- t -

• t : protocols::hybridization::TMalign
• T_ : core::scoring::ResidualDipolarCoupling , protocols::toolbox::InteratomicVarianceMatrix
• t_ang_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• T_bins : core::scoring::dna::DirectReadoutPotential
• T_ndx : protocols::moves::ReplicaExchangeMC
• T_rev : protocols::moves::ReplicaExchangeMC
• T_tag : protocols::moves::ReplicaExchangeMC
• TAB_DIR : protocols::sparta::Sparta::SpartaLib
• table_ : core::scoring::DenseEnergyContainer , core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::OneToAllEnergyContainer , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• table_size_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• tables_ : core::scoring::PolymerBondedEnergyContainer
• taboo_ : protocols::residue_optimization::MetapatchEnumeration
• 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
• tabooed_ : protocols::residue_optimization::MetapatchEnumeration
• tag : core::conformation::signals::ConnectionEvent , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::optimization::EItem , protocols::qsar::qsarOptData
• tag_ : core::fragment::CacheWrapper< T, XCacheUnit > , core::pose::full_model_info::SubMotifInfo , core::scoring::methods::BBDepCartBondedParameters , core::scoring::packstat::MultiProbePoseAccumulator , protocols::comparative_modeling::Align_RotamerEvaluator , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::electron_density::DockIntoDensityMover , protocols::evaluation::AlignEvaluator , protocols::grafting::AnchoredGraftMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::SingleStructureData , protocols::pockets::PocketGrid , protocols::pose_length_moves::NearNativeLoopCloser , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::simple_filters::ChiWellRmsdEvaluator , protocols::simple_filters::EvaluatedTrialMover , protocols::simple_filters::PoseMetricEvaluator< T > , protocols::simple_filters::RDC_Evaluator , protocols::simple_filters::RmsdEvaluator , protocols::simple_filters::SelectGdtEvaluator , protocols::simple_filters::SelectMaxsubEvaluator , protocols::simple_filters::SelectRDC_Evaluator , protocols::simple_filters::SelectRmsdEvaluator , protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::screener::TagDefinition , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer
• 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::Ligand_info , protocols::ligand_docking::Rotate_info
• tag_definition_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::AnchorSugarScreener
• 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::farna::RNA_DeNovoProtocol , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• tag_list : protocols::cluster::GatherPosesMover
• tag_map_ : protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug
• tag_name_ : protocols::matdes::SchemePlaceMotifsMover
• tag_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• tag_prefix_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• tag_residues_ : protocols::features::DatabaseJobInputter
• tag_structures_ : protocols::features::DatabaseJobInputter
• tag_to_source_map_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• tag_to_source_map_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• tags_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::scoring::rna::RNA_SuitePotential , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug , protocols::toolbox::KClusterData
• tail_residue_name_ : protocols::helical_bundle::MakeBundleHelix
• tail_segment_ : protocols::protein_interface_design::movers::LoopLengthChange
• tailresidues_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• takeoff_atom_ : core::scoring::loop_graph::LoopScoreInfo
• takeoff_domain_ : core::scoring::loop_graph::Loop
• takeoff_pos_ : core::scoring::loop_graph::Loop
• 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_ : core::chemical::ReplaceMainchainAtom , protocols::cryst::SetRefinementOptionsMover , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::noesy_assign::PeakCalibrator , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::simple_moves::MutateResidue
• 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::indexed_structure_store::filters::FragmentLookupFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::seeded_abinitio::SeedFoldTree , protocols::simple_moves::AlignChainMover
• target_conformer_ : protocols::motifs::MotifHit
• 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_end_ : protocols::simple_moves::SuperimposeMover
• target_function_ : core::scoring::cryst::PhenixInterface
• 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_jump_ : protocols::rigid::UniformRigidBodyMover
• target_lookup_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• target_path_ : core::indexed_structure_store::BinaryFragmentStoreBackend
• target_pose_start_ : protocols::grafting::simple_movers::ReplaceRegionMover
• 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_region_ : protocols::simple_filters::DomainInterfaceFilter
