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

- t -

• T_ : core::scoring::ResidualDipolarCoupling
• t_ : protocols::hybridization::TMalign
• T_ : protocols::toolbox::InteratomicVarianceMatrix
• t_ang_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• T_bins : core::scoring::dna::DirectReadoutPotential
• t_jump() : protocols::moves::SimulatedTempering
• T_ndx : protocols::moves::ReplicaExchangeMC
• t_predicate_func : protocols::flexpep_docking::FlexPepDockingPoseMetrics
• T_rev : protocols::moves::ReplicaExchangeMC
• T_SURFACE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• T_tag : protocols::moves::ReplicaExchangeMC
• T_xx_ : core::scoring::nmr::NMRTensor
• T_xy_ : core::scoring::nmr::NMRTensor
• T_xz_ : core::scoring::nmr::NMRTensor
• T_yy_ : core::scoring::nmr::NMRTensor
• T_yz_ : core::scoring::nmr::NMRTensor
• 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_name_ : protocols::features::SimpleMetricFeatures
• table_size_ : core::pack::interaction_graph::AminoAcidNeighborSparseMatrix< T >
• tableID() : core::scoring::tableID
• TableLookupEtableEnergy() : core::scoring::etable::TableLookupEtableEnergy
• TableLookupEvaluator() : core::scoring::etable::TableLookupEvaluator
• 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
• tabooed_ : protocols::residue_optimization::MetapatchEnumeration
• TabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• tabulate() : core::scoring::saxs::FormFactor , core::scoring::saxs::FormFactorManager
• Tag : core::conformation::signals::ConnectionEvent
• tag : core::conformation::signals::ConnectionEvent
• Tag : core::conformation::signals::IdentityEvent
• tag : core::conformation::signals::IdentityEvent
• Tag : core::conformation::signals::LengthEvent
• tag : core::conformation::signals::LengthEvent , core::import_pose::libraries::BasePairStepSequence , core::import_pose::libraries::BasePairType , core::optimization::EItem
• Tag : core::pack::palette::PackerPaletteFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperationFactory
• tag() : core::pose::full_model_info::SubMotifInfo , core::pose::PDBInfo , core::scoring::motif::ResPairMotif , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::AlignEvaluator
• Tag : protocols::filters::FilterFactory , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory
• tag() : protocols::ligand_docking::ga_ligand_dock::AtomProperties
• Tag : protocols::moves::MoverFactory
• tag() : protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::SingleStructureData
• Tag : protocols::parser::FragmentReader
• tag : protocols::qsar::qsarOptData
• Tag : protocols::qsar::scoring_grid::GridFactory , protocols::rna::movers::ErraserMinimizerMover , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory
• tag() : protocols::stepwise::screener::TagDefinition , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer
• 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::ligand_docking::ga_ligand_dock::AtomProperties , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::SingleStructureData , protocols::pockets::PocketGrid , 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_chain_ids() : protocols::ligand_docking::Rotate_info
• tag_along_chains_ : protocols::ligand_docking::Rotate_info , protocols::ligand_docking::Translate
• tag_along_jumps() : protocols::ligand_docking::Rotate_info
• tag_along_residues : protocols::ligand_docking::Ligand_info , protocols::ligand_docking::Rotate_info
• tag_definition_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::AnchorSugarScreener
• tag_disulfide() : protocols::denovo_design::DisulfidizeMover
• tag_disulfides() : protocols::denovo_design::DisulfidizeMover
• tag_for_cluster_metric_ : protocols::multistage_rosetta_scripts::MRSJob
• tag_for_stage_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• tag_idx_ : core::import_pose::atom_tree_diffs::AtomTreeDiff
• TAG_IN_FILE : protocols::jd2::archive::ArchiveBase
• tag_is_done_ : protocols::rna::denovo::RNA_DeNovoProtocol , protocols::rna::setup::RNA_MonteCarloJobDistributor
• tag_list : protocols::cluster::GatherPosesMover
• tag_list_for_input_pose_id() : protocols::multistage_rosetta_scripts::TagManager
• tag_list_for_input_pose_id_ : protocols::multistage_rosetta_scripts::TagManager
• tag_manager() : protocols::multistage_rosetta_scripts::MRSJobQueen
• tag_manager_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• tag_map_ : protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug
• TAG_NAME : protocols::denovo_design::components::SegmentPairing
• 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_residue_number_ : core::scoring::nmr::pcs::PCSMultiSet
• tag_residues_ : protocols::features::DatabaseJobInputter
• tag_structures_ : protocols::features::DatabaseJobInputter
• tag_time() : protocols::simple_moves::DumpPdb
• tag_to_source_map_ONE_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• tag_to_source_map_TWO_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• TagCOP : core::pack::palette::PackerPaletteFactory , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::ResLvlTaskOperationFactory , core::pack::task::operation::TaskOperation , core::pack::task::operation::TaskOperationFactory , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfacePacker , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::evolution::EvolutionaryDynamicsMover , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::moves::DsspMover , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::parser::FragmentReader , protocols::pose_creation::MakePolyXMover , protocols::pose_metric_calculators::FragQualCalculator , protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::rosetta_scripts::RosettaScriptsParser , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::splice::SampleRotamersFromPDB , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::SeqprofConsensusOperation
• TagCOPs : protocols::rosetta_scripts::RosettaScriptsParser
• TagDefinition() : protocols::stepwise::screener::TagDefinition
• TagList : protocols::toolbox::KClusterData
• TagManager() : protocols::multistage_rosetta_scripts::TagManager
• TagOP : core::pack::palette::PackerPaletteFactory , core::pack::task::operation::ResFilterFactory , core::pack::task::operation::TaskOperationFactory
• TagPoseWithRefinementStatsMover() : protocols::cryst::TagPoseWithRefinementStatsMover
• TagPtr : protocols::indexed_structure_store::filters::FragmentLookupFilter
• tags() : core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentFileData
• Tags : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• tags() : protocols::moves::TrialCounter
• tags_ : core::import_pose::pose_stream::SilentFilePoseInputStream , core::scoring::rna::RNA_SuitePotential , core::scoring::rna::TNA_SuitePotential , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug , protocols::toolbox::KClusterData
• tail() : protocols::protein_interface_design::movers::LoopLengthChange
• tail_dbase_subset_ : protocols::splice::SpliceInTail
• tail_diff_ : protocols::splice::SpliceInAntibody
• tail_fold_tree() : protocols::splice::Splice
• tail_mover() : protocols::splice::SpliceOut
• tail_seg() : protocols::splice::SpliceManager
• tail_seg_ : protocols::splice::SpliceManager
• tail_segment() : protocols::splice::ResidueBBDofs
• tail_segment_ : protocols::protein_interface_design::movers::LoopLengthChange , protocols::splice::ResidueBBDofs , protocols::splice::Splice
• tail_submover_ : protocols::splice::SpliceOutAntibody
• tail_torsion_database_ : protocols::splice::Splice , protocols::splice::SpliceIn
• tailfunctions_ : core::scoring::netcharge_energy::NetChargeEnergySetup
• tailresidues_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• TailSegmentMover() : protocols::splice::TailSegmentMover
• TailsScoreMover() : protocols::simple_moves::TailsScoreMover
• take_coordinates_from_pose() : core::scoring::BB_Pos , protocols::fldsgn::topology::BB_Pos
• take_out_cutpoints() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• takeoff_atom_id_ : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator
• takeoff_domain() : core::scoring::loop_graph::Loop
• takeoff_domain_ : core::scoring::loop_graph::Loop
• takeoff_pos() : core::scoring::loop_graph::Loop
• takeoff_pos_ : core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator , core::scoring::loop_graph::Loop
• TalosSSSimilarity() : protocols::frag_picker::scores::TalosSSSimilarity
• targ_ang() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_ang_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base2_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base2_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base_atom_names() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_base_atom_names_ : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_dih() : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_dih_ : protocols::forge::remodel::ResidueVicinityInfo , protocols::toolbox::match_enzdes_util::ResInteractions
• targ_res() : protocols::toolbox::match_enzdes_util::ResInteractions
• targ_res_ : protocols::toolbox::match_enzdes_util::ResInteractions
• TARGET : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• target() : protocols::simple_moves::MutateResidue
• target_ : core::chemical::ReplaceMainchainAtom , protocols::cryst::SetRefinementOptionsMover , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::ligand_docking::ga_ligand_dock::LigandAligner , protocols::noesy_assign::PeakCalibrator , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::simple_moves::MutateResidue
• target_accept_ratio() : protocols::abinitio::IterativeBase
• target_accept_ratio_ : protocols::abinitio::IterativeBase
• target_Ashifts_ : protocols::frag_picker::scores::AmbigCSScore
• target_atom_name_ : protocols::simple_filters::SimpleHbondsToAtomFilter
• target_atoms() : protocols::denovo_design::movers::RotateSegmentMover
• target_bb_atom_ids_ : protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover
• 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::simple_moves::AlignChainMover
• 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_clash_pdb() : core::scoring::methods::EnergyMethodOptions
• target_clash_pdb_ : core::scoring::methods::EnergyMethodOptions , protocols::scoring::methods::TargetClashEnergy
• target_conformer() : protocols::motifs::MotifHit
• target_conformer_ : protocols::motifs::MotifHit
• target_conformers_map() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_conformers_map_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_distance_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover
• target_downstream_coords_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_downstream_res_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_end_ : protocols::simple_moves::SuperimposeMover
• target_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_ : protocols::indexed_structure_store::BinaryFragmentStoreBackend
• target_pose_start() : protocols::grafting::simple_movers::ReplaceRegionMover
• target_pose_start_ : protocols::grafting::simple_movers::ReplaceRegionMover
• target_positions() : protocols::motifs::BuildPosition , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_positions_ : protocols::motifs::BuildPosition , protocols::motifs::IRCollection , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_proximity_to_native_conformation_ : protocols::enzdes::EnzdesFlexibleRegion
• target_proximity_to_other_conformations_ : protocols::enzdes::EnzdesFlexibleRegion
• target_region() : protocols::simple_filters::DomainInterfaceFilter
• target_region_ : protocols::simple_filters::DomainInterfaceFilter
• target_region_str_ : protocols::simple_filters::DomainInterfaceFilter
• target_region_string() : protocols::simple_filters::DomainInterfaceFilter
• target_res() : protocols::pockets::PocketConstraint
• target_res_ : protocols::enzdes::RepackWithoutLigandFilter
• target_res_for_geom_cst() : protocols::toolbox::match_enzdes_util::InvrotTarget
• target_res_index_ : protocols::simple_moves::CopyRotamerMover
• target_residue_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::SimpleHbondsToAtomFilter
• target_residue_type_ : core::pack::task::ResidueLevelTask_
• target_residues() : protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::PackRotamersMoverPartGreedy
• target_residues_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::PackRotamersMoverPartGreedy
• 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_selector_ : protocols::simple_filters::InterfaceHydrophobicResidueContactsFilter
• target_selectors_ : protocols::denovo_design::movers::AlignResiduesMover
• target_seq() : protocols::simple_filters::SequenceDistance
• target_seq_ : protocols::simple_filters::SequenceDistance
• target_seqpos_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• target_sequence() : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::task_operations::DatabaseThread , protocols::task_operations::ThreadSequenceOperation
• target_sequence_ : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::hybridization::FoldTreeHybridize , protocols::rna::movers::RNAThreadAndMinimizeMover , protocols::task_operations::DatabaseThread , protocols::task_operations::ThreadSequenceOperation
• target_sequences_ : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• target_shifts_ : protocols::frag_picker::scores::CSScore
• target_sign_ : protocols::noesy_assign::PeakCalibrator
• target_start_ : protocols::simple_moves::SuperimposeMover
• target_stub : protocols::hotspot_hashing::ConstPattern
• target_total_residue() : protocols::abinitio::Templates
• target_type() : core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_ , protocols::cyclic_peptide::RamaMutationSelector
• target_type_ : protocols::cyclic_peptide::RamaMutationSelector
• target_values_ : protocols::noesy_assign::PeakCalibrator
• target_xyz_in_takeoff_frame_ : core::scoring::rna::RNA_StubCoordinateEnergy
• TargetClashEnergy() : protocols::scoring::methods::TargetClashEnergy
• targeted_dna() : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• targeted_dna_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::motifs::MotifDnaPacker
• TargetPocketGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid , protocols::pockets::TargetPocketGrid
• targetPocketHeuristicScore() : protocols::pockets::PocketGrid
• targetPocketHydrophobicProteinSurface() : protocols::pockets::PocketGrid
• targetPocketPolarProteinSurface() : protocols::pockets::PocketGrid
• targetPocketProteinSurface() : protocols::pockets::PocketGrid
• targetPocketSolventSurface() : protocols::pockets::PocketGrid
• targetPocketVolume() : protocols::pockets::PocketGrid
• TargetRotamerCoords() : protocols::match::downstream::TargetRotamerCoords
• targets_ : protocols::protein_interface_design::filters::DisulfideFilter
• TargetValues : protocols::noesy_assign::PeakCalibrator
• task : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ReweightData , core::pack::rotamer_set::RotamerSets , protocols::calc_taskop_movers::DesignRepackMover , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelWorkingSet , protocols::mean_field::EnergiesByTaskCalculator , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• task1_ : protocols::task_operations::StoreCombinedStoredTasksMover
• task2_ : protocols::task_operations::StoreCombinedStoredTasksMover
