- t -

• TableLookupEtableEnergy() : core::scoring::etable::TableLookupEtableEnergy
• TableLookupEvaluator() : core::scoring::etable::TableLookupEvaluator
• TabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• tabulate() : core::scoring::saxs::FormFactor , core::scoring::saxs::FormFactorManager
• tag() : protocols::evaluation::AlignEvaluator , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::OptEPositionData , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::topology_broker::ConstraintClaimer
• tag_format_string() : protocols::outputter::SilentFileOutputter
• tag_time() : protocols::simple_moves::DumpPdb
• tags() : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• 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_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_dih() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_res() : protocols::toolbox::match_enzdes_util::ResInteractions
• target_accept_ratio() : protocols::abinitio::IterativeBase
• target_conformer() : protocols::motifs::MotifHit
• target_conformers_map() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_positions() : protocols::motifs::BuildPosition , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_res() : protocols::pockets::PocketConstraint
• target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget
• target_residues() : protocols::enzdes::PackRotamersMoverPartGreedy
• target_sequence() : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::toolbox::task_operations::ThreadSequenceOperation
• target_total_residue() : protocols::abinitio::Templates
• target_type() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , core::pack::task::PackerTask_
• targeted_dna() : protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::DesignProteinBackboneAroundDNA
• 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
• task() : 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_factory() : 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 , 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
• task_factory_set() : protocols::protein_interface_design::filters::Torsion
• task_initialized() : protocols::simple_moves::sidechain_moves::SidechainMover
• task_is_valid() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover
• task_mode() : core::pack::task::ResidueLevelTask_
• task_string() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• TaskAwareCsts() : protocols::protein_interface_design::movers::TaskAwareCsts
• TaskAwareMinMover() : protocols::simple_moves::TaskAwareMinMover
• TaskFactory() : core::pack::task::TaskFactory
• TaskOperationFactory() : core::pack::task::operation::TaskOperationFactory
• TaskOperationLoader() : protocols::jd2::parser::TaskOperationLoader
• TaskOperationMPM() : protocols::match::TaskOperationMPM
• TaskOperationRegistrator() : core::pack::task::operation::TaskOperationRegistrator< T >
• Tau() : core::scoring::FACTSPotential
• 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::pose::UnrecognizedAtomRecord , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::simple_moves::TorsionDOFMover
• temp1() : core::scoring::AtomNeighbor
• temp2() : core::scoring::AtomNeighbor
• temp3() : core::scoring::AtomNeighbor
• temp4() : core::scoring::AtomNeighbor
• temp_file() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor
• temp_final() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_initial() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temperature() : 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
• 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
• TemperatureController() : protocols::canonical_sampling::TemperatureController
• TemperedDocking() : protocols::docking::TemperedDocking
• tempering() : protocols::canonical_sampling::MetropolisHastingsMover
• TemperingBase() : protocols::canonical_sampling::TemperingBase
• Template() : protocols::abinitio::Template
• template_atom_inds() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• template_file() : protocols::protein_interface_design::movers::Splice
• template_index() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_name() : protocols::id::AlignmentID
• template_number() : protocols::hybridization::ChunkTrialMover
• template_pose() : protocols::comparative_modeling::ThreadingMover
• template_poses() : protocols::jd2::InnerMultiThreadingJob
• template_res_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_size() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_size() : protocols::jumping::MembraneJump
• TemplateFragmentClaimer() : protocols::topology_broker::TemplateFragmentClaimer
• TemplateHistory() : protocols::hybridization::TemplateHistory
• TemplateJumpClaimer() : protocols::topology_broker::TemplateJumpClaimer
• TemplateJumpSetup() : protocols::abinitio::TemplateJumpSetup
• Templates() : protocols::abinitio::Templates
• 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
• tenA_neighbor_graph() : core::scoring::Energies
• TenANeighborEdge() : core::scoring::TenANeighborEdge
• TenANeighborGraph() : core::scoring::TenANeighborGraph
• TenANeighborNode() : core::scoring::TenANeighborNode
• tensor() : core::scoring::ResidualDipolarCoupling
• TensorsOptimizer() : protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizer
• TensorsOptimizerFix() : protocols::scoring::methods::pcs2::TensorsOptimizerFix
• TensorsOptimizerSvd() : protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• 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_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
