- s -

• ScaffoldRotamerPair : protocols::match::output::UpstreamHitCacher
• ScaffoldRotamerTuple : protocols::match::output::UpstreamHitCacher
• Score : core::scoring::motif::XformScore
• ScoreConstIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoredFrag : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoredList : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreFunction : core::energy_methods::AACompositionEnergy , core::energy_methods::AARepeatEnergy , core::energy_methods::DNATorsionEnergy , core::energy_methods::FACTSEnergy , core::energy_methods::RNA_CoarseDistEnergy , core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::PDBOutput , protocols::evolution::EvolutionaryDynamicsMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets , 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::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::matdes::SymDofMover , protocols::minimization_packing::GreenPacker , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pre::PREEnergy , protocols::nmr::rdc::RDCEnergy , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , 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::protein_interface_design::Revert , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::task_operations::LimitAromaChi2_RotamerSetOperation
• ScoreFunctionCOP : core::fragment::picking_old::vall::eval::EnergyEval , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FlxbbDesignPack , protocols::forge::remodel::RemodelAccumulator , protocols::matdes::SymDofMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::MinMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RepackSidechainsMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::moves::MonteCarlo , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::normalmode::NormalModeMinimizer , protocols::pack_daemon::PackDaemon , 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::protein_interface_design::Revert , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::switches::GraftSwitchMover
• ScoreFunctionFactory : protocols::forge::remodel::RemodelAccumulator
• ScoreFunctionInfo : core::scoring::Energies
• ScoreFunctionOP : core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::DnaInterfacePacker , protocols::dna::PDBOutput , protocols::enzdes::BackboneSampler , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::evolution::EvolutionaryDynamicsMover , 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_Layer , protocols::flxbb::DesignTask_Normal , 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::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::matdes::SymDofMover , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::moves::MonteCarlo , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREMover , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::Revert , protocols::rna::movers::ErraserMinimizerMover , protocols::simple_moves::ScoreMover , protocols::switches::GraftSwitchMover
• ScoreIterator : core::fragment::picking_old::vall::VallLibrarian
• ScoreList : core::fragment::CacheWrapper< T, XCacheUnit >
• ScoreMap : core::scoring::motif::XformScore , protocols::qsar::scoring_grid::GridSet
• ScorerMap : protocols::legacy_sewing::scoring::LegacyAssemblyScoreFunction
• Scores : core::fragment::picking_old::vall::VallLibrarian , protocols::sic_dock::RigidScore
• ScoreType : core::scoring::Energies , protocols::simple_ddg::ddG
• ScoreTypes : protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::AACompositionEnergyCreator , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator , protocols::minimization_packing::GreenPacker , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::WrapperOptEMultifunc
• ScoringSchemeTypes : core::sequence::ScoringSchemeFactory
• Screw : core::kinematics::jacobian::ModuleType1
• ScValue : core::scoring::sc::MolecularSurfaceCalculator
• SecondaryCreatorList : protocols::jd3::pose_outputters::PoseOutputterFactory
• SecondaryOutputterMap : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::pose_outputters::PoseOutputterFactory
• SecondaryRepresentativeOutputterMap : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• SecStruct : protocols::task_operations::DsspDesignOperation
• SecstructAbegoMap : protocols::denovo_design::components::IdealAbegoGenerator
• SecStructResidues : protocols::task_operations::DsspDesignOperation
• Segment : core::pose::datacache::SpecialSegmentsObserver
• SegmentName : protocols::denovo_design::components::StructureData
• SegmentNameSet : protocols::denovo_design::components::StructureData
• SegmentPair : protocols::denovo_design::connection::ConnectionArchitect
• SegmentPairs : protocols::denovo_design::connection::ConnectionArchitect
• SegmentToNodeMap : protocols::denovo_design::components::FoldGraph
• SeqLabelMap : core::environment::SequenceAnnotation
• SeqposTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• SequenceAnnotation : protocols::environment::Environment
