- p -

• PackerEnergy : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• PackerPalette : core::pack::task::TaskFactory
• PackerPaletteCOP : core::pack::task::TaskFactory
• PackerPaletteCreatorMap : core::pack::palette::PackerPaletteFactory
• PackerPaletteOP : core::pack::task::TaskFactory
• PackerPaletteOPs : core::pack::palette::PackerPaletteFactory
• PackerTask : core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::evolution::EvolutionaryDynamicsMover , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelRotamerLinks , protocols::hbnet::ConstrainHBondNetwork , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::motifs::LigandMotifSearch , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::SeqprofConsensusOperation
• PackerTaskCOP : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::PDBOutput , protocols::evolution::EvolutionaryDynamicsMover , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesignPack , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::MinPackMover , protocols::minimization_packing::PackRotamersMover , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::switches::GraftSwitchMover , protocols::task_operations::LimitAromaChi2_RotamerSetOperation
• PackerTaskOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::evolution::EvolutionaryDynamicsMover , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::minimization_packing::BoltzmannRotamerMover , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::RotamerizeMover , protocols::minimization_packing::RotamerTrialsMinMover , protocols::minimization_packing::RotamerTrialsMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::scoring::Interface
• Page : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallResidues
• PageConstIterator : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , 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::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• PageIterator : 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::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::VallSection
• Pairings : protocols::abinitio::AlternativePairings
• PairingsInfo : protocols::denovo_design::architects::BetaSheetArchitect
• PairingsInfoVector : protocols::denovo_design::architects::BetaSheetArchitect
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• PairList : protocols::sparta::PDB
• ParaIon : core::scoring::nmr::pre::PREMultiSet
• ParaIonCOP : core::scoring::nmr::pre::PREMultiSet
• ParaIonOP : core::scoring::nmr::pre::PREMultiSet
• ParameterizationCalculatorProperties : protocols::helical_bundle::BundleParametrizationCalculator
• Parameters : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParametersCOP : core::conformation::Conformation
• ParametersOP : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParametersSet : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• ParametersSetCOP : core::conformation::Conformation
• ParametersSetOP : core::conformation::Conformation , protocols::helical_bundle::BundleGridSampler , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::MakeBundleHelix , protocols::helical_bundle::parameters::BundleParameters , protocols::helical_bundle::parameters::BundleParametersSet , protocols::helical_bundle::PerturbBundle , protocols::helical_bundle::PerturbBundleHelix
• Params : core::scoring::dna::DNA_BasePotential
• parent : core::chemical::rotamers::RotamerLibrarySpecificationRegistrator< T > , core::conformation::RotamerSetBase , core::energy_methods::AromaticBackboneRestraintEnergy , core::energy_methods::AspartimidePenaltyEnergy , core::energy_methods::BranchEnergy , core::energy_methods::Burial_v2Energy , core::energy_methods::CartesianBondedEnergy , core::energy_methods::CenHBEnergy , core::energy_methods::CenPairEnergy , core::energy_methods::CenPairMotifDegreeEnergy , core::energy_methods::CenPairMotifEnergy , core::energy_methods::CenRotEnvEnergy , core::energy_methods::CenRotPairEnergy , core::energy_methods::CentroidDisulfideEnergy , core::energy_methods::ChainbreakEnergy , core::energy_methods::ChemicalShiftAnisotropyEnergy , core::energy_methods::ContactOrderEnergy , core::energy_methods::ContextDependentGeometricSolEnergy , core::energy_methods::ContextIndependentGeometricSolEnergy , core::energy_methods::CovalentLabelingEnergy , core::energy_methods::CovalentLabelingFAEnergy , core::energy_methods::CustomAtomPairEnergy , core::energy_methods::D2H_SA_Energy , core::energy_methods::dfire::DFIRE_Energy , core::energy_methods::DipolarCouplingEnergy , core::energy_methods::DirectReadoutEnergy , core::energy_methods::DistanceChainbreakEnergy , core::energy_methods::DisulfideMatchingEnergy , core::energy_methods::DNA_BaseEnergy , core::energy_methods::DNA_DihedralEnergy , core::energy_methods::DNA_EnvPairEnergy , core::energy_methods::DNA_ReferenceEnergy , core::energy_methods::DNAChiEnergy , core::energy_methods::DNATorsionEnergy , core::energy_methods::ElecDensAllAtomCenEnergy , core::energy_methods::ElecDensAtomwiseEnergy , core::energy_methods::ElecDensCenEnergy , core::energy_methods::ElecDensEnergy , core::energy_methods::EnvEnergy , core::energy_methods::EnvSmoothEnergy , core::energy_methods::ExactOccludedHbondSolEnergy , core::energy_methods::FA_ElecEnergyAroAll , core::energy_methods::FA_ElecEnergyAroAro , core::energy_methods::FA_GrpElecEnergy , core::energy_methods::Fa_MbenvEnergy , core::energy_methods::Fa_MbsolvEnergy , core::energy_methods::FACTSEnergy , core::energy_methods::FaMPEnvEnergy , core::energy_methods::FaMPEnvSmoothEnergy , core::energy_methods::FaMPSolvEnergy , core::energy_methods::FastDensEnergy , core::energy_methods::FastSAXSEnergy , core::energy_methods::FiberDiffractionEnergy , core::energy_methods::FiberDiffractionEnergyDens , core::energy_methods::FreeDOF_Energy , core::energy_methods::FullatomDisulfideEnergy , core::energy_methods::GaussianOverlapEnergy , core::energy_methods::GenBornEnergy , core::energy_methods::GenericBondedEnergy , core::energy_methods::GoapEnergy , core::energy_methods::HackAroEnergy , core::energy_methods::HolesEnergy , core::energy_methods::HRFDynamicsEnergy , core::energy_methods::HybridVDW_Energy , core::energy_methods::HydroxylTorsionEnergy , core::energy_methods::IntermolEnergy , core::energy_methods::LinearBranchEnergy , core::energy_methods::LinearChainbreakEnergy , core::energy_methods::LK_hack , core::energy_methods::LK_PolarNonPolarEnergy , core::energy_methods::LoopCloseEnergy , core::energy_methods::MembraneCbetaEnergy , core::energy_methods::MembraneCenPairEnergy , core::energy_methods::MembraneEnvEnergy , core::energy_methods::MembraneEnvPenalties , core::energy_methods::MembraneEnvSmoothEnergy , core::energy_methods::MembraneLipo , core::energy_methods::MgEnergy , core::energy_methods::MissingEnergy , core::energy_methods::MotifDockEnergy , core::energy_methods::MPCbetaEnergy , core::energy_methods::MPEnvEnergy , core::energy_methods::MPHelicalityEnergy , core::energy_methods::MPPairEnergy , core::energy_methods::MPResidueLipophilicityEnergy , core::energy_methods::MPSpanAngleEnergy , core::energy_methods::MPSpanInsertionEnergy , core::energy_methods::MultipoleElecEnergy , core::energy_methods::NPDHBondEnergy , core::energy_methods::OccludedHbondSolEnergy , core::energy_methods::OccludedHbondSolEnergy_onebody , core::energy_methods::OmegaTetherEnergy , core::energy_methods::OtherPoseEnergy , core::energy_methods::P_AA_Energy , core::energy_methods::P_AA_pp_Energy , core::energy_methods::P_AA_ss_Energy , core::energy_methods::PackStatEnergy , core::energy_methods::PairEnergy , core::energy_methods::PeptideBondEnergy , core::energy_methods::pHEnergy , core::energy_methods::PointWaterEnergy , core::energy_methods::PoissonBoltzmannEnergy , core::energy_methods::ProClosureEnergy , core::energy_methods::ProQ_Energy , core::energy_methods::RamachandranEnergy2B , core::energy_methods::RamachandranEnergy , core::energy_methods::RamaPreProEnergy , core::energy_methods::ReferenceEnergy , core::energy_methods::ReferenceEnergyNoncanonical , core::energy_methods::ResidualDipolarCouplingEnergy , core::energy_methods::ResidualDipolarCouplingEnergy_Rohl , core::energy_methods::RG_Energy_Fast , core::energy_methods::RG_Energy_RNA , core::energy_methods::RingClosureEnergy , core::energy_methods::RMS_Energy , core::energy_methods::RNA_BulgeEnergy , core::energy_methods::RNA_ChemicalMappingEnergy , core::energy_methods::RNA_ChemicalShiftEnergy , core::energy_methods::RNA_DataBackboneEnergy , core::energy_methods::RNA_FA_ElecEnergy , core::energy_methods::RNA_FullAtomStackingEnergy , core::energy_methods::RNA_FullAtomVDW_BasePhosphate , core::energy_methods::RNA_JR_SuiteEnergy , core::energy_methods::RNA_LJ_BaseEnergy , core::energy_methods::RNA_MgPointEnergy , core::energy_methods::RNA_PairwiseLowResolutionEnergy , core::energy_methods::RNA_StubCoordinateEnergy , core::energy_methods::RNA_SugarCloseEnergy , core::energy_methods::RNA_SuiteEnergy , core::energy_methods::RNA_TorsionEnergy , core::energy_methods::RNA_VDW_Energy , core::energy_methods::RNP_LowResEnergy , core::energy_methods::RNP_LowResPairDistEnergy , core::energy_methods::RNP_LowResStackEnergy , core::energy_methods::SA_Energy , core::energy_methods::SASAEnergy , core::energy_methods::SecondaryStructureEnergy , core::energy_methods::SequenceDependentRefEnergy , core::energy_methods::SmoothCenPairEnergy , core::energy_methods::SmoothEnvEnergy , core::energy_methods::SplitUnfoldedTwoBodyEnergy , core::energy_methods::SSElementMotifContactEnergy , core::energy_methods::StackElecEnergy , core::energy_methods::SuckerEnergy , core::energy_methods::SurfEnergy , core::energy_methods::SurfVolEnergy , core::energy_methods::SymmetricLigandEnergy , core::energy_methods::TNA_SuiteEnergy , core::energy_methods::UnfoldedStateEnergy , core::energy_methods::VdWTinkerEnergy , core::energy_methods::WaterAdductHBondEnergy , core::energy_methods::WaterAdductIntraEnergy , core::energy_methods::WaterSpecificEnergy , core::energy_methods::XtalMLEnergy , core::energy_methods::YHHPlanarityEnergy
• Parent : core::environment::EXCN_Env_Exception , core::environment::EXCN_FTSketchGraph , core::fragment::AnnotatedFragData , core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD , core::fragment::ConstantLengthFragSet , core::fragment::DownJumpSRFD , core::fragment::FragCache< T > , core::fragment::FragSetCollection , core::fragment::FragStore< T > , core::fragment::MinimalFragSet , core::fragment::NonContinuousFrame , core::fragment::OrderedFragSet , core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parent : core::io::silent::SilentStructRegistrator< T >
• Parent : core::kinematics::EXCN_InvalidFoldTree
• parent : core::optimization::MinimizerMap , core::optimization::Multifunc , core::optimization::NumDerivCheckData , core::optimization::NumericalDerivCheckResult , core::optimization::SingleResidueMultifunc , core::pack::annealer::FASTERAnnealer , core::pack::dunbrack::BBDepSemiRotamericData< T, N > , core::pack::dunbrack::BBIndSemiRotamericData< T, N > , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::DunbrackRotamer< S, N, P > , core::pack::dunbrack::PackedDunbrackRotamer< S, N, P > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N > , core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchEnergy , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondEdge< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondNode< V, E, G > , core::pack::interaction_graph::NPDHBSimpleEdge , core::pack::interaction_graph::NPDHBSimpleInteractionGraph , core::pack::interaction_graph::NPDHBSimpleNode , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceEnergy , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::palette::CustomBaseTypePackerPalette , core::pack::palette::DefaultPackerPalette , core::pack::palette::NCAADefaultPackerPalette , core::pack::palette::NoDesignPackerPalette , core::pack::palette::PackerPaletteRegistrator< T > , core::pack::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , core::pack::rotamers::SingleResidueRotamerLibraryRegistrator< T > , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::AllResFilter , core::pack::task::operation::AnyResFilter , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::ChainIs , core::pack::task::operation::ChainIsnt , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraChiCutoffRLT , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ExtraRotamersGenericRLT , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::IncludeCurrentRLT , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeFromOptionCollection , core::pack::task::operation::NoResFilter , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreserveCBetaRLT , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::ProhibitSpecifiedBaseResidueTypes , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResFilterRegistrator< T > , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueIndexIsnt , core::pack::task::operation::ResidueLacksProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueName3Isnt , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBIndexIsnt , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResiduePDBInfoLacksLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperationRegistrator< T > , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASExceptNativeRLT , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , core::pack::task::operation::RestrictToResidueProperties , core::pack::task::operation::RestrictToSpecifiedBaseResidueTypes , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::TaskOperationRegistrator< T > , core::pack::task::operation::UseMultiCoolAnnealer , core::pack::task::TaskFactory
• Parent : core::pose::datacache::SpecialSegmentsObserver
