoring::constraints::AmbiguousConstraint
• temp_energies : protocols::vip::VIP_Mover
• temp_file() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor
• temp_final() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_final_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_initial() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_initial_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_positions : protocols::vip::VIP_Mover
• temp_residues : protocols::vip::VIP_Mover
• temp_trial_count_ : protocols::canonical_sampling::TemperingBase
• temperature : core::io::pdb::AtomInformation , core::pose::PDBInfo::AtomRecord , protocols::ligand_docking::Transform_info , core::pose::PDBInfo , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::TemperingBase , protocols::forge::remodel::RemodelLoopMover , protocols::moves::MonteCarlo , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::BackboneMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• temperature0_ : protocols::simple_moves::sidechain_moves::SidechainMover
• Temperature_ : protocols::antibody2::CDRsMinPackMin , protocols::antibody2::H3PerturbCCD
• temperature_ : core::pack::annealer::SimAnnealerBase , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::FixedTemperatureController , protocols::docking::ConformerSwitchMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::forge::remodel::RemodelLoopMover , protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::moves::CanonicalSamplingMover , protocols::moves::MonteCarlo , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::BackboneMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::surface_docking::CentroidRelaxMover , protocols::surface_docking::FullatomRelaxMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• temperature_jumps_ : protocols::canonical_sampling::SimulatedTempering
• temperature_level() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• temperature_move() : protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::FixedTemperatureController
• temperature_stride_ : protocols::canonical_sampling::TemperingBase
• TemperatureController() : protocols::canonical_sampling::TemperatureController
• temperatures_ : protocols::canonical_sampling::TemperingBase , protocols::simple_moves::GenericMonteCarloMover
• TemperedDocking() : protocols::docking::TemperedDocking
• tempering() : protocols::canonical_sampling::MetropolisHastingsMover
• tempering_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::docking::TemperedDocking
• TemperingBase() : protocols::canonical_sampling::TemperingBase
• Template() : protocols::abinitio::Template
• template_atom_inds() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• template_chunks_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• template_clusterID_ : protocols::hybridization::HybridizeProtocol
• template_contigs_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• template_core_chunk_indices_ : protocols::hybridization::HybridizeFoldtreeDynamic
• template_cst_fn_ : protocols::hybridization::HybridizeProtocol
• template_cst_reses_ : protocols::hybridization::HybridizeProtocol
• template_end_ : protocols::antibody::GraftOneMover
• template_file() : protocols::protein_interface_design::movers::Splice
• template_file_ : protocols::protein_interface_design::movers::Splice
• template_fn_ : protocols::hybridization::HybridizeProtocol
• TEMPLATE_HYBRIDIZATION_HISTORY : core::pose::datacache::CacheableDataType
• template_id_ : protocols::hybridization::InsertChunkMover
• template_index() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_index_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_name() : protocols::id::AlignmentID
• template_name_ : protocols::antibody::GraftOneMover , protocols::id::AlignmentID
• template_number() : protocols::hybridization::ChunkTrialMover
• template_number_ : protocols::hybridization::ChunkTrialMover
• template_pdb_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• template_pose() : protocols::comparative_modeling::ThreadingMover
• template_pose_ : protocols::antibody::CDRH3Modeler , protocols::antibody::GraftOneMover , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::hybridization::InsertChunkMover , protocols::protein_interface_design::movers::Splice
• template_poses() : protocols::jd2::InnerMultiThreadingJob
• template_poses_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter , protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::jd2::InnerMultiThreadingJob
• template_presence : protocols::seeded_abinitio::GrowPeptides
• template_presence_ : protocols::seeded_abinitio::CAcstGenerator
• template_res_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_size() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_scores : protocols::cluster::GatherPosesMover
• template_size() : protocols::jumping::MembraneJump
• template_size_ : protocols::jumping::MembraneJump
• template_start_ : protocols::antibody::GraftOneMover
• template_weights_ : protocols::hybridization::HybridizeProtocol
• template_weights_sum_ : protocols::hybridization::HybridizeProtocol
• template_wts_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• TemplateFragmentClaimer() : protocols::topology_broker::TemplateFragmentClaimer
• TemplateHistory() : protocols::hybridization::TemplateHistory
• TemplateJumpClaimer() : protocols::topology_broker::TemplateJumpClaimer
• TemplateJumpSetup() : protocols::abinitio::TemplateJumpSetup
• TemplateList : protocols::abinitio::Templates
• TemplateMap : protocols::abinitio::Templates
• TemplatePoseMap : protocols::antibody2::Ab_TemplateInfo
• Templates() : protocols::abinitio::Templates
• templates_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::TemplateJumpSetup , protocols::abinitio::Templates , protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol , protocols::jumping::MembraneJump , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• templates_poses_ : protocols::antibody2::Ab_TemplateInfo
• templates_with_incorrect_strand_pairings_ : protocols::hybridization::FoldTreeHybridize
• temporarily_fix_everything() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• temporarily_set_pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• temporary_file_name() : protocols::jd2::FileSystemJobDistributor
• Temps : core::io::pdb::FileData
• temps : core::io::pdb::ResidueInformation
• tenA_ : core::scoring::TenANeighborGraph
• tenA_edge_pool_ : core::scoring::TenANeighborGraph
• tenA_neighbor_graph() : core::scoring::Energies
• tenA_squared_ : core::scoring::TenANeighborGraph
• TenANeighborEdge() : core::scoring::TenANeighborEdge
• TenANeighborGraph() : core::scoring::TenANeighborGraph
• TenANeighborNode() : core::scoring::TenANeighborNode
• tensor() : core::scoring::ResidualDipolarCoupling
• Tensor : core::scoring::ResidualDipolarCoupling
• Tensor5 : core::scoring::ResidualDipolarCoupling
• tensorDa : core::scoring::data_structDa , core::scoring::data_structDaR
• tensorR : core::scoring::data_structR , core::scoring::data_structDaR
• TensorsOptimizer() : protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizer
• TensorsOptimizerFix() : protocols::scoring::methods::pcs2::TensorsOptimizerFix