• target_region_str_ : protocols::simple_filters::DomainInterfaceFilter
• target_res_ : protocols::enzdes::RepackWithoutLigandFilter
• target_residue_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::simple_filters::NeighborTypeFilter
• target_residue_type_ : core::pack::task::ResidueLevelTask_
• 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_seqpos_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• target_sequence_ : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::hybridization::FoldTreeHybridize , protocols::toolbox::task_operations::DatabaseThread , 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_values_ : protocols::noesy_assign::PeakCalibrator
• targeted_dna_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::motifs::MotifDnaPacker
• targets_ : protocols::protein_interface_design::filters::DisulfideFilter
• task : protocols::forge::remodel::RemodelWorkingSet
• task1_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• task2_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• task_ : core::pack::rotamer_set::RotamerSets , protocols::docking::SidechainMinMover , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flexpack::FlexPacker , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::RandomMutation , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerizeMover , 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::loop_modeling::ToolboxKeys
• task_factory : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC
• task_factory_ : protocols::anchored_design::AnchorMoversData , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::features::ReportToDB , protocols::features::RotamerRecoveryFeatures , protocols::floppy_tail::FloppyTailMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::matdes::ClashCheckFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::optimize_weights::IterativeOptEDriver , protocols::pack_daemon::DaemonSet , 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::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::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::toolbox::task_operations::StoreTaskMover
• task_factory_set_ : protocols::protein_interface_design::filters::Torsion
• task_factoryA_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• task_factoryB_ : protocols::protein_interface_design::filters::AtomicContactCountFilter
• task_initialized_ : protocols::simple_moves::sidechain_moves::SidechainMover
• task_invalidated_ : protocols::simple_filters::PackerNeighborGraphFilter
• task_layers_ : protocols::flxbb::LayerDesignOperation
• task_name_ : protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover
• task_op_ : protocols::match::TaskOperationMPM
• task_operation_creator_map_ : core::pack::task::operation::TaskOperationFactory
• task_operations_ : protocols::flxbb::CombinedTaskOperation , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign
• task_scaling_ : protocols::simple_moves::GenericMonteCarloMover
• task_segments_ : protocols::relax::AtomCoordinateCstMover
• taskfactory_ : protocols::simple_filters::TotalSasaFilter
• taskops_ : protocols::features::TaskOperationFeatures
• tasks_ : protocols::toolbox::task_operations::STMStoredTask
• Tau_ : core::scoring::FACTSPotential
• tau_ : protocols::md::Thermostat , protocols::normalmode::NormalMode
• tau_angles : core::chemical::rings::RingConformer
• tccw : core::scoring::packstat::Circle
• tcw : core::scoring::packstat::Circle
• tell_vlb_to_not_touch_fold_tree_ : protocols::fldsgn::BluePrintBDR
• temp : core::scoring::APBSConfig::R_PARAM
• temp0 : protocols::md::MDscheduleData
• temp0_ : protocols::md::MDBase , protocols::md::Thermostat
• temp1_ : core::scoring::AtomNeighbor
• temp2_ : core::scoring::AtomNeighbor
• temp3_ : core::scoring::AtomNeighbor
• temp4_ : core::scoring::AtomNeighbor
• temp_ : core::pose::UnrecognizedAtomRecord , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::cryst::DockLatticeMover , protocols::denovo_design::filters::SSPredictionFilter , protocols::hybridization::CartesianSampler , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::PeriodicBoxMover , 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_cycles_ : protocols::loop_modeling::LoopProtocol
• temp_EMap_ : core::scoring::constraints::AmbiguousConstraint
• temp_energies : protocols::vip::VIP_Mover
• temp_final_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_id_ : protocols::moves::SimulatedTempering
• 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_stage1_ : protocols::hybridization::FoldTreeHybridize
• temp_trial_count_ : protocols::canonical_sampling::TemperingBase
• tempdir_ : core::scoring::cryst::PhenixInterface
• temperature : core::io::AtomInformation , core::pose::PDBInfo::AtomRecord , protocols::ligand_docking::Transform_info
• temperature0_ : protocols::simple_moves::sidechain_moves::SidechainMover
• temperature_ : core::pack::annealer::SimAnnealerBase , protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• Temperature_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::H3PerturbCCD