• task_ : core::pack::rotamer_set::RotamerSets , protocols::calc_taskop_movers::DesignRepackMover , protocols::docking::SidechainMinMover , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::evolution::NucleotideMutation , protocols::flexpack::FlexPacker , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::hbnet::HBNet , protocols::mean_field::EnergiesByTaskCalculator , protocols::mean_field::GenMeanFieldMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::minimization_packing::TaskAwareMinMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::RandomMutation , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_ddg::ddG , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::symmetric_docking::SymSidechainMinMover
• task_begin() : protocols::task_operations::StoreCompoundTaskMover
• task_clear() : protocols::task_operations::StoreCompoundTaskMover
• task_end() : protocols::task_operations::StoreCompoundTaskMover
• task_factory() : protocols::backrub::BackrubSidechainMover , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_movers::DesignRepackMover , protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::evolution::NucleotideMutation , protocols::hbnet::HBNet , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• TASK_FACTORY : protocols::loop_modeling::ToolboxKeys
• task_factory : protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub , protocols::loops::loop_mover::refine::LoopMover_Refine_KIC , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::matdes::ClashCheckFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::mean_field::GenMeanFieldMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , 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::TaskAwareCsts , protocols::recon_design::FindConsensusSequence , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::splice::Splice , protocols::splice::SpliceManager , protocols::switches::GraftSwitchMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• task_factory_ : protocols::anchored_design::AnchorMoversData , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::calc_taskop_movers::DesignRepackMover , protocols::chemically_conjugated_docking::UBQ_GTPaseMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::evolution::NucleotideMutation , protocols::features::ReportToDB , protocols::features::RotamerRecoveryFeatures , protocols::floppy_tail::FloppyTailMover , protocols::hbnet::HBNet , 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::matdes::SchemePlaceMotifsMover , protocols::mean_field::GenMeanFieldMover , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::optimize_weights::IterativeOptEDriver , protocols::pack_daemon::DaemonSet , protocols::pose_creation::MergePDBMover , 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::quantum_annealing::InteractionGraphSummaryMetric , protocols::recon_design::FindConsensusSequence , protocols::relax::RelaxProtocolBase , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::RotamerDump::RotamerDumpMover , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter , protocols::simple_ddg::DdGScan , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ExplicitWaterMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::splice::Splice , protocols::splice::SpliceManager , protocols::splice::SpliceOut , protocols::splice::TailSegmentMover , protocols::switches::GraftSwitchMover , protocols::task_operations::StoreTaskMover
• task_factory_set() : protocols::protein_interface_design::filters::Torsion
• 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_initialized_ : protocols::simple_moves::sidechain_moves::SidechainMover
• task_is_valid() : protocols::hbnet::HBNet , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover
• task_iterator : protocols::task_operations::StoreCompoundTaskMover
• task_layers_ : protocols::flxbb::LayerDesignOperation
• task_mode() : core::pack::task::ResidueLevelTask_
• task_name() : protocols::task_operations::StoreCompoundTaskMover
• task_name_ : protocols::task_operations::RetrieveStoredTaskOperation , protocols::task_operations::StoreCombinedStoredTasksMover , protocols::task_operations::StoreCompoundTaskMover , protocols::task_operations::StoreTaskMover
• task_op_ : protocols::match::TaskOperationMPM
• task_op_loader_ct_namer() : protocols::parser::TaskOperationLoader
• task_operation_creator_map_ : core::pack::task::operation::TaskOperationFactory
• task_operation_is_unpublished() : core::pack::task::operation::TaskOperation
• task_operation_provides_citation_info() : core::pack::task::operation::TaskOperation
• task_operation_xml_schema_group_name() : core::pack::task::operation::TaskOperationFactory
• task_operations_ : protocols::flxbb::CombinedTaskOperation , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::rosetta_scripts::XmlObjects
• task_scaling() : protocols::monte_carlo::GenericMonteCarloMover
• task_scaling_ : protocols::monte_carlo::GenericMonteCarloMover
• task_segments_ : protocols::relax::AtomCoordinateCstMover
• task_string() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• TaskAwareCsts() : protocols::protein_interface_design::movers::TaskAwareCsts
• TaskAwareMinMover() : protocols::minimization_packing::TaskAwareMinMover
• TaskAwareSASAFilter() : protocols::simple_filters::TaskAwareSASAFilter
• TaskAwareScoreTypeFilter() : protocols::simple_filters::TaskAwareScoreTypeFilter
• TaskAwareSymMinMover() : protocols::minimization_packing::symmetry::TaskAwareSymMinMover
• taskFactOP_ : protocols::hybridization::detailedControlsTagSetting
• TaskFactory() : core::pack::task::TaskFactory , protocols::minimization_packing::GreenPacker
• taskfactory_ : protocols::simple_filters::TotalSasaFilter
• TaskFactoryCOP : protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::switches::GraftSwitchMover
• TaskFactoryOP : protocols::constraint_movers::AddConstraintsToCurrentConformationMover , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::evolution::EvolutionaryDynamicsMover , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::minimization_packing::GreenPacker , protocols::monte_carlo::GenericMonteCarloMover , protocols::switches::GraftSwitchMover
• TaskLayer : protocols::flxbb::LayerDesignOperation
• TaskLayers : protocols::flxbb::LayerDesignOperation
• Taskop_id_name_factory_() : protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• TaskOperation : core::pack::task::operation::ReplicateTask , core::pack::task::TaskFactory , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::InterfaceTaskOperation , protocols::simple_task_operations::RestrictToInterface , protocols::splice::SampleRotamersFromPDB , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictOperationsBase , protocols::task_operations::SeqprofConsensusOperation
• TaskOperationCOP : core::pack::task::TaskFactory
• TaskOperationCreatorMap : core::pack::task::operation::TaskOperationFactory
• TaskOperationFactory() : core::pack::task::operation::TaskOperationFactory
• TaskOperationFeatures() : protocols::features::TaskOperationFeatures
• TaskOperationLoader() : protocols::parser::TaskOperationLoader
• TaskOperationMPM() : protocols::match::TaskOperationMPM
• TaskOperationOP : core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::ReplicateTask , core::pack::task::TaskFactory , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::flxbb::CombinedTaskOperation , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::hbnet::ConstrainHBondNetwork , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::InterfaceTaskOperation , protocols::simple_task_operations::RestrictToInterface , protocols::splice::SampleRotamersFromPDB , protocols::task_operations::DsspDesignOperation , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::task_operations::RestrictOperationsBase , protocols::task_operations::SeqprofConsensusOperation
• TaskOperationOPs : core::pack::task::operation::TaskOperationFactory
• TaskOperationRegistrator() : core::pack::task::operation::TaskOperationRegistrator< T >
• taskops_ : protocols::features::TaskOperationFeatures
• tasks() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• tasks_ : protocols::fold_from_loops::movers::DisplayPoseLabelsMover , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::task_operations::STMStoredTask
• TaskSelector() : protocols::residue_selectors::TaskSelector
• Tau() : core::scoring::FACTSPotential
• Tau_ : core::scoring::FACTSPotential
• tau_ : protocols::md::Thermostat , protocols::normalmode::NormalMode
• tau_angles : core::chemical::rings::RingConformer
• tau_c_ : core::scoring::nmr::pre::PREMultiSet
• tau_c_max_ : core::scoring::nmr::pre::PREMultiSet
• tau_c_min_ : core::scoring::nmr::pre::PREMultiSet
• tau_e_ : core::io::nmr::ParaIon
• tau_r_ : core::scoring::nmr::pre::PREMultiSet
• tau_t_ : core::scoring::nmr::pre::PREMultiSet
• TautomerizeAnomerMover() : protocols::carbohydrates::TautomerizeAnomerMover
• tbmb_constraints_energy_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TBMB_Helper() : protocols::cyclic_peptide::crosslinker::TBMB_Helper
• tbmb_positions_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• tbmb_sidechain_distance_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TCacheUnit : core::fragment::CacheWrapper< T, XCacheUnit >
• TCacheUnitAP : core::fragment::CacheWrapper< T, XCacheUnit >
• TCacheUnitOP : core::fragment::CacheWrapper< T, XCacheUnit >
• tccw : core::scoring::packstat::Circle
• tcr_graft_model() : protocols::tcr::TCRmodel
• tcr_graft_model_ : protocols::tcr::TCRmodel
• tcr_loop_model() : protocols::tcr::TCRmodel
• tcr_loop_model_ : protocols::tcr::TCRmodel
• tcr_model() : protocols::tcr::TCRmodel
• tcr_model_ : protocols::tcr::TCRmodel
• TCRmodel() : protocols::tcr::TCRmodel
• tcw : core::scoring::packstat::Circle
• tdb : protocols::tcr::TCRmodel::tmpltinfo
• 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
• tell_vlb_to_not_touch_fold_tree_ : protocols::fldsgn::BluePrintBDR
• temp() : core::pose::UnrecognizedAtomRecord , core::scoring::APBSConfig::R_PARAM , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::multistate_design::PartitionAggregateFunction , protocols::simple_moves::TorsionDOFMover
• temp0() : protocols::md::MDBase , protocols::md::MDscheduleData
• temp0_ : protocols::md::MDBase , protocols::md::Thermostat
• temp1() : core::scoring::AtomNeighbor
• temp1_ : core::scoring::AtomNeighbor
• temp2() : core::scoring::AtomNeighbor
• temp2_ : core::scoring::AtomNeighbor
• temp3() : core::scoring::AtomNeighbor
• temp3_ : core::scoring::AtomNeighbor
• temp4() : core::scoring::AtomNeighbor
• temp4_ : core::scoring::AtomNeighbor
• temp_ : core::pose::UnrecognizedAtomRecord , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::denovo_design::filters::SSPredictionFilter , protocols::hybridization::CartesianSampler , protocols::multistate_design::PartitionAggregateFunction , protocols::recces::scratch::ThermalMinimizer , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::PeriodicBoxMover , protocols::simple_moves::TorsionDOFMover
• 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_f_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• temp_file() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor
• temp_final() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::splice::TailSegmentMover
• temp_final_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::splice::TailSegmentMover
• temp_i_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• temp_id() : protocols::moves::SimulatedTempering
• temp_id_ : protocols::moves::SimulatedTempering
• temp_initial() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::splice::TailSegmentMover
• temp_initial_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::splice::TailSegmentMover
• temp_positions : protocols::vip::VIP_Mover
• temp_residues : protocols::vip::VIP_Mover
• temp_stage1_ : protocols::hybridization::FoldTreeHybridize
• temp_step_ : protocols::monte_carlo::GenericSimulatedAnnealer
• temp_trial_count_ : protocols::canonical_sampling::TemperingBase
• tempdir_ : core::scoring::cryst::PhenixInterface
• temperature() : core::conformation::membrane::ImplicitLipidInfo , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::io::AtomInformation , core::pose::PDBInfo::AtomRecord , core::pose::PDBInfo , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::forge::remodel::RemodelLoopMover , protocols::ligand_docking::Transform_info , protocols::ligand_docking::TransformEnsemble_info , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::magnesium::MgMonteCarlo , protocols::md::MDBase , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::moves::MonteCarlo , protocols::moves::SimulatedTempering , protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• temperature0_ : protocols::simple_moves::sidechain_moves::SidechainMover
• temperature_ : core::conformation::membrane::ImplicitLipidInfo , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::pack::annealer::SimAnnealerBase , core::scoring::nmr::pre::PREMultiSet , 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::calc_taskop_filters::RotamerBoltzmannWeight , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::FixedTemperatureController , protocols::docking::ConformerSwitchMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , 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::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::membrane::AddMembraneMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo , protocols::pose_metric_calculators::RotamerBoltzCalculator , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::CoupledMover , 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::MulliganPNearEvaluator , protocols::toolbox::RotamerBoltzmannWeightEvaluator , protocols::ub_e2c::ubi_e2c_modeler
• temperature_jumps_ : protocols::canonical_sampling::SimulatedTempering
• temperature_level() : protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase
• temperature_move() : protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperatureController
• temperature_stride_ : protocols::canonical_sampling::TemperingBase
• TemperatureController() : protocols::canonical_sampling::TemperatureController
• temperatures() : protocols::monte_carlo::GenericMonteCarloMover , protocols::recces::options::RECCES_Options
• temperatures_ : protocols::canonical_sampling::TemperingBase , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::SimulatedTempering , protocols::recces::options::RECCES_Options
• TemperedDocking() : protocols::docking::TemperedDocking
• tempering() : protocols::canonical_sampling::MetropolisHastingsMover
• tempering_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::docking::TemperedDocking
• TemperingBase() : protocols::canonical_sampling::TemperingBase
• templ() : protocols::abinitio::abscript::RigidChunkCM
• templ_selector() : protocols::abinitio::abscript::RigidChunkCM
• templ_selector_ : protocols::abinitio::abscript::RigidChunkCM
• templ_target() : protocols::abinitio::abscript::RigidChunkCM
• templ_target_ : protocols::abinitio::abscript::RigidChunkCM
• Template() : protocols::abinitio::Template
• template_ : protocols::abinitio::abscript::RigidChunkCM
• template_atom_inds() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• 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_cys_pos_ : protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• template_end_ : protocols::antibody_legacy::GraftOneMover
• template_file() : protocols::splice::Splice , protocols::splice::SpliceManager , protocols::task_operations::DatabaseThread
• template_file_ : protocols::splice::Splice , protocols::splice::SpliceManager , protocols::task_operations::DatabaseThread
• template_fns_ : protocols::hybridization::HybridizeProtocol
• template_from_res() : protocols::splice::SpliceManager