• TensorsOptimizerSvd() : protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• terCount : core::io::pdb::AtomInformation , core::io::pdb::ResidueInformation
• terminal_res_ : protocols::swa::rna::StepWiseRNA_BaseCentroidScreener , protocols::swa::StepWisePoseSetup
• termini_penalty() : core::scoring::MembranePotential
• TerminusDistanceFilter() : protocols::simple_filters::TerminusDistanceFilter
• test() : protocols::toolbox::DummyClass
• test_broker_settings() : protocols::abinitio::IterativeBase
• test_chunk() : protocols::frag_picker::AllowPdbIdFilter , protocols::frag_picker::DenyPdbIdFilter , protocols::frag_picker::VallChunkFilter
• test_control_mode_ : protocols::grafting::AnchoredGraftMover
• test_count_one : protocols::swa::rna::SillyCountStruct
• test_count_two : protocols::swa::rna::SillyCountStruct
• test_cycles_ : protocols::relax::FastRelax
• test_flexbb_rotamer_sets() : protocols::enzdes::EnzdesFlexBBProtocol
• test_for_stage_end() : protocols::abinitio::IterativeBase
• test_loop_sample() : protocols::loophash::LoopHashLibrary
• test_matches() : protocols::rna::RNA_ChunkLibrary
• test_move() : protocols::contact_map::ContactMap , protocols::moves::_BoolMover , protocols::moves::Mover , protocols::moves::NullMover , protocols::simple_moves::SmallMover , protocols::simple_moves::ShearMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::sidechain_moves::SidechainMover
• test_round() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• test_saving_library() : protocols::loophash::LoopHashLibrary
• test_sequence_recovery() : protocols::optimize_weights::IterativeOptEDriver
• test_upstream_only_hit_incompatibility() : protocols::match::Matcher
• test_weight_sensitivity() : protocols::optimize_weights::IterativeOptEDriver
• testCartesianDerivatives() : protocols::cartesian::MolecularDynamics
• testing_phase : protocols::simple_moves::ShakeStructureMover
• testNeighbor() : protocols::pockets::PCluster
• TestPattern() : protocols::hotspot_hashing::TestPattern
• tether_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• tether_ligands() : protocols::ligand_docking::HighResDocker
• TetherLigand() : protocols::ligand_docking::TetherLigand
• tf2() : protocols::docking::DockingHighRes
• tf2_ : protocols::docking::DockingHighRes
• tf_ : protocols::antibody::AntibodyModeler , protocols::antibody::CDRH3Modeler , protocols::antibody::LoopRlxMover , protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::CDRsMinPackMin , protocols::antibody2::GraftCDRLoopsProtocol , protocols::antibody2::H3RefineCCD , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHSnugFitLegacy , protocols::antibody2::ModelCDRH3 , protocols::antibody2::RefineBetaBarrel , protocols::antibody2::RefineOneCDRLoop , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::rbsegment_relax::AutoRBMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymSidechainMinMover
• tgt_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgt_pos_ : protocols::constraints_additional::BindingSiteConstraint
• tgt_pos_centroid_ : protocols::constraints_additional::BindingSiteConstraint
• tgtD_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgtE_ : protocols::simple_moves::symmetry::SetupNCSMover
• the_cdr_loop_ : protocols::antibody2::RefineOneCDRLoopCentroid
• the_config_file_ : core::scoring::saxs::SAXSEnergy
• the_loop_ : protocols::antibody2::H3RefineCCD
• the_mover_ : protocols::wum::WorkUnit_MoverWrapper
• theArchive_ : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• thenfilters_ : protocols::filters::IfThenFilter
• THEORETICAL_MODEL : core::io::pdb::HeaderInformation
• TheozymeInvrotTree() : protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• thermal_accepts_ : protocols::moves::MoverStatistics
• ThermodynamicMover() : protocols::canonical_sampling::ThermodynamicMover
• ThermodynamicObserver() : protocols::canonical_sampling::ThermodynamicObserver
• theta : protocols::simple_moves::MinimalRotamer , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , protocols::fldsgn::topology::DimerPairing
• theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• THETA_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• theta_ : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::chemical::AddConnect , core::chemical::SetICoor , core::kinematics::tree::BondedAtom , protocols::fldsgn::topology::DimerPairing
• theta_near_0_ : protocols::match::VoxelSetIterator
• theta_near_180_ : protocols::match::VoxelSetIterator
• thickness() : core::scoring::Membrane_FAEmbed
• thickness_ : core::scoring::hbonds::HBondEnergy , core::scoring::Membrane_FAEmbed , core::scoring::packstat::Slice
• third_atom_ : protocols::frag_picker::scores::FourAtomsConstraintData
• third_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• ThirdLoop() : core::scoring::sc::MolecularSurfaceCalculator
• this_aa() : protocols::optimize_weights::PNatAAOptERotamerData
• this_aa_ : protocols::optimize_weights::PNatAAOptERotamerData
• this_batch_job_inputter_ : protocols::jd2::BatchJobInputter
• this_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• this_weak_ptr() : core::kinematics::tree::Atom_
• this_weak_ptr_ : core::kinematics::AtomTree , core::kinematics::tree::Atom_
• thread() : protocols::simple_filters::RelativePoseFilter
• thread_ : protocols::simple_filters::RelativePoseFilter
• thread_seq() : protocols::simple_filters::RelativePoseFilter
• ThreadingJob() : protocols::comparative_modeling::ThreadingJob
• ThreadingJobInputter() : protocols::comparative_modeling::ThreadingJobInputter
• ThreadingMover() : protocols::comparative_modeling::ThreadingMover
• ThreadSequenceOperation() : protocols::toolbox::task_operations::ThreadSequenceOperation
• threashold_ : protocols::filters::CompoundFilter
• three_prime_atom : protocols::swa::rna::Jump_point
• three_prime_seq_num : protocols::swa::rna::Jump_point
• threeD_projection_ : protocols::match::OccupiedSpaceHash
• threshold : protocols::viewer::triangleIterator , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::MatchResidues , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::Operator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::Sigmoid
• threshold_ : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::constraints_additional::ConstraintEvaluator , protocols::dna::RotamerDNAHBondFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::filters::CombinedFilter , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::MatchResidues , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::Operator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::Sigmoid , protocols::simple_moves::MinMover , protocols::toolbox::KMedoid
• THRESHOLD_ACCEPTANCE_RATE_FOR_RPE_STORAGE : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• threshold_probabilities_per_residue_ : protocols::simple_filters::RotamerBoltzmannWeight
• threshold_probability() : protocols::simple_filters::RotamerBoltzmannWeight
• tic_ : protocols::filters::TimeFilter
• tight_minimize() : protocols::rna::RNA_LoopCloser
• tighten_memory() : core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::pose::PDBInfo
• tilt() : protocols::dna::DNABasestep
• tilt_ : protocols::dna::DNABasestep
• time_ : protocols::checkpoint::Timer
• time_for_temp_move() : protocols::canonical_sampling::TemperingBase