• temperature_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::FixedTemperatureController , protocols::docking::ConformerSwitchMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::farna::options::RNA_FragmentMonteCarloOptions , protocols::forge::remodel::RemodelLoopMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::magnesium::MgMonteCarlo , protocols::md::MDBase , protocols::moves::MonteCarlo , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::BackboneMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::ub_e2c::ubi_e2c_modeler
• temperature_jumps_ : protocols::canonical_sampling::SimulatedTempering
• temperature_stride_ : protocols::canonical_sampling::TemperingBase
• temperatures_ : protocols::canonical_sampling::TemperingBase , protocols::moves::SimulatedTempering , protocols::simple_moves::GenericMonteCarloMover
• tempering_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::docking::TemperedDocking
• templ_selector_ : protocols::abinitio::abscript::RigidChunkCM
• templ_target_ : protocols::abinitio::abscript::RigidChunkCM
• template_ : protocols::abinitio::abscript::RigidChunkCM
• template_chunks_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• template_contigs_ : protocols::hybridization::CartesianHybridize , 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_legacy::GraftOneMover
• template_file_ : protocols::toolbox::task_operations::DatabaseThread
• template_fn_ : protocols::hybridization::HybridizeProtocol
• template_id_ : protocols::hybridization::InsertChunkMover
• template_index_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_mini_pose_ : protocols::simple_moves::CopyDofMover
• template_name_ : protocols::antibody_legacy::GraftOneMover , protocols::toolbox::task_operations::AlignedThreadOperation
• template_names_ : protocols::protein_interface_design::filters::RmsdFilter
• 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::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::GraftOneMover , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::hybridization::InsertChunkMover , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::CopyDofMover , protocols::toolbox::task_operations::DatabaseThread
• 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_scores : protocols::cluster::GatherPosesMover
• template_size_ : protocols::jumping::MembraneJump
• template_start_ : protocols::antibody_legacy::GraftOneMover
• template_stem1_ : protocols::simple_filters::SSMotifFinder
• template_stem2_ : protocols::simple_filters::SSMotifFinder
• template_weights_ : protocols::hybridization::HybridizeProtocol
• template_wts_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• 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_aln_ : protocols::hybridization::HybridizeProtocol
• templates_poses_ : protocols::antibody::Ab_TemplateInfo
• templates_with_incorrect_strand_pairings_ : protocols::hybridization::FoldTreeHybridize
• temps_ : core::io::ResidueInformation
• tenA_ : core::scoring::TenANeighborGraph
• tenA_edge_pool_ : core::scoring::TenANeighborGraph
• tenA_squared_ : core::scoring::TenANeighborGraph
• tensorDa : core::scoring::data_struct
• tensorR : core::scoring::data_struct
• terCount : core::io::AtomInformation
• terCount_ : core::io::ResidueInformation
• term_length_ : core::scoring::methods::NMerSVMEnergy
• terminal_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• terminate_ : protocols::wum::MPI_WorkUnitManager_Slave
• termination_broadcasted_ : protocols::mpi_refinement::MPI_Refine_Emperor
• terminus_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• test_ : protocols::carbohydrates::GlycanRelaxMover
• test_all_moves_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• test_control_mode_ : protocols::grafting::AnchoredGraftMover
• test_count_one : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• test_count_two : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• test_cycles_ : protocols::relax::FastRelax
• test_run_ : protocols::loop_modeling::LoopProtocol
• testing_phase : protocols::simple_moves::ShakeStructureMover
• testmap_ : protocols::electron_density::ReportFSC
• tether_jump_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• tether_ligand_ : protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDockProtocol
• tether_to_closest_res_ : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• tetrahedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• tf : protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• tf2_ : protocols::docking::DockingHighRes
• tf_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::design::GeneralAntibodyModeler , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::rbsegment_relax::AutoRBMover , protocols::residue_selectors::TaskSelector , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::ub_e2c::ubi_e2c_modeler
• tf_set_ : protocols::antibody::design::GeneralAntibodyModeler