• template_from_res_ : protocols::splice::SpliceManager
• template_group_ : protocols::task_operations::LinkResidues
• TEMPLATE_HYBRIDIZATION_HISTORY : core::pose::datacache::CacheableDataType
• template_id_ : protocols::hybridization::InsertChunkMover
• template_identity_cutoff_ : protocols::tcr::TCRmodel
• template_index() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_index_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_insertion_ranges() : protocols::fold_from_loops::NubInitioMover
• template_label() : protocols::fold_from_loops::utils::Nub
• template_mini_pose_ : protocols::simple_moves::CopyDofMover
• template_name() : protocols::task_operations::AlignedThreadOperation
• template_name_ : protocols::antibody_legacy::GraftOneMover , protocols::task_operations::AlignedThreadOperation
• template_names_ : protocols::protein_interface_design::filters::RmsdFilter
• template_number() : protocols::hybridization::ChunkTrialMover
• template_number_ : protocols::hybridization::ChunkTrialMover
• template_pdb_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• template_pdb_fname() : protocols::splice::RBOutMover
• template_pdb_fname_ : protocols::splice::RBOutMover
• template_pose() : protocols::comparative_modeling::ThreadingMover , protocols::denovo_design::components::Segment , protocols::fold_from_loops::NubInitioMover , protocols::splice::AlignEndsMover , protocols::splice::SpliceManager
• template_pose_ : protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::GraftOneMover , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::PartialThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::denovo_design::components::Segment , protocols::fold_from_loops::NubInitioMover , protocols::hybridization::InsertChunkMover , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::CopyDofMover , protocols::splice::AlignEndsMover , protocols::splice::Splice , protocols::splice::SpliceManager , protocols::task_operations::DatabaseThread
• template_poses() : protocols::jd2::InnerMultiThreadingJob
• template_poses_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter , protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::jd2::InnerMultiThreadingJob
• template_presence : protocols::seeded_abinitio::GrowPeptides
• template_presence_ : protocols::seeded_abinitio::CAcstGenerator
• template_res_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_size() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_index_ : protocols::simple_moves::CopyRotamerMover
• template_resid() : protocols::denovo_design::components::Segment
• template_residues_ : core::pack::rotamer_set::RotamerLinks
• template_rmsd() : protocols::fold_from_loops::NubInitioMover
• template_scores : protocols::cluster::GatherPosesMover
• template_selector() : protocols::fold_from_loops::NubInitioMover
• template_selector_ : protocols::fold_from_loops::NubInitioMover
• template_selectors_ : protocols::denovo_design::movers::AlignResiduesMover
• template_sequence_from_alignment_ : protocols::rna::movers::RNAThreadAndMinimizeMover
• template_size() : protocols::jumping::MembraneJump
• template_size_ : protocols::jumping::MembraneJump
• template_start_ : protocols::antibody_legacy::GraftOneMover
• template_stem1() : protocols::simple_filters::SSMotifFinder
• template_stem1_ : protocols::simple_filters::SSMotifFinder
• template_stem2() : protocols::simple_filters::SSMotifFinder
• template_stem2_ : protocols::simple_filters::SSMotifFinder
• template_to_res() : protocols::splice::SpliceManager
• template_to_res_ : protocols::splice::SpliceManager
• template_to_unfolded_mapping() : protocols::fold_from_loops::utils::Nub
• template_weights_ : protocols::hybridization::HybridizeProtocol
• template_wts_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize
• TemplateFragmentClaimer() : protocols::topology_broker::TemplateFragmentClaimer
• TemplateHistory() : protocols::hybridization::TemplateHistory
• TemplateJumpClaimer() : protocols::topology_broker::TemplateJumpClaimer
• TemplateJumpSetup() : protocols::abinitio::TemplateJumpSetup
• TemplateList : protocols::abinitio::Templates
• TemplateMap : protocols::abinitio::Templates
• TemplatePoseMap : protocols::antibody::Ab_TemplateInfo
• Templates() : protocols::abinitio::Templates
• templates_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::TemplateJumpSetup , protocols::abinitio::Templates , protocols::hybridization::CartesianHybridize , protocols::hybridization::HybridizeProtocol , protocols::jumping::MembraneJump , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• templates_aln_ : protocols::hybridization::HybridizeProtocol
• templates_poses_ : protocols::antibody::Ab_TemplateInfo
• templates_with_incorrect_strand_pairings_ : protocols::hybridization::FoldTreeHybridize
• temporarily_fix_everything() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• temporarily_set_pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• temporary_file_name() : protocols::jd2::FileSystemJobDistributor
• temps() : core::io::ResidueInformation
• temps_ : core::io::ResidueInformation , protocols::recces::scratch::ThermalSamplingMover
• tenA_ : core::scoring::TenANeighborGraph
• tenA_edge_pool_ : core::scoring::TenANeighborGraph
• tenA_neighbor_graph() : core::scoring::Energies
• tenA_squared_ : core::scoring::TenANeighborGraph
• TenANeighborEdge() : core::scoring::TenANeighborEdge
• TenANeighborGraph() : core::scoring::TenANeighborGraph
• TenANeighborNode() : core::scoring::TenANeighborNode
• tensor() : core::scoring::ResidualDipolarCoupling
• Tensor : core::scoring::ResidualDipolarCoupling
• Tensor5 : core::scoring::ResidualDipolarCoupling
• tensor_ : core::scoring::loop_graph::evaluator::SixDTransRotPotential , core::scoring::nmr::pcs::PCSSingleSet , core::scoring::nmr::rdc::RDCMultiSet , protocols::qsar::scoring_grid::PCSSingleGrid
• tensor_const_ : core::scoring::constraints::ResidueCouplingConstraint
• tensor_file_ : protocols::simple_moves::AddResidueCouplingConstraint
• tensor_fixed() : core::scoring::nmr::rdc::RDCMultiSet
• tensor_index1_ : core::scoring::constraints::ResidueCouplingConstraint
• tensor_index2_ : core::scoring::constraints::ResidueCouplingConstraint
• tensor_name() : core::scoring::nmr::NMRTensor , core::scoring::nmr::pcs::PCSTensor , core::scoring::nmr::rdc::RDCTensor
• tensorDa : core::scoring::data_struct
• tensorR : core::scoring::data_struct
• tensors_fixed() : core::scoring::nmr::pcs::PCSMultiSet
• TensorsOptimizer() : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs::TensorsOptimizer
• TensorsOptimizer_Ts1() : protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1
• TensorsOptimizer_Ts2() : protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2
• TensorsOptimizer_Ts3() : protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3
• TensorsOptimizer_Ts4() : protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• TensorsOptimizerFix() : protocols::scoring::methods::pcs2::TensorsOptimizerFix
• TensorsOptimizerSvd() : protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• terCount : core::io::AtomInformation , core::io::ResidueInformation
• terCount_ : core::io::ResidueInformation
• term_ : protocols::simple_moves::ReportXYZ
• term_length() : core::scoring::methods::NMerSVMEnergy
• term_length_ : core::scoring::methods::NMerSVMEnergy
• term_name_ : protocols::simple_filters::ReadPoseExtraScoreFilter
• term_w_bb : protocols::hbnet::HBondNetStruct
• term_w_cycle : protocols::hbnet::HBondNetStruct
• term_w_start : protocols::hbnet::HBondNetStruct
• terminal_pair() : protocols::topology_broker::SequenceNumberResolver
• terminal_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• terminal_res_ : core::import_pose::FullModelPoseBuilder , protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• terminal_types_ : core::pack::palette::PackerPalette
• terminate_ : protocols::wum::MPI_WorkUnitManager_Slave
• termination_broadcasted_ : protocols::mpi_refinement::MPI_Refine_Emperor
• termini() : protocols::denovo_design::components::StructureData
• termini_feature() : core::scoring::methods::ProQ_Energy
• termini_penalty() : core::scoring::MembranePotential
• TerminiConstraintGenerator() : protocols::constraint_generator::TerminiConstraintGenerator
• terminus() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• terminus_ : protocols::sewing::scoring::TerminusMotifScorer , protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• terminus_motif_score() : protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::TerminusMotifScorer
• TerminusDistanceFilter() : protocols::simple_filters::TerminusDistanceFilter
• TerminusMotifScorer() : protocols::sewing::scoring::TerminusMotifScorer
• test() : protocols::sewing::requirements::AssemblyRequirement , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LigandAssemblyRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::SizeInSegmentsRequirement , protocols::toolbox::DummyClass
• test_ : protocols::carbohydrates::GlycanSampler
• test_AA() : protocols::recon_design::FindConsensusSequence
• test_all_mg_hydration_frames() : protocols::stepwise::options::StepWiseBasicOptions
• test_all_mg_hydration_frames_ : protocols::stepwise::options::StepWiseBasicOptions
• test_all_moves() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• test_all_moves_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• test_all_moves_recursively() : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• test_broker_settings() : protocols::abinitio::IterativeBase
• test_chunk() : protocols::frag_picker::AllowPdbIdFilter , protocols::frag_picker::DenyPdbIdFilter , protocols::frag_picker::VallChunkFilter
• test_control_mode() : protocols::grafting::AnchoredGraftMover
• test_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_epigraft_and_contextStructure_clashes() : protocols::motif_grafting::movers::MotifGraftMover
• test_flexbb_rotamer_sets() : protocols::enzdes::EnzdesFlexBBProtocol
• test_for_stage_end() : protocols::abinitio::IterativeBase
• test_loop_sample() : protocols::loophash::LoopHashLibrary
• test_move() : protocols::contact_map::ContactMap , protocols::moves::Mover , protocols::moves::NullMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::sidechain_moves::SidechainMover
• test_results_ : protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::SizeInSegmentsRequirement
• test_round() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• test_run_ : protocols::loop_modeling::LoopProtocol
• 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
• TestCompositeRealMetric() : core::simple_metrics::TestCompositeRealMetric
• TestCompositeStringMetric() : core::simple_metrics::TestCompositeStringMetric
• testing_phase : protocols::simple_moves::ShakeStructureMover
• testmap_ : protocols::electron_density::ReportFSC
• testNeighbor() : protocols::pockets::CCluster , protocols::pockets::PCluster
• TestPattern() : protocols::hotspot_hashing::TestPattern
• TestPerResidueRealMetric() : core::simple_metrics::TestPerResidueRealMetric
• TestPerResidueStringMetric() : core::simple_metrics::TestPerResidueStringMetric
• TestRealMetric() : core::simple_metrics::TestRealMetric
• TestStringMetric() : core::simple_metrics::TestStringMetric
• tether_jump() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• 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_ligands() : protocols::ligand_docking::HighResDocker
• tether_to_closest_res() : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• tether_to_closest_res_ : protocols::magnesium::MgScanner , protocols::magnesium::SampleGrid
• TetherLigand() : protocols::ligand_docking::TetherLigand
• tetrahedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• tetrahedral_metal_constraints_energy_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• tetrahedral_metal_positions_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• tetrahedral_metal_sidechain_distance_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TetrahedralMetal_Helper() : protocols::cyclic_peptide::crosslinker::TetrahedralMetal_Helper
• tf : protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• tf2() : protocols::docking::DockingHighRes
• 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::RefineBetaBarrel , protocols::antibody::snugdock::SnugDock , protocols::antibody::snugdock::SnugDockProtocol , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::GlycanSampler , 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::symmetry::SetupNCSMover
• TGT_AA__TGT_ATOM : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_amino_ : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_atom_ : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_pos_ : protocols::constraints_additional::BindingSiteConstraint
• tgt_pos_centroid_ : protocols::constraints_additional::BindingSiteConstraint
• TGT_RES : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgt_res_idxs_ : protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator
• tgtD_ : protocols::symmetry::SetupNCSMover
• tgtE_ : protocols::symmetry::SetupNCSMover
• the_archive() : protocols::jd2::archive::BaseArchiveManager
• 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
• TheozymeInvrotTree() : protocols::toolbox::match_enzdes_util::TheozymeInvrotTree
• thermal_accepts_ : protocols::moves::MoverStatistics
• thermal_sampler_mode() : protocols::recces::options::RECCES_Options
• thermal_sampler_mode_ : protocols::recces::options::RECCES_Options
• thermal_sampler_output_min_pose() : protocols::stepwise::options::StepWiseBasicOptions
• thermal_sampler_output_min_pose_ : protocols::stepwise::options::StepWiseBasicOptions
• thermal_sampler_temperature() : protocols::stepwise::options::StepWiseBasicOptions
• thermal_sampler_temperature_ : protocols::stepwise::options::StepWiseBasicOptions
• ThermalMinimizer() : protocols::recces::scratch::ThermalMinimizer
• ThermalSamplingMover() : protocols::recces::scratch::ThermalSamplingMover
• thermodynamic_data_ : protocols::simple_moves::PeriodicBoxMover
• ThermodynamicMover() : protocols::canonical_sampling::ThermodynamicMover
• ThermodynamicObserver() : protocols::canonical_sampling::ThermodynamicObserver
• Thermostat() : protocols::md::Thermostat
• theta() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::MutableICoorRecord , core::chemical::orbitals::ICoorOrbitalData , core::pose::Pose , protocols::fldsgn::topology::DimerPairing , protocols::minimization_packing::MinimalRotamer
• theta0() : core::scoring::mm::MMBondAngleResidueTypeParam
• theta0_ : core::scoring::mm::MMBondAngleResidueTypeParam
• theta_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::MutableICoorRecord , core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor , core::kinematics::tree::BondedAtom , core::scoring::carbohydrates::OmegaPreferencesFunction , 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
• theta_terms_ : core::scoring::epr_deer::DEERDecayData
• thickness() : core::scoring::Membrane_FAEmbed
• 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
• ThirdLoop() : core::scoring::sc::MolecularSurfaceCalculator
• this_aa() : protocols::optimize_weights::PNatAAOptERotamerData
• this_aa_ : protocols::optimize_weights::PNatAAOptERotamerData
• this_batch_job_inputter_ : protocols::jd2::BatchJobInputter
• this_nodes_job_ : protocols::jd2::VectorPoseJobDistributor
• 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
• thole_ : core::scoring::MultipoleParameter
• thread() : protocols::calc_taskop_filters::RelativePoseFilter
• thread_ : protocols::calc_taskop_filters::RelativePoseFilter