• time_to_checkpoint() : protocols::checkpoint::Timer
• TIME_TO_UPDATE : core::scoring::TenANeighborNode
• TimeEvaluator() : protocols::evaluation::TimeEvaluator
• TimeFilter() : protocols::filters::TimeFilter
• Timer() : protocols::checkpoint::Timer
• TimeStampedChannel : protocols::jd2::MpiFileBuffer
• TIMING_CPU : protocols::wum::MPI_WorkUnitManager
• TIMING_end : protocols::wum::MPI_WorkUnitManager
• TIMING_IDLE : protocols::wum::MPI_WorkUnitManager
• TIMING_IO_READ : protocols::wum::MPI_WorkUnitManager
• TIMING_IO_WRITE : protocols::wum::MPI_WorkUnitManager
• timing_last_start_time_ : protocols::wum::MPI_WorkUnitManager
• timing_last_type_ : protocols::wum::MPI_WorkUnitManager
• timing_total_ : protocols::wum::MPI_WorkUnitManager
• TIMING_TRANSFER_RECV : protocols::wum::MPI_WorkUnitManager
• TIMING_TRANSFER_SEND : protocols::wum::MPI_WorkUnitManager
• TIMING_WAIT : protocols::wum::MPI_WorkUnitManager
• title() : core::io::pdb::HeaderInformation
• title_ : core::io::pdb::HeaderInformation
• titrate_stack_bonus_ : protocols::rna::RNA_DeNovoProtocol
• tlevel2rank_ : protocols::canonical_sampling::ParallelTempering
• Tlist_ : protocols::moves::ReplicaExchangeMC
• TM3 : protocols::hybridization::TMalign
• TM4 : protocols::hybridization::TMalign
• TM5 : protocols::hybridization::TMalign
• tm_projection_ : core::scoring::MembraneEmbed
• tm_projection_penalty() : core::scoring::MembranePotential
• TMap : core::fragment::MapCacheUnit< T >
• tmh_inserted() : core::scoring::MembraneTopology
• tmh_inserted_ : core::scoring::MembraneTopology
• tmhelix() : core::scoring::MembraneTopology
• tmregion() : core::scoring::MembraneTopology
• tmregion_ : core::scoring::MembraneTopology
• TMscore() : protocols::hybridization::TMalign
• TMscore8_search() : protocols::hybridization::TMalign
• to_all_atom() : protocols::docking::DockingProtocol
• to_all_atom_ : protocols::docking::DockingProtocol
• to_allatom() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• to_be_closed_cuts_ : protocols::topology_broker::TopologyBroker
• to_be_relaxed_ : protocols::loophash::MPI_LoopHashRefine_Master
• to_centroid() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::nonlocal::SingleFragmentMover
• to_centroid_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• to_chain_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• to_do() : protocols::jd2::Job
• to_res() : protocols::protein_interface_design::movers::Splice
• to_res_ : protocols::protein_interface_design::movers::Splice
• to_string() : core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::NamedAtomID , core::id::SequenceMapping , core::scoring::constraints::Constraint , core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::id::AlignmentID , protocols::genetic_algorithm::EntityElement , protocols::multistate_design::PosType
• toc_ : protocols::filters::TimeFilter
• toggle() : protocols::topology_broker::DofClaim , protocols::topology_broker::BBClaim , protocols::topology_broker::JumpClaim
• Tokens : core::coarse::Rule
• tokens_ : core::coarse::Rule::BeadAdder
• tol() : core::scoring::constraints::FlatHarmonicFunc
• tol_ : core::scoring::constraints::FlatHarmonicFunc
• tolerance : core::optimization::DFPMinConvergedFractional , core::optimization::DFPMinConvergedAbsolute , protocols::branch_angle::BranchAngleOptimizer , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::simple_moves::MinMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::simple_moves::MinMover
• tolerance_ : protocols::branch_angle::BranchAngleOptimizer , protocols::docking::FaDockingSlideIntoContact , protocols::loops::loop_closure::ccd::CcdLoopClosureMover , protocols::moves::JumpOutMover , protocols::noesy_assign::PeakCalibrator , protocols::rotamer_recovery::RRComparerChiDiff , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::surface_docking::FaSlideIntoSurface , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::surface_docking::FaSlideAwayFromSurface , protocols::branch_angle::BranchParam1
• tolerate_off_range_atom_bin_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• tolerated_overlap() : protocols::match::output::MatchCollisionFilter
• tolerated_overlap_ : protocols::match::output::MatchCollisionFilter
• too_far() : protocols::constraints_additional::MaxSeqSepConstraintSet
• top() : protocols::dna::DnaPosition , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• top_ : core::fragment::FragmentIO , protocols::dna::DnaPosition
• top_count_of_all_inputs_ : protocols::features::TopPercentOfAllInputs
• top_count_of_each_input_ : protocols::features::TopPercentOfEachInput
• top_entities_ : protocols::pack_daemon::MultistateFitnessFunction
• top_fragments() : core::fragment::picking_old::vall::VallLibrarian
• top_level_pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• top_n_big_frag_ : protocols::hybridization::FoldTreeHybridize
• top_n_small_frag_ : protocols::hybridization::FoldTreeHybridize
• top_netstates_ : core::pack::annealer::MultiCoolAnnealer
• top_to_keep : core::pack::annealer::MultiCoolAnnealer
• TopCountOfAllInputs() : protocols::features::TopCountOfAllInputs
• TopCountOfEachInput() : protocols::features::TopCountOfEachInput
• TOPO_RESAMPLING : protocols::abinitio::IterativeBase
• topol_score_ : protocols::abinitio::Template
• topological_match_to() : core::kinematics::AtomTree
• topological_match_to_ : core::kinematics::AtomTree
• topological_observers() : core::kinematics::AtomTree
• topological_observers_ : core::kinematics::AtomTree
• Topologies : protocols::abinitio::PairingStatistics
• topology() : protocols::abinitio::PairingStatistics
• topology_broker() : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_broker_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_score() : protocols::abinitio::Template
• TopologyBroker() : protocols::topology_broker::TopologyBroker
• TopologyClaimer() : protocols::topology_broker::TopologyClaimer
• TopologyClaimerCAPs : protocols::topology_broker::ClaimerMessage
• TopologyClaimerFactory() : protocols::topology_broker::TopologyClaimerFactory
• TopologyClaimers : protocols::topology_broker::TopologyBroker
• topols_ : protocols::abinitio::PairingStatistics
• TopOutFunc() : core::scoring::constraints::TopOutFunc
• TopPercentOfAllInputs() : protocols::features::TopPercentOfAllInputs
• TopPercentOfEachInput() : protocols::features::TopPercentOfEachInput
• tor_for_dof() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• tor_U1D3() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U1D3_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U1D3_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U1D3_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U2D2_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U3D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• toroidal : core::scoring::sc::_RESULTS
• torsion : protocols::rna::suite_info , core::conformation::Conformation , core::id::TorsionID , core::pose::Pose , protocols::protein_interface_design::filters::Torsion
• Torsion() : protocols::protein_interface_design::filters::Torsion
• torsion() : core::fragment::BBTorsionSRFD
• torsion2big_bin() : protocols::comparative_modeling::features::TorsionFeature , protocols::toolbox::pose_metric_calculators::RotamerRecovery , protocols::rotamer_recovery::PerNativeRRReporterHuman