• tgt_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgt_amino_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_atom_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_pos_ : protocols::constraints_additional::BindingSiteConstraint
• tgt_pos_centroid_ : protocols::constraints_additional::BindingSiteConstraint
• tgt_res_idxs_ : protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgtD_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgtE_ : protocols::simple_moves::symmetry::SetupNCSMover
• the_cdr_loop_ : protocols::antibody::RefineOneCDRLoopCentroid
• the_config_file_ : core::scoring::saxs::SAXSEnergy
• the_loop_ : protocols::antibody::H3RefineCCD
• the_mover_ : protocols::wum::WorkUnit_MoverWrapper
• theArchive_ : protocols::jd2::archive::BaseArchiveManager , protocols::jd2::archive::MPIArchiveJobDistributor
• thenfilters_ : protocols::filters::IfThenFilter
• thermal_accepts_ : protocols::moves::MoverStatistics
• thermodynamic_data_ : protocols::simple_moves::PeriodicBoxMover
• theta : protocols::simple_moves::MinimalRotamer
• theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• theta_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor , core::kinematics::tree::BondedAtom , protocols::fldsgn::topology::DimerPairing
• THETA_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• theta_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• theta_near_0_ : protocols::match::VoxelSetIterator
• theta_near_180_ : protocols::match::VoxelSetIterator
• thickness_ : core::conformation::membrane::MembraneInfo , core::scoring::hbonds::HBondEnergy , core::scoring::Membrane_FAEmbed , core::scoring::packstat::Slice , protocols::membrane::AddMembraneMover , protocols::membrane::visualize::VisualizeMembraneMover
• third_atom_ : protocols::frag_picker::scores::FourAtomsConstraintData
• third_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• 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::environment::FoldTreeSketch::Node , core::kinematics::AtomTree
• thole_ : core::scoring::MultipoleParameter
• thread_ : protocols::simple_filters::RelativePoseFilter
• thread_sequence_ : protocols::simple_moves::SimpleThreadingMover
• threashold_ : protocols::filters::CompoundFilter
• three_prime_atom : protocols::stepwise::modeler::rna::Jump_point
• three_prime_chain_break_res_ : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• three_prime_phosphate_res_input_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• three_prime_seq_num : protocols::stepwise::modeler::rna::Jump_point
• three_prime_xyz_ : protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener
• threeD_projection_ : protocols::match::OccupiedSpaceHash
• threshold : protocols::viewer::triangleIterator
• threshold_ : core::select::residue_selector::NumNeighborsSelector , protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::dna::RotamerDNAHBondFilter , protocols::docking::SlideIntoContact , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RemoveLigandFilter , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::MatchResidues , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::residue_optimization::MetapatchEnumeration , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::Operator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::MinMover , protocols::toolbox::KMedoid , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation
• 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_score_of_complete_cycle_ : protocols::sewing::RepeatAssemblyMover
• throw_on_double_registration_ : core::select::residue_selector::ResidueSelectorFactory
• tic_ : protocols::filters::TimeFilter
• tightness_ : protocols::simple_filters::DisulfideEntropyFilter
• tilt1_center_ : protocols::docking::DockingInitialPerturbation , protocols::rigid::RigidBodyTiltMover
• tilt1_mag_ : protocols::rigid::RigidBodyTiltMover
• tilt2_center_ : protocols::docking::DockingInitialPerturbation , protocols::rigid::RigidBodyTiltMover
• tilt2_mag_ : protocols::rigid::RigidBodyTiltMover
• tilt_ : protocols::dna::DNABasestep , protocols::docking::DockingInitialPerturbation
• time_ : protocols::checkpoint::Timer
• time_data_mean_ : core::scoring::methods::D2H_SA_Energy
• time_data_std_ : core::scoring::methods::D2H_SA_Energy
• time_minobj_ : protocols::md::MDBase
• TIME_TO_UPDATE : core::scoring::TenANeighborNode
• timestamp_ : protocols::jd2::Job
• timing_last_start_time_ : protocols::wum::MPI_WorkUnitManager
• timing_last_type_ : protocols::wum::MPI_WorkUnitManager
• timing_total_ : protocols::wum::MPI_WorkUnitManager
• title_ : core::io::HeaderInformation
• titrate_stack_bonus_ : protocols::farna::options::RNA_FragmentMonteCarloOptions
• tlevel2rank_ : protocols::canonical_sampling::ParallelTempering
• Tlist_ : protocols::moves::ReplicaExchangeMC
• TM : core::scoring::TMscoreStore
• TM10 : core::scoring::TMscoreStore
• TM10_max : core::scoring::TMscoreStore
• TM_max : core::scoring::TMscoreStore
• TM_sum : core::scoring::TMscoreStore
• TM_sum10 : core::scoring::TMscoreStore
• tmh_inserted_ : core::scoring::MembraneTopology
