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

- t -

• t : protocols::hybridization::TMalign
• T_ : protocols::toolbox::InteratomicVarianceMatrix
• t_ang_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::legacy::modeler::rna::RNA_AnalyticLoopCloser , protocols::stepwise::sampler::rna::RNA_KinematicCloser
• 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
• TAB_DIR : protocols::sparta::Sparta::SpartaLib
• taboo_map_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• taboo_map_max_capacity_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• taboo_master_map_ : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• TabooSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber
• tag() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::AlignEvaluator
• Tag : protocols::filters::FilterFactory
• tag() : protocols::grafting::AnchoredGraftMover
• Tag : protocols::jd2::parser::FragmentReader , protocols::moves::MoverFactory
• tag() : protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::SingleStructureData
• Tag : protocols::protein_interface_design::DockDesignFilterFactory
• tag : protocols::qsar::qsarOptData
• Tag : protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory
• tag() : protocols::stepwise::screener::TagDefinition , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer
• tag_ : protocols::comparative_modeling::Align_RotamerEvaluator , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::evaluation::AlignEvaluator , protocols::grafting::AnchoredGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::SingleStructureData , protocols::pockets::PocketGrid , protocols::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::StepWiseRNA_VirtualSugarSampler , protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::screener::TagDefinition , protocols::toolbox::match_enzdes_util::GeomSampleInfo , protocols::topology_broker::ConstraintClaimer
• tag_activity_selection_ : protocols::qsar::qsarOptFunc
• tag_along_chains : protocols::ligand_docking::Rotate_info
• tag_along_jumps : protocols::ligand_docking::Rotate_info
• tag_along_jumps_ : protocols::ligand_docking::Translate
• tag_along_residues : protocols::ligand_docking::Ligand_info , protocols::ligand_docking::Rotate_info
• tag_definition_ : protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::screener::AnchorSugarScreener
• tag_format_string() : protocols::outputter::SilentFileOutputter
• tag_format_string_ : protocols::outputter::SilentFileOutputter
• TAG_IN_FILE : protocols::jd2::archive::ArchiveBase
• tag_is_done_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol , protocols::farna::RNA_DeNovoProtocol , protocols::stepwise::setup::StepWiseMonteCarloJobDistributor
• tag_list : protocols::cluster::GatherPosesMover
• tag_map_ : protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug
• tag_name_ : protocols::matdes::SchemePlaceMotifsMover
• tag_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• tag_prefix_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• tag_residues_ : protocols::features::DatabaseJobInputter
• tag_structures_ : protocols::features::DatabaseJobInputter
• tag_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 : protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfacePacker , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , 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::jd2::parser::FragmentReader , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::moves::DsspMover , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::protein_interface_design::DockDesignFilterFactory , protocols::qsar::scoring_grid::GridFactory , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• TagCOPs : protocols::rosetta_scripts::RosettaScriptsParser
• TagDefinition() : protocols::stepwise::screener::TagDefinition
• TagList : protocols::toolbox::KClusterData
• TagPoseWithRefinementStatsMover() : protocols::cryst::TagPoseWithRefinementStatsMover
• TagPtr : protocols::indexed_structure_store::filters::FragmentLookupFilter
• Tags : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• tags() : protocols::moves::TrialCounter
• tags_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::frag_picker::quota::QuotaSelector , protocols::frag_picker::QuotaDebug , protocols::inputter::SilentFileInputter , protocols::toolbox::KClusterData
• tail() : protocols::protein_interface_design::movers::LoopLengthChange
• tail_residue_name() : protocols::helical_bundle::MakeBundleHelix
• tail_residue_name_ : protocols::helical_bundle::MakeBundleHelix
• tail_segment_ : protocols::protein_interface_design::movers::LoopLengthChange
• tailresidues_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• TailsScoreMover() : protocols::simple_moves::TailsScoreMover
• take_coordinates_from_pose() : protocols::fldsgn::topology::BB_Pos
• take_out_cutpoints() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• 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::cryst::SetRefinementOptionsMover , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::noesy_assign::PeakCalibrator , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::simple_moves::MutateResidue
• target_accept_ratio() : protocols::abinitio::IterativeBase
• target_accept_ratio_ : protocols::abinitio::IterativeBase
• target_Ashifts_ : protocols::frag_picker::scores::AmbigCSScore
• target_Bshifts_ : protocols::frag_picker::scores::AmbigCSScore
• target_ca_dev_ : protocols::frag_picker::scores::PCS_FragDistance
• target_ca_dist_ : protocols::frag_picker::scores::PCS_FragDistance
• target_chain() : protocols::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_conformer() : protocols::motifs::MotifHit
• target_conformer_ : protocols::motifs::MotifHit
• target_conformers_map() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_conformers_map_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• target_distance_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover
• target_downstream_coords_ : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• target_downstream_res() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_downstream_res_ : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• target_end_ : protocols::simple_moves::SuperimposeMover
• target_geomcst_coords_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_geomcst_id_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_end_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_for_focused_build_point_begin_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_hits_for_focused_build_point_end_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_jump_ : protocols::rigid::UniformRigidBodyMover