• testNeighbor() : protocols::pockets::PCluster
• TestPattern() : protocols::hotspot_hashing::TestPattern
• tether_ligands() : protocols::ligand_docking::HighResDocker
• TetherLigand() : protocols::ligand_docking::TetherLigand
• tf2() : protocols::docking::DockingHighRes
• TheozymeInvrotTree() : protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• ThermodynamicMover() : protocols::canonical_sampling::ThermodynamicMover
• ThermodynamicObserver() : protocols::canonical_sampling::ThermodynamicObserver
• theta() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , protocols::fldsgn::topology::DimerPairing
• theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• thickness() : core::scoring::Membrane_FAEmbed
• ThirdLoop() : core::scoring::sc::MolecularSurfaceCalculator
• this_aa() : protocols::optimize_weights::PNatAAOptERotamerData
• this_weak_ptr() : core::kinematics::tree::Atom_
• 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
• threshold() : 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_probability() : protocols::simple_filters::RotamerBoltzmannWeight
• 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
• time_for_temp_move() : protocols::canonical_sampling::TemperingBase
• time_to_checkpoint() : protocols::checkpoint::Timer
• TimeEvaluator() : protocols::evaluation::TimeEvaluator
• TimeFilter() : protocols::filters::TimeFilter
• Timer() : protocols::checkpoint::Timer
• title() : core::io::pdb::HeaderInformation
• tm_projection_penalty() : core::scoring::MembranePotential
• tmh_inserted() : core::scoring::MembraneTopology
• tmhelix() : core::scoring::MembraneTopology
• tmregion() : core::scoring::MembraneTopology
• TMscore() : protocols::hybridization::TMalign
• TMscore8_search() : protocols::hybridization::TMalign
• to_all_atom() : protocols::docking::DockingProtocol
• to_allatom() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• to_centroid() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::nonlocal::SingleFragmentMover
• to_do() : protocols::jd2::Job
• 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
• toggle() : protocols::topology_broker::DofClaim , protocols::topology_broker::BBClaim , protocols::topology_broker::JumpClaim
• tol() : core::scoring::constraints::FlatHarmonicFunc
• tolerance() : protocols::branch_angle::BranchAngleOptimizer , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::simple_moves::MinMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• 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_fragments() : core::fragment::picking_old::vall::VallLibrarian
• top_level_pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• TopCountOfAllInputs() : protocols::features::TopCountOfAllInputs
• TopCountOfEachInput() : protocols::features::TopCountOfEachInput
• topological_match_to() : core::kinematics::AtomTree
• topological_observers() : core::kinematics::AtomTree
• topology() : protocols::abinitio::PairingStatistics
• topology_broker() : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_score() : protocols::abinitio::Template
• TopologyBroker() : protocols::topology_broker::TopologyBroker
• TopologyClaimer() : protocols::topology_broker::TopologyClaimer
• TopologyClaimerFactory() : protocols::topology_broker::TopologyClaimerFactory
• 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_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• torsion() : core::conformation::Conformation , core::fragment::BBTorsionSRFD , core::id::TorsionID , core::pose::Pose , protocols::protein_interface_design::filters::Torsion
• Torsion() : protocols::protein_interface_design::filters::Torsion
• torsion2big_bin() : protocols::comparative_modeling::features::TorsionFeature , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::toolbox::pose_metric_calculators::RotamerRecovery
• 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_angle() : core::conformation::Conformation , core::kinematics::AtomTree
• torsion_angle_dof_id() : core::kinematics::AtomTree
• torsion_angles_within_cutoffs() : protocols::swa::rna::RNA_LoopCloseSampler
• torsion_bin() : protocols::comparative_modeling::features::TorsionFeature
• torsion_database() : protocols::protein_interface_design::movers::Splice
• torsion_database_fname() : protocols::protein_interface_design::movers::Splice
• 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_begin() : core::kinematics::MoveMap
• torsion_id_end() : core::kinematics::MoveMap
• torsion_id_ranges() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::rigid::RigidBodyMover , protocols::simple_moves::SmallMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• torsion_ids() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• torsion_is_independent() : core::conformation::symmetry::SymmetryInfo
• torsion_name() : protocols::simple_moves::SetTorsion
• torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
• torsion_scale_factor() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• torsion_type_begin() : core::kinematics::MoveMap
• torsion_type_end() : core::kinematics::MoveMap
• 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::id::TorsionID
• TorsionID_Range() : core::id::TorsionID_Range
• TorsionRestrictedKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• torsions() : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• 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
• TorsionSweepingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• total() : core::scoring::saxs::DistanceHistogram
• total_accepts() : protocols::jd2::archive::ArchiveBase