• torsion2big_bin_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• torsion2index() : core::util::ABEGOManager
• torsion2index_level1() : core::util::ABEGOManager
• torsion2index_level2() : core::util::ABEGOManager
• torsion2index_level3() : core::util::ABEGOManager
• torsion2index_level4() : core::util::ABEGOManager
• torsion_ : core::id::TorsionID , protocols::protein_interface_design::filters::Torsion
• torsion_angle() : core::conformation::Conformation , core::kinematics::AtomTree
• torsion_angle_dof_id() : core::kinematics::AtomTree
• torsion_angles_within_cutoffs() : protocols::swa::rna::RNA_LoopCloseSampler
• torsion_atom_ : core::chemical::AddConnect
• torsion_bin() : protocols::comparative_modeling::features::TorsionFeature
• torsion_bin_ : protocols::comparative_modeling::features::TorsionFeature
• torsion_database() : protocols::protein_interface_design::movers::Splice
• torsion_database_ : protocols::protein_interface_design::movers::Splice
• torsion_database_fname() : protocols::protein_interface_design::movers::Splice
• torsion_database_fname_ : protocols::protein_interface_design::movers::Splice
• torsion_delta_ : protocols::loops::loop_closure::ccd::CcdLoopClosureMover
• torsion_features_string() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_mover::LoopMover
• torsion_id() : core::id::TorsionID_Range , core::optimization::DOF_Node
• torsion_id_ : core::id::TorsionID_Range , core::optimization::DOF_Node
• torsion_id_begin() : core::kinematics::MoveMap
• torsion_id_end() : core::kinematics::MoveMap
• torsion_id_map_ : core::kinematics::MoveMap
• torsion_id_ranges() : protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::rigid::RigidBodyMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover , protocols::backrub::BackrubMover
• torsion_ids() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• torsion_ids_ : protocols::canonical_sampling::MetricRecorder , protocols::swa::rna::StepWiseRNA_RotamerGenerator
• torsion_increment_ : protocols::swa::rna::RNA_LoopCloseSampler
• torsion_info_ : protocols::swa::rna::RNA_LoopCloseSampler
• torsion_is_independent() : core::conformation::symmetry::SymmetryInfo
• torsion_name() : protocols::simple_moves::SetTorsion
• torsion_name_ : protocols::simple_moves::SetTorsion
• torsion_parameter : core::scoring::methods::ResidueCartBondedParameters
• torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
• torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• torsion_range_ : protocols::swa::rna::RNA_LoopCloseSampler
• torsion_scale_factor() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• torsion_source_name : protocols::rna::TorsionSet
• torsion_type_begin() : core::kinematics::MoveMap
• torsion_type_end() : core::kinematics::MoveMap
• torsion_type_map_ : core::kinematics::MoveMap
• torsionA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• torsionAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• torsionB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• TorsionBinIO() : protocols::frag_picker::TorsionBinIO
• TorsionBinPool() : protocols::frag_picker::quota::TorsionBinPool
• TorsionBinSimilarity() : protocols::frag_picker::scores::TorsionBinSimilarity
• TorsionDOFMover() : protocols::simple_moves::TorsionDOFMover
• TorsionFeature() : protocols::comparative_modeling::features::TorsionFeature
• TorsionFourierComponent() : core::scoring::dna::TorsionFourierComponent
• TorsionFragment() : protocols::frags::TorsionFragment
• TorsionFragmentLibrary() : protocols::frags::TorsionFragmentLibrary
• TorsionID : core::conformation::symmetry::SymmetryInfo , core::kinematics::MoveMap , core::optimization::DOF_Node , core::id::TorsionID , core::pose::Pose , core::conformation::Conformation
• TorsionID_Map : core::kinematics::MoveMap
• TorsionID_Range() : core::id::TorsionID_Range
• TorsionIDs : core::conformation::symmetry::SymmetryInfo
• TorsionRestrictedKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• torsions : protocols::rna::TorsionSet , protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• torsions_ : protocols::frags::TorsionFragment , core::fragment::BBTorsionSRFD
• torsions_indep_ : core::scoring::methods::IdealParametersDatabase
• torsions_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• torsions_monte_carlo_minimize() : protocols::flexpep_docking::FlexPepDockingProtocol
• TorsionSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• TorsionSet() : protocols::rna::TorsionSet
• torsionsMCM : protocols::flexpep_docking::FlexPepDockingFlags
• TorsionSweepingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• TorsionType : core::kinematics::MoveMap
• TorsionTypeMap : core::kinematics::MoveMap
• tot_rotamer_count : protocols::swa::rna::SillyCountStruct
• tot_surf : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• tot_vol : core::scoring::packing::SurfVolDeriv , core::scoring::packing::SurfVol
• total() : core::scoring::saxs::DistanceHistogram
• total_accepts() : protocols::jd2::archive::ArchiveBase
• total_accepts_ : protocols::jd2::archive::ArchiveBase
• total_area : core::scoring::packstat::AreaAccumulator
• total_assigned_distances_ : protocols::noesy_assign::DistanceScoreMover
• total_base_axis_score_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• total_base_pair_score_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• total_base_stack_axis_score_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• total_base_stack_score_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• total_base_stagger_score_ : core::scoring::rna::RNA_FilteredBaseBaseInfo
• total_bin : protocols::swa::rna::SillyCountStruct
• total_cdr_loops_ : protocols::antibody2::AntibodyInfo
• total_chain_break_score : protocols::forge::remodel::RemodelData
• total_charge_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_clashes_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• total_completed_nstruct_ : protocols::jd2::BOINCJobDistributor
• total_count : protocols::swa::rna::Filterer_Count
• total_count_ : protocols::canonical_sampling::SimulatedTempering
• total_energies() : core::scoring::Energies
• total_energies_ : core::scoring::Energies
• total_energy() : core::pack::interaction_graph::SimpleInteractionGraph , core::scoring::Energies , core::scoring::saxs::SAXSEnergy , core::scoring::Energies
• total_energy_ : core::scoring::Energies
• total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_alternate_state_assignment_ : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph
• total_energy_current_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_current_state_assignment_ : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph
• total_exp_chemical_shift_data_points_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• total_frames_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• total_goodfrags_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• total_hb_E_ : protocols::analysis::InterfaceAnalyzerMover
• total_helices : core::scoring::Helices
• total_HH_dimer : core::scoring::Helices
• total_hpatch_score_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• total_input_struct_pair_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• total_mc_trial_count : protocols::boinc::BoincSharedMemory