• thread_limit() : core::pack::task::operation::RestrictInteractionGraphThreadsOperation
• thread_original_sequence() : protocols::splice::Splice , protocols::splice::SpliceManager , protocols::splice::SpliceOut
• thread_original_sequence_ : protocols::splice::Splice , protocols::splice::SpliceManager , protocols::splice::SpliceOut
• thread_seq() : protocols::calc_taskop_filters::RelativePoseFilter
• thread_sequence_ : protocols::simple_moves::SimpleThreadingMover
• threadable_residues_ : protocols::switches::GraftSwitchMover
• threadable_residues_selector_ : protocols::switches::GraftSwitchMover
• ThreadingJob() : protocols::comparative_modeling::ThreadingJob
• ThreadingJobInputter() : protocols::comparative_modeling::ThreadingJobInputter
• ThreadingMover() : protocols::comparative_modeling::ThreadingMover
• ThreadSequenceOperation() : protocols::task_operations::ThreadSequenceOperation
• three_letter_code() : core::io::nmr::SpinlabelDatabaseEntry
• three_letter_code_ : core::io::nmr::SpinlabelDatabaseEntry , core::scoring::nmr::NMRSpinlabel
• three_param_func : protocols::mean_field::jagged_array< T, A >::func_T2< T_2 > , protocols::mean_field::jagged_array< T, A >
• three_prime_atom : protocols::stepwise::modeler::rna::Jump_point
• three_prime_chain_break_res() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker
• 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
• thresh_ : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• threshes_ : core::scoring::mhc_epitope_energy::AlleleMatrix
• threshold() : core::select::residue_selector::CloseContactResidueSelector , core::select::residue_selector::NumNeighborsSelector , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::Sigmoid
• THRESHOLD : protocols::cluster::calibur::Clustering
• threshold() : protocols::evolution::AASynthesisFitnessCost , protocols::filters::CalculatorFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::MatchResidues , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::recon_design::FitnessFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::task_operations::SelectByDeltaScoreOperation
• threshold_ : core::select::residue_selector::NumNeighborsSelector , protocols::calc_taskop_filters::MultipleSigmoids , protocols::calc_taskop_filters::Operator , protocols::calc_taskop_filters::Sigmoid , protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::constraint_filters::ConstraintScoreFilter , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::denovo_design::filters::PreProlineFilter , protocols::denovo_design::filters::SSPredictionFilter , protocols::dna::RotamerDNAHBondFilter , protocols::docking::DockingSlideIntoContact , protocols::docking::SlideIntoContact , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RemoveLigandFilter , protocols::evolution::AASynthesisFitnessCost , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::filters::HelixBendFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::MatchResidues , protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter , protocols::frag_picker::FragmentScoreFilter , protocols::hbnet::HBNetScore , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , 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::recon_design::FitnessFilter , protocols::residue_optimization::MetapatchEnumeration , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::ChainBreak , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::MembAccesResidueLipophilicityFilter , protocols::simple_filters::MPSpanAngleFilter , protocols::simple_filters::ReadPoseExtraScoreFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueLipophilicityFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SequenceDistance , protocols::simple_filters::SpanTopologyMatchPoseFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TMsAACompFilter , protocols::simple_filters::TMsSpanMembraneFilter , protocols::task_operations::SelectByDeltaScoreOperation , protocols::task_operations::SelectByDensityFitOperation , protocols::toolbox::KMedoid , protocols::viewer::triangleIterator
• THRESHOLD_ACCEPTANCE_RATE_FOR_RPE_STORAGE : core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode
• threshold_probabilities_per_residue_ : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• threshold_probability() : protocols::calc_taskop_filters::RotamerBoltzmannWeight
• threshold_score_of_complete_cycle_ : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• throw_on_double_registration_ : core::select::jump_selector::JumpSelectorFactory , core::select::residue_selector::ResidueSelectorFactory , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterFactory , protocols::jd3::full_model_inputters::FullModelInputterFactory , protocols::jd3::pose_inputters::PoseInputterFactory , protocols::jd3::pose_outputters::PoseOutputterFactory , protocols::multistage_rosetta_scripts::cluster::ClusterMetricFactory
• throw_on_fail_ : protocols::pdbinfo_manipulations::AlignPDBInfoToSequences
• tic_ : protocols::filters::TimeFilter
• tid : protocols::tcr::TCRmodel::tmpltinfo
• tighten_memory() : core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::pose::PDBInfo
• tightness() : protocols::simple_filters::DisulfideEntropyFilter
• tightness_ : protocols::simple_filters::DisulfideEntropyFilter
• tilt() : protocols::dna::DNABasestep , protocols::rigid::RigidBodyTiltMover
• tilt1_center() : protocols::rigid::RigidBodyTiltMover
• tilt1_center_ : protocols::docking::DockingInitialPerturbation , protocols::rigid::RigidBodyTiltMover
• tilt1_mag() : protocols::rigid::RigidBodyTiltMover
• tilt1_mag_ : protocols::rigid::RigidBodyTiltMover
• tilt2_center() : protocols::rigid::RigidBodyTiltMover
• tilt2_center_ : protocols::docking::DockingInitialPerturbation , protocols::rigid::RigidBodyTiltMover
• tilt2_mag() : protocols::rigid::RigidBodyTiltMover
• tilt2_mag_ : protocols::rigid::RigidBodyTiltMover
• tilt_ : protocols::dna::DNABasestep , protocols::docking::DockingInitialPerturbation
• TiltMover() : protocols::membrane::TiltMover
• time_ : protocols::checkpoint::Timer
• time_data_mean_ : core::scoring::methods::D2H_SA_Energy
• time_data_std_ : core::scoring::methods::D2H_SA_Energy
• time_for_temp_move() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperingBase
• time_minobj() : protocols::md::MDBase
• time_minobj_ : protocols::md::MDBase
• time_points_sqd() : core::scoring::epr_deer::DEERDecayData
• time_pts_sqd() : core::scoring::epr_deer::DEERDecayData
• time_pts_sqd_ : core::scoring::epr_deer::FittingInfo
• time_to_checkpoint() : protocols::checkpoint::Timer
• TIME_TO_UPDATE : core::scoring::TenANeighborNode
• TimeEvaluator() : protocols::evaluation::TimeEvaluator
• TimeFilter() : protocols::filters::TimeFilter
• Timer() : protocols::checkpoint::Timer
• timestamp() : protocols::jd2::Job
• timestamp_ : protocols::jd2::Job
• TimeStampedChannel : protocols::jd2::MpiFileBuffer
• TIMING_CPU : protocols::wum::MPI_WorkUnitManager
• TIMING_end : protocols::wum::MPI_WorkUnitManager
• TIMING_IDLE : protocols::wum::MPI_WorkUnitManager
• TIMING_IO_READ : protocols::wum::MPI_WorkUnitManager
• TIMING_IO_WRITE : protocols::wum::MPI_WorkUnitManager
• timing_last_start_time_ : protocols::wum::MPI_WorkUnitManager
• timing_last_type_ : protocols::wum::MPI_WorkUnitManager
• timing_total_ : protocols::wum::MPI_WorkUnitManager
• TIMING_TRANSFER_RECV : protocols::wum::MPI_WorkUnitManager
• TIMING_TRANSFER_SEND : protocols::wum::MPI_WorkUnitManager
• TIMING_WAIT : protocols::wum::MPI_WorkUnitManager
• TimingProfileMetric() : core::simple_metrics::metrics::TimingProfileMetric
• title() : core::io::HeaderInformation , protocols::relax::DatabaseRelaxScript
• title_ : core::io::HeaderInformation
• title_width() : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• title_width_ : protocols::fold_from_loops::movers::DisplayPoseLabelsMover
• titrate_stack_bonus() : core::import_pose::options::RNA_FragmentMonteCarloOptions
• titrate_stack_bonus_ : core::import_pose::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_alpha_ : protocols::membrane::MPLipidAccessibility
• TM_max : core::scoring::TMscoreStore
• tm_num_ : protocols::simple_filters::MPSpanAngleFilter
• tm_projection_penalty() : core::scoring::MembranePotential
• TM_sum : core::scoring::TMscoreStore
• TM_sum10 : core::scoring::TMscoreStore
• tma_constraints_energy_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TMA_Helper() : protocols::cyclic_peptide::crosslinker::TMA_Helper
• tma_positions_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• tma_sidechain_distance_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TMalign() : protocols::hybridization::TMalign
• TMap : core::fragment::MapCacheUnit< T >
• tmh_inserted() : core::scoring::MembraneTopology
• tmh_inserted_ : core::scoring::MembraneTopology
• tmhelix() : core::scoring::MembraneTopology
• tmhelix_ : protocols::topology_broker::TMHTopologySamplerClaimer
• TMHTopologySamplerClaimer() : protocols::topology_broker::TMHTopologySamplerClaimer
• tmp_energies_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• tmp_weights_ : core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleNode
• tmregion() : core::scoring::MembraneTopology
• tmregion_ : core::scoring::MembraneTopology
• TMsAACompFilter() : protocols::simple_filters::TMsAACompFilter
• TMscore() : core::scoring::TMscore , protocols::hybridization::TMalign
• TMscore8_search() : protocols::hybridization::TMalign
• TMscoreStore() : core::scoring::TMscoreStore
• TMsSpanMembraneFilter() : protocols::simple_filters::TMsSpanMembraneFilter
• tna_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• tna_suite_potential_ : core::scoring::rna::TNA_SuiteEnergy , core::scoring::ScoringManager
• TNA_SuiteEnergy() : core::scoring::rna::TNA_SuiteEnergy
• TNA_SuitePotential() : core::scoring::rna::TNA_SuitePotential
• tna_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• to_ : core::select::residue_selector::SliceResidueSelector
• to_add_element() : protocols::electron_density::ResultDB< T, Tcomp >
• to_all_atom() : protocols::docking::DockingProtocol
• to_all_atom_ : protocols::docking::DockingProtocol
• to_allatom() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• to_be_closed_cuts_ : protocols::topology_broker::TopologyBroker
• to_be_relaxed_ : protocols::loophash::MPI_LoopHashRefine_Master
• to_centroid() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::nonlocal::SingleFragmentMover
• to_centroid_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::surface_docking::SurfaceDockingProtocol
• to_chain() : protocols::indexed_structure_store::movers::DirectSegmentLookupMover
• to_chain_ : protocols::indexed_structure_store::movers::DirectSegmentLookupMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• to_do() : protocols::jd2::Job , protocols::jd3::LarvalJob
• to_entry() : protocols::protein_interface_design::PatchdockReader , protocols::splice::RBInMover
• to_entry_ : protocols::protein_interface_design::PatchdockReader , protocols::splice::RBInMover
• to_full_atom_ : protocols::surface_docking::SurfaceDockingProtocol
• to_minipose() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• to_multichain_pose() : protocols::legacy_sewing::Assembly
• to_pose() : protocols::legacy_sewing::Assembly , protocols::ligand_docking::ga_ligand_dock::LigandConformer , protocols::sewing::data_storage::SmartAssembly
• to_pose_from_db() : protocols::legacy_sewing::Model
• to_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::splice::Splice
• to_res_ : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::splice::Splice
• to_residue_ : core::select::residue_selector::GlycanPositionSelector
• to_scheme_ : protocols::antibody::AntibodyNumberingConverterMover
• to_sequence_profile() : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• to_string() : core::fragment::picking_old::vall::scores::VallFragmentScore , core::id::NamedAtomID , core::id::SequenceMapping , core::io::mmtf::sd_index , core::kinematics::FoldTree , core::optimization::DOF_Node , core::pack::annealer::Value , core::scoring::constraints::Constraint , core::select::residue_selector::ResidueRange , core::sequence::CompositeSequence , core::sequence::Sequence , core::sequence::SequenceAlignment , protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::ligand_docking::ga_ligand_dock::LigandConformer , protocols::multistate_design::PosType
• to_xml() : protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StrandPairing
• toc_ : protocols::filters::TimeFilter
• toggle() : protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::topology_broker::claims::BBClaim , protocols::topology_broker::claims::DofClaim , protocols::topology_broker::claims::JumpClaim
• token : protocols::jd3::dag_node_managers::ResultElements
• tokenize_connected() : protocols::pockets::SmallMol
• tol() : core::scoring::func::FlatHarmonicFunc
• tol_ : core::scoring::func::FlatHarmonicFunc , protocols::nmr::pre::PREDistanceRecord
• tolerance : core::optimization::DFPMinConvergedAbsolute , core::optimization::DFPMinConvergedFractional , protocols::branch_angle::BranchAngleOptimizer , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::minimization_packing::MinMover , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::simple_filters::ChainBreak , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• tolerance_ : protocols::branch_angle::BranchAngleOptimizer , protocols::branch_angle::BranchParam1 , protocols::docking::FaDockingSlideIntoContact , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::membrane::AqueousPoreFinder , protocols::minimization_packing::symmetry::TaskAwareSymMinMover , protocols::moves::JumpOutMover , protocols::noesy_assign::PeakCalibrator , protocols::rotamer_recovery::RRComparerChiDiff , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_filters::ChainBreak , protocols::splice::Splice , protocols::splice::SpliceOut , protocols::symmetry::FaSymDockingSlideTogether , 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
• tolerated_overlap_ : protocols::match::output::MatchCollisionFilter
• too_far() : protocols::constraints_additional::MaxSeqSepConstraintSet
• too_similar() : protocols::ncbb::SecStructFinder
• toolbox_ : protocols::loop_modeling::LoopMover
• top() : protocols::dna::DnaPosition , protocols::electron_density::ResultDB< T, Tcomp > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• top_ : core::fragment::FragmentIO , protocols::dna::DnaPosition
• top_count_of_all_inputs_ : protocols::features::TopPercentOfAllInputs
• top_count_of_each_input_ : protocols::features::TopPercentOfEachInput
• top_designs_ : protocols::antibody::design::AntibodyDesignMover
• top_entities_ : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• top_fragments() : core::fragment::picking_old::vall::VallLibrarian
• top_level_pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• top_n_big_frag_ : protocols::hybridization::FoldTreeHybridize
• top_n_small_frag_ : protocols::hybridization::FoldTreeHybridize
• top_netstates_ : core::pack::annealer::MultiCoolAnnealer
• top_outputed_ : protocols::pose_length_moves::NearNativeLoopCloser
• top_scores_ : protocols::antibody::design::AntibodyDesignMover
• top_to_keep : core::pack::annealer::MultiCoolAnnealer
• toparse_ : core::scoring::BondOrderParser
• TopCountOfAllInputs() : protocols::features::TopCountOfAllInputs
• TopCountOfEachInput() : protocols::features::TopCountOfEachInput
• TopEntitySet() : protocols::pack_daemon::TopEntitySet
• TopNByProperty() : protocols::pose_selectors::TopNByProperty
• topNfilter_ : protocols::electron_density::DockIntoDensityMover
