- p -

• PackerEnergy : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• PackerTask : core::pack::task::operation::OptCysHG , protocols::enzdes::AddLigandMotifRotamers , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::flxbb::LayerDesignOperation , core::pack::task::operation::OptH , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::forge::remodel::RemodelRotamerLinks , protocols::motifs::LigandMotifSearch , protocols::dna::WatsonCrickRotamerCouplings , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::enzdes::SetCatalyticResPackBehavior , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::enzdes::DetectProteinLigandInterface , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::JointSequenceOperation , core::pack::task::operation::NoRepackDisulfides , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::enzdes::AddRigidBodyLigandConfs , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• PackerTaskCOP : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::PDBOutput , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesignPack , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• PackerTaskOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Normal , protocols::flxbb::DesignTask_Layer , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::QuickRepacker , protocols::scoring::Interface , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• Page : core::fragment::picking_old::vall::VallResidues , core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library >
• 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
• Pairings : protocols::abinitio::AlternativePairings
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• Params : core::scoring::dna::DNA_BasePotential
• parent : core::pack::task::operation::NoResFilter , core::scoring::methods::OneBodyEnergy
• Parent : protocols::abinitio::IterativeFullatom , protocols::abinitio::JumpingFoldConstraints
• parent : core::scoring::methods::P_AA_Energy
• Parent : protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraintsWrapper
• parent : core::pack::task::operation::ResidueTypeFilter , core::scoring::methods::P_AA_pp_Energy
• Parent : protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::HamiltonianExchange
• parent : core::scoring::methods::PackStatEnergy
• Parent : protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder
• parent : core::pack::task::operation::ResidueHasProperty , core::scoring::methods::PairEnergy
• Parent : protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder
• parent : core::scoring::methods::PeptideBondEnergy
• Parent : protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase
• parent : core::pack::task::operation::ResidueLacksProperty , core::scoring::methods::pHEnergy
• Parent : protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::evaluation::MetaPoseEvaluator
• parent : core::scoring::methods::PoissonBoltzmannEnergy
• Parent : protocols::fldsgn::topology::Strand , protocols::fldsgn::topology::Helix
• parent : core::pack::task::operation::ResidueName3Is , core::scoring::methods::ProClosureEnergy
• Parent : protocols::fldsgn::topology::Loop , protocols::jd2::archive::EvaluatedArchive
• parent : core::scoring::methods::RamachandranEnergy
• Parent : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::archive::NormalizedEvaluatedArchive
• parent : core::pack::task::operation::ResidueName3Isnt , core::scoring::methods::RamachandranEnergy2B
• Parent : protocols::jd2::archive::VarianceStatisticsArchive , protocols::jd2::MPIFileBufJobDistributor
• parent : core::scoring::methods::ReferenceEnergy
• Parent : protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::parser::FragmentReader
• parent : core::pack::task::operation::ResidueIndexIs , core::scoring::methods::ReferenceEnergyNoncanonical
• Parent : protocols::loops::EXCN_Loop_not_closed , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• parent : core::scoring::methods::ResidualDipolarCouplingEnergy
• Parent : protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• parent : core::pack::task::operation::ResidueIndexIsnt , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl
• Parent : protocols::match::output::PDBWriter , protocols::moves::ReplicaExchangeMC
• parent : core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments
• Parent : protocols::noesy_assign::EXCN_NoesyAssign , protocols::noesy_assign::FloatingResonance
• parent : core::pack::task::operation::ResiduePDBIndexIs , core::scoring::methods::RG_Energy_Fast
• Parent : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::rigid::RigidBodyPerturbNoCenterMover
• parent : core::scoring::methods::RMS_Energy
• Parent : protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• parent : core::pack::task::operation::ResiduePDBIndexIsnt , core::scoring::methods::SA_Energy
• Parent : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• parent : core::scoring::methods::SecondaryStructureEnergy
• Parent : protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::WobbleMover
• parent : core::pack::task::operation::ChainIs , core::scoring::methods::SequenceDependentRefEnergy
• Parent : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::topology_broker::AsymFoldandDockClaimer
• parent : core::scoring::methods::ShortRangeTwoBodyEnergy
• Parent : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• parent : core::pack::task::operation::ChainIsnt , core::scoring::methods::SmoothCenPairEnergy