• parent : core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::ConstraintNode , core::scoring::constraints::ConstraintRegistrator< T > , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::ContextGraph , core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::DockingScoreFunction , core::scoring::elec::CountPairRepresentative , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPair2B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairCrossover34 , core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover3full , core::scoring::etable::count_pair::CountPairCrossover4 , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator > , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator > , core::scoring::func::FourPointsFunc
• PARENT : core::scoring::hbonds::graph::HBondGraph
• parent : core::scoring::hbonds::NPDHBondSet , core::scoring::methods::ContextDependentLRTwoBodyEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextDependentTwoBodyEnergy , core::scoring::methods::ContextIndependentLRTwoBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::ContextIndependentTwoBodyEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodRegistrator< T > , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerSVMEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinimizationNode , core::scoring::MinScoreScoreFunction , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::solid_surface::SurfaceEnergies , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode , core::select::jump_selector::JumpSelectorRegistrator< T > , core::select::residue_selector::ResidueSelectorRegistrator< T > , core::sequence::SequenceRegistrator< T > , core::simple_metrics::SimpleMetricRegistrator< T >
• Parent : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid , protocols::abinitio::IterativeFullatom , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• parent : protocols::calc_taskop_filters::ConservedPosMutationFilter , protocols::calc_taskop_filters::RelativePoseFilter , protocols::calc_taskop_filters::RotamerBoltzmannWeight
• Parent : protocols::canonical_sampling::AsyncMPITemperingBase , protocols::canonical_sampling::BiasedMonteCarlo , protocols::canonical_sampling::BiasEnergy::Histogram< T > , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::WTEBiasEnergy
• parent : protocols::constraint_filters::ConstraintScoreCutoffFilter , protocols::constraint_filters::SavePoseConstraintToFileFilter , protocols::constraint_generator::ConstraintGeneratorRegistrator< T >
• Parent : protocols::constraints_additional::MaxSeqSepConstraintSet
• parent : protocols::dna::RestrictDesignToProteinDNAInterface
• Parent : protocols::environment::AutoCutData , protocols::environment::claims::ClaimStrength , protocols::environment::claims::CutBiasClaim , protocols::environment::claims::JumpClaim , protocols::environment::claims::TorsionClaim , protocols::environment::claims::VirtResClaim , protocols::environment::claims::XYZClaim , protocols::environment::Environment , protocols::environment::EXCN_Env_Passport , protocols::environment::EXCN_Env_Security_Exception , protocols::environment::ProtectedConformation
• parent : protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::DiversifyStoredRBConfs , protocols::enzdes::EnzdesJobOutputter , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::ModifyStoredRBConfs , protocols::evaluation::EvaluatorRegistrator< T >
• Parent : protocols::evaluation::MetaPoseEvaluator
• parent : protocols::features::DatabaseJobOutputter , protocols::features::FeaturesReporterRegistrator< T > , protocols::filters::ContingentFilter , protocols::filters::FilterRegistrator< T > , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy
• Parent : protocols::fldsgn::topology::Helix , protocols::fldsgn::topology::Loop , protocols::fldsgn::topology::Strand
• parent : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::OtherContextScoreFunction , protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::flxbb::LayerDesignOperation , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::EntityElementRegistrator< T > , protocols::genetic_algorithm::Mutate1Randomizer , protocols::hotspot_hashing::SearchPatternRotSetOp
• Parent : protocols::jd2::archive::ArchiveManager , protocols::jd2::archive::EvaluatedArchive , protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::archive::NormalizedEvaluatedArchive , protocols::jd2::archive::VarianceStatisticsArchive
• parent : protocols::jd2::FileJobOutputter , protocols::jd2::JobInputterRegistrator< T > , protocols::jd2::JobOutputterRegistrator< T > , protocols::jd2::mmCIFJobOutputter , protocols::jd2::mmtfJobOutputter