• topNfinal_ : protocols::electron_density::DockIntoDensityMover
• TopNMotifScorer() : protocols::sewing::scoring::TopNMotifScorer
• 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_RESAMPLING : protocols::abinitio::IterativeBase
• topo_up_ : protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately
• topol_score_ : protocols::abinitio::Template
• topological_match_to() : core::kinematics::AtomTree
• topological_match_to_ : core::kinematics::AtomTree
• topological_observers() : core::kinematics::AtomTree
• topological_observers_ : core::kinematics::AtomTree
• Topologies : protocols::abinitio::PairingStatistics
• topology() : protocols::abinitio::PairingStatistics
• topology_ : core::conformation::membrane::SpanningTopology , core::scoring::methods::ProQ_Energy , protocols::membrane::AddMembraneMover
• topology_broker() : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_broker_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_feature() : core::scoring::methods::ProQ_Energy
• topology_root_res_ : protocols::topology_broker::TMHTopologySamplerClaimer
• topology_score() : protocols::abinitio::Template
• TopologyBroker() : protocols::topology_broker::TopologyBroker
• TopologyBrokerMover() : protocols::protein_interface_design::movers::TopologyBrokerMover
• TopologyClaimer() : protocols::topology_broker::TopologyClaimer
• TopologyClaimerCAPs : protocols::topology_broker::ClaimerMessage
• TopologyClaimerFactory() : protocols::topology_broker::TopologyClaimerFactory
• TopologyClaimers : protocols::topology_broker::TopologyBroker
• topols_ : protocols::abinitio::PairingStatistics
• TopOutFunc() : core::scoring::func::TopOutFunc
• TopPercentOfAllInputs() : protocols::features::TopPercentOfAllInputs
• TopPercentOfEachInput() : protocols::features::TopPercentOfEachInput
• tor1 : protocols::normalmode::ContactStruct
• tor2 : protocols::normalmode::ContactStruct
• tor_for_dof() : core::pack::scmin::AtomTreeSCMinMinimizerMap , core::pack::scmin::CartSCMinMinimizerMap , core::pack::scmin::SCMinMinimizerMap
• tor_step_ : protocols::simple_moves::PeriodicBoxMover
• tor_U1D3 : protocols::toolbox::match_enzdes_util::SingleConstraint
• tor_U1D3_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U1D3_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2 : protocols::toolbox::match_enzdes_util::SingleConstraint
• tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1 : protocols::toolbox::match_enzdes_util::SingleConstraint
• tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• torID_ : protocols::normalmode::NormalMode
• toroidal : core::scoring::sc::_RESULTS
• tors_iterator : core::scoring::HydroxylTorsionPotential
• tors_lookup_ : core::scoring::GenericBondedPotential
• tors_pot_ : core::scoring::GenericBondedPotential
• torsion() : core::conformation::Conformation , core::fragment::BBTorsionSRFD , core::id::TorsionID , core::pose::Pose , core::pose::rna::RNA_SuiteInfo , protocols::normalmode::NormalMode
• Torsion() : protocols::protein_interface_design::filters::Torsion
• torsion() : protocols::protein_interface_design::filters::Torsion
• torsion2big_bin() : protocols::comparative_modeling::features::TorsionFeature , protocols::pose_metric_calculators::RotamerRecovery , protocols::rotamer_recovery::PerNativeRRReporterHuman
• torsion2big_bin_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• torsion2index() : core::sequence::ABEGOManager
• torsion2index_level1() : core::sequence::ABEGOManager
• torsion2index_level2() : core::sequence::ABEGOManager
• torsion2index_level3() : core::sequence::ABEGOManager
• torsion2index_level4() : core::sequence::ABEGOManager
• torsion_ : core::id::TorsionID , protocols::constraint_generator::DihedralConstraintGenerator , protocols::normalmode::NormalMode , protocols::protein_interface_design::filters::Torsion
• torsion_angle() : core::conformation::Conformation , core::kinematics::AtomTree
• torsion_angle_dof_id() : core::kinematics::AtomTree
• torsion_angles_ : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• torsion_assigned_ : protocols::cyclic_peptide::PeptideCyclizeMover
• torsion_atom_ : core::chemical::AddConnect
• torsion_atoms_ : protocols::simple_moves::SetTorsion
• torsion_bin() : protocols::comparative_modeling::features::TorsionFeature
• torsion_bin_ : protocols::comparative_modeling::features::TorsionFeature
• torsion_changes_move_other_monomers() : core::conformation::symmetry::SymmetryInfo
• torsion_changes_move_other_monomers_ : core::conformation::symmetry::SymmetryInfo
• torsion_ct_name() : protocols::simple_moves::SetTorsion
• torsion_database() : protocols::splice::Splice
• torsion_database_ : protocols::splice::Splice , protocols::splice::SpliceIn
• torsion_database_fname() : protocols::splice::Splice
• torsion_database_fname_ : protocols::splice::Splice
• torsion_degree_ : protocols::backbone_moves::local_backbone_mover::free_peptide_movers::ShearFreePeptideMover
• torsion_delta() : protocols::loops::loop_closure::ccd::CCDLoopClosureMover
• torsion_features_string() : protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::loops::loop_mover::LoopMover
• torsion_id() : core::id::TorsionID_Range , core::optimization::DOF_Node , protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_id_ : core::id::TorsionID_Range , core::optimization::DOF_Node , protocols::recces::sampler::MC_OneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• torsion_id_begin() : core::kinematics::MoveMap
• torsion_id_end() : core::kinematics::MoveMap
• torsion_id_list_ : protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover
• torsion_id_map_ : core::kinematics::MoveMap
• torsion_id_ranges() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , protocols::rigid::RigidBodyMover , protocols::rigid::UniformRigidBodyMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SmallMover
• torsion_ids_ : core::scoring::rna::TNA_SuitePotential , protocols::canonical_sampling::MetricRecorder , protocols::recces::sampler::rna::MC_RNA_Suite , protocols::simple_moves::TorsionSetMover
• torsion_info_ : core::import_pose::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• torsion_is_independent() : core::conformation::symmetry::SymmetryInfo
• torsion_lower_vals_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_name() : protocols::simple_moves::SetTorsion
• torsion_name_ : protocols::simple_moves::SetTorsion
• torsion_parameter : core::scoring::methods::ResidueCartBondedParameters
• torsion_parameters() : core::scoring::methods::ResidueCartBondedParameters
• torsion_params_ : core::scoring::HydroxylTorsionPotential , core::scoring::methods::ResidueCartBondedParameters
• torsion_potential() : core::scoring::rna::RNA_EnergyMethodOptions
• torsion_potential_ : core::scoring::rna::RNA_EnergyMethodOptions
• torsion_sample_vals_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_sample_value() : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_samples_ : protocols::helical_bundle::BackboneGridSamplerHelper
• torsion_scale_factor() : core::optimization::MinimizerMap , core::optimization::symmetry::SymMinimizerMap
• torsion_screen_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• torsion_source_name : core::fragment::rna::TorsionSet
• torsion_specs_ : protocols::canonical_sampling::MetricRecorder
• torsion_type() : core::scoring::GenTorsionParams
• torsion_type_ : core::scoring::GenTorsionParams , protocols::simple_moves::bb_sampler::BBDihedralSamplerBase
• torsion_type_begin() : core::kinematics::MoveMap
• torsion_type_end() : core::kinematics::MoveMap
• 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
• TorsionBinIO() : protocols::frag_picker::TorsionBinIO
• TorsionBinSimilarity() : protocols::frag_picker::scores::TorsionBinSimilarity
• TorsionClaim() : protocols::environment::claims::TorsionClaim
• TorsionDOFMover() : protocols::simple_moves::TorsionDOFMover
• TorsionFeature() : protocols::comparative_modeling::features::TorsionFeature
• TorsionFourierComponent() : core::scoring::dna::TorsionFourierComponent
• TorsionFragment() : protocols::frags::TorsionFragment
• TorsionFragmentLibrary() : protocols::frags::TorsionFragmentLibrary
• TorsionFragmentMover() : protocols::frags::TorsionFragmentMover
• TorsionID : core::conformation::Conformation , core::conformation::symmetry::SymmetryInfo , core::id::TorsionID , core::kinematics::MoveMap , core::optimization::DOF_Node , core::pose::Pose
• TorsionID_Map : core::kinematics::MoveMap
• TorsionID_Range() : core::id::TorsionID_Range
• TorsionIDs : core::conformation::symmetry::SymmetryInfo , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler
• TorsionList : protocols::toolbox::SamplerPlusPlus
• TorsionRestrictedKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• torsions() : core::fragment::rna::FullAtomRNA_Fragments , core::fragment::rna::TorsionSet
• torsions_ : core::fragment::BBTorsionSRFD , protocols::frags::TorsionFragment
• torsions_indep_ : core::scoring::methods::IdealParametersDatabase
• torsions_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• torsions_monte_carlo_minimize() : protocols::flexpep_docking::FlexPepDockingProtocol
• 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
• TorsionSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• TorsionSet() : core::fragment::rna::TorsionSet
• TorsionSetMover() : protocols::simple_moves::TorsionSetMover
• TorsionsIndepSubmap : core::scoring::methods::IdealParametersDatabase
• torsionsMCM : protocols::flexpep_docking::FlexPepDockingFlags
• TorsionSweepingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• TorsionType : core::kinematics::MoveMap
• TorsionTypeMap : core::kinematics::MoveMap
• torsmutationRate_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• tot_rotamer_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• tot_score() : core::scoring::motif::XformScore
• tot_surf : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• tot_vol : core::scoring::packing::SurfVol , core::scoring::packing::SurfVolDeriv
• total() : core::scoring::saxs::DistanceHistogram , protocols::mean_field::EnergiesByTaskCalculator
• total_ : core::scoring::mhc_epitope_energy::MHCEpitopeEnergy
• total_accepts() : protocols::jd2::archive::ArchiveBase
• total_accepts_ : protocols::jd2::archive::ArchiveBase
• total_area : core::scoring::packstat::AreaAccumulator
• total_assigned_distances_ : protocols::noesy_assign::DistanceScoreMover
• total_atoms() : core::pose::Pose
• total_base_axis_score_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• total_base_pair_score_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• total_base_stack_axis_score_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• total_base_stack_score_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• total_base_stagger_score_ : core::pose::rna::RNA_FilteredBaseBaseInfo
• total_bin : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• total_buried_volume() : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• total_buried_volume_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• total_cdr_loops_ : protocols::antibody::AntibodyInfo
• total_chain_break_score : protocols::forge::remodel::RemodelData
• total_charge_ : protocols::pose_metric_calculators::ChargeCalculator
• total_clashes_ : protocols::pose_metric_calculators::ClashCountCalculator
• total_completed_nstruct_ : protocols::jd2::BOINCJobDistributor
• total_count : protocols::stepwise::modeler::rna::Filterer_Count
• total_count_ : protocols::canonical_sampling::SimulatedTempering , protocols::matdes::MotifHitsRotamersOperation
• total_counts_ : core::scoring::bin_transitions::BinTransitionData
• total_embed() : protocols::membrane::geometry::Embedding
• total_embed_ : protocols::membrane::geometry::Embedding
• total_energies() : core::scoring::Energies
• total_energies_ : core::scoring::Energies
• total_energy() : core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::scoring::Energies , core::scoring::loop_graph::LoopGraph , core::scoring::saxs::SAXSEnergy
• total_energy_ : core::scoring::Energies , core::scoring::loop_graph::LoopGraph
• total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_alternate_state_assignment_ : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , 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() : 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::NPDHBondInteractionGraph< V, E, G > , 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_cutoff_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• 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::GlycanSampler
• total_goodfrags_ : protocols::pose_metric_calculators::FragQualCalculator
• total_hb_E : protocols::analysis::InterfaceData
• total_hbonds : protocols::hbnet::HBondNetStruct
• total_helices : core::scoring::Helices
• total_HH_dimer : core::scoring::Helices
• total_hpatch_score_ : protocols::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::pose_metric_calculators::ChargeCalculator
• total_net_change_in_rama_score_over_range() : protocols::loops::loop_closure::ccd::RamaCheckBase
• total_nlcontacts_ : protocols::pose_metric_calculators::NonlocalContactsCalculator
• total_nr_jobs() : protocols::jd2::JobDistributor
• total_num_mc_runs_ : protocols::hbnet::HBNet
• total_num_slides_ : protocols::symmetry::SymmetrySlider
• total_number_abego() : core::sequence::ABEGOManager
• total_number_pres_ : core::scoring::nmr::pre::PREMultiSet
• total_number_rdc_ : core::scoring::nmr::rdc::RDCMultiSet
• total_packstat_ : protocols::pose_metric_calculators::PackstatCalculator
• total_partitions_ : protocols::hotspot_hashing::PartitionedSearchPattern
• total_permutations_ : protocols::antibody::design::AntibodyDesignMover
• total_polar_atoms : protocols::hbnet::HBondNetStruct
• total_pos_charges_ : protocols::pose_metric_calculators::ChargeCalculator
• total_positions_ : protocols::optimize_weights::IterativeOptEDriver
• TOTAL_PRECISION : protocols::frag_picker::scores::FragmentScoreManager
• total_proposed() : protocols::jd2::archive::ArchiveBase
• total_proposed_ : protocols::jd2::archive::ArchiveBase
• total_ref_resids_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• total_rel_hsasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• total_res() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• total_residue() : core::fragment::SecondaryStructure , core::kinematics::ResidueCoordinateChangeList , core::pack::rotamer_set::ContinuousRotamerSets , core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::UnboundRotamersOperation , core::pack::task::PackerTask , core::pack::task::PackerTask_ , core::pack_basic::RotamerSetsBase , core::pose::Pose , core::scoring::trie::TrieCollection , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::legacy_sewing::Assembly , protocols::noesy_assign::PeakAssignmentResidueMap , protocols::parser::BluePrint
• 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::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::optimize_weights::PNatStructureOptEData , protocols::parser::BluePrint
• total_residue_wolig() : protocols::parser::BluePrint
• total_residue_wolig_ : protocols::parser::BluePrint
• total_residues_ : protocols::loop_grower::LoopGrower
• total_rot_ : core::pack::rotamer_set::UnboundRotamersOperation
• total_rotamer_positions_ : protocols::optimize_weights::IterativeOptEDriver
• total_rotamers_2_unique_rotamers() : core::scoring::trie::RotamerTrie< AT, CPDATA >
• total_rotamers_2_unique_rotamers_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• total_sampled_ : protocols::recces::scratch::ThermalSamplingMover