• tmhelix_ : protocols::topology_broker::TMHTopologySamplerClaimer
• tmregion_ : core::scoring::MembraneTopology
• to_all_atom_ : protocols::docking::DockingProtocol
• 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::surface_docking::SurfaceDockingProtocol
• to_chain_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• to_entry_ : protocols::protein_interface_design::PatchdockReader
• to_full_atom_ : protocols::surface_docking::SurfaceDockingProtocol
• to_res_ : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• toc_ : protocols::filters::TimeFilter
• tol_ : core::scoring::func::FlatHarmonicFunc
• tolerance : core::optimization::DFPMinConvergedAbsolute , core::optimization::DFPMinConvergedFractional
• tolerance_ : protocols::branch_angle::BranchAngleOptimizer , protocols::branch_angle::BranchParam1 , protocols::docking::FaDockingSlideIntoContact , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::moves::JumpOutMover , protocols::noesy_assign::PeakCalibrator , protocols::rotamer_recovery::RRComparerChiDiff , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• tolerate_off_range_atom_bin_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• tolerated_overlap_ : protocols::match::output::MatchCollisionFilter
• toolbox_ : protocols::loop_modeling::LoopMover
• top_ : core::fragment::FragmentIO , protocols::dna::DnaPosition
• top_count_of_all_inputs_ : protocols::features::TopPercentOfAllInputs
• top_count_of_each_input_ : protocols::features::TopPercentOfEachInput
• top_designs_ : protocols::antibody::design::AntibodyDesignMover
• top_entities_ : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• top_n_big_frag_ : protocols::hybridization::FoldTreeHybridize
• top_n_small_frag_ : protocols::hybridization::FoldTreeHybridize
• top_netstates_ : core::pack::annealer::MultiCoolAnnealer
• top_outputed_ : protocols::pose_length_moves::NearNativeLoopCloser
• top_scores_ : protocols::antibody::design::AntibodyDesignMover
• top_to_keep : core::pack::annealer::MultiCoolAnnealer
• topNfilter_ : protocols::electron_density::DockIntoDensityMover
• topNfinal_ : protocols::electron_density::DockIntoDensityMover
• topNtrans_ : protocols::electron_density::DockIntoDensityMover
• topo_ : protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately
• topo_down_ : protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately
• topo_up_ : protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately
• topol_score_ : protocols::abinitio::Template
• topological_match_to_ : core::kinematics::AtomTree
• topological_observers_ : core::kinematics::AtomTree
• topology_ : core::conformation::membrane::SpanningTopology , core::scoring::methods::ProQ_Energy , protocols::membrane::AddMembraneMover
• topology_broker_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_root_res_ : protocols::topology_broker::TMHTopologySamplerClaimer
• topols_ : protocols::abinitio::PairingStatistics
• tor1 : protocols::normalmode::ContactStruct
• tor2 : protocols::normalmode::ContactStruct
• tor_step_ : protocols::simple_moves::PeriodicBoxMover
• 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
• torID_ : protocols::normalmode::NormalMode
• toroidal : core::scoring::sc::_RESULTS
• torsion : core::pose::rna::RNA_SuiteInfo
• torsion_ : core::id::TorsionID , protocols::normalmode::NormalMode , protocols::protein_interface_design::filters::Torsion
• torsion_angles_ : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• torsion_atom_ : core::chemical::AddConnect
• torsion_atoms_ : protocols::simple_moves::SetTorsion
• torsion_bin_ : protocols::comparative_modeling::features::TorsionFeature
• torsion_changes_move_other_monomers_ : core::conformation::symmetry::SymmetryInfo
• torsion_id_ : core::id::TorsionID_Range , core::optimization::DOF_Node , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• torsion_id_list_ : protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover
• torsion_id_map_ : core::kinematics::MoveMap
• torsion_ids_ : core::scoring::rna::RNA_SuitePotential , protocols::canonical_sampling::MetricRecorder , protocols::simple_moves::TorsionSetMover , protocols::stepwise::sampler::rna::RNA_MC_Suite
• torsion_info_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• torsion_lower_vals_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_name_ : protocols::simple_moves::SetTorsion
• torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• torsion_potential_ : core::scoring::rna::RNA_EnergyMethodOptions
• torsion_sample_vals_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_samples_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_screen_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• torsion_source_name : protocols::farna::fragments::TorsionSet
• torsion_type_ : protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• torsion_type_map_ : core::kinematics::MoveMap
• torsion_upper_vals_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_values_ : protocols::simple_moves::TorsionSetMover
