- s -

• ScaffoldRotamerPair : protocols::match::output::UpstreamHitCacher
• ScaffoldRotamerTuple : protocols::match::output::UpstreamHitCacher
• ScoreConstIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoredFrag : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoredList : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreFunction : core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::TryRotamers , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::dna::PDBOutput , protocols::flxbb::FlxbbDesign , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::flxbb::InterlockAroma , protocols::fldsgn::BluePrintBDR , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , core::fragment::picking_old::vall::eval::EnergyEval , protocols::fldsgn::potentials::AACompositionEnergy , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , core::pack::interaction_graph::OnTheFlyInteractionGraph , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::Revert , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::MapHotspot
• ScoreFunctionCOP : protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FlxbbDesignPack , protocols::forge::remodel::RemodelAccumulator , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::Revert , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• ScoreFunctionFactory : protocols::forge::remodel::RemodelAccumulator
• ScoreFunctionInfo : core::scoring::Energies
• ScoreFunctionOP : protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Normal , protocols::flxbb::DesignTask_Layer , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::moves::MonteCarlo , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::protein_interface_design::Revert , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::RepackMinimize , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::enzdes::PackRotamersMoverPartGreedy
• ScoreIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoreList : core::fragment::CacheWrapper< T, XCacheUnit >
• Scores : core::fragment::picking_old::vall::VallLibrarian , protocols::sic_dock::RigidScore
• ScoreType : core::scoring::Energies , protocols::simple_moves::ddG
• ScoreTypes : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , protocols::simple_moves::GreenPacker
• ScoringSchemeTypes : core::sequence::ScoringSchemeFactory
• ScValue : core::scoring::sc::MolecularSurfaceCalculator
• Segment : core::pose::datacache::SpecialSegmentsObserver
• SeqposTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• SequenceCoupling : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCouplingCOP : protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCouplingOP : protocols::constraints_additional::SequenceCouplingConstraint
• SequenceCreatorMap : core::sequence::SequenceFactory
• SequenceLigPosMap : protocols::match::output::SameSequenceAndDSPositionGrouper
• SequenceMap : protocols::match::output::SameSequenceGrouper
• SequenceMapping : core::scoring::constraints::Obsolet_NamedAtomPairConstraint , core::scoring::constraints::SequenceProfileConstraint , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::forge::build::BuildManager
• SequenceMappingCOP : protocols::forge::build::BuildManager
• SequenceMappingOP : protocols::forge::build::BuildManager
• SequenceProfile : core::scoring::constraints::SequenceProfileConstraint
• SequenceProfileCOP : core::scoring::constraints::SequenceProfileConstraint
• SerializedLoopList : protocols::loops::Loops
• SheetSetCOP : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• SheetTopology : protocols::jumping::SheetBuilder
• SilentInfoList : protocols::simple_filters::EvaluatedTrialMover
• SilentStructCreatorMap : core::io::silent::SilentStructFactory
• SilentStructs : protocols::abinitio::HedgeArchive , protocols::jd2::archive::ArchiveBase
• SilentStructVector : protocols::abinitio::IterativeBase , protocols::jd2::archive::VarianceStatisticsArchive
• SingleConstraints : protocols::noesy_assign::DistanceScoreMover
• Size : protocols::match::output::ProcessorFactory , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::ResidueKinemageWriter , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::SampleStrategyData , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover , protocols::moves::ReplicaExchangeMC , protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::nonlocal::SingleFragmentMover , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::PNatAAOptERotamerData , core::conformation::ResidueKinWriter , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData , core::conformation::signals::IdentityEvent , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::OptEData , core::conformation::signals::LengthEvent , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::WrapperOptEMultifunc , core::fragment::IndependentBBTorsionSRFD , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFunc , core::fragment::picking_old::concepts::Book< Pages > , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::MultistateFitnessFunction , core::fragment::picking_old::concepts::Extent< PageIterator > , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::ReportSequenceDifferences , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , core::fragment::picking_old::concepts::Library< Books > , protocols::protein_interface_design::ReportPSSMDifferences , protocols::scoring::ResidualDipolarCouplingRigidSegments , core::fragment::picking_old::vall::gen::LengthGen , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , core::fragment::picking_old::vall::gen::SecStructGen , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ConsensusDesignMover , core::fragment::picking_old::vall::gen::VallFragmentGen , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::GenericMonteCarloMover , core::fragment::picking_old::vall::VallLibrarian , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::GroupDiscriminator , core::fragment::picking_old::vall::VallLibrary , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::simple_moves::GreenPacker , core::fragment::picking_old::vall::VallResidue , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , core::id::AtomID_Map< T > , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst , core::id::DOF_ID_Map< T > , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::InvrotTree , core::pack::task::operation::OptH , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::LigandConformer , core::pose::datacache::SpecialSegmentsObserver , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , core::pose::datacache::ObserverCache , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations , core::pose::PDBInfo , protocols::topology_broker::DofClaim , core::pose::PDBPoseMap , core::scoring::ChemicalShiftAnisotropy , core::scoring::DipolarCoupling , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::util::ABEGOManager , protocols::enzdes::ModifyStoredRBConfs , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::MyAtom , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::Interval , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frag_picker::VallResidue , protocols::genetic_algorithm::EntityElement , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::loophash::FastGapMover , protocols::match::Bool3DGridKinemageWriter , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::match::downstream::TargetRotamerCoords , protocols::match::Matcher , protocols::match::MatcherMover , protocols::match::MatcherTask , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::match_lite_hasher , protocols::match::OccupiedSpaceHash , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchConsolidator , protocols::match::output::BestMatchesCollection , protocols::match::output::PoseInserter
• Size2 : core::scoring::methods::ResidueCartBondedParameters , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size2Tuple : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size3 : core::scoring::methods::ResidueCartBondedParameters , protocols::match::OccupiedSpaceHash
• Size4 : core::scoring::methods::ResidueCartBondedParameters
• Size6 : protocols::match::VoxelSetIterator
• size_type : boost::unordered_object_pool< T, UserAllocator > , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T >
• SizeFilter_map : protocols::protein_interface_design::movers::MapHotspot
• SizeList : core::scoring::dssp::StrandPairing
• SizePair : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::output::PDBWriter
• SizeRealPair : protocols::pack_daemon::DaemonSet , protocols::enzdes::EnzdesFlexibleRegion
• SizeRealPairs : protocols::pack_daemon::DaemonSet
• Sizes : core::scoring::methods::LK_BallEnergy , protocols::motifs::MotifSearch , protocols::sic_dock::RigidScore , protocols::motifs::LigandMotifSearch
• SizeSet : protocols::toolbox::task_operations::RestrictToNeighborhoodOperation
• Sphere : protocols::match::BumpGrid
• SpinAssignments : protocols::noesy_assign::CrossPeak::Spin
• SRFD_List : core::fragment::FragData
• SRFD_Types : core::fragment::FragFactory
• SS_Info2 : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• SS_Info2_COP : protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::StrandPairingSet , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::filters::InterlockingAromaFilter
• SS_Info2_OP : protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::filters::SheetTopologyFilter
• StageID : protocols::topology_broker::TopologyBroker
• StateEnergies : protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction
• StateEnergiesAndNPDs : protocols::pack_daemon::MultistateFitnessFunction
• StateEsAndNPDs : protocols::pack_daemon::DaemonSet
• StateIndices : protocols::pack_daemon::MultistateAggregateFunction
• Storage : protocols::simple_moves::LoggedFragmentMover
• StrandPairings : core::scoring::dssp::StrandPairingSet
• StrandPairingSet : protocols::fldsgn::topology::SheetSet , protocols::fldsgn::filters::SheetTopologyFilter
• StrandPairingSetCOP : protocols::fldsgn::topology::SheetSet , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• StrandPairingSetOP : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::filters::SheetTopologyFilter
• String : protocols::fldsgn::topology::HelixPairingSet , protocols::toolbox::SelectResiduesByLayer , protocols::simple_filters::HolesFilter , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::simple_moves::GenericMonteCarloMover , protocols::forge::remodel::RemodelMover , core::util::ABEGOManager , protocols::jd2::parser::BluePrint , protocols::forge::components::BDRSegmentInfo , protocols::forge::remodel::RemodelLoopMover
• string : core::scoring::dna::DirectReadoutPotential
• String : protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentInsert , protocols::forge::build::RelativeConnectRight , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::forge::build::ConnectRight , protocols::fldsgn::topology::HSSTripletSet , protocols::flxbb::FlxbbDesign , protocols::flxbb::LayerDesignOperation , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::flxbb::DesignTask , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::BluePrintBDR , core::fragment::picking_old::vall::VallResidue , protocols::flxbb::InterlockAroma
• string : core::io::silent::SilentStruct
• String : protocols::forge::components::VarLengthBuild
• string : core::sequence::CompositeSequence