• SequenceAnnotationCOP : protocols::environment::EnvClaimBroker , protocols::environment::Environment , protocols::environment::ProtectedConformation
• SequenceAnnotationOP : protocols::environment::EnvClaimBroker , protocols::environment::Environment
• 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
• ShapeComplementarityCalculator : protocols::simple_filters::ShapeComplementarityFilter
• ShapeComplementarityCalculatorResults : protocols::simple_filters::ShapeComplementarityFilter
• ShapeSimilarityCalculatorResults : core::simple_metrics::metrics::ShapeSimilarityMetric
• SheetSetCOP : protocols::fldsgn::topology::BetaAlphaBetaMotifSet
• SheetTopology : protocols::jumping::SheetBuilder
• SignedResid : protocols::denovo_design::residue_selectors::NamedSegmentSelector
• SignedResidSet : protocols::denovo_design::residue_selectors::NamedSegmentSelector
• 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
• SixDCoordinateBinner : core::scoring::motif::MotifHash , core::scoring::motif::XformScore , core::scoring::motif::XfragSet
• Size : core::conformation::ResidueKinWriter , core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::concepts::Library< Books > , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallResidue , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , core::pack::task::operation::OptH , core::pose::datacache::ObserverCache , core::pose::datacache::SpecialSegmentsObserver , core::pose::PDBInfo , core::pose::PDBPoseMap , core::scoring::ChemicalShiftAnisotropy , core::scoring::DipolarCoupling , core::scoring::ResidualDipolarCoupling , core::scoring::ResidualDipolarCoupling_Rohl , core::select::util::SelectResiduesByLayer , core::sequence::ABEGOManager , core::sequence::SSManager , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::enzdes::ModifyStoredRBConfs , protocols::evolution::EvolutionaryDynamicsMover , 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::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::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintGenerator , 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::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbNode , 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::NtoCConstraintGenerator , protocols::forge::constraints::RemoveRemodelCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragment , protocols::frags::TorsionFragmentLibrary , protocols::frags::TorsionFragmentMover , protocols::genetic_algorithm::EntityElement , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::loophash::FastGapMover , protocols::match::Bool3DGrid , 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::HitHasher , protocols::match::HitNeighborFinder , protocols::match::match_lite_hasher , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherMover , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::output::BestMatchesCollection , protocols::match::output::DownstreamRMSEvaluator , protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchConsolidator , protocols::match::output::PoseInserter , protocols::match::output::ProcessorFactory , protocols::match::output::ResidueKinemageWriter , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::WriteUpstreamCoordinateKinemage , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::SampleStrategyData , protocols::match::upstream::ScaffoldBuildPoint , protocols::match::upstream::UpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::matdes::SymDofMover , protocols::matdes::SymDofMoverSampler , protocols::mean_field::jagged_array< T, A > , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::GroupDiscriminator , protocols::minimization_packing::MinimalRotamer , protocols::minimization_packing::UserDefinedGroupDiscriminator , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover , protocols::moves::MonteCarlo , protocols::moves::ReplicaExchangeMC , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pcs::PCSTensorOptimizer , protocols::nmr::pre::PREDistanceRecord , protocols::nmr::pre::PREEnergy , protocols::nmr::pre::PREMover , protocols::nmr::rdc::RDCEnergy , protocols::nonlocal::Chunk , protocols::nonlocal::Region , protocols::nonlocal::SingleFragmentMover , protocols::optimize_weights::IterativeOptEDriver , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::parser::BluePrint , protocols::parser::FragmentReader , protocols::pose_metric_calculators::FragQualCalculator , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::recces::scratch::ThermalMinimizer , protocols::recces::scratch::ThermalSamplingMover , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sic_dock::RigidScore , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::DME_FilterMover , protocols::task_operations::LinkResidues , protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover , protocols::toolbox::match_enzdes_util::AllowedSeqposForGeomCst , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::InvrotTree , protocols::toolbox::match_enzdes_util::InvrotTreeNode , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::topology_broker::claims::DofClaim