• torsionA_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• torsionAB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• torsionB_ : protocols::toolbox::match_enzdes_util::EnzConstraintParameters
• torsions : protocols::farna::fragments::TorsionSet
• torsions_ : core::fragment::BBTorsionSRFD , protocols::frags::TorsionFragment
• torsions_indep_ : core::scoring::methods::IdealParametersDatabase
• torsions_to_fix_ : protocols::helical_bundle::BackboneGridSampler
• torsions_to_sample_ : protocols::helical_bundle::BackboneGridSampler
• torsions_using_ : protocols::normalmode::NormalMode
• torsions_using_assigned_ : protocols::normalmode::NormalMode
• torsionsMCM : protocols::flexpep_docking::FlexPepDockingFlags
• tot_rotamer_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• tot_surf : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• tot_vol : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• 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::stepwise::modeler::rna::StepWiseRNA_CountStruct
• total_cdr_loops_ : protocols::antibody::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::stepwise::modeler::rna::Filterer_Count
• total_count_ : protocols::canonical_sampling::SimulatedTempering
• total_counts_ : core::scoring::bin_transitions::BinTransitionData
• total_embed_ : protocols::membrane::geometry::Embedding
• total_energies_ : core::scoring::Energies
• total_energy_ : core::scoring::Energies , core::scoring::loop_graph::LoopGraph
• total_energy_alternate_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::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , 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::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_exp_chemical_shift_data_points_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• total_frames_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• total_glycan_residues_ : protocols::carbohydrates::GlycanRelaxMover
• total_goodfrags_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• total_hb_E : protocols::analysis::InterfaceData
• total_helices : core::scoring::Helices
• total_HH_dimer : core::scoring::Helices
• total_hpatch_score_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• total_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• total_hsasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• total_input_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• total_jobs_ : protocols::jd2::JobsContainer
• total_jobs_set_ : protocols::jd2::JobsContainer
• total_mc_trial_count : protocols::boinc::BoincSharedMemory
• total_metropolis_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_metropolis_accepts_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• 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_num_slides_ : protocols::simple_moves::symmetry::SymmetrySlider
• total_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• total_partitions_ : protocols::hotspot_hashing::PartitionedSearchPattern
• total_permutations_ : protocols::antibody::design::AntibodyDesignMover
• 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_ref_resids_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• total_rel_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• 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::constraints::ConstraintSet , core::scoring::solid_surface::SurfaceEnergies , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::optimize_weights::PNatStructureOptEData
• 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_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc
• total_sasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• total_score : core::scoring::motif::MotifHits
• total_score_ : protocols::analysis::LoopAnalyzerMover , protocols::simple_filters::ScoreCutoffFilter
• total_score_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• total_score_of_last_considered_pose_ : protocols::moves::MonteCarlo
• total_search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• total_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• total_SS_dimer : core::scoring::Strands
• total_strands : core::scoring::Strands
• total_structures_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_structures_relax_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_surface_energy_ : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• total_tmhelix_ : core::scoring::MembraneTopology
• total_trials_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• total_updates_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• total_updates_so_far_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• total_violation_count_ : protocols::noesy_assign::DistanceScoreMover
• total_weight_ : protocols::jumping::JumpSelector
• totalres_ : protocols::pockets::PocketConstraint
• totaltime_batchrelax_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• totaltime_loophash_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• totnum_abego_ : core::sequence::ABEGOManager
• trace_ : core::io::rna::RDAT , core::scoring::packstat::Event , core::scoring::ResidualDipolarCoupling