• target_lookup_ : protocols::indexed_structure_store::filters::FragmentLookupFilter
• 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_residue_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::hotspot_hashing::movers::PlaceProbeMover , protocols::simple_filters::NeighborTypeFilter
• target_residues() : protocols::enzdes::PackRotamersMoverPartGreedy
• target_residues_ : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::DesignRepackMover
• target_resnum_ : protocols::hotspot_hashing::HotspotStubSet , protocols::protein_interface_design::movers::HotspotHasherMover
• target_restype_index_map_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• target_restypes_ : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::TargetRotamerCoords
• target_seqpos_ : protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers
• target_sequence() : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::ThreadSequenceOperation
• target_sequence_ : protocols::abinitio::IterativeBase , protocols::abinitio::Templates , protocols::hybridization::FoldTreeHybridize , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::ThreadSequenceOperation
• target_shifts_ : protocols::frag_picker::scores::CSScore
• target_sign_ : protocols::noesy_assign::PeakCalibrator
• target_start_ : protocols::simple_moves::SuperimposeMover
• target_stub : protocols::hotspot_hashing::ConstPattern
• target_total_residue() : protocols::abinitio::Templates
• target_values_ : protocols::noesy_assign::PeakCalibrator
• targeted_dna() : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface
• targeted_dna_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::motifs::MotifDnaPacker
• 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() : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelWorkingSet , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• task1_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• task2_ : protocols::toolbox::task_operations::StoreCombinedStoredTasksMover
• task_ : protocols::docking::SidechainMinMover , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flexpack::FlexPacker , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::hybridization::HybridizeProtocol , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::RandomMutation , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::PackerNeighborGraphFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::symmetric_docking::SymSidechainMinMover
• task_begin() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• task_clear() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• task_end() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• task_factory() : protocols::backrub::BackrubSidechainMover , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::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::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::seeded_abinitio::SeedSetupMover , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol
• task_factory_ : protocols::anchored_design::AnchorMoversData , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::features::ReportToDB , protocols::features::RotamerRecoveryFeatures , protocols::floppy_tail::FloppyTailMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::matdes::ClashCheckFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::optimize_weights::IterativeOptEDriver , protocols::outputter::ResFileOutputter , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::relax::RelaxProtocolBase , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::RotamerDump::RotamerDumpMover , protocols::seeded_abinitio::SeedSetupMover , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DdGScan , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::toolbox::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_invalidated_ : protocols::simple_filters::PackerNeighborGraphFilter
• task_is_valid() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover
• task_iterator : protocols::toolbox::task_operations::StoreCompoundTaskMover
• task_layers_ : protocols::flxbb::LayerDesignOperation
• task_name() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• task_name_ : protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover
• task_op_ : protocols::match::TaskOperationMPM
• task_operations_ : protocols::flxbb::CombinedTaskOperation , protocols::flxbb::DesignTask , protocols::flxbb::FlxbbDesign
• task_scaling() : protocols::simple_moves::GenericMonteCarloMover
• task_scaling_ : protocols::simple_moves::GenericMonteCarloMover
• task_segments_ : protocols::relax::AtomCoordinateCstMover
• TaskAwareCsts() : protocols::protein_interface_design::movers::TaskAwareCsts
• TaskAwareMinMover() : protocols::simple_moves::TaskAwareMinMover
• TaskAwareSASAFilter() : protocols::simple_filters::TaskAwareSASAFilter
• TaskAwareScoreTypeFilter() : protocols::simple_filters::TaskAwareScoreTypeFilter
• TaskAwareSymMinMover() : protocols::simple_moves::symmetry::TaskAwareSymMinMover
• TaskFactory : protocols::simple_moves::GreenPacker
• taskfactory_ : protocols::simple_filters::TotalSasaFilter
• TaskFactoryCOP : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• TaskFactoryOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker
• TaskLayer : protocols::flxbb::LayerDesignOperation
• TaskLayers : protocols::flxbb::LayerDesignOperation
• Taskop_id_name_factory_() : protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• TaskOperation : protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::SeqprofConsensusOperation
• TaskOperationFeatures() : protocols::features::TaskOperationFeatures
• TaskOperationFeaturesCreator() : protocols::features::TaskOperationFeaturesCreator
• TaskOperationLoader() : protocols::jd2::parser::TaskOperationLoader
• TaskOperationMPM() : protocols::match::TaskOperationMPM
• TaskOperationOP : 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::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::SeqprofConsensusOperation
• taskops_ : protocols::features::TaskOperationFeatures
• tasks_ : protocols::toolbox::task_operations::STMStoredTask
• tau_ : protocols::md::Thermostat , protocols::normalmode::NormalMode
• tear_down() : protocols::nonlocal::StarTreeBuilder , protocols::nonlocal::TreeBuilder
• tear_down_kinematics() : protocols::star::StarAbinitio
• tell_vlb_to_not_touch_fold_tree_ : protocols::fldsgn::BluePrintBDR
