- p -

• PackerTask : core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH
• PackerTaskCOP : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• 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
• PairFuncMap : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• Params : core::scoring::dna::DNA_BasePotential
• parent : core::conformation::RotamerSetBase
• 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::NonContinuousFrame , core::fragment::OrderedFragSet , core::fragment::SecstructSRFD , core::fragment::UpJumpSRFD
• parent : core::graph::Graph
• Parent : 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 > , core::pack::dunbrack::BBIndSemiRotamericData< T > , core::pack::dunbrack::cenrot::CenRotDunEnergy , core::pack::dunbrack::DunbrackEnergy , core::pack::dunbrack::DunbrackRotamer< S, P > , core::pack::dunbrack::PackedDunbrackRotamer< S, P > , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , 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::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::rotamer_set::ContinuousRotamerSet , core::pack::rotamer_set::FixbbRotamerSets , core::pack::rotamer_set::RotamerSet , 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::DockingNoRepack1 , core::pack::task::operation::DockingNoRepack2 , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::NoResFilter , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::PreventRepackingRLT , 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::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToInterface , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictToRepackingRLT , 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::residue_selector::ResidueSelectorRegistrator< T > , 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::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::elec::ElecAtom , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::EnergyNode , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover4 , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , 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 , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , 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::CustomAtomPairEnergy , core::scoring::methods::D2H_SA_Energy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodRegistrator< T > , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::FreeMoietyEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GoapEnergy , core::scoring::methods::HybridVDW_Energy , core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LK_PolarNonPolarEnergy , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , 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::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::OtherPoseEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::methods::YHHPlanarityEnergy , 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::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TenANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::scoring::TwelveANeighborNode , core::sequence::SequenceRegistrator< T >
• PBIter : core::conformation::PseudoBondCollection
• PBLifetimeCache : core::scoring::methods::PoissonBoltzmannEnergy
• PBLifetimeCacheOP : core::scoring::methods::PoissonBoltzmannEnergy
• Pdb2Pose : core::pose::PDBPoseMap
• pointer : core::io::silent::SilentFileData::const_iterator , core::io::silent::SilentFileData::iterator
• Pose : 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::Rama2BOffset , core::scoring::Ramachandran2B , core::scoring::Ramachandran , core::util::ABEGOManager
• PoseOP : core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph
• Position : core::kinematics::tree::Atom
• PositionMap : core::sequence::AnnotatedSequence
• PosList : core::fragment::NonContinuousFrame
• Probability_AA : core::scoring::P_AA
• Probability_AA_n : core::scoring::P_AA
• Probability_AA_pp : core::scoring::P_AA