• tracer_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover
• tracer_output_stream_ : protocols::rpc::JSON_RPC
• tracer_visible_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• traces_ : core::scoring::packstat::Slice
• traffic_total_received_ : protocols::wum::MPI_WorkUnitManager
• traffic_total_sent_ : protocols::wum::MPI_WorkUnitManager
• traits_ : protocols::genetic_algorithm::Entity
• trajectories_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectory_ : core::pack::annealer::DebuggingAnnealer
• trajectory_file_name_ : core::pack::annealer::FixbbSimAnnealer
• trajectory_map_features_reporter_ : protocols::features::TrajectoryReportToDB
• Trajectory_state : protocols::viewer::GraphicsState
• trajectory_stream_ : protocols::canonical_sampling::PDBTrajectoryRecorder
• trans_ : protocols::rigid::WholeBodyTranslationMover
• trans_away_vec_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• trans_axis_ : protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover
• trans_back_vec_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• trans_chi4_mean_ : core::scoring::methods::ProClosureEnergy
• trans_chi4_sd_ : core::scoring::methods::ProClosureEnergy
• trans_mag_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::cryst::DockLatticeMover , protocols::farna::MultipleDomainMover , protocols::membrane::RandomPositionTranslationMover , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• trans_mag_in_ : protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::topology_broker::RigidBodyRandomTMHMover
• trans_mag_smooth_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover
• trans_magnitude_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::docking::DockingPrepackProtocol , protocols::docking::DockMCMCycle , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes
• TRANS_OMG_LOWER_RANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• TRANS_OMG_UPPER_RANGE : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• trans_packed_rotno_2_sorted_rotno_ : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• trans_rotamers_ : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• trans_step_ : protocols::simple_moves::PeriodicBoxMover
• trans_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• TRANS_UPPER_CIS_LOWER_SPLIT : core::pack::rotamers::RotamericSingleResiduePeptoidLibrary< T, N >
• trans_wt_ : protocols::simple_filters::SymmetricMotifFilter
• TRANS_X : core::kinematics::Jump
• TRANS_Y : core::kinematics::Jump
• TRANS_Z : core::kinematics::Jump
• transfer_buf_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• transform_info_ : protocols::ligand_docking::Transform
• transformed_residues : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• transforms_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transforms_uptodate_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transition_threshold_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• translate_ : protocols::rigid::RollMover
• translate_Ang_ : protocols::ligand_docking::RigidSearchMover
• translate_by_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• translate_index : protocols::forge::remodel::RemodelWorkingSet
• translate_info_ : protocols::ligand_docking::Translate
• translates_ : protocols::ligand_docking::CompoundTranslate
• translation : core::kinematics::RT , protocols::protein_interface_design::Transformation , Transformation
• translation_ : protocols::dna::SeparateDnaFromNonDna
• translation_axes_ : protocols::matdes::SymDofMover
• translation_mag_ : protocols::rigid::UniformRigidBodyMover , protocols::topology_broker::TMHTopologySamplerClaimer
• translation_magnitude_ : protocols::simple_moves::CoupledMover
• translation_matrices_ : core::conformation::symmetry::SymmData
• translation_vector_ : protocols::membrane::TranslationMover
• translocation_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• transM : protocols::sparta::RingData
• transparent_facets_ : protocols::match::Bool3DGridKinemageWriter
• tree_ : protocols::rigid::RigidBodyMotionMover
• treeatom_map_ : core::chemical::RerootRestypeVisitor
• triage_filter_ : protocols::protein_interface_design::filters::FilterScanFilter
• triage_positions_ : protocols::protein_interface_design::movers::PlaceStubMover
• triage_threshold_ : protocols::protein_interface_design::filters::BoltzmannFilter
• trial_counter_ : protocols::canonical_sampling::TemperingBase , protocols::moves::TrialCounter , protocols::simple_moves::GenericMonteCarloMover
• trial_large_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_positions_ : protocols::enzdes::SecondaryMatchProtocol
• trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_pack_ : protocols::abinitio::ClassicAbinitio
• trial_small_top25_ : protocols::abinitio::MembraneAbinitio
• trials_ : protocols::abinitio::hConvergenceCheck , protocols::denovo_design::connection::Connection , protocols::hybridization::hConvergenceCheck , protocols::seeded_abinitio::CloseFold