• temp() : protocols::multistate_design::PartitionAggregateFunction< T > , protocols::simple_moves::TorsionDOFMover
• temp0() : protocols::md::MDBase , protocols::md::MDscheduleData
• temp0_ : protocols::md::MDBase , protocols::md::Thermostat
• temp_ : protocols::hybridization::CartesianSampler , protocols::multistate_design::PartitionAggregateFunction< T > , protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::TorsionDOFMover
• temp_coord_for_evaluation_ : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• temp_coords_ : protocols::canonical_sampling::mc_convergence_checks::DataBuffer
• temp_cycles_ : protocols::loop_modeling::LoopProtocol
• temp_energies : protocols::vip::VIP_Mover
• temp_file() : protocols::jobdist::BaseJobDistributor , protocols::jobdist::PlainPdbJobDistributor
• temp_final() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_final_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_id() : protocols::moves::SimulatedTempering
• temp_id_ : protocols::moves::SimulatedTempering
• temp_initial() : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_initial_ : protocols::dna::DesignProteinBackboneAroundDNA , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• temp_positions : protocols::vip::VIP_Mover
• temp_residues : protocols::vip::VIP_Mover
• temp_trial_count_ : protocols::canonical_sampling::TemperingBase
• temperature() : protocols::canonical_sampling::FixedTemperatureController , protocols::canonical_sampling::TemperatureController , protocols::canonical_sampling::TemperingBase , protocols::forge::remodel::RemodelLoopMover , protocols::ligand_docking::Transform_info , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::moves::MonteCarlo , protocols::moves::SimulatedTempering , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::BackboneMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator
• temperature0_ : protocols::simple_moves::sidechain_moves::SidechainMover
• temperature_ : protocols::abinitio::abscript::AbscriptStageMover , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• Temperature_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::H3PerturbCCD
• temperature_ : protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::CanonicalSamplingMover , protocols::canonical_sampling::FixedTemperatureController , protocols::docking::ConformerSwitchMover , protocols::docking::DockingHighResLegacy , protocols::docking::DockingLowRes , protocols::forge::remodel::RemodelLoopMover , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::ligand_docking::RigidSearchMover , protocols::loops::loop_closure::ccd::LoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::md::MDBase , protocols::moves::MonteCarlo , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::BackboneMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::ub_e2c::ubi_e2c_modeler
• temperature_jumps_ : protocols::canonical_sampling::SimulatedTempering
• temperature_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::simple_moves::GenericMonteCarloMover
• temperatures_ : protocols::canonical_sampling::TemperingBase , protocols::moves::SimulatedTempering , protocols::simple_moves::GenericMonteCarloMover
• TemperedDocking() : protocols::docking::TemperedDocking
• tempering() : protocols::canonical_sampling::MetropolisHastingsMover
• tempering_ : protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::MultiTemperatureTrialCounter , protocols::docking::TemperedDocking
• TemperingBase() : protocols::canonical_sampling::TemperingBase
• 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::HybridizeSetup
• template_chunks_ : protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_clusterID_ : protocols::hybridization::HybridizeProtocol
• template_contigs() : protocols::hybridization::HybridizeSetup
• template_contigs_ : protocols::hybridization::CartesianHybridize , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_core_chunk_indices_ : protocols::hybridization::HybridizeFoldtreeDynamic
• template_cst_fn() : protocols::hybridization::HybridizeSetup
• template_cst_fn_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_cst_reses_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_end_ : protocols::antibody_legacy::GraftOneMover
• template_file() : protocols::toolbox::task_operations::DatabaseThread
• template_file_ : protocols::toolbox::task_operations::DatabaseThread
• template_file_names() : protocols::hybridization::HybridizeSetup
• template_fn_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_id_ : protocols::hybridization::InsertChunkMover
• template_index() : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_index_ : protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover
• template_mini_pose_ : protocols::simple_moves::CopyDofMover
• template_name() : protocols::toolbox::task_operations::AlignedThreadOperation
• template_name_ : protocols::antibody_legacy::GraftOneMover , protocols::toolbox::task_operations::AlignedThreadOperation
• template_number() : protocols::hybridization::ChunkTrialMover
• template_number_ : protocols::hybridization::ChunkTrialMover
• template_pdb_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::SeedFoldTree
• template_pose() : protocols::comparative_modeling::ThreadingMover
• template_pose_ : protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::GraftOneMover , protocols::comparative_modeling::ExtraThreadingMover , protocols::comparative_modeling::ThreadingMover , protocols::hybridization::InsertChunkMover , protocols::simple_filters::SSMotifFinder , protocols::simple_moves::CopyDofMover , protocols::toolbox::task_operations::DatabaseThread
• template_poses() : protocols::hybridization::HybridizeSetup , protocols::jd2::InnerMultiThreadingJob
• template_poses_ : protocols::comparative_modeling::MultiThreadingMover , protocols::comparative_modeling::ThreadingJobInputter , protocols::hybridization::ChunkTrialMover , protocols::hybridization::FoldTreeHybridize , protocols::jd2::InnerMultiThreadingJob
• template_presence : protocols::seeded_abinitio::GrowPeptides
• template_presence_ : protocols::seeded_abinitio::CAcstGenerator
• template_res_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_res_cache_size() : protocols::toolbox::match_enzdes_util::EnzdesCstParamCache
• template_scores : protocols::cluster::GatherPosesMover
• template_size() : protocols::jumping::MembraneJump
• template_size_ : protocols::jumping::MembraneJump