• Size2 : core::energy_methods::ResidueCartBondedParameters , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size2Tuple : protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• Size3 : core::energy_methods::ResidueCartBondedParameters , protocols::match::OccupiedSpaceHash
• Size4 : core::energy_methods::ResidueCartBondedParameters
• Size6 : protocols::match::VoxelSetIterator
• size_type : core::conformation::Conformation , core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T > , core::id::NamedAtomID_Map< T > , protocols::mean_field::jagged_array< T, A >
• SizeDIET : protocols::jd3::JobTracker
• SizeFilter_map : protocols::protein_interface_design::movers::MapHotspot
• SizeList : core::scoring::dssp::StrandPairing , protocols::jd3::job_distributors::JobExtractor
• SizePair : protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::output::PDBWriter
• SizeRealPair : protocols::enzdes::EnzdesFlexibleRegion , protocols::pack_daemon::DaemonSet
• SizeRealPairs : protocols::pack_daemon::DaemonSet
• Sizes : core::scoring::lkball::LK_BallEnergy , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::sic_dock::RigidScore
• SizeSet : protocols::task_operations::RestrictToNeighborhoodOperation
• SizeToStringMap : protocols::environment::EnvClaimBroker
• Solution : protocols::denovo_design::components::FoldGraph
• Solutions : protocols::denovo_design::components::FoldGraph
• Sphere : protocols::match::BumpGrid
• SpinAssignments : protocols::noesy_assign::CrossPeak::Spin
• SpinlabelDatabaseMap : core::io::nmr::SpinlabelDatabaseHandler
• SpinlabelHistogramMap : protocols::nmr::pre::PREMover
• SpinlabelToPREDistances : protocols::nmr::pre::PREMover
• SpinPairCoordinates : core::scoring::nmr::rdc::RDCMultiSet
• SRFD_List : core::fragment::FragData
• SRFD_Types : core::fragment::FragFactory
• SS_Info2 : protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::DimerPairings , protocols::fldsgn::topology::StrandPairingSet
• SS_Info2_COP : protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet
• SS_Info2_OP : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::topology::StrandPairing
• SSize : protocols::mean_field::jagged_array< T, A >
• ssize_type : protocols::mean_field::jagged_array< T, A >
• StageID : protocols::topology_broker::TopologyBroker
• StateEnergies : protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• StateEnergiesAndNPDs : protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::TopEntitySet
• StateEsAndNPDs : protocols::pack_daemon::DaemonSet
• StateIndices : protocols::pack_daemon::MultistateAggregateFunction
• Stats : protocols::sic_dock::scores::MotifHashRigidScore
• Storage : protocols::simple_moves::LoggedFragmentMover
• StrandArchitectOPs : protocols::denovo_design::architects::BetaSheetArchitect
• StrandExtension : protocols::denovo_design::architects::BetaSheetArchitect
• StrandExtensionsMap : protocols::denovo_design::architects::BetaSheetArchitect
• StrandOrientation : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::StrandArchitect , protocols::denovo_design::movers::FoldArchitectMover
• StrandOrientations : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::StrandArchitect
• StrandPairings : core::scoring::dssp::StrandPairingSet
• StrandPairingSet : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::topology::SheetSet
• StrandPairingSetCOP : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::topology::SheetSet
• StrandPairingSetOP : protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential
• String : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::VallResidue
• string : core::import_pose::pose_stream::LazySilentFilePoseInputStream , core::import_pose::pose_stream::SilentFilePoseInputStream , core::io::silent::SilentStruct
• String : core::pose::PDBInfo
• string : core::scoring::dna::DirectReadoutPotential
• String : core::select::util::SelectResiduesByLayer , core::sequence::ABEGO , core::sequence::ABEGOManager
• string : core::sequence::ChemicalShiftSequence , core::sequence::CompositeSequence , core::sequence::SequenceCoupling , core::sequence::SequenceProfile
• String : core::sequence::SSManager , protocols::evolution::EvolutionaryDynamicsMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::SheetFoldTypeManager , protocols::fldsgn::topology::SS_Info2 , protocols::fldsgn::topology::StrandPairing , protocols::fldsgn::topology::StrandPairingSet , protocols::flxbb::DesignTask , protocols::flxbb::FilterStructs , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , 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::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frag_picker::VallResidue , protocols::monte_carlo::GenericMonteCarloMover , protocols::parser::BluePrint , protocols::parser::FragmentReader