• triangles_ : protocols::viewer::ConformationViewer
• triazolamer_post_pos_ : protocols::simple_moves::triazolamer::TriazolamerMover
• triazolamer_pre_pos_ : protocols::simple_moves::triazolamer::TriazolamerMover
• triazolamer_seq_positions_ : protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• trie_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• tried_centroid_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tried_fullatom_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tries_ : core::scoring::trie::TrieCollection , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::TorsionDOFMover
• triggers_ : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• trim_proportion_ : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trimmedArea : core::scoring::sc::_RESULTS
• tripFileName : protocols::sparta::Sparta::SpartaLib
• triplet_fingerprint_data_ : protocols::pockets::FingerprintBase
• TRIPLET_Tab : protocols::sparta::Sparta::SpartaLib
• trj_ : protocols::md::MDBase
• trj_score_only_ : protocols::md::MDBase
• trj_scratch_ : protocols::md::MDBase
• true_behavior_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• true_mover_ : protocols::moves::IfMover
• truncate_only_ : protocols::electron_density::ScaleMapIntensities
• trust_current_temp_ : protocols::canonical_sampling::TemperingBase
• trust_fold_tree_ : protocols::loop_modeling::LoopMover
• try_all_disulfides_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• Tsymm_ : core::conformation::symmetry::SymmetricConformation
• turn_off_rna_chem_map_during_optimize_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• turnoff_minimization_ : protocols::antibody::CDRsMinPackMin
• tVal : protocols::sparta::Sparta::SpartaLib
• TvecA : protocols::motif_grafting::movers::motif2scaffold_data
• TvecB : protocols::motif_grafting::movers::motif2scaffold_data
• twelveA_ : core::scoring::TwelveANeighborGraph
• twelveA_squared_ : core::scoring::TwelveANeighborGraph
• twin_law_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• twist_ : protocols::dna::DNABasestep , protocols::make_rot_lib::RotData
• two_body_energies_ : core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::PDEdge
• two_parts_chain1_ : protocols::protein_interface_design::movers::SetAtomTree
• two_stage_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• two_step_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• twobody_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_enmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• twochains_ : protocols::seeded_abinitio::SeedFoldTree
• twoD_histogram_ : core::scoring::orbitals::OrbitalsStatistics
• tX_ : core::grid::CartGrid< T >
• tY_ : core::grid::CartGrid< T >
• type : core::io::raw_data::DisulfideFile::ResNum , core::scoring::packstat::SimplePDB_Atom , core::scoring::sc::_DOT , protocols::dna::PositionType , protocols::dna::Reversion , protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::environment::claims::DOFElement , protocols::environment::claims::JumpElement , protocols::environment::claims::ResidueElement , protocols::kinmatch::KRSQuery , protocols::ligand_docking::ligand_options::InterfaceInfo , protocols::md::MDscheduleData
• type1_id_ : core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint
• type2_id_ : core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint
• type3_id_ : core::scoring::constraints::NamedAngleConstraint
• type_ : core::chemical::ICoorAtomID , core::conformation::Atom , core::conformation::orbitals::OrbitalXYZCoords , core::conformation::symmetry::SymmetryInfo , core::id::DOF_ID , core::id::TorsionID , core::scoring::constraints::BoundFunc , core::scoring::DC , core::scoring::methods::UnfoldedStateEnergy , core::scoring::motif::MotifHash , core::scoring::motif::ResPairMotif , core::scoring::MultipoleElecResidueInfo , core::scoring::RDC , core::scoring::RDC_Rohl , core::scoring::rna::data::RNA_Reactivity , core::sequence::Cell , core::sequence::ScoringScheme , protocols::checkpoint::CheckPointer , protocols::dna::DesignProteinBackboneAroundDNA , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::topology::Loop , protocols::frag_picker::Contact , protocols::moves::Mover , protocols::moves::PyMolObserver , protocols::multistate_design::PosType , protocols::qsar::qsarPoint , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::FragmentCost
• type_list_ : protocols::toolbox::KClusterElement
• type_lookup_ : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• type_map_ : core::scoring::packstat::AtomRadiusMap , protocols::qsar::qsarMap
• type_of_computation : core::scoring::data_struct
• type_set_name_ : protocols::simple_filters::JScoreEvaluator
• type_set_tag_ : protocols::simple_moves::SwitchResidueTypeSetMover
• types_ : core::chemical::Metapatch , core::chemical::Patch , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory
• typGrid_ : protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::NonPlaidFingerprint
• tZ_ : core::grid::CartGrid< T >