• template_start_ : protocols::antibody_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_weights_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_weights_sum_ : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• template_wts() : protocols::hybridization::HybridizeSetup
• 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::hybridization::HybridizeSetup , protocols::jumping::MembraneJump , protocols::topology_broker::TemplateFragmentClaimer , protocols::topology_broker::TemplateJumpClaimer
• templates_poses_ : protocols::antibody::Ab_TemplateInfo
• templates_with_incorrect_strand_pairings_ : protocols::hybridization::FoldTreeHybridize
• temporary_file_name() : protocols::jd2::FileSystemJobDistributor
• 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
• terminal_pair() : protocols::topology_broker::SequenceNumberResolver
• terminal_res() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• terminal_res_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• terminate_ : protocols::wum::MPI_WorkUnitManager_Slave
• termination_broadcasted_ : protocols::mpi_refinement::MPI_Refine_Emperor
• terminus() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• terminus_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• TerminusDistanceFilter() : protocols::simple_filters::TerminusDistanceFilter
• test() : protocols::toolbox::DummyClass
• test_broker_settings() : protocols::abinitio::IterativeBase
• test_chunk() : protocols::frag_picker::AllowPdbIdFilter , protocols::frag_picker::DenyPdbIdFilter , protocols::frag_picker::VallChunkFilter
• test_control_mode() : protocols::grafting::AnchoredGraftMover
• test_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::ScoreMover , protocols::simple_moves::ShearMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::SmallMover
• 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
• testing_phase : protocols::simple_moves::ShakeStructureMover
• testmap_ : protocols::electron_density::ReportFSC
• testNeighbor() : protocols::pockets::CCluster , protocols::pockets::PCluster
• TestPattern() : protocols::hotspot_hashing::TestPattern
• 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
• TetherLigand() : protocols::ligand_docking::TetherLigand
• tetrahedral_constraints_ : protocols::metal_interface::AddZincSiteConstraints
• tf : protocols::features::TaskOperationFeatures::Taskop_id_name_factory_
• tf2() : protocols::docking::DockingHighRes
• tf2_ : protocols::docking::DockingHighRes
• tf_ : protocols::antibody::CDRsMinPackMin , protocols::antibody::design::AntibodyDesignModeler , protocols::antibody::design::AntibodyDesignMoverGenerator , protocols::antibody::GraftCDRLoopsProtocol , protocols::antibody::H3RefineCCD , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::antibody::ModelCDRH3 , protocols::antibody::RefineBetaBarrel , protocols::antibody::RefineOneCDRLoop , protocols::antibody_legacy::AntibodyModeler , protocols::antibody_legacy::CDRH3Modeler , protocols::antibody_legacy::LoopRlxMover , protocols::docking::DockingHighRes , protocols::docking::DockMCMCycle , protocols::loops::loop_mover::refine::LoopRefineInnerCycle , protocols::rbsegment_relax::AutoRBMover , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymSidechainMinMover , protocols::ub_e2c::ubi_e2c_modeler
• tgt_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgt_pos_ : protocols::constraints_additional::BindingSiteConstraint
• tgt_pos_centroid_ : protocols::constraints_additional::BindingSiteConstraint
• tgtD_ : protocols::simple_moves::symmetry::SetupNCSMover
• tgtE_ : protocols::simple_moves::symmetry::SetupNCSMover
• the_archive() : protocols::jd2::archive::BaseArchiveManager
• the_cdr_loop_ : protocols::antibody::RefineOneCDRLoopCentroid
• 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
• ThermodynamicMover() : protocols::canonical_sampling::ThermodynamicMover
• ThermodynamicObserver() : protocols::canonical_sampling::ThermodynamicObserver
• Thermostat() : protocols::md::Thermostat
• theta() : protocols::fldsgn::topology::DimerPairing , protocols::simple_moves::MinimalRotamer
• theta_ : protocols::fldsgn::topology::DimerPairing
• THETA_ : protocols::frag_picker::JCouplingIO , protocols::frag_picker::scores::JCoupling
• theta_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• theta_near_0_ : protocols::match::VoxelSetIterator
• theta_near_180_ : protocols::match::VoxelSetIterator
• thickness_ : protocols::membrane::visualize::VisualizeMembraneMover
• third_atom_ : protocols::frag_picker::scores::FourAtomsConstraintData
• third_offset_ : protocols::frag_picker::scores::FourAtomsConstraintData
• this_aa() : protocols::optimize_weights::PNatAAOptERotamerData
• this_aa_ : protocols::optimize_weights::PNatAAOptERotamerData
• this_batch_job_inputter_ : protocols::jd2::BatchJobInputter
• this_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• thread() : protocols::simple_filters::RelativePoseFilter
• thread_ : protocols::simple_filters::RelativePoseFilter
• thread_seq() : protocols::simple_filters::RelativePoseFilter
• ThreadingJob() : protocols::comparative_modeling::ThreadingJob
• ThreadingJobInputter() : protocols::comparative_modeling::ThreadingJobInputter
• ThreadingMover() : protocols::comparative_modeling::ThreadingMover
• ThreadSequenceOperation() : protocols::toolbox::task_operations::ThreadSequenceOperation
• threashold_ : protocols::filters::CompoundFilter
• three_prime_atom : protocols::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
• threshold() : protocols::filters::CalculatorFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::MatchResidues , protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::Operator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::viewer::triangleIterator
• threshold_ : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::dna::RotamerDNAHBondFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::RemoveLigandFilter , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::IfThenFilter , protocols::filters::ReplicateFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::MatchResidues , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::matdes::ClashCheckFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::Operator , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::MinMover , protocols::toolbox::KMedoid , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation
• threshold_probabilities_per_residue_ : protocols::simple_filters::RotamerBoltzmannWeight
• threshold_probability() : protocols::simple_filters::RotamerBoltzmannWeight
• tic_ : protocols::filters::TimeFilter
• tight_minimize() : protocols::farna::RNA_LoopCloser
