- r -

• RBConfLists : protocols::enzdes::ModifyStoredRBConfs
• RCR : protocols::sic_dock::Rose
• RDC_lines : core::scoring::ResidualDipolarCoupling_Rohl , protocols::scoring::ResidualDipolarCouplingRigidSegments , core::scoring::ResidualDipolarCoupling
• RDC_Segments : protocols::scoring::ResidualDipolarCouplingRigidSegments
• Real : core::fragment::picking_old::vall::eval::EnergyEval , core::scoring::ResidualDipolarCoupling , protocols::fldsgn::filters::NcontactsFilter , protocols::flxbb::FlxbbDesign , protocols::optimize_weights::OptEData , protocols::optimize_weights::OptEMultifunc , protocols::flxbb::InterlockAroma , protocols::optimize_weights::WrapperOptEMultifunc , protocols::pack_daemon::MultistateFitnessFunction , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::flxbb::LayerDesignOperation , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::ReportSequenceDifferences , protocols::forge::build::Bridge , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , core::scoring::ResidualDipolarCoupling_Rohl , protocols::fldsgn::MatchResidues , protocols::forge::build::BuildInstruction , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::forge::build::SegmentInsert , protocols::protein_interface_design::movers::RepackMinimize , Transformation , protocols::fldsgn::MatchResiduesMover , protocols::forge::build::SegmentRebuild , protocols::protein_interface_design::Transformation , protocols::protein_interface_design::ReportPSSMDifferences , protocols::forge::components::BDR , protocols::rosetta_scripts::ParsedProtocol , protocols::scoring::Interface , core::fragment::picking_old::vall::eval::IdentityEval , core::util::ABEGO , protocols::fldsgn::NcontactsCalculator , protocols::forge::components::VarLengthBuild , protocols::scoring::ResidualDipolarCouplingRigidSegments , protocols::sic_dock::RigidScore , protocols::forge::constraints::NtoC_RCG , protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::forge::constraints::RemoveCsts , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::forge::remodel::RemodelAccumulator , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::BackboneMover , core::util::ABEGOManager , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::forge::remodel::RemodelDesignMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ddG , protocols::forge::remodel::RemodelLoopMover , protocols::simple_moves::DME_FilterMover , protocols::simple_moves::GenericMonteCarloMover , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::forge::remodel::RemodelMover , protocols::simple_moves::MinimalRotamer , protocols::simple_moves::GreenPacker , protocols::frag_picker::VallResidue , protocols::simple_moves::MinMover , protocols::simple_moves::MonteCarloRecover , core::fragment::picking_old::vall::scores::VallFragmentScore , protocols::docking::DockingHighRes , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::idealize::IdealizeMover , protocols::simple_moves::MonteCarloTest , protocols::surface_docking::FullatomRelaxMover , protocols::jd2::parser::BluePrint , protocols::symmetric_docking::SymDockingHiRes , protocols::symmetric_docking::SymDockingLowRes , protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential , protocols::loophash::FastGapMover , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::match::Bool3DGrid , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::docking::DockingHighResLegacy , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::match::BumpGrid , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::JointSequenceOperation , protocols::match::Bool3DGridKinemageWriter , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::match::downstream::ActiveSiteGrid , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::match::downstream::ClassicMatchAlgorithm , protocols::toolbox::task_operations::SeqprofConsensusOperation , core::fragment::picking_old::vall::VallResidue , protocols::docking::DockMCMCycle , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::match::downstream::SecMatchEvaluatorFactory , protocols::match::downstream::SecMatchResiduePairEvaluator , protocols::docking::DockMCMProtocol , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::match::Matcher , protocols::match::MatcherMover , protocols::fldsgn::SheetConstraintsRCG , protocols::match::MatcherTask , protocols::match::HitHasher , core::pose::PDBInfo , protocols::enzdes::ModifyStoredRBConfs , protocols::fldsgn::topology::BetaAlphaBetaMotif , protocols::match::HitNeighborFinder , protocols::match::MatchCounter , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::match::OccupiedSpaceHash , protocols::match::output::MatchConsolidator , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::topology::DimerPairing , protocols::match::output::BestMatchesCollection , protocols::match::output::MatchEvaluator , protocols::fldsgn::topology::HelixPairing , protocols::match::output::MatchGrouper , protocols::match::output::ProcessorFactory , core::scoring::constraints::NonResidueTypeConstraint , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::topology::HSSTriplet , protocols::match::output::SameChiBinComboGrouper , protocols::match::output::SameRotamerComboGrouper , protocols::fldsgn::topology::Sheet , protocols::match::output::SameSequenceGrouper , protocols::match::output::MatchCollisionFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::topology::SheetSet , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::fldsgn::topology::SS_Base , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::SampleStrategyData , core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::constraints::ResidueTypeConstraint , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::topology::StrandPairing , protocols::match::upstream::BuildSet , protocols::match::upstream::FullChiSampleSet , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::match::upstream::ProteinUpstreamBuilder , protocols::match::upstream::UpstreamResTypeGeometry , protocols::fldsgn::filters::HelixPairingFilter , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::match::VoxelSetIterator , protocols::motifs::LigandMotifSearch , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::motifs::MotifSearch , protocols::moves::MonteCarlo , core::scoring::constraints::ResidueTypeLinkingConstraint , protocols::fldsgn::filters::HSSTripletFilter , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::moves::RampingFunc , protocols::moves::TrialMover , protocols::flxbb::FilterStructs , protocols::nonlocal::SingleFragmentMover , protocols::optimize_weights::IterativeOptEDriver , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::flxbb::FilterStructs_Packstat , protocols::optimize_weights::PNatAAOptERotamerData , protocols::optimize_weights::PNatRotOptERotamerData , protocols::flxbb::FilterStructs_TotalCharge , protocols::optimize_weights::SingleStructureData , protocols::optimize_weights::OptEPositionData
• 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 : core::id::AtomID_Map< T > , core::id::DOF_ID_Map< T >
• reference : core::id::DOF_ID_Map< T > , core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP > , core::id::AtomID_Map< T >
• Remarks : core::pose::PDBInfo
• RemodelConstraintGeneratorOP : protocols::forge::components::VarLengthBuild
• RemodelData : protocols::forge::components::VarLengthBuild , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelAccumulator
• RemodelWorkingSet : protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelMover
• ResAtomIndex : core::scoring::custom_pair_distance::RespairInteractions , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• ResAtomIndexFuncMap : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy , core::scoring::custom_pair_distance::RespairInteractions
• ResAtomIndexTuple : core::scoring::custom_pair_distance::RespairInteractions , core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• ResConnID : core::conformation::PseudoBond
• ResfileContentsOP : protocols::pack_daemon::DaemonSet
• ResFilterCreatorMap : core::pack::task::operation::ResFilterFactory
• ResIDList : protocols::pack_daemon::EntityCorrespondence
• ResIDListConstIter : protocols::pack_daemon::EntityCorrespondence
• Residue : protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::fldsgn::potentials::AACompositionEnergy , protocols::protein_interface_design::movers::MapHotspot , core::scoring::MinimizationNode , core::scoring::FACTSPoseInfo , core::pack::dunbrack::RotamerLibrary , core::scoring::constraints::FourPointsFunc , core::scoring::dna::DNA_BasePotential , core::scoring::constraints::XYZ_Func , core::pose::Pose , core::scoring::constraints::ConstraintSet , core::scoring::constraints::Constraints , core::scoring::GenBornPotential , core::scoring::FACTSRotamerSetInfo , core::chemical::ICoorAtomID , core::scoring::FACTSPotential , core::scoring::GenBornPoseInfo , core::scoring::GenBornResidueInfo , core::scoring::GenBornRotamerSetInfo , protocols::dna::PDBOutput , core::scoring::WaterAdductHBondPotential , core::scoring::MinimizationEdge , protocols::fldsgn::NcontactsCalculator , core::scoring::FACTSResidueInfo , protocols::protein_interface_design::movers::TryRotamers , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::MinimalRotamer , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• ResidueAuction : protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• ResidueAuctionItem : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlacementAuctionMover
• ResidueCoords : core::io::pdb::FileData
• ResidueCOP : core::pack::rotamer_set::RotamerSet_ , protocols::flexpack::interaction_graph::OTFFlexbbNode , core::pack::rotamer_set::RotamerSubset
• ResidueCOPs : protocols::viewer::ConformationViewer