• total_sasa_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc , protocols::vardist_solaccess::VarSolDistSasaCalculator
• total_sasa_sc_ : core::pose::metrics::simple_calculators::SasaCalculator2 , core::scoring::sasa::SasaCalc
• total_score : core::scoring::motif::MotifHits , protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager , protocols::qsar::scoring_grid::GridSet
• total_score_ : protocols::analysis::LoopAnalyzerMover , protocols::mean_field::EnergiesByTaskCalculator , protocols::score_filters::ScoreCutoffFilter
• total_score_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• total_score_of_last_considered_pose() : protocols::moves::MonteCarlo
• total_score_of_last_considered_pose_ : protocols::moves::MonteCarlo
• total_search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• total_sfr_atoms() : core::io::pose_to_sfr::PoseToStructFileRepConverter
• total_size() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• total_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• total_SS_dimer : core::scoring::Strands
• total_standard_cycles() : protocols::forge::remodel::RemodelLoopMover
• total_stored_solutions() : protocols::generalized_kinematic_closure::GeneralizedKIC
• 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::pose_metric_calculators::SurfaceCalculator
• total_tmhelix_ : core::scoring::MembraneTopology
• total_trials() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::evolution::EvolutionaryDynamicsMover , protocols::moves::MonteCarlo , protocols::moves::TrialCounter
• total_trials_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::evolution::EvolutionaryDynamicsMover
• total_updates_ : protocols::rna::setup::RNA_CSA_JobDistributor
• total_updates_so_far_ : protocols::rna::setup::RNA_CSA_JobDistributor
• total_violation_count_ : protocols::noesy_assign::DistanceScoreMover
• total_volume_ : protocols::denovo_design::calculators::CavityCalculator
• total_weight_ : protocols::jumping::JumpSelector , protocols::monte_carlo::MonteCarloInterface
• TotalEnergyMetric() : core::simple_metrics::metrics::TotalEnergyMetric
• totalinnervox_ : core::scoring::atomic_depth::AtomicDepth
• totalres_ : protocols::pockets::PocketConstraint
• TotalSasaFilter() : protocols::simple_filters::TotalSasaFilter
• TotalScoreFeatures() : protocols::features::TotalScoreFeatures
• totalsurfacevox_ : core::scoring::atomic_depth::AtomicDepth
• totaltime_batchrelax_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• totaltime_loophash() : 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
• touchesPS() : protocols::pockets::PocketGrid
• touchesSolvent() : protocols::pockets::PocketGrid
• touchesSS() : protocols::pockets::PocketGrid
• touchesSurface() : protocols::pockets::PocketGrid
• tournament_select() : protocols::genetic_algorithm::GeneticAlgorithmBase
• TP_BURIED : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• TP_EDGE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• TP_POCKET : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• TP_SURF : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• tpdb : protocols::tcr::TCRmodel::tmpltinfo
• tpdb_db_ : protocols::tcr::TCRmodel
• tpiece : protocols::tcr::TCRmodel::tmpltinfo
• 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 , 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
• trace() : core::io::rna::RDAT , core::scoring::epr_deer::DEERDecayData , core::scoring::packstat::trace
• trace_ : core::io::rna::RDAT , core::scoring::epr_deer::DEERDecayData , core::scoring::epr_deer::Simulated4PDEERTrace , core::scoring::packstat::Event , core::scoring::ResidualDipolarCoupling
• traceback() : core::sequence::Aligner
• tracer() : protocols::rpc::JSON_RPC
• tracer_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover , protocols::loops::filters::LoopAnalyzerFilter
• tracer_output_stream_ : protocols::rpc::JSON_RPC
• traces_ : core::scoring::packstat::Slice
• track_completed_job() : protocols::jd3::JobTracker
• track_deallocated_input_pose() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• track_hpatch_E_min() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• track_job_completed() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• track_job_node_assigned() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• track_job_node_being_assigned() : protocols::jd3::standard::PreliminaryLarvalJobTracker
• track_max_magnitude_surface_deltaE() : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G >
• track_npd_hbond_E_min() : core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >
• track_starting_job_list() : protocols::jd3::JobTracker
• track_surface_E_min() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• trackfragments_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• traffic_total_received_ : protocols::wum::MPI_WorkUnitManager
• traffic_total_sent_ : protocols::wum::MPI_WorkUnitManager
• train() : core::scoring::func::CircularSplineFunc
• TraitEntityHashMap : protocols::genetic_algorithm::GeneticAlgorithmBase
• traits() : protocols::genetic_algorithm::Entity
• traits_ : protocols::genetic_algorithm::Entity
• traits_string() : protocols::genetic_algorithm::Entity
• trajectory_ : core::pack::annealer::DebuggingAnnealer , protocols::backrub::BackrubProtocol
• trajectory_apply_mover_ : protocols::backrub::BackrubProtocol
• trajectory_file_name() : core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::SequenceSymmetricAnnealer , core::pack::annealer::SmartFixbbSimAnnealer
• trajectory_file_name_ : core::pack::annealer::FixbbSimAnnealer , core::pack::annealer::SequenceSymmetricAnnealer , core::pack::annealer::SmartFixbbSimAnnealer
• trajectory_gz_ : protocols::backrub::BackrubProtocol
• trajectory_map_features_reporter_ : protocols::features::TrajectoryReportToDB
• Trajectory_state : protocols::viewer::GraphicsState
• trajectory_stream_ : protocols::canonical_sampling::PDBTrajectoryRecorder
• trajectory_stride_ : protocols::backrub::BackrubProtocol
• TrajectoryLogger() : protocols::loop_modeling::utilities::TrajectoryLogger
• TrajectoryMapFeatures() : protocols::features::TrajectoryMapFeatures
• TrajectoryRecorder() : protocols::canonical_sampling::TrajectoryRecorder
• TrajectoryReportToDB() : protocols::features::TrajectoryReportToDB
• trans() : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• 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
• 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::membrane::RandomPositionTranslationMover , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rna::denovo::coarse::MultipleDomainMover , protocols::rna::denovo::movers::RNA_HelixMover , 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::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover
• 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_movers_ : protocols::rna::denovo::movers::RNA_HelixMover
• trans_step_ : protocols::ligand_docking::ga_ligand_dock::LigandAligner , protocols::nmr::pcs::PCSLigandTransformMover , protocols::simple_moves::PeriodicBoxMover
• trans_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• trans_wt_ : protocols::simple_filters::SymmetricMotifFilter
• TRANS_X : core::kinematics::Jump , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric
• TRANS_Y : core::kinematics::Jump , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric
• TRANS_Z : core::kinematics::Jump , protocols::multistage_rosetta_scripts::cluster::metrics::JumpMetric
• TRANSFER : core::conformation::signals::ConnectionEvent
• transfer_conformation() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• transfer_constraint_set() : core::pose::Pose
• transfer_jumps() : protocols::jumping::JumpSample
• transfer_to_residue_vector() : protocols::loops::Loops
• transfer_unfolded_conformation() : protocols::fold_from_loops::utils::Nub
• transform() : core::conformation::UltraLightResidue , 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_info_ : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• transform_ligand() : protocols::ligand_docking::Transform , protocols::ligand_docking::TransformEnsemble
• transform_model() : protocols::legacy_sewing::Hasher
• transform_pose() : protocols::protein_interface_design::PatchdockReader
• transform_pose_into_membrane() : protocols::docking::membrane::MPDockingSetupMover
• transform_segment_coords() : protocols::legacy_sewing::LegacyRepeatAssemblyMover
• transform_segments() : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::Hasher
• transform_single_residue() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• transformed_residues : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• transformed_water_thickness_ : core::conformation::membrane::ImplicitLipidInfo
• TransformEnsemble() : protocols::ligand_docking::TransformEnsemble
• TransformEnsemble_info() : protocols::ligand_docking::TransformEnsemble_info
• TransformIntoMembraneMover() : protocols::membrane::TransformIntoMembraneMover
• transforms_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transforms_uptodate() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• transforms_uptodate_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• TransientCutpointHandler() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• transition_threshold() : protocols::canonical_sampling::CanonicalSamplingMover
• transition_threshold_ : protocols::canonical_sampling::CanonicalSamplingMover
• translate() : core::grid::CartGrid< T > , protocols::backbone_moves::local_backbone_mover::FreePeptide
• Translate() : protocols::ligand_docking::Translate
• translate_ : protocols::rigid::RollMover
• translate_Ang_ : protocols::ligand_docking::RigidSearchMover
• translate_by() : protocols::membrane::geometry::EmbeddingDef , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter
• translate_by_ : protocols::features::InterfaceDdGMover , protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter
• translate_index : protocols::forge::remodel::RemodelWorkingSet
• Translate_info() : protocols::ligand_docking::Translate_info
• translate_info_ : protocols::ligand_docking::Translate
• translate_ligand() : protocols::ligand_docking::TransformEnsemble , protocols::ligand_docking::Translate
• translate_virt_to_CoM() : protocols::hybridization::FoldTreeHybridize
• translateDSSP_ABEGO() : protocols::forge::remodel::RemodelData
• translation : core::kinematics::RT , protocols::dna::SeparateDnaFromNonDna , protocols::ligand_docking::RigidSearchMover , protocols::protein_interface_design::Transformation , Transformation
• translation_ : protocols::dna::SeparateDnaFromNonDna , protocols::loop_grower::SheetPositions
• translation_along_axis() : core::kinematics::Jump
• translation_axes_ : protocols::matdes::SymDofMover
• translation_mag_ : protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::rigid::UniformRigidBodyMover , protocols::topology_broker::TMHTopologySamplerClaimer
• translation_magnitude_ : protocols::simple_moves::CoupledMover
• translation_matrices_ : core::conformation::symmetry::SymmData
• translation_vector_ : protocols::membrane::TranslationMover
• TranslationFreePeptideMover() : protocols::backbone_moves::local_backbone_mover::free_peptide_movers::TranslationFreePeptideMover
• TranslationMover() : protocols::membrane::TranslationMover
• TranslationRotationMover() : protocols::membrane::TranslationRotationMover
• translations_ : protocols::ligand_docking::CompoundTranslate
• translocation_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• transM : protocols::sparta::RingData
• transmutWidth_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• transparent_facets_ : protocols::match::Bool3DGridKinemageWriter
• traverse_IG() : protocols::hbnet::HBNet
• traverse_native() : protocols::hbnet::HBNet
• treat_L_as_D_ : protocols::fldsgn::filters::SecondaryStructureFilter
• tree_ : core::conformation::carbohydrates::GlycanTree , protocols::rigid::RigidBodyMotionMover
• tree_based_min_pack_ : protocols::carbohydrates::GlycanSampler
• tree_edge() : core::chemical::RerootRestypeVisitor
• tree_from_jumps_and_cuts() : core::kinematics::FoldTree
• tree_set_observer_ : core::conformation::Conformation
• tree_start_residue_ : core::conformation::carbohydrates::GlycanNode
• treeatom_map_ : core::chemical::RerootRestypeVisitor
• trees_to_model_ : protocols::carbohydrates::GlycanTreeModeler
• TreeVizBuilder() : core::kinematics::TreeVizBuilder
• triage_filter() : protocols::protein_interface_design::filters::FilterScanFilter
• triage_filter_ : protocols::protein_interface_design::filters::FilterScanFilter
• triage_positions_ : protocols::protein_interface_design::movers::PlaceStubMover
• triage_threshold() : protocols::protein_interface_design::filters::BoltzmannFilter
• triage_threshold_ : protocols::protein_interface_design::filters::BoltzmannFilter
• trial() : protocols::moves::TrialCounter
• trial_counter() : protocols::canonical_sampling::TemperingBase , protocols::hybridization::ChunkTrialMover , protocols::hybridization::InsertChunkMover , protocols::monte_carlo::GenericMonteCarloMover
• trial_counter_ : protocols::canonical_sampling::TemperingBase , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::TrialCounter
• trial_large() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_large_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_positions_ : protocols::enzdes::SecondaryMatchProtocol
• trial_small() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• trial_small_pack_ : protocols::abinitio::ClassicAbinitio
• trial_small_top25() : protocols::abinitio::MembraneAbinitio
• trial_small_top25_ : protocols::abinitio::MembraneAbinitio
• trial_smooth() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio
• TrialCounter() : protocols::moves::TrialCounter
• TrialCounterObserver() : protocols::canonical_sampling::TrialCounterObserver
• TrialMover() : protocols::moves::TrialMover
• trials() : protocols::seeded_abinitio::CloseFold
• trials_ : protocols::abinitio::hConvergenceCheck , protocols::fold_from_loops::NubInitioMover , protocols::hybridization::hConvergenceCheck , protocols::seeded_abinitio::CloseFold
• triangle() : protocols::viewer::triangle
• triangleIterator() : protocols::viewer::triangleIterator
• triazolamer_post_pos_ : protocols::simple_moves::triazolamer::TriazolamerMover
• triazolamer_pre_pos_ : protocols::simple_moves::triazolamer::TriazolamerMover
• triazolamer_seq_positions_ : protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• TriazolamerMover() : protocols::simple_moves::triazolamer::TriazolamerMover
• TriazolamerRandomSmallMover() : protocols::simple_moves::triazolamer::TriazolamerRandomSmallMover
• trie() : core::scoring::trie::TrieCollection
• trie_ : core::scoring::trie::RotamerTrie< AT, CPDATA >
• trie_vs_path() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase
• trie_vs_trie() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , 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
• tried_centroid_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tried_fullatom_pose_ : protocols::constraints_additional::ConstraintEvaluator
• TrieNode() : core::scoring::trie::TrieNode< AT, CPDATA >
• tries() : protocols::simple_moves::TorsionDOFMover
• tries_ : core::scoring::trie::TrieCollection , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::TorsionDOFMover
• TrieVsTrieCachedDataContainerBase() : core::scoring::trie::TrieVsTrieCachedDataContainerBase
• trigger_accept() : protocols::rbsegment_relax::SequenceShiftMover