• tightness() : protocols::simple_filters::DisulfideEntropyFilter
• tightness_ : protocols::simple_filters::DisulfideEntropyFilter
• tilt() : protocols::dna::DNABasestep
• tilt_ : protocols::dna::DNABasestep
• time_ : protocols::checkpoint::Timer
• time_for_temp_move() : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::TemperingBase
• time_minobj_ : protocols::md::MDBase
• time_to_checkpoint() : protocols::checkpoint::Timer
• 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
• titrate_stack_bonus_ : protocols::farna::RNA_DeNovoProtocol
• tlevel2rank_ : protocols::canonical_sampling::ParallelTempering
• Tlist_ : protocols::moves::ReplicaExchangeMC
• tmhelix_ : protocols::topology_broker::TMHTopologySamplerClaimer
• TMHTopologySamplerClaimer() : protocols::topology_broker::TMHTopologySamplerClaimer
• TMscore() : protocols::hybridization::TMalign
• TMscore8_search() : protocols::hybridization::TMalign
• to_all_atom() : protocols::docking::DockingProtocol
• to_all_atom_ : protocols::docking::DockingProtocol
• to_allatom() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• to_be_closed_cuts_ : protocols::topology_broker::TopologyBroker
• to_be_relaxed_ : protocols::loophash::MPI_LoopHashRefine_Master
• to_centroid() : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes , protocols::nonlocal::SingleFragmentMover
• to_centroid_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking , protocols::surface_docking::SurfaceDockingProtocol
• to_chain_ : protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::SwapSegment
• to_do() : protocols::jd2::Job
• to_entry() : protocols::protein_interface_design::PatchdockReader
• to_entry_ : protocols::protein_interface_design::PatchdockReader
• to_full_atom_ : protocols::surface_docking::SurfaceDockingProtocol
• to_res() : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• to_res_ : protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder
• to_string() : protocols::genetic_algorithm::Entity , protocols::genetic_algorithm::EntityElement , protocols::multistate_design::PosType
• 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
• tokenize_connected() : protocols::pockets::SmallMol
• tolerance() : protocols::branch_angle::BranchAngleOptimizer , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::noesy_assign::CrossPeak , protocols::noesy_assign::Resonance , protocols::simple_moves::MinMover , 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::moves::JumpOutMover , protocols::noesy_assign::PeakCalibrator , protocols::rotamer_recovery::RRComparerChiDiff , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_moves::symmetry::FaSymDockingSlideTogether , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• tolerate_off_range_atom_bin_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• tolerated_overlap() : protocols::match::output::MatchCollisionFilter
• tolerated_overlap_ : protocols::match::output::MatchCollisionFilter
• too_far() : protocols::constraints_additional::MaxSeqSepConstraintSet
• toolbox_ : protocols::loop_modeling::LoopMover
• top() : protocols::dna::DnaPosition , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• top_ : protocols::dna::DnaPosition
• top_count_of_all_inputs_ : protocols::features::TopPercentOfAllInputs
• top_count_of_each_input_ : protocols::features::TopPercentOfEachInput
• top_designs_ : protocols::antibody::design::AntibodyGraftDesignMover
• top_entities_ : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• 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_scores_ : protocols::antibody::design::AntibodyGraftDesignMover
• TopCountOfAllInputs() : protocols::features::TopCountOfAllInputs
• TopCountOfEachInput() : protocols::features::TopCountOfEachInput
• TopEntitySet() : protocols::pack_daemon::TopEntitySet
• TopNByProperty() : protocols::pose_selectors::TopNByProperty
• TOPO_RESAMPLING : protocols::abinitio::IterativeBase
• topol_score_ : protocols::abinitio::Template
• Topologies : protocols::abinitio::PairingStatistics
• topology() : protocols::abinitio::PairingStatistics
• topology_ : protocols::membrane::AddMembraneMover , protocols::membrane::TransformIntoMembraneMover
• topology_broker() : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• topology_broker_ : protocols::abinitio::AbrelaxMover , protocols::abinitio::FragmentSampler
• 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
• TopPercentOfAllInputs() : protocols::features::TopPercentOfAllInputs
• TopPercentOfEachInput() : protocols::features::TopPercentOfEachInput
• tor1 : protocols::normalmode::ContactStruct
• tor2 : protocols::normalmode::ContactStruct
• tor_U1D3() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U1D3_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U1D3_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U1D3_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U2D2_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U2D2_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U2D2_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U3D1_ : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• tor_U3D1_samples() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• tor_U3D1_samples_ : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• torID_ : protocols::normalmode::NormalMode
• torsion() : protocols::normalmode::NormalMode , protocols::protein_interface_design::filters::Torsion
• Torsion() : protocols::protein_interface_design::filters::Torsion
• torsion2big_bin() : protocols::comparative_modeling::features::TorsionFeature , protocols::rotamer_recovery::PerNativeRRReporterHuman , protocols::toolbox::pose_metric_calculators::RotamerRecovery
• torsion2big_bin_() : protocols::frag_picker::scores::LAMBEGO_Similarity , protocols::frag_picker::scores::TorsionBinSimilarity
• torsion_ : protocols::normalmode::NormalMode , protocols::protein_interface_design::filters::Torsion
• torsion_angles_ : protocols::kinematic_closure::ClosureSolution , protocols::kinematic_closure::perturbers::LogFilePerturber
• torsion_atoms_ : protocols::simple_moves::SetTorsion
• torsion_bin() : protocols::comparative_modeling::features::TorsionFeature
• torsion_bin_ : protocols::comparative_modeling::features::TorsionFeature
• 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_ : protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneTorsion
• torsion_id_list_ : protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover
• 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_ : protocols::canonical_sampling::MetricRecorder , protocols::simple_moves::TorsionSetMover , protocols::stepwise::sampler::rna::RNA_MC_Suite