• ResidueFeatureTypes : protocols::comparative_modeling::features::ResidueFeatureFactory
• ResidueIndices : core::pack::task::operation::OperateOnCertainResidues
• ResidueList : protocols::noesy_assign::PeakAssignmentResidueMap
• ResidueMap : core::id::AtomID_Map< T > , protocols::noesy_assign::ResonanceList
• ResidueMatcherCOP : core::pack::rotamer_set::RotamerCouplings
• ResidueOP : core::scoring::FACTSRotamerSetInfo , core::scoring::GenBornPoseInfo , core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset , core::scoring::FACTSPoseInfo , core::scoring::GenBornRotamerSetInfo
• ResiduePairConstraints : core::scoring::constraints::ConstraintSet
• ResiduePairConstraintsIterator : core::scoring::constraints::ConstraintSet
• ResidueRecords : core::pose::PDBInfo
• ResidueTemps : core::io::pdb::FileData
• ResidueType : core::conformation::Residue , protocols::simple_moves::MinimalRotamer , core::scoring::methods::LK_BallEnergy , core::pack::dunbrack::RotamerLibrary , core::pack::rotamer_set::WaterAnchorInfo
• ResidueTypeCOPList : core::pack::task::ResidueLevelTask
• ResidueTypeCOPListConstIter : core::pack::task::ResidueLevelTask
• ResidueTypeCOPListIter : core::pack::task::ResidueLevelTask
• ResidueTypeSet : protocols::forge::build::BuildInstruction
• ResidueTypeSetAP : core::coarse::TranslatorSet
• ResidueTypeSetCAP : protocols::forge::build::ConnectRight , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::BuildInstruction , protocols::forge::build::Bridge , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• ResidueTypeSets : core::chemical::ChemicalManager
• reslibrary_iterator : core::pack::dunbrack::RotamerLibrary
• ResLibraryMap : core::pack::dunbrack::RotamerLibrary
• ResName : core::coarse::TranslatorSet
• ResonanceIDs : protocols::noesy_assign::ResonanceList
• Resonances : protocols::noesy_assign::ResonanceList
• ResourceDescription : protocols::loops::LoopsFileFallbackConfiguration
• Restraints : protocols::ligand_docking::UnconstrainedTorsionsMover
• ResTypePair : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• ResTypePairTuple : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• RestypeToTemplateAtomsMap : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• ring_conf_def : protocols::simple_moves::carbohydrates::RingConformationMover
• RLTOC_Map : core::pack::task::operation::ResLvlTaskOperationFactory
• RotamerAssignment : protocols::pack_daemon::PackDaemon
• RotamerAssignmentAndEnergy : protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::PackDaemon
• RotamerComboCountMap : protocols::match::output::SameRotamerComboGrouper , protocols::match::output::LimitHitsPerRotamerFilter
• RotamerCouplingsCOP : core::pack::task::PackerTask , core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• RotamerCouplingsOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer
• RotamerLibrary : core::pack::dunbrack::DunbrackEnergy , core::coarse::TranslatorSet
• RotamerLinksCOP : core::pack::task::PackerTask , core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerLinksOP : core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerList : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• Rotamers : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSet : core::scoring::FACTSRotamerSetInfo , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSetBase : core::scoring::GenBornRotamerSetInfo
• RotamerSetCOP : core::pack::annealer::FixbbCoupledRotamerSimAnnealer , core::pack::annealer::FixbbLinkingRotamerSimAnnealer
• RotamerSetOP : protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::TryRotamers
• RotamerSetOperationOP : protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• RotamerSets : protocols::simple_moves::GreenPacker , protocols::pack_daemon::PackDaemon
• RotamerSetsBaseCOP : core::pack::annealer::SimAnnealerBase
• RotamerSetsCOP : core::pack::annealer::FixbbLinkingRotamerSimAnnealer , protocols::simple_moves::PackRotamersMover , core::pack::annealer::FixbbCoupledRotamerSimAnnealer , protocols::pack_daemon::PackDaemon
• RotamerSetsOP : protocols::simple_moves::GreenPacker , protocols::simple_moves::PackRotamersMover , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::PackDaemon
• RotamerSetVector : core::pack::rotamer_set::FixbbRotamerSets
• RotamersForAA : core::pack::rotamer_set::ContinuousRotamerSet
• RotamerSubsetsOP : protocols::pack_daemon::RotamerSubsetRepacker
• RotamerTrieBaseOP : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• Row : core::sequence::DP_Matrix
• RRComparerCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRProtocolCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RRReporterCreatorMap : protocols::rotamer_recovery::RotamerRecoveryFactory
• RT : protocols::forge::build::ConnectRight
• RuleMap : core::coarse::RuleSet
• rvec : protocols::evaluation::PCA , core::scoring::ResidualDipolarCoupling
• rvec5 : core::scoring::ResidualDipolarCoupling