• total_metropolis_ : protocols::loophash::MPI_LoopHashRefine
• total_metropolis_accepts_ : protocols::loophash::MPI_LoopHashRefine
• total_moves_ : protocols::loops::loop_closure::ccd::CcdMover
• total_mpi_wait_time_ : protocols::canonical_sampling::ParallelTempering
• total_neg_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• total_nr_jobs() : protocols::jd2::JobDistributor
• total_num_slides_ : protocols::simple_moves::symmetry::SymmetrySlider
• total_number_abego() : core::util::ABEGOManager
• total_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• total_partitions_ : protocols::hotspot_hashing::PartitionedSearchPattern
• total_pos_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_positions_ : protocols::optimize_weights::IterativeOptEDriver
• TOTAL_PRECISION : protocols::frag_picker::scores::FragmentScoreManager
• total_proposed() : protocols::jd2::archive::ArchiveBase
• total_proposed_ : protocols::jd2::archive::ArchiveBase
• total_ref_resids_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• total_res() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• total_residue() : protocols::jumping::JumpSetup , core::fragment::SecondaryStructure , core::kinematics::ResidueCoordinateChangeList , core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pose::MiniPose , core::pose::Pose , core::scoring::trie::TrieCollection , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSample , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::noesy_assign::PeakAssignmentResidueMap , core::scoring::trie::TrieCollection , core::pack::rotamer_set::RotamerSetsBase , core::kinematics::ResidueCoordinateChangeList
• total_residue_ : core::fragment::SecondaryStructure , core::kinematics::ResidueCoordinateChangeList , core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::scoring::dssp::Dssp , core::scoring::solid_surface::SurfaceEnergies , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::optimize_weights::PNatStructureOptEData , protocols::jumping::JumpsFromAllPairings , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• total_residue_wolig() : protocols::jd2::parser::BluePrint
• total_residue_wolig_ : protocols::jd2::parser::BluePrint
• total_rot_ : core::pack::rotamer_set::UnboundRotamersOperation
• total_rotamer_positions_ : protocols::optimize_weights::IterativeOptEDriver
• total_rotamers_2_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• total_rotamers_2_unique_rotamers_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• total_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator , protocols::analysis::InterfaceAnalyzerMover
• total_score() : protocols::qsar::scoring_grid::GridManager , protocols::frag_picker::scores::FragmentScoreManager , protocols::frag_picker::FragmentPicker , protocols::qsar::scoring_grid::GridManager
• total_score_ : protocols::simple_filters::ScoreCutoffFilter
• total_score_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• total_score_of_last_considered_pose() : protocols::moves::MonteCarlo
• total_score_of_last_considered_pose_ : protocols::moves::MonteCarlo
• total_search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• total_size() : protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::ABEGO_SS_Pool
• total_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• total_SS_dimer : core::scoring::Strands
• total_standard_cycles() : protocols::forge::remodel::RemodelLoopMover
• total_strands : core::scoring::Strands
• total_structures_ : protocols::loophash::MPI_LoopHashRefine
• total_structures_relax_ : protocols::loophash::MPI_LoopHashRefine
• total_surface_energy_ : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• total_tmhelix_ : core::scoring::MembraneTopology
• total_trials() : protocols::abinitio::ClassicAbinitio , protocols::moves::MonteCarlo , protocols::moves::TrialCounter , protocols::abinitio::MembraneAbinitio
• total_trials_ : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler
• total_variation_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• total_violation_count_ : protocols::noesy_assign::DistanceScoreMover
• total_weight_ : protocols::jumping::JumpSelector
• totalres_ : protocols::pockets::PocketConstraint
• totaltime_batchrelax_ : protocols::loophash::MPI_LoopHashRefine
• totaltime_loophash() : protocols::loophash::MPI_LoopHashRefine
• totaltime_loophash_ : protocols::loophash::MPI_LoopHashRefine
• totnum_abego_ : core::util::ABEGOManager
• touchesPS() : protocols::pockets::PocketGrid
• touchesSolvent() : protocols::pockets::PocketGrid
• touchesSS() : protocols::pockets::PocketGrid
• touchesSurface() : protocols::pockets::PocketGrid
• tournament_select() : protocols::genetic_algorithm::GeneticAlgorithm
• TP_BURIED : protocols::pockets::PocketGrid
• TP_EDGE : protocols::pockets::PocketGrid
• TP_POCKET : protocols::pockets::PocketGrid
• TP_SURF : protocols::pockets::PocketGrid
• tr() : protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• TR_ : core::fragment::picking_old::vall::VallLibrarian
• trace() : core::scoring::packstat::trace
• trace_ : core::scoring::packstat::Event , core::scoring::ResidualDipolarCoupling
• traceback() : core::sequence::Aligner
• tracer_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover
• tracer_visible_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• traces_ : core::scoring::packstat::Slice
• track_hpatch_E_min() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• track_max_magnitude_surface_deltaE() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• track_surface_E_min() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• traffic_total_received_ : protocols::wum::MPI_WorkUnitManager
• traffic_total_sent_ : protocols::wum::MPI_WorkUnitManager
• TraitEntityHashMap : protocols::genetic_algorithm::GeneticAlgorithm
• traits() : protocols::genetic_algorithm::Entity
• traits_ : protocols::genetic_algorithm::Entity
• trajectories_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectories_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectory_idx() : protocols::wum2::WorkUnit
• trajectory_idx_ : protocols::wum2::WorkUnit
• Trajectory_state : protocols::viewer::GraphicsState
• trajectory_stream_ : protocols::canonical_sampling::PDBTrajectoryRecorder
• TrajectoryRecorder() : protocols::canonical_sampling::TrajectoryRecorder
• trans_ : protocols::rigid::WholeBodyTranslationMover
• trans_away_vec_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• trans_axis() : protocols::rigid::RigidBodyTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyTransMover
• trans_axis_ : protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyTransMover
• trans_back_vec_ : protocols::docking::DockingPrepackProtocol , protocols::docking::DockingEnsemblePrepackProtocol
• trans_chi4_mean_ : core::scoring::methods::ProClosureEnergy
• trans_chi4_sd_ : core::scoring::methods::ProClosureEnergy
• trans_mag_ : protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::LHRepulsiveRamp , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::RigidBodyPerturbMover , protocols::antibody2::LHSnugFitLegacy , protocols::rigid::RigidBodyDofPerturbMover , protocols::rna::MultipleDomainMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::rigid::RigidBodyDofSeqPerturbMover