• Parent : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor
• parent : protocols::jd2::PDBJobOutputter , protocols::jd2::RNA_DeNovoJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jd2::wwPDBJobOutputter , protocols::jd3::chunk_library_inputters::ChunkLibraryInputterRegistrator< T > , protocols::jd3::full_model_inputters::FullModelInputterRegistrator< T > , protocols::jd3::JobDigraph , protocols::jd3::JobDirectedEdge , protocols::jd3::JobDirectedNode , protocols::jd3::pose_inputters::PoseInputterRegistrator< T > , protocols::jd3::pose_outputters::PoseOutputterRegistrator< T > , protocols::jd3::pose_outputters::SecondaryPoseOutputterRegistrator< T > , protocols::jd3::standard::StandardInnerLarvalJob , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor , protocols::legacy_sewing::LegacyAppendAssemblyMover , protocols::legacy_sewing::LegacyEnumerateAssemblyMover , protocols::legacy_sewing::LegacyGivenPathAssemblyMover , protocols::legacy_sewing::LegacyGreedyAssemblyMover , protocols::legacy_sewing::LegacyMonteCarloAssemblyMover , protocols::legacy_sewing::LegacyReadNativeRotamersFile , protocols::legacy_sewing::LegacyRepeatAssemblyMover , protocols::legacy_sewing::sampling::requirements::LegacyRequirementRegistrator< T > , protocols::ligand_docking::rdf::RDFFunctionRegistrator< T >
• Parent : protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• parent : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• Parent : protocols::loops::loop_mover::LoopCM
• parent : protocols::loops::loops_definers::LoopsDefinerRegistrator< T > , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::CloudPDBWriter
• Parent : protocols::match::output::PDBWriter
• parent : protocols::match::output::PoseMatchOutputWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::match::upstream::BuildSet , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::matdes::InterfacePackingFilter , protocols::md::MDBase , protocols::mean_field::GenMeanFieldMover , protocols::membrane::scoring::FaWaterToBilayerEnergy
• Parent : protocols::minimization_packing::MinMover , protocols::moves::MoveMapMover , protocols::moves::MoverApplyingMover
• parent : protocols::moves::MoverRegistrator< T >
• Parent : protocols::moves::ReplicaExchangeMC
• parent : protocols::multistage_rosetta_scripts::cluster::ClusterMetricRegistrator< T > , protocols::multistate_design::PosType
• Parent : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::LabelResonance , protocols::noesy_assign::ProtonResonance
• parent : protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::FASTER_IG_Repacker , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::Mean , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PowExpression , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::RotamerSubsetRepacker , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VectorExpressionCreator , protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction , protocols::pack_daemon::VMax , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMin , protocols::pack_daemon::VMinBy , protocols::parser::DataLoaderRegistrator< T >
• Parent : protocols::parser::FragmentReader
• parent : protocols::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter
• Parent : protocols::protein_interface_design::filters::StubScoreLoopsFilter
• parent : protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::qsar::scoring_grid::GridRegistrator< T > , protocols::relax::AcceptToBestMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::ClassicRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , protocols::rigid::RigidBodyDeterministicSpinMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover
• Parent : protocols::rigid::RigidBodyPerturbNoCenterMover
• parent : protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyTiltMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::rna::AlignmentEnergy , protocols::rosetta_scripts::PosePropertyReporterRegistrator< T > , protocols::rosetta_scripts::PoseSelectorRegistrator< T > , protocols::rosetta_scripts::RosettaScriptsJobQueen , protocols::rotamer_recovery::RotamerRecoveryRegistrator< T > , protocols::score_filters::ScoreCutoffFilter , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4 , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::SpecialRotamerEnergy , protocols::scoring::methods::TargetClashEnergy , protocols::scoring::VDW_GridEnergy , protocols::sewing::requirements::AssemblyRequirementRegistrator< T > , protocols::sewing::scoring::AssemblyScorerRegistrator< T > , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::ChainCountFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• Parent : protocols::simple_moves::FragmentMover , protocols::simple_moves::LoggedFragmentMover