• Parent : protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::EXCN_TopologyBroker
• parent : core::scoring::methods::SmoothEnvEnergy
• Parent : protocols::topology_broker::EXCN_Input , protocols::topology_broker::EXCN_FailedBroking
• parent : core::pack::task::operation::ResLvlTaskOperationRegistrator< T > , core::scoring::methods::SuckerEnergy
• Parent : protocols::topology_broker::EXCN_FilterFailed , protocols::topology_broker::FibrilModelingClaimer
• parent : core::scoring::methods::SymmetricLigandEnergy
• Parent : protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer
• parent : core::pack::task::operation::RestrictToRepackingRLT , core::scoring::methods::TwoBodyEnergy
• Parent : protocols::topology_broker::JumpClaimer , protocols::topology_broker::MembraneTopologyClaimer
• parent : core::scoring::methods::UnfoldedStateEnergy
• Parent : protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController
• parent : core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::scoring::methods::VDW_Energy
• Parent : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer
• parent : core::scoring::methods::WaterAdductHBondEnergy , core::pack::task::operation::DisallowIfNonnativeRLT , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WholeStructureEnergy , core::pack::task::operation::PreventRepackingRLT , core::scoring::methods::YHHPlanarityEnergy , core::scoring::MinimizationNode , core::pack::task::operation::AddBehaviorRLT , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::pack::task::operation::DockingNoRepack1 , core::scoring::MinScoreScoreFunction , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::pack::task::operation::DockingNoRepack2 , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::pack::task::operation::RestrictToInterface , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::pack::task::operation::TaskOperationRegistrator< T > , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::solid_surface::SurfaceEnergies , core::pack::task::operation::RestrictToRepacking , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborNode , core::pack::task::operation::RestrictResidueToRepacking , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::scoring::TwelveANeighborNode , core::scoring::TwelveANeighborEdge , core::pack::task::operation::DisallowIfNonnative , core::scoring::TwelveANeighborGraph , core::sequence::SequenceRegistrator< T > , core::pack::task::operation::RotamerExplosion , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::enzdes::EnzdesJobOutputter , core::pack::task::operation::InitializeFromCommandline , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::GenerateStoredRBConfs , core::pack::task::operation::InitializeExtraRotsFromCommandline , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::MinimizeStoredRBConfs , core::pack::task::operation::IncludeCurrent , protocols::enzdes::DiversifyStoredRBConfs , protocols::evaluation::EvaluatorRegistrator< T > , core::pack::task::operation::ExtraRotamersGeneric , protocols::features::DatabaseJobOutputter , protocols::features::FeaturesReporterRegistrator< T > , core::pack::task::operation::ReadResfile , protocols::filters::ContingentFilter , protocols::filters::FilterRegistrator< T > , core::pack::task::operation::ReadResfileAndObeyLengthEvents , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , core::pack::task::operation::SetRotamerCouplings , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::task::operation::SetRotamerLinks , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , core::pack::task::operation::AppendRotamer , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::pack::task::operation::AppendRotamerSet , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::task::operation::AppendResidueRotamerSet , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , core::pack::task::operation::PreserveCBeta , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::OtherContextScoreFunction , core::pack::task::operation::PreventRepacking , protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::flxbb::LayerDesignOperation , core::pack::task::operation::RestrictYSDesign , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::EntityElementRegistrator< T > , core::pack::task::operation::ExtraRotamers , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::jd2::FileJobOutputter , core::pack::task::operation::ExtraChiCutoff , protocols::jd2::JobInputterRegistrator< T > , protocols::jd2::JobOutputterRegistrator< T > , core::pack::task::TaskFactory , protocols::jd2::parser::DataLoaderRegistrator< T > , protocols::jd2::PDBJobOutputter , core::scoring::constraints::PeriodicBoundFunc , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , core::scoring::constraints::OffsetPeriodicBoundFunc , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , core::conformation::RotamerSetBase , core::scoring::constraints::ConstraintRegistrator< T > , protocols::jobdist::PlainSilentFileJobDistributor , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , core::scoring::constraints::ConstraintNode , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , core::graph::Graph , core::scoring::constraints::ConstraintEdge , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , core::scoring::constraints::ConstraintGraph
• Parent : protocols::abinitio::IterativeCentroid , protocols::abinitio::IterativeBase , protocols::abinitio::IterativeAbrelax , protocols::abinitio::HedgeArchive , protocols::abinitio::FragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::ConstraintFragmentSampler