• trans_magnitude() : protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover
• trans_magnitude_ : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::docking::DockingLowRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol , protocols::docking::DockMCMCycle
• trans_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• trans_wt_ : protocols::simple_filters::SymmetricMotifFilter
• TRANS_X : core::kinematics::Jump
• TRANS_Y : core::kinematics::Jump
• TRANS_Z : core::kinematics::Jump
• TRANSFER : core::conformation::signals::ConnectionEvent
• transfer_buf_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• transfer_constraint_set() : core::pose::Pose
• transfer_jumps() : protocols::jumping::JumpSample
• transfer_to_residue_vector() : protocols::loops::Loops
• TransferBuffer() : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• Transform() : protocols::ligand_docking::Transform
• transform() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::hotspot_hashing::SearchPatternTransform
• Transform() : protocols::ligand_docking::Transform
• transform() : protocols::hybridization::TMalign
• transform_Ax_plus_b_recursive() : core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• Transform_info() : protocols::ligand_docking::Transform_info
• transform_info_ : protocols::ligand_docking::Transform
• transform_ligand() : protocols::ligand_docking::Transform
• transforms_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transforms_uptodate() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transforms_uptodate_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transition_threshold() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• transition_threshold_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD , protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• Translate() : protocols::ligand_docking::Translate
• translate() : core::grid::CartGrid< T >
• translate_ : protocols::rigid::RollMover
• translate_Ang_ : protocols::ligand_docking::RigidSearchMover
• translate_by_ : protocols::simple_moves::ddG , protocols::simple_filters::DdgFilter
• translate_index : protocols::forge::remodel::WorkingRemodelSet
• Translate_info() : protocols::ligand_docking::Translate_info
• translate_info_ : protocols::ligand_docking::Translate
• translate_ligand() : protocols::ligand_docking::Translate
• translate_virt_to_CoM() : protocols::hybridization::FoldTreeHybridize
• translateDSSP_ABEGO() : protocols::forge::remodel::RemodelData
• translates_ : protocols::ligand_docking::CompoundTranslate
• translation() : protocols::dna::SeparateDnaFromNonDna , Transformation , protocols::protein_interface_design::Transformation , protocols::ligand_docking::RigidSearchMover , core::kinematics::RT , protocols::ligand_docking::RigidSearchMover
• translation_ : protocols::dna::SeparateDnaFromNonDna
• translation_along_axis() : core::kinematics::Jump
• translation_matrices_ : core::conformation::symmetry::SymmData
• Translator() : core::coarse::Translator
• TranslatorMap : core::coarse::TranslatorSet
• TranslatorSet() : core::coarse::TranslatorSet
• translocation_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• transM : protocols::sparta::RingData
• transparent_facets_ : protocols::match::Bool3DGridKinemageWriter
• tree_ : protocols::rigid::RigidBodyMotionMover
• tree_from_jumps_and_cuts() : core::kinematics::FoldTree
• TreeVizBuilder() : core::kinematics::TreeVizBuilder
• triage_filter() : protocols::protein_interface_design::filters::FilterScanFilter
• triage_filter_ : protocols::protein_interface_design::filters::FilterScanFilter
• triage_positions_ : protocols::protein_interface_design::movers::PlaceStubMover
• triage_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• triage_threshold_ : protocols::protein_interface_design::filters::BoltzmannFilter
• trial() : protocols::moves::TrialCounter
• trial_ : protocols::canonical_sampling::MetropolisHastingsMover
• trial_counter() : protocols::hybridization::InsertChunkMover , protocols::hybridization::ChunkTrialMover
• trial_counter_ : protocols::simple_moves::GenericMonteCarloMover , protocols::moves::TrialCounter
• trial_large() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• trial_large_ : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• trial_positions_ : protocols::enzdes::SecondaryMatchProtocol
• trial_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_top25() : protocols::abinitio::MembraneAbinitio
• trial_small_top25_ : protocols::abinitio::MembraneAbinitio
• trial_smooth() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• TrialCounter() : protocols::moves::TrialCounter
• TrialCounterObserver() : protocols::canonical_sampling::TrialCounterObserver
• TrialMover() : protocols::moves::TrialMover
• trials() : protocols::seeded_abinitio::CloseFold
• trials_ : protocols::hybridization::hConvergenceCheck , protocols::seeded_abinitio::CloseFold , protocols::abinitio::hConvergenceCheck
• triangle() : protocols::viewer::triangle
• triangleIterator() : protocols::viewer::triangleIterator
• triangles_ : protocols::viewer::ConformationViewer
• trie() : core::scoring::trie::TrieCollection
• trie_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• trie_vs_path() : core::scoring::etable::TableLookupEvaluator , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA >
• trie_vs_trie() : core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA >
• TrieCountPair1BC3() : core::scoring::etable::etrie::TrieCountPair1BC3
• TrieCountPair1BC4() : core::scoring::etable::etrie::TrieCountPair1BC4
• TrieCountPairAll() : core::scoring::etable::etrie::TrieCountPairAll
• TrieCountPairGeneric() : core::scoring::etable::etrie::TrieCountPairGeneric
• tried_centroid_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tried_fullatom_pose_ : protocols::constraints_additional::ConstraintEvaluator
• TrieNode() : core::scoring::trie::TrieNode< AT, CPDATA >
• tries() : protocols::simple_moves::TorsionDOFMover
• tries_ : protocols::seeded_abinitio::SegmentHybridizer , core::scoring::trie::TrieCollection , protocols::simple_moves::BackboneMover , protocols::simple_moves::TorsionDOFMover
• triggers_ : protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::GenericMonteCarloMover
• trilinear_gradient() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• trilinear_interpolation() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• trim() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trim_based_on_known_ligand() : protocols::pockets::NonPlaidFingerprint
• trim_cter() : protocols::ub_e2c::ubi_e2c_modeler
• trim_proportion_ : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trimmedArea : core::scoring::sc::_RESULTS
• TrimPeripheralBand() : core::scoring::sc::ShapeComplementarityCalculator
• TrimPeripheralBandCheckDot() : core::scoring::sc::ShapeComplementarityCalculator
• tripFileName : protocols::sparta::Sparta::SpartaLib
• triplet_fingerprint_data() : protocols::pockets::FingerprintBase
• triplet_fingerprint_data_ : protocols::pockets::FingerprintBase
• TRIPLET_Tab : protocols::sparta::Sparta::SpartaLib
• true_mover_ : protocols::moves::IfMover
• TrueFilter() : protocols::filters::TrueFilter
• truncate_cenlist_values() : core::scoring::EnvPairPotential