• torsion_info_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler , protocols::stepwise::modeler::rna::phosphate::PhosphateMover , protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• torsion_name() : protocols::simple_moves::SetTorsion
• torsion_name_ : protocols::simple_moves::SetTorsion
• torsion_screen_ : protocols::stepwise::sampler::rna::RNA_KIC_Sampler
• torsion_source_name : protocols::farna::TorsionSet
• 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
• TorsionFragment() : protocols::frags::TorsionFragment
• TorsionFragmentLibrary() : protocols::frags::TorsionFragmentLibrary
• TorsionFragmentMover() : protocols::frags::TorsionFragmentMover
• TorsionList : protocols::stepwise::sampler::StepWiseSamplerBase
• TorsionNormalModeMover() : protocols::normalmode::TorsionNormalModeMover
• TorsionRestrictedKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• torsions() : protocols::farna::FullAtomRNA_Fragments , protocols::farna::TorsionSet
• torsions_ : protocols::frags::TorsionFragment
• torsions_monte_carlo() : protocols::flexpep_docking::FlexPepDockingAbInitio , protocols::flexpep_docking::FlexPepDockingLowRes
• torsions_monte_carlo_minimize() : protocols::flexpep_docking::FlexPepDockingProtocol
• torsions_using_ : protocols::normalmode::NormalMode
• torsions_using_assigned_ : protocols::normalmode::NormalMode
• TorsionSamplingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• TorsionSet() : protocols::farna::TorsionSet
• TorsionSetMover() : protocols::simple_moves::TorsionSetMover
• torsionsMCM : protocols::flexpep_docking::FlexPepDockingFlags
• TorsionSweepingKinematicPerturber() : protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• tot_rotamer_count : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• total_accepts() : protocols::jd2::archive::ArchiveBase
• total_accepts_ : protocols::jd2::archive::ArchiveBase
• total_assigned_distances_ : protocols::noesy_assign::DistanceScoreMover
• total_bin : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• total_cdr_loops_ : protocols::antibody::AntibodyInfo
• total_chain_break_score : protocols::forge::remodel::RemodelData
• total_charge_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_clashes_ : protocols::toolbox::pose_metric_calculators::ClashCountCalculator
• total_completed_nstruct_ : protocols::jd2::BOINCJobDistributor
• total_count : protocols::stepwise::modeler::rna::Filterer_Count
• total_count_ : protocols::canonical_sampling::SimulatedTempering
• total_embed() : protocols::membrane::geometry::Embedding
• total_embed_ : protocols::membrane::geometry::Embedding
• total_energy_alternate_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_alternate_state_assignment_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_current_state_assignment() : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_energy_current_state_assignment_ : protocols::flexpack::interaction_graph::FlexbbInteractionGraph
• total_frames_ : protocols::hybridization::WeightedFragmentSmoothTrialMover , protocols::hybridization::WeightedFragmentTrialMover
• total_goodfrags_ : protocols::toolbox::pose_metric_calculators::FragQualCalculator
• total_hb_E : protocols::analysis::InterfaceData
• total_hpatch_score_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• total_input_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• total_mc_trial_count : protocols::boinc::BoincSharedMemory
• total_metropolis_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_metropolis_accepts_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_mpi_wait_time_ : protocols::canonical_sampling::ParallelTempering
• total_neg_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_net_change_in_rama_score_over_range() : protocols::loops::loop_closure::ccd::RamaCheckBase
• total_nlcontacts_ : protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator
• total_nr_jobs() : protocols::jd2::JobDistributor
• total_num_slides_ : protocols::simple_moves::symmetry::SymmetrySlider
• total_packstat_ : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• total_partitions_ : protocols::hotspot_hashing::PartitionedSearchPattern
• total_permutations_ : protocols::antibody::design::AntibodyGraftDesignMover
• total_pos_charges_ : protocols::toolbox::pose_metric_calculators::ChargeCalculator
• total_positions_ : protocols::optimize_weights::IterativeOptEDriver
• TOTAL_PRECISION : protocols::frag_picker::scores::FragmentScoreManager
• total_proposed() : protocols::jd2::archive::ArchiveBase
• total_proposed_ : protocols::jd2::archive::ArchiveBase
• total_ref_resids_ : protocols::frag_picker::scores::FragmentAllAtomCrmsd
• total_res() : protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints
• total_residue() : protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::noesy_assign::PeakAssignmentResidueMap
• total_residue_ : protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::jd2::parser::BluePrint , protocols::jumping::JumpSample , protocols::jumping::JumpSetup , protocols::jumping::JumpsFromAllPairings , protocols::jumping::ResiduePairJumpSetup , protocols::jumping::SameStrand , protocols::jumping::SheetBuilder , protocols::optimize_weights::PNatStructureOptEData
• total_residue_wolig() : protocols::jd2::parser::BluePrint
• total_residue_wolig_ : protocols::jd2::parser::BluePrint
• total_rotamer_positions_ : protocols::optimize_weights::IterativeOptEDriver
• total_score() : protocols::frag_picker::FragmentPicker , protocols::frag_picker::scores::FragmentScoreManager , protocols::qsar::scoring_grid::GridManager
• total_score_ : protocols::analysis::LoopAnalyzerMover , protocols::simple_filters::ScoreCutoffFilter
• total_score_cutoff_ : protocols::match::downstream::ScoringSecMatchRPE
• total_score_of_last_considered_pose() : protocols::moves::MonteCarlo
• total_score_of_last_considered_pose_ : protocols::moves::MonteCarlo
• total_search_partition_ : protocols::hotspot_hashing::movers::PlaceProbeMover
• total_size() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• total_size_ : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool
• total_standard_cycles() : protocols::forge::remodel::RemodelLoopMover
• total_structures_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_structures_relax_ : protocols::loophash::MPI_LoopHashRefine , protocols::mpi_refinement::MPI_Refinement
• total_surface_energy_ : protocols::toolbox::pose_metric_calculators::SurfaceCalculator