• triggers_ : protocols::monte_carlo::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• trigonal_planar_metal_constraints_energy_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• trigonal_planar_metal_positions_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• trigonal_planar_metal_sidechain_distance_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• trigonal_pyramidal_metal_constraints_energy_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• trigonal_pyramidal_metal_positions_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• trigonal_pyramidal_metal_sidechain_distance_filter_multiplier_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• TrigonalPlanarMetal_Helper() : protocols::cyclic_peptide::crosslinker::TrigonalPlanarMetal_Helper
• TrigonalPyramidalMetal_Helper() : protocols::cyclic_peptide::crosslinker::TrigonalPyramidalMetal_Helper
• trilinear_gradient() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• trilinear_interpolation() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• trim() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trim_additional_rotamers() : protocols::hbnet::HBNet
• trim_back_repeat_to_repair_scar() : protocols::simple_moves::RepeatPropagationMover
• trim_based_on_known_ligand() : protocols::pockets::NonPlaidFingerprint
• trim_chunks() : protocols::pose_creation::SliceToMiniProteinMover
• trim_cter() : protocols::ub_e2c::ubi_e2c_modeler
• trim_db_pose() : protocols::legacy_sewing::Model
• trim_dots_to_resl() : core::scoring::sc::ElectrostaticComplementarityCalculator
• trim_pose() : protocols::features::ModelFeatures , protocols::pose_creation::MakeJunctionsMover
• trim_proportion_ : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trim_rotamers() : protocols::hbnet::HBNet
• trim_scores() : protocols::legacy_sewing::Hasher
• trim_subbin_edges_and_rescale_subbin() : core::scoring::bin_transitions::BinTransitionData
• trim_target_pose() : protocols::hybridization::MRMover
• trim_terminal_segments() : protocols::sewing::data_storage::SmartAssembly
• trim_to_heterogeneous_clusters() : protocols::simple_moves::AtomHash
• trim_to_single_repeat() : protocols::cyclic_peptide::SymmetricCycpepAlign
• trim_to_single_repeat_ : protocols::cyclic_peptide::SymmetricCycpepAlign
• trimFiberDiffractionData() : core::scoring::fiber_diffraction::FiberDiffraction
• trimmed_dots : core::scoring::sc::MolecularSurfaceCalculator
• trimmedArea : core::scoring::sc::_RESULTS
• TrimPeripheralBand() : core::scoring::sc::ShapeComplementarityCalculator
• TrimPeripheralBandCheckDot() : core::scoring::sc::ShapeComplementarityCalculator
• trimRegion() : protocols::pose_length_moves::PossibleLoop
• tripFileName : protocols::sparta::Sparta::SpartaLib
• triplet_fingerprint_data() : protocols::pockets::FingerprintBase
• triplet_fingerprint_data_ : protocols::pockets::FingerprintBase
• TRIPLET_Tab : protocols::sparta::Sparta::SpartaLib
• TripletID() : protocols::fldsgn::topology::TripletID
• TripletMap : protocols::fldsgn::topology::HSSTripletSet
• TrisBpyScore() : protocols::sic_dock::scores::TrisBpyScore
• trj() : protocols::md::MDBase
• trj_ : protocols::md::MDBase
• trj_score_only() : protocols::md::MDBase
• trj_score_only_ : protocols::md::MDBase
• trj_scratch() : protocols::md::MDBase
• trj_scratch_ : protocols::md::MDBase
• true_behavior() : protocols::task_operations::StoreCompoundTaskMover
• true_behavior_ : protocols::task_operations::StoreCompoundTaskMover
• true_mover_ : protocols::moves::IfMover
• trueD() : protocols::cluster::calibur::Clustering
• TrueFilter() : protocols::filters::TrueFilter
• TrueResidueSelector() : core::select::residue_selector::TrueResidueSelector
• truly_floating_base() : protocols::stepwise::modeler::StepWiseConnectionSampler
• truncate_cenlist_values() : core::scoring::EnvPairPotential
• truncate_only_ : protocols::electron_density::ScaleMapIntensities
• TruncatedScoreEvaluator() : protocols::simple_filters::TruncatedScoreEvaluator
• trust() : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• trust_ : protocols::fold_from_loops::movers::NubInitioLoopClosureMover
• trust_current_temp_ : protocols::canonical_sampling::TemperingBase
• trust_fold_tree() : protocols::loop_modeling::LoopMover
• trust_fold_tree_ : protocols::loop_modeling::LoopMover
• try_all_conformers() : protocols::docking::DockingLowResEnsemble
• try_all_disulfides_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• try_all_pairs() : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• try_all_pairs_ : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• try_elongating_helix() : protocols::helical_bundle_predict::HBPHelixAssignments
• try_for_more() : protocols::motifs::IRCollection
• try_move_to_idle() : core::scoring::util_methods::DumpTrajectoryEnergy
• try_nucleating_helix() : protocols::helical_bundle_predict::HBPHelixAssignments
• try_perturbing_global_helix_parameters() : protocols::helical_bundle_predict::HBPHelixAssignments
• try_perturbing_local_helix_parameters() : protocols::helical_bundle_predict::HBPHelixAssignments
• try_point_mutants() : protocols::vip::VIP_Mover
• try_retracting_helix() : protocols::helical_bundle_predict::HBPHelixAssignments
• try_to_slide_into_contact() : protocols::rna::denovo::coarse::MultipleDomainMover
• TryDisulfPermutations() : protocols::cyclic_peptide::TryDisulfPermutations
• TryRotamers() : protocols::protein_interface_design::movers::TryRotamers
• trySeveral_ciBRs() : core::pack::annealer::FASTERAnnealer
• trywait_semaphore() : protocols::boinc::Boinc
• TS1_PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• TS2_PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• TS3_PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• TS4_PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• tscore : protocols::tcr::TCRmodel::tmpltinfo
• tseq : protocols::tcr::TCRmodel::tmpltinfo
• tseq_db_ : protocols::tcr::TCRmodel
• tsinfo : protocols::tcr::TCRmodel
• Tsymm_ : core::conformation::symmetry::SymmetricConformation
• Tumble() : protocols::simple_moves::Tumble
• turn_expression_ASTs_into_expressions() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• turn_off_flank_relax() : protocols::antibody::H3RefineCCD
• turn_off_for_chunks() : protocols::rna::movers::ErraserMinimizerMover
• turn_off_H3_filter() : protocols::antibody::H3PerturbCCD
• turn_off_h3_filter() : protocols::antibody::H3RefineCCD
• turn_off_repulsive_ramp() : protocols::antibody::RefineBetaBarrel
• turn_off_rna_chem_map_during_optimize() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• turn_off_rna_chem_map_during_optimize_ : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• turn_off_rotation_dependence_ : core::scoring::loop_graph::evaluator::SixDTransRotPotential
• turn_on_benchmark() : protocols::antibody::H3RefineCCD
• turnoff_minimization_ : protocols::antibody::CDRsMinPackMin
• tVal : protocols::sparta::Sparta::SpartaLib
• TvecA : protocols::motif_grafting::movers::motif2scaffold_data
• TvecB : protocols::motif_grafting::movers::motif2scaffold_data
• TVector : core::fragment::VectorCacheUnit< T >
• twelveA_ : core::scoring::TwelveANeighborGraph
• twelveA_neighbor_graph() : core::scoring::Energies
• twelveA_squared_ : core::scoring::TwelveANeighborGraph
• TwelveANeighborEdge() : core::scoring::TwelveANeighborEdge
• TwelveANeighborGraph() : core::scoring::TwelveANeighborGraph
• TwelveANeighborNode() : core::scoring::TwelveANeighborNode
• twin_law_ : core::scoring::cryst::PhenixInterface , protocols::cryst::SetRefinementOptionsMover
• twist() : protocols::dna::DNABasestep
• twist_ : protocols::dna::DNABasestep , protocols::make_rot_lib::RotData
• twist_level() : protocols::fldsgn::filters::StrandCurvatureByLevels
• twist_level_ : protocols::fldsgn::filters::StrandCurvatureByLevels
• Two : core::chemical::gasteiger::GasteigerAtomTypeData
• TWO_B_MethodIterator : core::scoring::ScoreFunction
• TWO_B_Methods : core::scoring::ScoreFunction
• two_body_energies() : core::pack::interaction_graph::PDEdge
• 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_body_energies_map_ : protocols::loop_grower::LoopComparator
• two_param_func : protocols::mean_field::jagged_array< T, A >::func_T2< T_2 > , protocols::mean_field::jagged_array< T, A >
• two_parts_chain1() : protocols::protein_interface_design::movers::SetAtomTree
• two_parts_chain1_ : protocols::protein_interface_design::movers::SetAtomTree
• two_stage_clustering() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• two_stage_clustering_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• two_step() : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• two_step_ : protocols::protein_interface_design::movers::SaveAndRetrieveSidechains
• twobody_energies() : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_energies_ : protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_enmeths_ : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• TwoBodyEnergies : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• TwoBodyEnergiesIterator : core::scoring::MinimizationEdge , core::scoring::MinimizationNode
• TwoBodyEnergy() : core::scoring::methods::TwoBodyEnergy
• twochains_ : protocols::seeded_abinitio::SeedFoldTree
• twoD_histogram_ : core::scoring::orbitals::OrbitalsStatistics
• twoprime() : core::import_pose::RNA_DeNovoParameters
• twoprime_ : core::import_pose::RNA_DeNovoParameters
• twoprime_res() : core::pose::full_model_info::FullModelInfo
• twoprime_res_ : core::import_pose::FullModelPoseBuilder
• tX_ : core::grid::CartGrid< T >
• tY_ : core::grid::CartGrid< T >
• type() : core::chemical::ICoorAtomID , core::conformation::Atom , core::conformation::orbitals::OrbitalXYZCoords , core::conformation::Residue , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::DownJumpSRFD , core::fragment::Frame , core::fragment::JumpingFrame , core::fragment::SecstructSRFD , core::fragment::SingleResidueFragData , core::fragment::UpJumpSRFD , core::id::DOF_ID , core::id::TorsionID , core::import_pose::ImportPoseOptions , core::import_pose::options::RNA_BasicOptions , core::import_pose::options::RNA_DeNovoProtocolOptions , core::import_pose::options::RNA_FragmentMonteCarloOptions , core::import_pose::options::RNA_MinimizerOptions , core::io::raw_data::DisulfideFile::ResNum , core::io::StructFileReaderOptions , core::io::StructFileRepOptions , core::optimization::DOF_Node , core::pack::dunbrack::DunbrackConstraint , core::pack::dunbrack::RotamerConstraint , core::pose::rna::RNA_Reactivity , core::scoring::constraints::AmbiguousConstraint , core::scoring::constraints::AmbiguousNMRConstraint , core::scoring::constraints::AmbiguousNMRDistanceConstraint , core::scoring::constraints::AngleConstraint , core::scoring::constraints::AtomPairConstraint , core::scoring::constraints::BackboneStubConstraint , core::scoring::constraints::BackboneStubLinearConstraint , core::scoring::constraints::BasePairConstraint , core::scoring::constraints::BigBinConstraint , core::scoring::constraints::BoundFunc , core::scoring::constraints::ConstantConstraint , core::scoring::constraints::Constraint , core::scoring::constraints::CoordinateConstraint , core::scoring::constraints::DihedralConstraint , core::scoring::constraints::DihedralPairConstraint , core::scoring::constraints::DistancePairConstraint , core::scoring::constraints::FabConstraint , core::scoring::constraints::KofNConstraint , core::scoring::constraints::LocalCoordinateConstraint , core::scoring::constraints::MultiConstraint , core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint , core::scoring::constraints::NamedDihedralConstraint , core::scoring::constraints::RTConstraint , core::scoring::constraints::SequenceProfileConstraint , core::scoring::constraints::SiteConstraint , core::scoring::constraints::SiteConstraintResidues , core::scoring::DC , core::scoring::motif::MotifHash , core::scoring::motif::ResPairMotif , core::scoring::MultipoleElecResidueInfo , core::scoring::nmr::NMRDummySpinlabelAtom , core::scoring::nmr::VoxelGridPoint , core::scoring::nmr::VoxelGridPoint_AA , core::scoring::packstat::SimplePDB_Atom , core::scoring::RDC , core::scoring::RDC_Rohl , core::scoring::rna::RNA_Motif , core::scoring::sc::_DOT , core::select::residue_selector::SSElementSelector::SSElement , core::sequence::CompositeSequence , core::sequence::ScoringScheme , core::sequence::Sequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::canonical_sampling::TorsionSpec , protocols::checkpoint::CheckPointer , protocols::comparative_modeling::features::ResidueFeature , protocols::comparative_modeling::features::SSFeature , protocols::comparative_modeling::features::TorsionFeature , protocols::constraints_additional::AmbiguousMultiConstraint , protocols::constraints_additional::BindingSiteConstraint , protocols::constraints_additional::COMCoordinateConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::DeNovoArchitect , protocols::denovo_design::architects::DeNovoMotifArchitect , protocols::denovo_design::architects::HelixArchitect , protocols::denovo_design::architects::PoseArchitect , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::architects::StructureArchitect , protocols::denovo_design::components::HelixPairing , protocols::denovo_design::components::HelixSheetPairing , protocols::denovo_design::components::PoseFolder , protocols::denovo_design::components::SegmentCounts , protocols::denovo_design::components::SegmentPairing , protocols::denovo_design::components::StrandPairing , protocols::denovo_design::connection::ConnectionArchitect , protocols::dna::PositionType , protocols::dna::Reversion , protocols::electron_density::DensitySymmInfo , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::environment::claims::DOFElement , protocols::environment::claims::EnvClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::JumpElement , protocols::environment::claims::ResidueElement , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::fldsgn::topology::Loop , protocols::frag_picker::Contact , protocols::kinmatch::KRSQuery , protocols::ligand_docking::ligand_options::InterfaceInfo
• Type : protocols::ligand_docking::ligand_options::InterfaceInfo