• TruncatedScoreEvaluator() : protocols::simple_filters::TruncatedScoreEvaluator
• trust_current_temp_ : protocols::canonical_sampling::TemperingBase
• try_for_more() : protocols::motifs::IRCollection
• try_fragment() : protocols::frag_picker::quota::TorsionBinPool
• try_point_mutants() : protocols::vip::VIP_Mover
• try_to_slide_into_contact() : protocols::rna::MultipleDomainMover
• TryRotamers() : protocols::protein_interface_design::movers::TryRotamers
• trySeveral_ciBRs() : core::pack::annealer::FASTERAnnealer
• trywait_semaphore() : protocols::boinc::Boinc
• Tsymm_ : core::conformation::symmetry::SymmetricConformation
• turn_expression_ASTs_into_expressions() : protocols::pack_daemon::EntityFunc , protocols::pack_daemon::DynamicAggregateFunction
• turn_off_cter_insert() : protocols::antibody2::ModelCDRH3
• turn_off_flank_relax() : protocols::antibody2::H3RefineCCD
• turn_off_h3_filter() : protocols::antibody2::H3RefineCCD
• turn_off_H3_filter() : protocols::antibody2::H3PerturbCCD , protocols::antibody2::ModelCDRH3
• turn_off_repulsive_ramp() : protocols::antibody2::RefineBetaBarrel
• turn_on_benchmark() : protocols::antibody2::RefineOneCDRLoop , protocols::antibody2::H3RefineCCD
• turnoff_minimization_ : protocols::antibody2::CDRsMinPackMin
• tVal : protocols::sparta::Sparta::SpartaLib
• TVector : core::fragment::VectorCacheUnit< T >
• twelve_A_neighbors_ : protocols::enzdes::EnzdesFlexibleRegion
• twelveA_ : core::scoring::TwelveANeighborGraph
• twelveA_neighbor_graph() : core::scoring::Energies
• twelveA_squared_ : core::scoring::TwelveANeighborGraph
• TwelveANeighborEdge() : core::scoring::TwelveANeighborEdge
• TwelveANeighborGraph() : core::scoring::TwelveANeighborGraph
• TwelveANeighborNode() : core::scoring::TwelveANeighborNode
• twist() : protocols::dna::DNABasestep
• twist_ : protocols::dna::DNABasestep , protocols::MakeRotLib::RotData
• TWO_B_MethodIterator : core::scoring::ScoreFunction
• TWO_B_Methods : core::scoring::ScoreFunction
• two_body_energies_ : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge
• two_parts_chain1() : protocols::protein_interface_design::movers::SetAtomTree
• two_parts_chain1_ : protocols::protein_interface_design::movers::SetAtomTree
• two_stage_clustering() : protocols::swa::rna::StepWiseRNA_Clusterer
• two_stage_clustering_ : protocols::swa::rna::StepWiseRNA_Clusterer
• twobody_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_enmeths_ : core::scoring::MinimizationNode , core::scoring::MinimizationEdge
• TwoBodyEnergies : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• TwoBodyEnergiesIterator : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• TwoBodyEnergy() : core::scoring::methods::TwoBodyEnergy
• twochains_ : protocols::seeded_abinitio::SeedFoldTree
• twoD_histogram_ : core::scoring::orbitals::OrbitalsStatistics
• tX_ : core::grid::CartGrid< T >
• tY_ : core::grid::CartGrid< T >
• type() : protocols::optimize_weights::PNatLigPoseOptEData , core::id::TorsionID , core::scoring::constraints::SiteConstraintResidues , protocols::checkpoint::CheckPointer , protocols::topology_broker::RigidChunkClaimer , protocols::optimize_weights::PNatStructureOptEData , core::scoring::DC , protocols::constraints_additional::AmbiguousMultiConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::MultiConstraint , protocols::rbsegment_relax::RBResidueRange , protocols::moves::Mover , core::import_pose::ImportPoseOptions , protocols::topology_broker::PseudocontactShiftEnergyController , core::scoring::constraints::ConstantConstraint , core::fragment::JumpingFrame , protocols::topology_broker::FragmentClaimer , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::BigBinConstraint , core::fragment::SecstructSRFD , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::topology_broker::AsymFoldandDockClaimer , protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::DensityScoringClaimer , core::io::pdb::PDB_DReaderOptions , protocols::comparative_modeling::features::SSFeature , protocols::topology_broker::CutClaim , core::optimization::DOF_Node , core::conformation::Atom , core::fragment::Frame , core::scoring::constraints::BackboneStubConstraint , Entry , core::id::DOF_ID , core::conformation::symmetry::SymmDataOptions , core::scoring::constraints::AtomPairConstraint , core::conformation::Residue , protocols::topology_broker::DofClaim , core::fragment::SingleResidueFragData , core::conformation::orbitals::OrbitalXYZCoords , protocols::topology_broker::BBClaim , core::io::raw_data::DisulfideFile::ResNum , core::conformation::Atom , protocols::dna::Reversion , protocols::dna::PositionType , core::chemical::ICoorAtomID , protocols::kinmatch::KRSQuery , core::io::pdb::Field , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::TopologyClaimer , protocols::topology_broker::SequenceClaimer
• Type : core::chemical::ICoorAtomID
• type() : protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::ClaimerMessage , core::scoring::packstat::SimplePDB_Atom
• Type : protocols::ligand_docking::ligand_options::InterfaceInfo
• type() : core::fragment::BBTorsionAndAnglesSRFD , core::sequence::Sequence , core::conformation::orbitals::OrbitalXYZCoords , protocols::topology_broker::ConstraintClaimer , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::frag_picker::Contact , core::scoring::constraints::Constraint , core::pack::dunbrack::DunbrackConstraint , core::sequence::ScoringScheme , core::scoring::constraints::DihedralConstraint , protocols::comparative_modeling::features::TorsionFeature , core::scoring::sc::_DOT , core::scoring::constraints::KofNConstraint , protocols::fldsgn::topology::Loop , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , core::scoring::constraints::AngleConstraint , protocols::topology_broker::DisulfJumpClaimer , protocols::moves::_BoolMover , core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::topology_broker::PcsEnergyController , protocols::optimize_weights::DGBindOptEData , protocols::multistate_design::PosType , protocols::optimize_weights::OptEPositionData , core::id::TorsionID , protocols::topology_broker::FoldandDockClaimer , core::pack::dunbrack::RotamerConstraint , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::simple_filters::RotamerBoltzmannWeight , protocols::topology_broker::MetalloClaimer , core::fragment::BBTorsionSRFD , protocols::topology_broker::JumpClaim , core::scoring::constraints::AmbiguousNMRConstraint , protocols::optimize_weights::DDGMutationOptEData , core::sequence::SequenceCoupling , protocols::pockets::PocketConstraint , protocols::topology_broker::JumpClaimer , core::fragment::UpJumpSRFD , core::chemical::ResidueLoaderOptions , protocols::optimize_weights::PNatRotOptEPositionData , core::fragment::DownJumpSRFD , protocols::simple_moves::FragmentCost , core::io::silent::SilentFileOptions , core::scoring::constraints::DistancePairConstraint , protocols::moves::Mover , core::scoring::RDC , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::optimize_weights::PSSMOptEPositionData , core::io::pdb::FileDataOptions , protocols::simple_filters::RotamerBoltzmannWeight , protocols::loops::LoopsFileOptions , core::scoring::electron_density::ElectronDensityOptions , protocols::optimize_weights::DDGBindOptEData , protocols::topology_broker::RootClaim , protocols::constraints_additional::SequenceCouplingConstraint , core::scoring::constraints::BoundFunc , protocols::topology_broker::MembraneTopologyClaimer , protocols::moves::_BoolMover , core::scoring::constraints::LocalCoordinateConstraint , protocols::topology_broker::LoopFragmentClaimer , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::FabConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::topology_broker::TemplateJumpClaimer , core::sequence::SequenceProfile , protocols::topology_broker::SequenceClaim , core::sequence::CompositeSequence , core::scoring::RDC_Rohl , core::scoring::constraints::SiteConstraint , protocols::comparative_modeling::features::ResidueFeature