• String : core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::gen::SecStructGen , core::pose::PDBInfo , core::util::ABEGO , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::FilterStructs , protocols::forge::build::Bridge , protocols::forge::build::BuildManager , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , core::fragment::picking_old::vall::eval::ABEGOEval , protocols::frag_picker::VallResidue , protocols::jd2::parser::FragmentReader , protocols::simple_filters::RangeFilter , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• string : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::sequence::ChemicalShiftSequence , core::sequence::SequenceCoupling , protocols::simple_moves::ExtendedPoseMover
• String : protocols::fldsgn::potentials::sspot::HSPairPotential
• string : core::sequence::SequenceProfile
• String : protocols::forge::constraints::ConstraintFileRCG , protocols::forge::build::GrowRight
• StringRealPairs : protocols::jd2::Job
• Strings : protocols::jd2::Job , protocols::moves::Mover , protocols::dna::PDBOutput , core::io::pdb::FileData
• StringsMap : protocols::dna::PDBOutput
• StringStringPairs : protocols::jd2::Job
• StructureMap : protocols::abinitio::StructureStore , protocols::features::ProteinSilentReport
• Stub : protocols::sic_dock::RigidScore
• StubID : core::kinematics::AtomTree
• Stubs : protocols::sic_dock::RigidScore
• StubsetStubPair : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• StubSetStubPos : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::filters::StubScoreFilter
• Super : protocols::forge::remodel::RemodelLoopMover , core::fragment::picking_old::vall::gen::LengthGen , protocols::fldsgn::filters::NcontactsFilter , core::fragment::picking_old::vall::gen::SecStructGen , protocols::flxbb::InterlockAroma , core::pose::datacache::CacheableObserver , core::pose::signals::EnergyEvent , core::fragment::picking_old::vall::eval::EnergyEval , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::forge::build::Bridge , core::fragment::picking_old::vall::gen::VallFragmentGen , core::pose::PDBInfo , protocols::enzdes::EnzdesFlexibleRegion , protocols::fldsgn::CircularPermutation , core::pose::datacache::ObserverCache , protocols::flxbb::FilterStructs_Packstat , core::fragment::picking_old::vall::VallSection , protocols::viewer::SilentObserver , core::kinematics::tree::BondedAtom , protocols::forge::build::BuildManager , protocols::fldsgn::filters::HelixKinkFilter , protocols::forge::build::GrowLeft , protocols::simple_filters::RangeFilter , core::fragment::IndependentBBTorsionSRFD , protocols::forge::components::BDR , protocols::forge::build::SegmentRebuild , protocols::simple_filters::HolesFilter , core::fragment::picking_old::vall::eval::VallFragmentEval , protocols::fldsgn::filters::SecondaryStructureFilter , core::fragment::picking_old::vall::VallLibrary , core::kinematics::tree::JumpAtom , protocols::fldsgn::filters::SheetTopologyFilter , core::conformation::signals::XYZEvent , core::pack::task::operation::NoRepackDisulfides , protocols::fldsgn::filters::HSSTripletFilter , core::pack::task::operation::OptCysHG , protocols::fldsgn::potentials::SetSecStructEnergies , core::pose::PDBPoseMap , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::simple_moves::GenericMonteCarloMover , core::kinematics::tree::Atom_ , protocols::simple_filters::PackStatFilter , protocols::fldsgn::NcontactsCalculator , core::conformation::signals::IdentityEvent , protocols::forge::remodel::RemodelMover , protocols::fldsgn::filters::HelixPairingFilter , core::conformation::signals::LengthEvent , protocols::fldsgn::BluePrintBDR , core::fragment::picking_old::vall::eval::ABEGOEval , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::forge::build::ConnectRight , core::pose::signals::ConformationEvent , protocols::forge::remodel::RemodelDesignMover , protocols::forge::components::VarLengthBuild , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , core::pack::task::operation::OptH , protocols::flxbb::FlxbbDesign , core::fragment::picking_old::vall::VallLibrarian , protocols::viewer::ConformationViewer , protocols::forge::build::BuildInstruction , protocols::forge::build::RelativeConnectRight , protocols::simple_filters::ShapeComplementarityFilter , core::fragment::picking_old::vall::eval::IdentityEval , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::forge::remodel::RemodelAccumulator , protocols::forge::build::SegmentSwap , protocols::fldsgn::filters::FragQualFilter , protocols::forge::build::SegmentInsert , protocols::flxbb::FilterStructs_TotalCharge , protocols::forge::build::GrowRight
• Super2 : core::fragment::IndependentBBTorsionSRFD
• SymmetricConformation : protocols::symmetric_docking::SymDockingHiRes , protocols::simple_moves::symmetry::SymRotamerTrialsMover , core::optimization::symmetry::SymAtomTreeMinimizer , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::scoring::symmetry::SymmetricEnergies , protocols::simple_moves::symmetry::SymmetricRMSMover , core::scoring::SecondaryStructurePotential , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetric_docking::SymDockProtocol , core::scoring::symmetry::SymmetricScoreFunction , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover
• SymmetricScoreFunction : core::scoring::ScoreFunctionFactory
• SymmetryInfo : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::SymDockingInitialPerturbation , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover
• SymmetryInfoCOP : core::optimization::symmetry::SymMinimizerMap , core::scoring::SecondaryStructurePotential , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::scoring::symmetry::SymmetricScoreFunction , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::scoring::symmetry::SymmetricEnergies
• SymmetryInfoOP : protocols::simple_moves::symmetry::SymmetricRMSMover , core::optimization::symmetry::SymAtomTreeMinimizer , protocols::fldsgn::potentials::SetSecStructEnergies