- r -

• RBConfLists : protocols::enzdes::ModifyStoredRBConfs
• RCR : protocols::sic_dock::Rose
• RDC_lines : protocols::scoring::ResidualDipolarCouplingRigidSegments
• RDC_Segments : protocols::scoring::ResidualDipolarCouplingRigidSegments
• RDFFunctionCreatorMap : protocols::ligand_docking::rdf::RDFFunctionFactory
• Real : protocols::docking::DockingHighRes , protocols::docking::DockingHighResLegacy , protocols::docking::DockMCMCycle , protocols::docking::DockMCMProtocol , protocols::enzdes::ModifyStoredRBConfs , 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::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , 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::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::DimerPairing , protocols::fldsgn::topology::HelixPairing , protocols::fldsgn::topology::HSSTriplet , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::SS_Base , protocols::fldsgn::topology::StrandPairing , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::SegmentInsert , protocols::forge::build::SegmentRebuild , 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::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::frag_picker::VallResidue , protocols::frags::FragLib , protocols::frags::SingleResidueTorsionFragmentLibrary , protocols::frags::TorsionFragment , protocols::frags::TorsionFragmentLibrary , protocols::frags::TorsionFragmentMover , protocols::idealize::IdealizeMover , protocols::jd2::parser::BluePrint , protocols::loophash::FastGapMover , protocols::match::Bool3DGrid , protocols::match::Bool3DGridKinemageWriter , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::match::HitHasher , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::match::Matcher , protocols::match::MatcherMover , protocols::match::MatcherTask , protocols::match::OccupiedSpaceHash , protocols::match::output::BestMatchesCollection , protocols::match::output::MatchCollisionFilter , protocols::match::output::MatchConsolidator , protocols::match::output::MatchEvaluator , protocols::match::output::MatchGrouper , protocols::match::output::ProcessorFactory , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::match::output::SameSequenceGrouper , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::SampleStrategyData , protocols::match::upstream::UpstreamResTypeGeometry , protocols::match::VoxelSetIterator , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::MonteCarlo , protocols::moves::RampingFunc , protocols::moves::TrialMover , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , 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::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::Transformation , protocols::rosetta_scripts::ParsedProtocol , protocols::scoring::Interface , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ddG , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::MinMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , Transformation
• Real3 : protocols::match::HitHasher , protocols::match::OccupiedSpaceHash , protocols::match::VoxelSetIterator
• Real6 : protocols::match::OccupiedSpaceHash , protocols::toolbox::match_enzdes_util::LigandConformer
• Reals : protocols::sic_dock::RigidScore
• Reference : protocols::jd2::utility::pointer::access_ptr< T >
• reference : protocols::jd2::utility::pointer::access_ptr< T > , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• RemodelConstraintGeneratorOP : protocols::forge::components::VarLengthBuild
• RemodelData : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelMover
• RemodelWorkingSet : protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelMover
• ResfileContentsOP : protocols::pack_daemon::DaemonSet
• ResIDList : protocols::pack_daemon::EntityCorrespondence
• ResidList : protocols::sparta::Sparta::SpartaLib
• ResIDListConstIter : protocols::pack_daemon::EntityCorrespondence
• Residue : protocols::dna::PDBOutput , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::potentials::AACompositionEnergy , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::MinimalRotamer
• ResidueAuction : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• ResidueAuctionItem : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• ResidueCOP : protocols::flexpack::interaction_graph::OTFFlexbbNode
• ResidueCOPs : protocols::viewer::ConformationViewer
• ResidueFeatureTypes : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueList : protocols::noesy_assign::PeakAssignmentResidueMap , protocols::sparta::GDB
• ResidueMap : protocols::noesy_assign::ResonanceList
• ResidueType : protocols::simple_moves::MinimalRotamer
• ResidueTypeConstraint : protocols::simple_moves::ResidueTypeConstraintMover
• ResidueTypeSet : protocols::forge::build::BuildInstruction
• ResidueTypeSetCAP : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , 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
• ResonanceIDs : protocols::noesy_assign::ResonanceList
• Resonances : protocols::noesy_assign::ResonanceList
• ResourceDescription : protocols::loops::LoopsFileFallbackConfiguration , protocols::surface_docking::SurfaceVectorFallbackConfiguration
• Restraints : protocols::ligand_docking::UnconstrainedTorsionsMover
• RestypeToTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• RotamerAssignment : protocols::pack_daemon::PackDaemon
• RotamerAssignmentAndEnergy : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker
• RotamerComboCountMap : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::SameRotamerComboGrouper
• RotamerList : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• Rotamers : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSet : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSetOP : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• RotamerSetOperationOP : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSets : protocols::pack_daemon::PackDaemon , protocols::simple_moves::GreenPacker
• RotamerSetsCOP : protocols::pack_daemon::PackDaemon , protocols::simple_moves::PackRotamersMover
• RotamerSetsOP : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::simple_moves::GreenPacker , protocols::simple_moves::PackRotamersMover
• RotamerSubsetsOP : protocols::pack_daemon::RotamerSubsetRepacker
• RRComparerCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRProtocolCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRReporterCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RT : protocols::forge::build::ConnectRight
• rvec : protocols::evaluation::PCA