• type1_id_ : core::scoring::constraints::NamedAtomPairConstraint
• type2_id_ : core::scoring::constraints::NamedAtomPairConstraint
• type_ : protocols::simple_moves::FragmentCost , core::conformation::symmetry::SymmetryInfo , protocols::dna::DesignProteinBackboneAroundDNA , core::chemical::sdf::atomTyper , core::id::DOF_ID , core::conformation::Atom , core::chemical::ICoorAtomID , core::id::TorsionID , core::conformation::orbitals::OrbitalXYZCoords , core::scoring::constraints::BoundFunc , protocols::qsar::scoring_grid::SingleGrid , protocols::frag_picker::Contact , protocols::moves::_BoolMover , protocols::multistate_design::PosType , core::scoring::RDC_Rohl , protocols::fldsgn::topology::Loop , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::qsar::qsarPoint , core::scoring::RDC , protocols::moves::Mover , protocols::filters::Filter , protocols::simple_filters::RotamerBoltzmannWeight , core::sequence::ScoringScheme , protocols::checkpoint::CheckPointer , protocols::qsar::scoring_grid::SolvationMetaGrid , core::scoring::methods::UnfoldedStateEnergy , core::sequence::Cell , core::scoring::DC
• type_list_ : protocols::toolbox::KClusterElement
• type_map_ : core::scoring::packstat::AtomRadiusMap , protocols::qsar::qsarMap
• type_name() : protocols::jumping::ResiduePairJumpSetup , protocols::features::ProtocolFeaturesCreator , protocols::features::ScoreFunctionFeatures , protocols::features::PoseCommentsFeaturesCreator , protocols::features::RadiusOfGyrationFeatures , protocols::features::PoseCommentsFeatures , protocols::features::PairFeatures , protocols::features::HBondParameterFeatures , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::features::ResidueSecondaryStructureFeatures , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::features::LoopAnchorFeatures , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::jumping::JumpSelector , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::features::PairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::BetaTurnDetectionFeatures , protocols::features::ResidueConformationFeatures , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::features::HBondFeatures , protocols::jumping::SheetBuilder , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::StructureFeatures , protocols::features::ProtocolFeatures , protocols::features::AtomTypesFeatures , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::features::ChargeChargeFeaturesCreator , protocols::features::ResidueScoresFeaturesCreator , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::PoseConformationFeaturesCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::evaluation::EvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::features::LoopAnchorFeaturesCreator , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueScoresFeatures , protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::features::FeaturesReporterCreator , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::BatchFeatures , protocols::features::HBondParameterFeaturesCreator , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ProteinBondGeometryFeatures , protocols::features::ScoreTypeFeaturesCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::features::ResidueFeaturesCreator , protocols::features::ChargeChargeFeatures , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::features::SmotifFeatures , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::features::SaltBridgeFeaturesCreator , protocols::features::OrbitalsFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::features::ProteinResidueConformationFeatures , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::ResidueTypesFeaturesCreator , protocols::abinitio::TemplateJumpSetup , protocols::features::UnrecognizedAtomFeatures , protocols::simple_filters::NativeEvaluatorCreator , protocols::features::AtomTypesFeaturesCreator , protocols::topology_broker::ConstraintEvaluatorWrapperCreator , protocols::rotamer_recovery::RRProtocolCreator , protocols::features::PdbDataFeaturesCreator , protocols::jumping::RandomSheetBuilder , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::ResidueBurialFeatures , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::PoseConformationFeatures , protocols::features::ProteinRMSDFeaturesCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::features::ProteinRMSDFeatures , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::jumping::BaseJumpSetup , protocols::features::SaltBridgeFeatures , protocols::features::RotamerFeaturesCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::features::JobDataFeatures , protocols::features::OrbitalsFeaturesCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::ScoreTypeFeatures , protocols::features::GeometricSolvationFeatures , protocols::features::GeometricSolvationFeaturesCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::features::ResidueGridScoresFeatures , protocols::rotamer_recovery::RRReporterCreator , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::FeaturesReporter , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::HBondFeaturesCreator , protocols::jumping::JumpSetup , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::StructureScoresFeaturesCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::features::SmotifFeaturesCreator , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::frag_picker::Contact , protocols::features::ResidueTypesFeatures , protocols::features::BatchFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerFeatures , protocols::features::ResidueConformationFeaturesCreator , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::JobDataFeaturesCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::StructureFeaturesCreator , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::PdbDataFeatures , protocols::features::ResidueFeatures , protocols::features::StructureScoresFeatures , protocols::simple_filters::PoolEvaluatorCreator , protocols::features::RotamerRecoveryFeatures , protocols::features::AtomAtomPairFeatures
• type_set_name_ : protocols::simple_filters::JScoreEvaluator
• type_set_tag() : protocols::simple_moves::SwitchResidueTypeSetMover
• type_set_tag_ : protocols::simple_moves::SwitchResidueTypeSetMover
• TypeCumulator : protocols::noesy_assign::PeakCalibrator
• types() : core::chemical::Patch
• types_ : protocols::features::FeaturesReporterFactory , core::chemical::Patch , protocols::loops::loops_definers::LoopsDefinerFactory , protocols::evaluation::EvaluatorFactory
• tZ_ : core::grid::CartGrid< T >