• parent : protocols::simple_moves::MembraneTopology , protocols::simple_moves::MutateResidue
• Parent : protocols::simple_moves::ResTypeFragmentMover
• parent : protocols::simple_moves::SetTorsion
• Parent : protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• parent : protocols::simple_moves::sidechain_moves::SetChiMover
• Parent : protocols::simple_moves::SmoothFragmentMover
• parent : protocols::simple_moves::StorePoseSnapshot
• Parent : protocols::simple_moves::WobbleMover
• parent : protocols::simple_task_operations::DockingNoRepack1 , protocols::simple_task_operations::DockingNoRepack2 , protocols::simple_task_operations::InterfaceTaskOperation , protocols::simple_task_operations::RestrictToInterface , protocols::simple_task_operations::RestrictToLoops , protocols::simple_task_operations::RestrictToLoopsAndNeighbors , protocols::splice::DesignInterfacesOperation , protocols::splice::FindEndpointsOperation , protocols::splice::SampleRotamersFromPDB , protocols::task_operations::AlignedThreadOperation , protocols::task_operations::DatabaseThread , protocols::task_operations::DesignAroundOperation , protocols::task_operations::DsspDesignOperation , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::InteractingRotamerExplosion , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::LinkResidues , protocols::task_operations::PreventChainFromRepackingOperation , protocols::task_operations::PreventResiduesFromRepackingOperation , protocols::task_operations::ProteinInterfaceDesignOperation , protocols::task_operations::ReadResfileFromDB , protocols::task_operations::RestrictByCalculatorsOperation , protocols::task_operations::RestrictChainToRepackingOperation
• Parent : protocols::task_operations::RestrictConservedLowDdgOperation
• parent : protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictInterGroupVectorOperation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::RestrictOperationsBase , protocols::task_operations::RestrictResiduesToRepackingOperation , protocols::task_operations::RestrictToAlignedSegmentsOperation , protocols::task_operations::RestrictToCDRH3Loop , protocols::task_operations::RestrictToInterfaceOperation , protocols::task_operations::RestrictToInterfaceVectorOperation , protocols::task_operations::RestrictToMoveMapChiOperation , protocols::task_operations::RestrictToNeighborhoodOperation , protocols::task_operations::SelectResiduesWithinChainOperation , protocols::task_operations::SeqprofConsensusOperation , protocols::task_operations::ThreadSequenceOperation , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::rotamer_set_operations::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO
• Parent : protocols::topology_broker::AsymFoldandDockClaimer , protocols::topology_broker::BasicJumpClaimer , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::FibrilModelingClaimer , protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer , protocols::topology_broker::FragmentJumpClaimer , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4 , protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer , protocols::topology_broker::SymmetryClaimer , protocols::topology_broker::TMHTopologySamplerClaimer
• parent1 : core::energy_methods::AACompositionEnergy , core::energy_methods::AARepeatEnergy , core::energy_methods::DumpTrajectoryEnergy , core::energy_methods::MHCEpitopeEnergy , core::energy_methods::NetChargeEnergy , core::energy_methods::RNA_PartitionEnergy , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::sap::SapConstraintEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• parent2 : core::energy_methods::AACompositionEnergy , core::energy_methods::AARepeatEnergy , core::energy_methods::DumpTrajectoryEnergy , core::energy_methods::MHCEpitopeEnergy , core::energy_methods::NetChargeEnergy , core::energy_methods::RNA_PartitionEnergy , core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty , core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy , core::pack::guidance_scoreterms::sap::SapConstraintEnergy , core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy
• ParentOP : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• ParsedProtocolOP : protocols::evolution::EvolutionaryDynamicsMover , protocols::monte_carlo::GenericMonteCarloMover