• string : protocols::pose_creation::ExtendedPoseMover
• String : protocols::pose_metric_calculators::FragQualCalculator , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LinkResidues , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::SeqprofConsensusOperation
• StringList : protocols::sparta::GDB
• StringRealMap : protocols::ligand_docking::InterfaceScoreCalculator
• StringRealPairs : protocols::jd2::Job
• Strings : core::io::StructFileRep , protocols::dna::PDBOutput , protocols::jd2::Job , protocols::moves::Mover
• StringsMap : protocols::dna::PDBOutput
• StringStringMap : protocols::jd3::chunk_library_inputters::ChunkLibraryInputSource , protocols::jd3::full_model_inputters::FullModelInputSource , protocols::jd3::pose_inputters::PoseInputSource
• StringStringPairs : protocols::jd2::Job
• StringToSizePairMap : protocols::environment::EnvClaimBroker
• StringToStringPairMap : protocols::environment::EnvClaimBroker
• StructureData : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::BlueprintArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::StrandArchitect
• StructureDataCOPs : protocols::denovo_design::architects::BetaSheetArchitect
• StructureDataMap : protocols::indexed_structure_store::search::StructureDatabase
• StructureDataOP : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::architects::DeNovoArchitect , protocols::denovo_design::architects::StrandArchitect
• StructureMap : protocols::abinitio::StructureStore , protocols::features::ProteinSilentReport
• StubID : core::kinematics::AtomTree
• StubsetStubPair : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• StubSetStubPos : protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• SubgraphContainer : core::pack::interaction_graph::MultiplexedAnnealableGraph
• SubMap : core::chemical::AtomRefMapping< FromRef, ToRef >
• SubPoseIDPair : protocols::fold_from_loops::movers::SplitAndMixPoseMover
• SummaryStatistics : protocols::indexed_structure_store::search::PairQueryExecutor , protocols::indexed_structure_store::search::SingleQueryExecutor
• Super : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::conformation::signals::XYZEvent , core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallLibrary , core::fragment::picking_old::vall::VallSection , core::kinematics::tree::Atom_ , core::kinematics::tree::BondedAtom , core::kinematics::tree::JumpAtom , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pose::datacache::CacheableObserver , core::pose::datacache::ObserverCache , core::pose::PDBInfo , core::pose::PDBPoseMap , core::pose::signals::ConformationEvent , core::pose::signals::EnergyEvent , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::enzdes::EnzdesFlexibleRegion , protocols::evolution::EvolutionaryDynamicsMover , 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::SecondaryStructureFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , 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::RelativeConnectRight , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLigandHandler , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter
• super : protocols::mean_field::jagged_array< T, A >
• Super : protocols::monte_carlo::GenericMonteCarloMover , protocols::pose_metric_calculators::FragQualCalculator , protocols::simple_ddg::SSElementBisectddGFilter , protocols::simple_filters::ContactMolecularSurfaceFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::LeastNativeLike9merFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::SecretionPredictionFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SSElementLengthFilter , protocols::simple_filters::SSElementMotifContactFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::viewer::SilentObserver
• Super2 : core::fragment::IndependentBBTorsionSRFD
• SurfaceExposureMap : protocols::sparta::Sparta::SpartaLib
• SurroundingSSMap : protocols::denovo_design::task_operations::ConsensusLoopDatabase
• SymmetricConformation : core::optimization::symmetry::SymAtomTreeMinimizer , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::scoring::SecondaryStructurePotential , core::scoring::symmetry::SymmetricEnergies , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetry::SymDockingInitialPerturbation , protocols::symmetry::SymmetricRMSMover
• SymmetryInfo : protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::symmetry::SymDockingInitialPerturbation
• SymmetryInfoCOP : core::optimization::symmetry::SymMinimizerMap , core::pack::rotamer_set::symmetry::SymmetricRotamerSet_ , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , core::scoring::SecondaryStructurePotential , core::scoring::symmetry::SymmetricEnergies , protocols::fldsgn::potentials::SetSecStructEnergies
• SymmetryInfoOP : core::optimization::symmetry::SymAtomTreeMinimizer , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::symmetry::SymmetricRMSMover