• total_energies() : core::scoring::Energies
• total_energy() : core::pack::interaction_graph::SimpleInteractionGraph , core::scoring::Energies , core::scoring::saxs::SAXSEnergy , core::scoring::Energies
• total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_current_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_nr_jobs() : protocols::jd2::JobDistributor
• total_number_abego() : core::util::ABEGOManager
• total_proposed() : protocols::jd2::archive::ArchiveBase
• total_res() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• total_residue() : core::fragment::SecondaryStructure , core::kinematics::ResidueCoordinateChangeList , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSetsBase , core::pack::rotamer_set::RotamerSubsets , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pose::MiniPose , core::pose::Pose , core::scoring::trie::TrieCollection , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::jumping::SameStrand , core::pack::rotamer_set::ContinuousRotamerSets , protocols::jd2::parser::BluePrint , core::pack::rotamer_set::UnboundRotamersOperation
• total_residue_wolig() : protocols::jd2::parser::BluePrint
• total_rotamers_2_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• total_score() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager , protocols::qsar::scoring_grid::GridManager
• total_score_of_last_considered_pose() : protocols::moves::MonteCarlo
• total_size() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• total_standard_cycles() : protocols::forge::remodel::RemodelLoopMover
• total_trials() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::moves::TrialCounter , protocols::moves::MonteCarlo
• totaltime_loophash() : protocols::loophash::MPI_LoopHashRefine
• touchesPS() : protocols::pockets::PocketGrid
• touchesSolvent() : protocols::pockets::PocketGrid
• touchesSS() : protocols::pockets::PocketGrid
• touchesSurface() : protocols::pockets::PocketGrid
• tournament_select() : protocols::genetic_algorithm::GeneticAlgorithm
• tr() : protocols::loop_build::LoopMover_SlidingWindow , protocols::loops::loop_mover::LoopMover , protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD , protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves , protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD
• trace() : core::scoring::packstat::trace
• traceback() : core::sequence::Aligner
• 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 >
• traits() : protocols::genetic_algorithm::Entity
• trajectories_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectory_idx() : protocols::wum2::WorkUnit
• TrajectoryRecorder() : protocols::canonical_sampling::TrajectoryRecorder
• trans_axis() : protocols::rigid::RigidBodyTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofSeqTransMover
• trans_magnitude() : protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover
• 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::hotspot_hashing::SearchPatternTransform , protocols::hybridization::TMalign
• Transform() : protocols::ligand_docking::Transform
• transform() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transform_Ax_plus_b_recursive() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• Transform_info() : protocols::ligand_docking::Transform_info
• transform_ligand() : protocols::ligand_docking::Transform
• transforms_uptodate() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transition_threshold() : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• translate() : core::grid::CartGrid< T >
• Translate() : protocols::ligand_docking::Translate
• Translate_info() : protocols::ligand_docking::Translate_info
• translate_ligand() : protocols::ligand_docking::Translate
• translate_virt_to_CoM() : protocols::hybridization::FoldTreeHybridize
• translateDSSP_ABEGO() : protocols::forge::remodel::RemodelData
• translation() : protocols::dna::SeparateDnaFromNonDna , protocols::ligand_docking::RigidSearchMover
• translation_along_axis() : core::kinematics::Jump
• Translator() : core::coarse::Translator
• TranslatorSet() : core::coarse::TranslatorSet
• tree_from_jumps_and_cuts() : core::kinematics::FoldTree
• TreeVizBuilder() : core::kinematics::TreeVizBuilder
• triage_filter() : protocols::protein_interface_design::filters::FilterScanFilter
• triage_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• trial() : protocols::moves::TrialCounter
• trial_counter() : protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover
• trial_large() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_top25() : protocols::abinitio::MembraneAbinitio
• trial_smooth() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio
• TrialCounter() : protocols::moves::TrialCounter
• TrialCounterObserver() : protocols::canonical_sampling::TrialCounterObserver
• TrialMover() : protocols::moves::TrialMover
• trials() : protocols::seeded_abinitio::CloseFold
• triangle() : protocols::viewer::triangle
• triangleIterator() : protocols::viewer::triangleIterator
• trie() : core::scoring::trie::TrieCollection
• trie_vs_path() : 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
• trie_vs_trie() : core::scoring::trie::RotamerTrieBase , core::scoring::trie::RotamerTrie< AT, CPDATA > , 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
• TrieCountPair1BC3() : core::scoring::etable::etrie::TrieCountPair1BC3
• TrieCountPair1BC4() : core::scoring::etable::etrie::TrieCountPair1BC4
• TrieCountPairAll() : core::scoring::etable::etrie::TrieCountPairAll