• ParsedProtocolStepVector : protocols::rosetta_scripts::ParsedProtocol
• PartialAtomID : core::conformation::Conformation
• PassportStack : protocols::environment::ClientMover
• PatchdockReaderOP : protocols::protein_interface_design::movers::PatchdockTransform
• PBIter : core::conformation::PseudoBondCollection
• PCSData : protocols::nmr::pcs::PCSEnergy , protocols::nmr::pcs::PCSLigandTransformMover
• PCSDataCOP : protocols::nmr::pcs::PCSLigandTransformMover
• PCSDataOP : protocols::nmr::pcs::PCSLigandTransformMover
• PCSMultiSet : protocols::nmr::pcs::PCSEnergy
• PCSSingle : protocols::qsar::scoring_grid::PCSSingleGrid
• PCSSingleOP : protocols::qsar::scoring_grid::PCSSingleGrid
• PCSSingleSetOP : protocols::nmr::pcs::PCSTensorOptimizer
• PCSTensor : protocols::qsar::scoring_grid::PCSSingleGrid
• PCSTensorCOP : protocols::qsar::scoring_grid::PCSSingleGrid
• PCSTensorOP : protocols::qsar::scoring_grid::PCSSingleGrid
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• PeptideStubMover : protocols::helical_bundle::BackboneGridSampler
• PeptideStubMoverCOP : protocols::helical_bundle::BackboneGridSampler
• PeptideStubMoverOP : protocols::helical_bundle::BackboneGridSampler
• Permutation : protocols::denovo_design::components::StructureDataPerturber
• Permutations : protocols::denovo_design::components::StructureDataPerturber
• PermutationsByPerturber : protocols::denovo_design::components::CompoundPerturber
• PermutationSelector : protocols::denovo_design::components::StructureDataPerturber
• PerResidueAAProbSet : protocols::task_operations::ResidueProbDesignOperation
• piecewise_poly : core::conformation::membrane::AqueousPoreParameters , core::conformation::membrane::ImplicitLipidInfo , protocols::membrane::AqueousPoreFinder
• pointer : core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• Pointer : protocols::mean_field::jagged_array< T, A >
• pointer : protocols::mean_field::jagged_array< T, A > , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• pop_const_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• Pose : core::energy_methods::RNA_CoarseDistEnergy , core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , core::pack::task::operation::ResFilter , core::pack::task::operation::TaskOperation , core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent , core::scoring::constraints::ConstraintSet , core::scoring::constraints::SequenceProfileConstraint , core::scoring::MinimizationEdge , core::scoring::MinimizationNode , core::scoring::OmegaTether , core::scoring::PointWaterPotential , core::scoring::Ramachandran2B , core::scoring::Ramachandran , core::scoring::RamaPrePro , core::select::util::SelectResiduesByLayer , core::sequence::ABEGOManager , protocols::boinc::BoincCurrentPoseObserver , protocols::calc_taskop_movers::ConsensusDesignMover , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::dna_dock::DNAClashCheckFilter , protocols::dna_dock::PropagateClashCheckFilter , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::evolution::EvolutionaryDynamicsMover , protocols::evolution::NucleotideMutation , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::fldsgn::filters::FragQualFilter , protocols::fldsgn::filters::HelixKinkFilter , protocols::fldsgn::filters::HelixPairingFilter , protocols::fldsgn::filters::HSSTripletFilter , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::filters::NcontactsFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::fldsgn::filters::SecondaryStructureCountFilter , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::SecondaryStructureHasResidueFilter , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::filters::StrandCurvatureByLevels , 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::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintGenerator , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::Sheet , protocols::fldsgn::topology::SS_Info2 , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Layer , protocols::flxbb::DesignTask_Normal , 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::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::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::forge::remodel::RemodelRotamerLinks , protocols::hbnet::ConstrainHBondNetwork , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::loophash::FastGapMover , protocols::match::output::PoseInserter , protocols::matdes::ClashCheckFilter , protocols::matdes::GetRBDOFValues , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::metal_interface::MatchGrafter , protocols::minimization_packing::GreenPacker , protocols::minimization_packing::GroupDiscriminator , 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::Mover , protocols::nmr::pcs::PCSEnergy , protocols::nmr::pcs::PCSLigandTransformMover , protocols::nmr::pre::PREEnergy , protocols::nmr::pre::PREMover , protocols::nmr::rdc::RDCEnergy , protocols::nonlocal::SingleFragmentMover , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::pack_interface::ProteinProteinInterfaceUpweighter , protocols::parser::BluePrint , protocols::parser::FragmentReader , protocols::pose_metric_calculators::FragQualCalculator , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::ReportSequenceDifferences , protocols::qsar::scoring_grid::PCSMultiGrid , protocols::qsar::scoring_grid::PCSSingleGrid , protocols::rna::movers::ErraserMinimizerMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , protocols::simple_ddg::ddG , 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::simple_moves::BBGaussianMover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::splice::SampleRotamersFromPDB , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation , protocols::splice::Splice , protocols::splice::SpliceOut , protocols::symmetry::DetectSymmetry , protocols::task_operations::ImportUnboundRotamersOperation , protocols::task_operations::JointSequenceOperation , protocols::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::task_operations::LimitAromaChi2Operation , protocols::task_operations::RestrictNativeResiduesOperation , protocols::task_operations::SeqprofConsensusOperation , protocols::viewer::SilentObserver
• PoseCOP : protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::pack_daemon::PackDaemon , protocols::sic_dock::Rose , protocols::simple_moves::BBGaussianMover
• PoseFolder : protocols::denovo_design::components::NullPoseFolder , protocols::denovo_design::components::RandomTorsionPoseFolder , protocols::denovo_design::components::RemodelLoopMoverPoseFolder
• PoseFolderOP : protocols::denovo_design::components::NullPoseFolder , protocols::denovo_design::components::RandomTorsionPoseFolder , protocols::denovo_design::components::RemodelLoopMoverPoseFolder
• PoseInputSourcesAndInputters : protocols::jd3::pose_inputters::PoseInputterFactory
• PoseInputterMap : protocols::jd3::pose_inputters::PoseInputterFactory
• PoseList : protocols::denovo_design::DisulfidizeMover
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMetricCalculatorOP : protocols::fldsgn::NcontactsCalculator , protocols::pose_metric_calculators::FragQualCalculator
• PoseOP : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::dna::PDBOutput , protocols::evolution::EvolutionaryDynamicsMover , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::forge::remodel::RemodelLoopMover , protocols::monte_carlo::GenericMonteCarloMover , protocols::monte_carlo::MonteCarloRecover , protocols::monte_carlo::MonteCarloReset , protocols::monte_carlo::MonteCarloTest , protocols::moves::MonteCarlo , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::simple_moves::BBGaussianMover , protocols::symmetry::DetectSymmetry
• PoseOPs : protocols::comparative_modeling::ThreadingJobInputter
• PoseOutputterMap : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::pose_outputters::PoseOutputterFactory
• PosePropertyReporterMap : protocols::rosetta_scripts::PosePropertyReporterFactory
• Poses : protocols::comparative_modeling::MultiThreadingMover
• PoseSelectorMap : protocols::rosetta_scripts::PoseSelectorFactory
• PoseVector : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator
• Position : core::kinematics::tree::Atom
• PositionMap : core::sequence::AnnotatedSequence
• Positions : 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::VarLengthBuild
• PosList : core::fragment::NonContinuousFrame
• PosType : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• PrecomputedPairEnergiesInteractionGraph : protocols::minimization_packing::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::minimization_packing::GreenPacker
• PREData : protocols::nmr::pre::PREMover
• PREDataCOP : protocols::nmr::pre::PREMover
• PREDataOP : protocols::nmr::pre::PREMover
• PREDistances : protocols::nmr::pre::PREMover
• PreparerSet : protocols::abinitio::abscript::AbscriptStageMover
• Probabilities : protocols::medal::MedalMover , protocols::nonlocal::BiasedFragmentMover
• Probability_AA : core::scoring::P_AA
• Probability_AA_n : core::scoring::P_AA
• Probability_AA_n_n : protocols::simple_moves::StructProfileMover
• Probability_AA_pp : core::scoring::P_AA
• ProjectionVector : protocols::evaluation::PCA
• PWM : core::scoring::mhc_epitope_energy::AlleleMatrix