• total_trials() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::moves::MonteCarlo , protocols::moves::TrialCounter
• total_trials_ : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• total_updates_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• total_updates_so_far_ : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• total_violation_count_ : protocols::noesy_assign::DistanceScoreMover
• total_weight_ : protocols::jumping::JumpSelector
• totalres_ : protocols::pockets::PocketConstraint
• TotalSasaFilter() : protocols::simple_filters::TotalSasaFilter
• TotalScoreFeatures() : protocols::features::TotalScoreFeatures
• 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
• 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
• 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() : protocols::analysis::PeptideDeriverBasicStreamOutputter , protocols::analysis::PeptideDeriverMarkdownStreamOutputter , protocols::analysis::PeptideDeriverOutputter , protocols::analysis::PeptideDeriverOutputterContainer , protocols::analysis::PeptideDeriverPoseOutputter
• tracer() : protocols::rpc::JSON_RPC
• tracer_ : protocols::analysis::InterfaceAnalyzerMover , protocols::analysis::LoopAnalyzerMover
• tracer_output_stream_ : protocols::rpc::JSON_RPC
• tracer_visible_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• traffic_total_received_ : protocols::wum::MPI_WorkUnitManager
• traffic_total_sent_ : protocols::wum::MPI_WorkUnitManager
• TraitEntityHashMap : protocols::genetic_algorithm::GeneticAlgorithmBase
• traits() : protocols::genetic_algorithm::Entity
• traits_ : protocols::genetic_algorithm::Entity
• traits_string() : protocols::genetic_algorithm::Entity
• trajectories_finished() : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectories_finished_ : protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• trajectory_idx() : protocols::wum2::WorkUnit
• trajectory_idx_ : protocols::wum2::WorkUnit
• trajectory_map_features_reporter_ : protocols::features::TrajectoryReportToDB
• Trajectory_state : protocols::viewer::GraphicsState
• trajectory_stream_ : protocols::canonical_sampling::PDBTrajectoryRecorder
• TrajectoryMapFeatures() : protocols::features::TrajectoryMapFeatures
• TrajectoryMapFeaturesCreator() : protocols::features::TrajectoryMapFeaturesCreator
• TrajectoryRecorder() : protocols::canonical_sampling::TrajectoryRecorder
• TrajectoryReportToDB() : protocols::features::TrajectoryReportToDB
• 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_mag_ : protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::LHSnugFitLegacy , protocols::farna::MultipleDomainMover , protocols::membrane::RandomPositionTranslationMover , protocols::rigid::MembraneCenterPerturbationMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• trans_mag_in_ : protocols::rigid::RigidBodyPerturbRandomJumpMover , protocols::topology_broker::RigidBodyRandomTMHMover
• trans_mag_smooth_ : protocols::symmetric_docking::SymFoldandDockRbTrialMover
• trans_magnitude() : protocols::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_thresh_ : protocols::simple_filters::SymmetricMotifFilter
• trans_wt_ : protocols::simple_filters::SymmetricMotifFilter
• transfer_buf_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• transfer_jumps() : protocols::jumping::JumpSample
• transfer_to_residue_vector() : protocols::loops::Loops
• TransferBuffer() : protocols::canonical_sampling::mc_convergence_checks::TransferBuffer
• transform() : protocols::hotspot_hashing::SearchPatternTransform , protocols::hybridization::TMalign
• Transform() : protocols::ligand_docking::Transform
• transform() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• Transform_info() : protocols::ligand_docking::Transform_info
• transform_info_ : protocols::ligand_docking::Transform
• transform_ligand() : protocols::ligand_docking::Transform
• transform_pose() : protocols::protein_interface_design::PatchdockReader
• transform_pose_into_membrane() : protocols::docking::membrane::MPDockingSetupMover
• transform_single_residue() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• transformed_residues : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives
• 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 , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• Translate() : protocols::ligand_docking::Translate
• translate_ : protocols::rigid::RollMover
• translate_Ang_ : protocols::ligand_docking::RigidSearchMover
• translate_by() : protocols::membrane::geometry::EmbeddingDef , protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• translate_by_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• translate_index : protocols::forge::remodel::RemodelWorkingSet
• Translate_info() : protocols::ligand_docking::Translate_info
• translate_info_ : protocols::ligand_docking::Translate
• translate_ligand() : protocols::ligand_docking::Transform , protocols::ligand_docking::Translate
• translate_virt_to_CoM() : protocols::hybridization::FoldTreeHybridize
• translateDSSP_ABEGO() : protocols::forge::remodel::RemodelData
• translates_ : protocols::ligand_docking::CompoundTranslate
• translation() : protocols::dna::SeparateDnaFromNonDna , protocols::ligand_docking::RigidSearchMover , protocols::protein_interface_design::Transformation , Transformation
• translation_ : protocols::dna::SeparateDnaFromNonDna
• translation_axes_ : protocols::matdes::SymDofMover
• translation_mag_ : protocols::rigid::UniformRigidBodyMover , protocols::topology_broker::TMHTopologySamplerClaimer
• translation_magnitude_ : protocols::simple_moves::CoupledMover
• translation_vector_ : protocols::membrane::TranslationMover
• TranslationMover() : protocols::membrane::TranslationMover
• TranslationRotationMover() : protocols::membrane::TranslationRotationMover
• translocation_sampling_ : protocols::hotspot_hashing::LSMSearchPattern
• transM : protocols::sparta::RingData
• transparent_facets_ : protocols::match::Bool3DGridKinemageWriter
• tree_ : protocols::rigid::RigidBodyMotionMover
• 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::simple_moves::GenericMonteCarloMover
• trial_counter_ : protocols::canonical_sampling::TemperingBase , protocols::moves::TrialCounter , protocols::simple_moves::GenericMonteCarloMover
• 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::hybridization::hConvergenceCheck , protocols::seeded_abinitio::CloseFold
• triangle() : protocols::viewer::triangle
• triangleIterator() : protocols::viewer::triangleIterator