• TrieCountPairGeneric() : core::scoring::etable::etrie::TrieCountPairGeneric
• TrieNode() : core::scoring::trie::TrieNode< AT, CPDATA >
• tries() : protocols::simple_moves::TorsionDOFMover
• 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
• TrimPeripheralBand() : core::scoring::sc::ShapeComplementarityCalculator
• TrimPeripheralBandCheckDot() : core::scoring::sc::ShapeComplementarityCalculator
• triplet_fingerprint_data() : protocols::pockets::FingerprintBase
• TrueFilter() : protocols::filters::TrueFilter
• truncate_cenlist_values() : core::scoring::EnvPairPotential
• TruncatedScoreEvaluator() : protocols::simple_filters::TruncatedScoreEvaluator
• 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
• turn_expression_ASTs_into_expressions() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• 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::H3RefineCCD , protocols::antibody2::RefineOneCDRLoop
• twelveA_neighbor_graph() : core::scoring::Energies
• TwelveANeighborEdge() : core::scoring::TwelveANeighborEdge
• TwelveANeighborGraph() : core::scoring::TwelveANeighborGraph
• TwelveANeighborNode() : core::scoring::TwelveANeighborNode
• twist() : protocols::dna::DNABasestep
• two_parts_chain1() : protocols::protein_interface_design::movers::SetAtomTree
• two_stage_clustering() : protocols::swa::rna::StepWiseRNA_Clusterer
• twobody_energies() : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• TwoBodyEnergy() : core::scoring::methods::TwoBodyEnergy
• type() : core::io::pdb::PDB_DReaderOptions , protocols::topology_broker::FoldandDockClaimer , protocols::optimize_weights::PNatLigPoseOptEData , core::conformation::Residue , core::conformation::orbitals::OrbitalXYZCoords , protocols::topology_broker::RigidChunkClaimer , core::chemical::ICoorAtomID , core::fragment::DownJumpSRFD , protocols::optimize_weights::DGBindOptEData , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::ConstraintClaimer , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::RDC_Rohl , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , core::conformation::orbitals::OrbitalXYZCoords , protocols::constraints_additional::BindingSiteConstraint , protocols::optimize_weights::DDGMutationOptEData , protocols::fldsgn::topology::Loop , core::chemical::ResidueLoaderOptions , core::scoring::RDC , protocols::topology_broker::LoopFragmentClaimer , protocols::moves::Mover , core::scoring::constraints::AngleConstraint , protocols::optimize_weights::OptEPositionData , protocols::frag_picker::Contact , protocols::simple_moves::FragmentCost , core::scoring::constraints::BoundFunc , protocols::multistate_design::PosType , protocols::topology_broker::SequenceClaim , protocols::topology_broker::DisulfJumpClaimer , core::scoring::constraints::DihedralConstraint , protocols::optimize_weights::DDGBindOptEData , protocols::topology_broker::DofClaim , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::JumpClaimer , protocols::topology_broker::JumpClaim , protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::AsymFoldandDockClaimer , core::scoring::constraints::SiteConstraint , protocols::topology_broker::CutClaim , core::import_pose::ImportPoseOptions , protocols::comparative_modeling::features::ResidueFeature , protocols::topology_broker::RootClaim , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , core::conformation::Atom , core::conformation::symmetry::SymmDataOptions , core::sequence::ScoringScheme , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::BBClaim , core::scoring::constraints::FabConstraint , protocols::topology_broker::ClaimerMessage , core::sequence::SequenceProfile , protocols::topology_broker::PcsEnergyController , core::fragment::SingleResidueFragData , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::comparative_modeling::features::TorsionFeature , protocols::loops::LoopsFileOptions , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::simple_filters::RotamerBoltzmannWeight , protocols::constraints_additional::SequenceCouplingConstraint , core::sequence::CompositeSequence , core::id::TorsionID , protocols::moves::_BoolMover , core::scoring::constraints::Constraint , core::scoring::constraints::BigBinConstraint , protocols::checkpoint::CheckPointer , core::optimization::DOF_Node , core::pack::dunbrack::RotamerConstraint , core::scoring::constraints::AmbiguousNMRConstraint , protocols::topology_broker::CoordConstraintClaimer , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::DistancePairConstraint , protocols::rbsegment_relax::RBResidueRange , core::scoring::DC , core::scoring::electron_density::ElectronDensityOptions , core::sequence::SequenceCoupling , protocols::topology_broker::MetalloClaimer , protocols::comparative_modeling::features::SSFeature , protocols::moves::Mover , core::sequence::ScoringScheme , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , core::scoring::constraints::KofNConstraint , protocols::simple_filters::RotamerBoltzmannWeight , protocols::topology_broker::DensityScoringClaimer , core::sequence::Sequence , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::FragmentClaimer , core::scoring::constraints::MultiConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::constraints::SequenceProfileConstraint , core::fragment::BBTorsionAndAnglesSRFD , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::DihedralPairConstraint , protocols::pockets::PocketConstraint , core::scoring::constraints::CoordinateConstraint , core::conformation::Atom , core::scoring::constraints::AmbiguousConstraint , protocols::optimize_weights::PNatRotOptEPositionData , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , protocols::topology_broker::TopologyClaimer , core::fragment::BBTorsionSRFD , core::id::TorsionID , core::pack::dunbrack::DunbrackConstraint , core::io::silent::SilentFileOptions , core::io::pdb::FileDataOptions , protocols::topology_broker::TemplateJumpClaimer , core::fragment::Frame , core::id::DOF_ID , core::fragment::JumpingFrame , core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD
• type_name() : protocols::features::PairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::FeaturesReporterCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::features::ProtocolFeatures , protocols::rotamer_recovery::RRComparerCreator , protocols::features::ScoreFunctionFeatures , protocols::features::ResidueScoresFeaturesCreator , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::features::StructureScoresFeaturesCreator , protocols::features::AtomTypesFeaturesCreator , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ScoreFunctionFeaturesCreator , protocols::jumping::ResiduePairJumpSetup , protocols::features::ChargeChargeFeatures , protocols::features::ResidueConformationFeatures , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::rotamer_recovery::RRProtocolCreator , protocols::evaluation::EvaluatorCreator , protocols::features::ResidueScoresFeatures , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::features::SaltBridgeFeatures , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::jumping::BaseJumpSetup , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueTypesFeatures , protocols::features::LoopAnchorFeaturesCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::features::PdbDataFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::SmotifFeaturesCreator , protocols::features::ResidueTotalScoresFeatures , protocols::topology_broker::ConstraintEvaluatorWrapperCreator , protocols::features::ResidueTypesFeaturesCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::features::GeometricSolvationFeatures , protocols::features::StructureFeatures , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::features::StructureFeaturesCreator , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::features::GeometricSolvationFeaturesCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::features::ResidueBurialFeaturesCreator , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::PoseCommentsFeatures , protocols::jumping::JumpSetup , protocols::features::FeaturesReporter , protocols::jumping::SheetBuilder , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::jumping::JumpSelector , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::abinitio::TemplateJumpSetup , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinRMSDFeatures , protocols::features::RotamerFeatures , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::features::PdbDataFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::PairFeatures , protocols::features::StructureScoresFeatures , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ResidueGridScoresFeaturesCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::features::SmotifFeatures , protocols::simple_filters::PoolEvaluatorCreator , protocols::features::ScoreTypeFeaturesCreator , protocols::features::BetaTurnDetectionFeatures , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::HBondFeaturesCreator , protocols::features::OrbitalsFeatures , protocols::features::PoseConformationFeatures , protocols::features::ResidueFeatures , protocols::features::BatchFeaturesCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator , protocols::features::ResidueConformationFeaturesCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::features::ProteinResidueConformationFeatures , protocols::features::AtomAtomPairFeatures , protocols::simple_filters::PalesEvaluatorCreator , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::features::JobDataFeaturesCreator , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::features::UnrecognizedAtomFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::features::RotamerFeaturesCreator , protocols::frag_picker::Contact , protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::features::RotamerRecoveryFeaturesCreator , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::features::RadiusOfGyrationFeatures , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::PoseCommentsFeaturesCreator , protocols::features::ProteinBondGeometryFeatures , protocols::rotamer_recovery::RRReporterCreator , protocols::features::HBondParameterFeaturesCreator , protocols::features::AtomTypesFeatures , protocols::features::LoopAnchorFeatures , protocols::rotamer_recovery::RRProtocolRTMinCreator , protocols::features::ResidueBurialFeatures , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::ScoreTypeFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::BatchFeatures , protocols::features::HBondFeatures , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::ProtocolFeaturesCreator , protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::features::JobDataFeatures , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::HBondParameterFeatures , protocols::jumping::RandomSheetBuilder , protocols::simple_filters::RdcEvaluatorCreator , protocols::features::ChargeChargeFeaturesCreator , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::features::OrbitalsFeaturesCreator
• type_set_tag() : protocols::simple_moves::SwitchResidueTypeSetMover
• types() : core::chemical::Patch