• type : protocols::md::MDscheduleData , protocols::mean_field::GenMeanFieldMover , protocols::moves::Mover , protocols::multistate_design::PosType , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::pockets::PocketConstraint , protocols::pose_creation::SliceToMiniProteinMover::SSElement , protocols::protein_interface_design::movers::VLBInstruction , protocols::rbsegment_relax::RBResidueRange , protocols::recces::options::RECCES_Options , protocols::recces::sampler::MC_Any , protocols::recces::sampler::MC_Comb , protocols::recces::sampler::MC_Loop , protocols::recces::sampler::MC_OneTorsion , protocols::recces::sampler::rna::MC_RNA_KIC_Sampler , protocols::recces::sampler::rna::MC_RNA_MultiSuite , protocols::recces::sampler::rna::MC_RNA_OneJump , protocols::recces::sampler::rna::MC_RNA_Sugar , protocols::recces::sampler::rna::MC_RNA_Suite , protocols::sic_dock::CBScore , protocols::sic_dock::ConstraintSetScore , protocols::sic_dock::JointScore , protocols::sic_dock::LinkerScore , protocols::sic_dock::RigidScore , protocols::sic_dock::scores::MotifHashRigidScore , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_moves::FragmentCost , protocols::stepwise::legacy::screener::ProteinAtrRepScreener , protocols::stepwise::legacy::screener::RNA_AtrRepScreener , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb , protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler , protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler , protocols::stepwise::sampler::jump::JumpStepWiseSampler , protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler , protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler , protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives , protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_KinematicCloser , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneDOF , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerRingConformer , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , protocols::stepwise::screener::AlignRMSD_Screener , protocols::stepwise::screener::AnchorSugarScreener , protocols::stepwise::screener::BaseBinMapUpdater , protocols::stepwise::screener::BaseCentroidScreener , protocols::stepwise::screener::BulgeApplier , protocols::stepwise::screener::CentroidDistanceScreener , protocols::stepwise::screener::FastForwardToNextResidueAlternative , protocols::stepwise::screener::FastForwardToNextRigidBody , protocols::stepwise::screener::IntegrationTestBreaker , protocols::stepwise::screener::O2PrimeScreener , protocols::stepwise::screener::PackScreener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PhosphateScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::ProteinCCD_ClosureScreener , protocols::stepwise::screener::ResidueContactScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryScreener , protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener , protocols::stepwise::screener::RNA_ChainClosureScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::StepWiseResiduePairScreener , protocols::stepwise::screener::StepWiseScreener , protocols::stepwise::screener::StubApplier , protocols::stepwise::screener::StubDistanceScreener , protocols::stepwise::screener::SugarInstantiator , protocols::stepwise::screener::TagDefinition , protocols::stepwise::screener::VDW_BinScreener , protocols::toolbox::SamplerPlusPlus , protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::ClaimerMessage , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::CutBiasClaimer , protocols::topology_broker::DensityScoringClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::LoopFragmentClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::MetalloClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::StartStructClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• type1() : core::scoring::motif::MotifHash , core::scoring::motif::ResPairMotif
• type1_id_ : core::scoring::constraints::NamedAngleConstraint , core::scoring::constraints::NamedAtomPairConstraint
• type2() : core::scoring::motif::MotifHash , core::scoring::motif::ResPairMotif
• 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::pose::rna::RNA_Reactivity , 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::RNA_Motif , core::sequence::Cell , core::sequence::ScoringScheme , protocols::calc_taskop_filters::RotamerBoltzmannWeight , protocols::checkpoint::CheckPointer , protocols::denovo_design::components::PoseFolder , protocols::dna::DesignProteinBackboneAroundDNA , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::topology::Loop , protocols::frag_picker::Contact , protocols::hybridization::detailedControlsTagSetting , protocols::jd3::deallocation::DeallocationMessage , protocols::mean_field::GenMeanFieldMover , protocols::moves::Mover , protocols::moves::PyMOLObserver , protocols::multistate_design::PosType , protocols::network::UIObserver , protocols::qsar::qsarPoint , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::sewing::data_storage::SmartSewingResidue , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::SimpleMetricFilter , protocols::simple_moves::FragmentCost
• type_for_fake_atoms() : core::chemical::gasteiger::GasteigerAtomTypeSet
• type_for_residuetype() : core::pack::rotamers::SingleResidueRotamerLibraryFactory
• type_info_map_ : core::scoring::FACTSRsdTypeMap
• type_list_ : protocols::toolbox::KClusterElement
• type_lookup_ : core::scoring::MultipoleElecPotential , core::scoring::VdWTinkerPotential
• type_map_ : core::scoring::packstat::AtomRadiusMap , protocols::qsar::qsarMap
• type_name() : protocols::abinitio::TemplateJumpSetup , protocols::antibody::AntibodyFeatures , protocols::antibody::AntibodyFeaturesCreator , protocols::antibody::clusters::CDRClusterFeatures , protocols::antibody::clusters::CDRClusterFeaturesCreator , protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator , protocols::constraints_additional::CombinedConstraintEvaluatorCreator , protocols::constraints_additional::ConstraintEvaluatorCreator , protocols::evaluation::EvaluatorCreator , protocols::features::AtomAtomPairFeatures , protocols::features::AtomAtomPairFeaturesCreator , protocols::features::AtomInResidueAtomInResiduePairFeatures , protocols::features::AtomInResidueAtomInResiduePairFeaturesCreator , protocols::features::AtomTypesFeatures , protocols::features::AtomTypesFeaturesCreator , protocols::features::BatchFeatures , protocols::features::BetaTurnDetection , protocols::features::BetaTurnDetectionFeatures , protocols::features::BetaTurnDetectionFeaturesCreator , protocols::features::ChargeChargeFeatures , protocols::features::ChargeChargeFeaturesCreator , protocols::features::DdGFeatures , protocols::features::DdGFeaturesCreator , protocols::features::FeaturesReporter , protocols::features::FeaturesReporterCreator , protocols::features::GeometricSolvationFeatures , protocols::features::GeometricSolvationFeaturesCreator , protocols::features::HBondFeatures , protocols::features::HBondFeaturesCreator , protocols::features::HBondParameterFeatures , protocols::features::HBondParameterFeaturesCreator , protocols::features::helixAssembly::ConcurrencyTest , protocols::features::helixAssembly::ConcurrencyTestCreator , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::helixAssembly::HelixBundleFeaturesCreator , protocols::features::HelixCapFeatures , protocols::features::HelixCapFeaturesCreator , protocols::features::InterfaceFeatures , protocols::features::InterfaceFeaturesCreator , protocols::features::JobDataFeatures , protocols::features::JobDataFeaturesCreator , protocols::features::LoopAnchorFeatures , protocols::features::LoopAnchorFeaturesCreator , protocols::features::ModelFeatures , protocols::features::ModelFeaturesCreator , protocols::features::OrbitalsFeatures , protocols::features::OrbitalsFeaturesCreator , protocols::features::PairFeatures , protocols::features::PairFeaturesCreator , protocols::features::PdbDataFeatures , protocols::features::PdbDataFeaturesCreator , protocols::features::PoseCommentsFeatures , protocols::features::PoseCommentsFeaturesCreator , protocols::features::PoseConformationFeatures , protocols::features::PoseConformationFeaturesCreator , protocols::features::ProteinBackboneAtomAtomPairFeatures , protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator , protocols::features::ProteinBackboneTorsionAngleFeatures , protocols::features::ProteinBackboneTorsionAngleFeaturesCreator , protocols::features::ProteinBondGeometryFeatures , protocols::features::ProteinBondGeometryFeaturesCreator , protocols::features::ProteinResidueConformationFeatures , protocols::features::ProteinResidueConformationFeaturesCreator , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDFeaturesCreator , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator , protocols::features::ProtocolFeatures , protocols::features::RadiusOfGyrationFeatures , protocols::features::RadiusOfGyrationFeaturesCreator , protocols::features::ResidueBurialFeatures , protocols::features::ResidueBurialFeaturesCreator , protocols::features::ResidueConformationFeatures , protocols::features::ResidueConformationFeaturesCreator , protocols::features::ResidueFeatures , protocols::features::ResidueFeaturesCreator , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueGridScoresFeaturesCreator , protocols::features::ResidueScoresFeatures , protocols::features::ResidueScoresFeaturesCreator , protocols::features::ResidueSecondaryStructureFeatures , protocols::features::ResidueSecondaryStructureFeaturesCreator , protocols::features::ResidueTotalScoresFeatures , protocols::features::ResidueTotalScoresFeaturesCreator , protocols::features::ResidueTypesFeatures , protocols::features::ResidueTypesFeaturesCreator , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerBoltzmannWeightFeaturesCreator , protocols::features::RotamerFeatures , protocols::features::RotamerFeaturesCreator , protocols::features::RotamerRecoveryFeatures , protocols::features::RotamerRecoveryFeaturesCreator , protocols::features::RuntimeFeatures , protocols::features::RuntimeFeaturesCreator , protocols::features::SaltBridgeFeatures , protocols::features::SaltBridgeFeaturesCreator , protocols::features::ScoreFunctionFeatures , protocols::features::ScoreFunctionFeaturesCreator , protocols::features::ScoreTypeFeatures , protocols::features::ScoreTypeFeaturesCreator , protocols::features::ScreeningFeatures , protocols::features::ScreeningFeaturesCreator , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SecondaryStructureSegmentFeaturesCreator , protocols::features::SimpleMetricFeatures , protocols::features::SimpleMetricFeaturesCreator , protocols::features::SmotifFeatures , protocols::features::SmotifFeaturesCreator , protocols::features::strand_assembly::SandwichFeatures , protocols::features::strand_assembly::SandwichFeaturesCreator , protocols::features::strand_assembly::StrandBundleFeatures , protocols::features::strand_assembly::StrandBundleFeaturesCreator , protocols::features::StructureFeatures , protocols::features::StructureFeaturesCreator , protocols::features::StructureScoresFeatures , protocols::features::StructureScoresFeaturesCreator , protocols::features::TaskOperationFeatures , protocols::features::TaskOperationFeaturesCreator , protocols::features::TotalScoreFeatures , protocols::features::TotalScoreFeaturesCreator , protocols::features::TrajectoryMapFeatures , protocols::features::TrajectoryMapFeaturesCreator , protocols::features::UnrecognizedAtomFeatures , protocols::features::UnrecognizedAtomFeaturesCreator , protocols::features::WaterFeatures , protocols::features::WaterFeaturesCreator , protocols::frag_picker::Contact , protocols::jumping::BaseJumpSetup , protocols::jumping::JumpSelector , protocols::jumping::JumpSetup , protocols::jumping::RandomSheetBuilder , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SheetBuilder , protocols::legacy_sewing::sampling::requirements::LegacyGlobalLengthRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyGlobalRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyIntraSegmentRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacyResidueRetentionRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentDsspRequirementCreator , protocols::legacy_sewing::sampling::requirements::LegacySegmentLengthRequirementCreator , protocols::ligand_docking::rdf::RDFBinaryHbondCreator , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunctionCreator , protocols::ligand_docking::rdf::RDFChargeCreator , protocols::ligand_docking::rdf::RDFElecCreator , protocols::ligand_docking::rdf::RDFEtableCreator , protocols::ligand_docking::rdf::RDFFunctionCreator , protocols::ligand_docking::rdf::RDFHbondCreator , protocols::ligand_docking::rdf::RDFOrbitalFunctionCreator , protocols::loops::loops_definers::LoopsDatabaseDefinerCreator , protocols::loops::loops_definers::LoopsDefinerCreator , protocols::loops::loops_definers::LoopsExplicitDefinerCreator , protocols::loops::loops_definers::LoopsFileDefinerCreator , protocols::loops::loops_definers::LoopsStringDefinerCreator , protocols::rotamer_recovery::RRComparerAutomorphicRMSDCreator , protocols::rotamer_recovery::RRComparerChiDiffCreator , protocols::rotamer_recovery::RRComparerCreator , protocols::rotamer_recovery::RRComparerElecDensDiffCreator , protocols::rotamer_recovery::RRComparerRotBinsCreator , protocols::rotamer_recovery::RRProtocolCreator , protocols::rotamer_recovery::RRProtocolMinPackCreator , protocols::rotamer_recovery::RRProtocolMoverCreator , protocols::rotamer_recovery::RRProtocolPackRotamersCreator , protocols::rotamer_recovery::RRProtocolReferenceStructureCreator , protocols::rotamer_recovery::RRProtocolRelaxCreator , protocols::rotamer_recovery::RRProtocolRotamerTrialsCreator , protocols::rotamer_recovery::RRProtocolRTMinCreator , protocols::rotamer_recovery::RRReporterCreator , protocols::rotamer_recovery::RRReporterHumanCreator , protocols::rotamer_recovery::RRReporterSimpleCreator , protocols::rotamer_recovery::RRReporterSQLiteCreator , protocols::sewing::requirements::ClashRequirement , protocols::sewing::requirements::DsspSpecificLengthRequirement , protocols::sewing::requirements::KeepLigandContactsRequirement , protocols::sewing::requirements::LengthInResiduesRequirement , protocols::sewing::requirements::LigandClashRequirement , protocols::sewing::requirements::NonTerminalStartingSegmentRequirement , protocols::sewing::requirements::SizeInSegmentsRequirement , protocols::sewing::scoring::InterModelMotifScorer , protocols::sewing::scoring::IntraDesignTerminusMotifScorer , protocols::sewing::scoring::LigandScorer , protocols::sewing::scoring::MotifScorer , protocols::sewing::scoring::PartnerMotifScorer , protocols::sewing::scoring::SegmentContactOrderScorer , protocols::sewing::scoring::StartingNodeMotifScorer , protocols::sewing::scoring::SubsetPartnerMotifScorer , protocols::sewing::scoring::TerminusMotifScorer , protocols::sewing::scoring::TopNMotifScorer , protocols::simple_filters::CamShiftEvaluatorCreator , protocols::simple_filters::ChiWellRmsdEvaluatorCreator , protocols::simple_filters::ContactMapEvaluatorCreator , protocols::simple_filters::ExtraScoreEvaluatorCreator , protocols::simple_filters::JScoreEvaluatorCreator , protocols::simple_filters::JumpNrEvaluatorCreator , protocols::simple_filters::NativeEvaluatorCreator , protocols::simple_filters::PalesEvaluatorCreator , protocols::simple_filters::PoolEvaluatorCreator , protocols::simple_filters::PredictedBurialFnEvaluatorCreator , protocols::simple_filters::RdcEvaluatorCreator , protocols::simple_filters::RdcSelectEvaluatorCreator , protocols::simple_filters::RdcTargetEvaluatorCreator , protocols::simple_filters::RmsdEvaluatorCreator , protocols::simple_filters::RmsdTargetEvaluatorCreator , protocols::simple_filters::StructureSimilarityEvaluatorCreator , protocols::sparta::ChemicalShiftEvaluatorCreator , protocols::topology_broker::ConstraintEvaluatorWrapperCreator
• type_of_computation : core::scoring::data_struct
• type_ptr() : core::conformation::Residue
• type_set_name_ : protocols::simple_filters::JScoreEvaluator
• type_set_tag() : protocols::simple_moves::SwitchResidueTypeSetMover
• type_set_tag_ : protocols::simple_moves::SwitchResidueTypeSetMover
• type_to_str() : protocols::denovo_design::components::SegmentPairing
• TypeCumulator : protocols::noesy_assign::PeakCalibrator
• TypeDifference : core::chemical::gasteiger::GasteigerAtomTypeData
• types() : core::chemical::Metapatch , core::chemical::Patch
• types_ : core::chemical::Metapatch , core::chemical::Patch , protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory
• types_to_avoid() : protocols::aa_composition::AddHelixSequenceConstraintsMover
• types_to_avoid_ : protocols::aa_composition::AddHelixSequenceConstraintsMover
• typGrid_ : protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::NonPlaidFingerprint
• tyr_hydroxyls_must_donate_ : protocols::hbnet::HBNet
• tZ_ : core::grid::CartGrid< T >