• triangles_ : protocols::viewer::ConformationViewer
• tried_centroid_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tried_fullatom_pose_ : protocols::constraints_additional::ConstraintEvaluator
• tries() : protocols::simple_moves::TorsionDOFMover
• tries_ : protocols::seeded_abinitio::SegmentHybridizer , protocols::simple_moves::BackboneMover , protocols::simple_moves::TorsionDOFMover
• trigger_accept() : protocols::rbsegment_relax::SequenceShiftMover
• triggers_ : protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::rational_mc::RationalMonteCarlo
• trim() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trim_based_on_known_ligand() : protocols::pockets::NonPlaidFingerprint
• trim_cter() : protocols::ub_e2c::ubi_e2c_modeler
• trim_proportion_ : protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• trim_target_pose() : protocols::hybridization::MRMover
• tripFileName : protocols::sparta::Sparta::SpartaLib
• triplet_fingerprint_data() : protocols::pockets::FingerprintBase
• triplet_fingerprint_data_ : protocols::pockets::FingerprintBase
• TRIPLET_Tab : protocols::sparta::Sparta::SpartaLib
• TrisBpyScore() : protocols::sic_dock::scores::TrisBpyScore
• trj_ : protocols::md::MDBase
• trj_score_only_ : protocols::md::MDBase
• trj_scratch_ : protocols::md::MDBase
• true_behavior() : protocols::toolbox::task_operations::StoreCompoundTaskMover
• true_behavior_ : protocols::toolbox::task_operations::StoreCompoundTaskMover
• true_mover_ : protocols::moves::IfMover
• TrueFilter() : protocols::filters::TrueFilter
• truly_floating_base() : protocols::stepwise::modeler::StepWiseConnectionSampler
• truncate_only_ : protocols::electron_density::ScaleMapIntensities
• TruncatedScoreEvaluator() : protocols::simple_filters::TruncatedScoreEvaluator
• trust_current_temp_ : protocols::canonical_sampling::TemperingBase
• trust_fold_tree() : protocols::loop_modeling::LoopMover
• trust_fold_tree_ : protocols::loop_modeling::LoopMover
• try_for_more() : protocols::motifs::IRCollection
• try_point_mutants() : protocols::vip::VIP_Mover
• try_to_slide_into_contact() : protocols::farna::MultipleDomainMover
• TryRotamers() : protocols::protein_interface_design::movers::TryRotamers
• trywait_semaphore() : protocols::boinc::Boinc
• Tumble() : protocols::simple_moves::Tumble
• turn_expression_ASTs_into_expressions() : protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc
• turn_off_cter_insert() : protocols::antibody::ModelCDRH3
• turn_off_flank_relax() : protocols::antibody::H3RefineCCD
• turn_off_H3_filter() : protocols::antibody::H3PerturbCCD
• turn_off_h3_filter() : protocols::antibody::H3RefineCCD
• turn_off_H3_filter() : protocols::antibody::ModelCDRH3
• 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_on_benchmark() : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop
• turnoff_minimization_ : protocols::antibody::CDRsMinPackMin
• tVal : protocols::sparta::Sparta::SpartaLib
• TvecA : protocols::motif_grafting::movers::motif2scaffold_data
• TvecB : protocols::motif_grafting::movers::motif2scaffold_data
• twin_law_ : protocols::cryst::SetRefinementOptionsMover
• twist() : protocols::dna::DNABasestep
• twist_ : protocols::dna::DNABasestep , protocols::make_rot_lib::RotData
• 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::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twobody_energies_ : protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator
• twochains_ : protocols::seeded_abinitio::SeedFoldTree
• type() : 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::dna::PositionType , protocols::dna::Reversion , 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::loophash::LoopHashLibraryOptions , protocols::loops::LoopsFileOptions , protocols::md::MDscheduleData , protocols::membrane::io::LipoFileOptions , protocols::membrane::io::SpanFileOptions , 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::rbsegment_relax::RBResidueRange , 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_filters::RotamerBoltzmannWeight , 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::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::JumpStepWiseSampler , protocols::stepwise::sampler::MC_OneTorsion , protocols::stepwise::sampler::NoOpStepWiseSampler , 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_MC_MultiSuite , protocols::stepwise::sampler::rna::RNA_MC_Sugar , protocols::stepwise::sampler::rna::RNA_MC_Suite , protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler , protocols::stepwise::sampler::StepWiseSamplerAny , protocols::stepwise::sampler::StepWiseSamplerBase , protocols::stepwise::sampler::StepWiseSamplerComb , protocols::stepwise::sampler::StepWiseSamplerOneTorsion , protocols::stepwise::sampler::StepWiseSamplerOneValue , protocols::stepwise::sampler::StepWiseSamplerOneValueComb , protocols::stepwise::sampler::StepWiseSamplerSized , protocols::stepwise::sampler::StepWiseSamplerSizedAny , protocols::stepwise::sampler::StepWiseSamplerSizedComb , 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::NativeRMSD_Screener , 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::surface_docking::SurfaceVectorOptions , 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
• type_ : protocols::checkpoint::CheckPointer , protocols::dna::DesignProteinBackboneAroundDNA , protocols::filters::Filter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::topology::Loop , protocols::frag_picker::Contact , protocols::moves::Mover , protocols::multistate_design::PosType , protocols::qsar::qsarPoint , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_moves::FragmentCost
• type_list_ : protocols::toolbox::KClusterElement
• type_map_ : 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::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::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::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::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::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_set_name_ : protocols::simple_filters::JScoreEvaluator
• type_set_tag() : protocols::simple_moves::SwitchResidueTypeSetMover
• type_set_tag_ : protocols::simple_moves::SwitchResidueTypeSetMover
• TypeCumulator : protocols::noesy_assign::PeakCalibrator
• types_ : protocols::evaluation::EvaluatorFactory , protocols::features::FeaturesReporterFactory , protocols::ligand_docking::rdf::RDFFunctionFactory , protocols::loops::loops_definers::LoopsDefinerFactory
• typGrid_ : protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::NonPlaidFingerprint