• parent : protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• Parent : core::pose::datacache::SpecialSegmentsObserver , core::kinematics::EXCN_InvalidFoldTree , core::fragment::SecstructSRFD , core::fragment::OrderedFragSet , core::fragment::DownJumpSRFD , core::fragment::UpJumpSRFD
• parent : protocols::loops::loops_definers::LoopsDefinerRegistrator< T > , core::io::silent::SilentStructRegistrator< T >
• Parent : core::fragment::AnnotatedFragData , core::fragment::FragStore< T > , core::fragment::FragCache< T > , core::fragment::ConstantLengthFragSet , core::fragment::BBTorsionSRFD , core::fragment::BBTorsionAndAnglesSRFD
• parent : protocols::toolbox::task_operations::ThreadSequenceOperation , core::scoring::constraints::FourPointsFunc , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , core::scoring::ContextGraph , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LayerOperations , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , core::optimization::MinimizerMap , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::MutateResidue , protocols::simple_moves::MembraneTopology , core::scoring::disulfides::FullatomDisulfidePotential , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AtomicContactFilter , protocols::scoring::methods::SpecialRotamerEnergy , core::scoring::dna::DNAChiEnergy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::EnsembleEnergy , protocols::rotamer_recovery::RotamerRecoveryRegistrator< T > , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::RigidBodyTransMover , core::optimization::Multifunc , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyMover , protocols::relax::RelaxProtocolBase , protocols::relax::MiniRelax , core::scoring::dna::DNATorsionEnergy , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::match::output::CloudPDBWriter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::pack_daemon::FASTER_IG_Repacker , protocols::pack_daemon::DoubleDenseIGRepacker , core::scoring::DockingScoreFunction , protocols::match::output::PoseMatchOutputWriter , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::pack_daemon::VectorExpressionCreator , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::LnExpression , core::optimization::NumDerivCheckData , core::scoring::EnergyNode , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::pack_daemon::VMin , protocols::pack_daemon::VMax , protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VectorFunction , protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::VectorExpression , core::scoring::EnergyEdge , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::multistate_design::PosType , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::OriginalBackboneBuildPoint , core::optimization::NumericalDerivCheckResult , core::scoring::EnergyGraph , protocols::match::upstream::BuildSet , protocols::moves::MoverRegistrator< T > , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator > , core::optimization::SingleResidueMultifunc , core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , protocols::optimize_weights::PSSMOptEPositionData , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::pack::annealer::FASTERAnnealer , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator > , core::pack::dunbrack::DunbrackEnergy , core::scoring::etable::CoarseEtableEnergy , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMinBy , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , protocols::pack_daemon::PowExpression , protocols::pack_daemon::ExpExpression , core::pack::dunbrack::DunbrackRotamer< S, P > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairCrossover3 , core::pack::dunbrack::PackedDunbrackRotamer< S, P > , core::scoring::etable::count_pair::CountPairCrossover4 , protocols::pack_daemon::DynamicAggregateFunction , core::scoring::etable::count_pair::CountPairGeneric , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::pack::dunbrack::BBDepSemiRotamericData< T > , core::scoring::etable::count_pair::CountPairIntraResC4 , protocols::pack_daemon::RotamerSubsetRepacker , protocols::pack_daemon::DenseIGRepacker , core::scoring::etable::count_pair::CountPairNone , core::pack::dunbrack::BBIndSemiRotamericData< T > , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , core::scoring::etable::etrie::EtableAtom , protocols::protein_interface_design::filters::DisulfideFilter , core::scoring::hackelec::ElecAtom , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::pack::interaction_graph::FASTERNode , core::scoring::hackelec::RNAHackElecEnergy , protocols::qsar::scoring_grid::GridRegistrator< T > , protocols::relax::ClassicRelax , core::scoring::methods::CartesianBondedEnergy , core::pack::interaction_graph::FASTEREdge , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::pack::interaction_graph::FASTERInteractionGraph , core::scoring::methods::ChainbreakEnergy , protocols::rigid::RigidBodyDeterministicSpinMover , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::pack::interaction_graph::HPatchEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::ContextDependentLRTwoBodyEnergy , core::pack::interaction_graph::HPatchNode< V, E, G > , core::scoring::methods::ContextDependentOneBodyEnergy , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , core::scoring::methods::ContextDependentTwoBodyEnergy , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::scoring::methods::ContextIndependentLRTwoBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::scoring::methods::ContextIndependentTwoBodyEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::CustomAtomPairEnergy , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::scoring::methods::DirectReadoutEnergy , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , core::scoring::methods::DistanceChainbreakEnergy , protocols::simple_filters::ScoreCutoffFilter , core::pack::interaction_graph::SurfaceEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::scoring::methods::EnergyMethodRegistrator< T > , protocols::toolbox::match_enzdes_util::LigandConformer , core::scoring::methods::EnvEnergy , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::scoring::methods::Fa_MbsolvEnergy , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , core::scoring::methods::FACTSEnergy , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::scoring::methods::HybridVDW_Energy , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , core::scoring::methods::LinearChainbreakEnergy , core::pack::rotamer_set::ContinuousRotamerSet , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::pack::rotamer_set::FixbbRotamerSets , core::scoring::methods::LK_hack , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::DockingNoRepack1 , core::scoring::methods::LongRangeTwoBodyEnergy , core::pack::rotamer_set::RotamerSet , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::pack::task::operation::OperateOnCertainResidues , core::scoring::methods::MembraneEnvEnergy , protocols::toolbox::task_operations::SeqprofConsensusOperation , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::NMerPSSMEnergy
• Parent : protocols::abinitio::ClassicAbinitio
• parent : core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMBondLengthEnergy
• Parent : core::fragment::NonContinuousFrame
• parent : core::scoring::methods::MembraneEnvPenalties , core::pack::task::operation::ReplicateTask , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::pack::task::operation::ResFilterRegistrator< T > , core::scoring::methods::MMBondAngleEnergy
• Parent : core::fragment::FragSetCollection
• parent : core::pack::task::operation::ResFilterComposition , core::pack::task::operation::AnyResFilter , core::scoring::methods::MMTorsionEnergy , core::pack::task::operation::AllResFilter
• PBIter : core::conformation::PseudoBondCollection
• PBLifetimeCache : core::scoring::methods::PoissonBoltzmannEnergy
• PBLifetimeCacheOP : core::scoring::methods::PoissonBoltzmannEnergy
• Pdb2Pose : core::pose::PDBPoseMap
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• pointer : core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• pop_const_const_iter : protocols::genetic_algorithm::GeneticAlgorithm
• pop_const_iter : protocols::genetic_algorithm::GeneticAlgorithm
• pop_iter : protocols::genetic_algorithm::GeneticAlgorithm
• Pose : protocols::simple_moves::MonteCarloRecover , core::pack::task::operation::OptH , protocols::design_opt::ParetoOptMutationMover , core::pack::task::operation::ResFilter , protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter , protocols::forge::build::SegmentRebuild , protocols::protein_interface_design::FavorNativeResidue , protocols::fldsgn::BluePrintBDR , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::seeded_abinitio::SwapSegment , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::DockDesignFilterFactory , protocols::forge::build::SegmentSwap , protocols::loophash::FastGapMover , protocols::nonlocal::SingleFragmentMover , protocols::match::output::PoseInserter , protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover , protocols::forge::components::VarLengthBuild , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::flxbb::FilterStructs_TotalCharge , protocols::forge::build::GrowLeft , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::forge::build::BuildInstruction , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::fldsgn::topology::Sheet , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::filters::InterlockingAromaFilter , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::filters::NcontactsFilter , protocols::flxbb::DesignTask , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::design_opt::PointMutationCalculator , core::pack::task::operation::TaskOperation , protocols::enzdes::BackboneSampler , protocols::toolbox::task_operations::LayerOperations , protocols::fldsgn::filters::HelixPairingFilter , protocols::design_opt::GreedyOptMutationMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::PDBOutput , core::pose::signals::DestructionEvent , protocols::seeded_abinitio::SegmentHybridizer , core::scoring::Ramachandran , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::BuildAlaPose , protocols::pack_daemon::DaemonSet , protocols::simple_filters::RangeFilter , protocols::jd2::Parser , protocols::idealize::IdealizeMover , protocols::forge::constraints::RemoveCsts , protocols::forge::constraints::NtoC_RCG , protocols::forge::build::Bridge , protocols::flxbb::LayerDesignOperation , protocols::flxbb::DesignTask_Layer , protocols::simple_moves::ConsensusDesignMover , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::filters::SheetTopologyFilter , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::simple_moves::GreenPacker , protocols::simple_moves::GenericMonteCarloMover , protocols::fldsgn::filters::HelixKinkFilter , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::task::operation::OptCysHG , protocols::simple_moves::GroupDiscriminator , protocols::constraints_additional::SequenceCoupling1BDConstraint , core::scoring::Ramachandran2B , core::pose::signals::GeneralEvent , core::scoring::MinimizationEdge , core::scoring::constraints::ConstraintSet , core::fragment::IndependentBBTorsionSRFD , protocols::fldsgn::filters::HSSTripletFilter , core::pack::task::operation::OperateOnCertainResidues , protocols::enzdes::DetectProteinLigandInterface , protocols::simple_moves::MonteCarloTest , protocols::enzdes::SetCatalyticResPackBehavior , protocols::fldsgn::filters::FragQualFilter , protocols::rosetta_scripts::ParsedProtocol , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::MatchResiduesMover , protocols::simple_moves::BBGaussianMover , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::SheetConstraintsRCG , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::FlxbbDesign , protocols::forge::build::RelativeConnectRight , protocols::moves::FilterMover , protocols::forge::remodel::RemodelDesignMover , protocols::simple_filters::PackStatFilter , protocols::moves::MoverFactory , protocols::pack_daemon::MultistateFitnessFunction , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::ReportPSSMDifferences , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::ReportSequenceDifferences , protocols::motifs::LigandMotifSearch , protocols::forge::build::ConnectRight , protocols::flxbb::InterlockAroma , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::MatchResidues , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::filters::FilterFactory , core::pack::task::operation::NoRepackDisulfides , protocols::motifs::MotifSearch , core::scoring::constraints::SequenceProfileConstraint , protocols::enzdes::ProteinLigandInterfaceUpweighter , core::fragment::picking_old::vall::eval::EnergyEval , protocols::moves::Mover , protocols::fldsgn::CircularPermutation , protocols::simple_filters::HolesFilter , protocols::toolbox::task_operations::JointSequenceOperation , protocols::moves::MonteCarlo , protocols::forge::build::BuildManager , protocols::simple_filters::ShapeComplementarityFilter , protocols::forge::remodel::RemodelLoopMover , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::simple_moves::ddG , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::sic_dock::RigidScore , protocols::simple_moves::symmetry::DetectSymmetry , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LimitAromaChi2Operation , core::util::ABEGOManager , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::PlaceFragments , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::LoopLengthChange , protocols::flxbb::DesignTask_Normal , protocols::jd2::parser::BluePrint , protocols::forge::build::GrowRight , core::scoring::OmegaTether , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::fldsgn::NcontactsCalculator , protocols::sic_dock::Rose , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::constraints_additional::SequenceCouplingConstraint , core::scoring::MinimizationNode , protocols::flxbb::FilterStructs , protocols::dna::WatsonCrickRotamerCouplings , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::boinc::BoincCurrentPoseObserver , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::remodel::RemodelAccumulator , protocols::fldsgn::topology::SS_Info2 , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::build::SegmentInsert , protocols::seeded_abinitio::CoordinateCst , protocols::protein_interface_design::movers::BackrubDDMover , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::viewer::SilentObserver , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::jd2::parser::FragmentReader
• PoseCOP : protocols::dna::PDBOutput , protocols::pack_daemon::PackDaemon , protocols::moves::Mover , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::moves::MonteCarlo , protocols::simple_moves::BBGaussianMover , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::sic_dock::Rose
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMetricCalculatorOP : protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::fldsgn::NcontactsCalculator
• PoseOP : protocols::simple_moves::BBGaussianMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::fldsgn::BluePrintBDR , protocols::pack_daemon::MultistateFitnessFunction , protocols::forge::remodel::RemodelLoopMover , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MonteCarloRecover , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::pack_daemon::QuickRepacker , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flxbb::FilterStructs , protocols::pack_daemon::PackDaemon , core::pack::interaction_graph::OnTheFlyInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::pack_daemon::DaemonSet , protocols::moves::MonteCarlo , protocols::dna::PDBOutput
• PoseOPs : protocols::comparative_modeling::ThreadingJobInputter
• Poses : protocols::comparative_modeling::MultiThreadingMover
• PoseSP : protocols::simple_moves::O2M_MutateMover
• PoseVector : protocols::noesy_assign::StructureDependentPeakCalibrator , protocols::noesy_assign::DistanceScoreMover
• Position : core::kinematics::tree::Atom
• PositionMap : core::sequence::AnnotatedSequence
• Positions : protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild , protocols::forge::build::ConnectRight , protocols::forge::components::VarLengthBuild , protocols::forge::build::SegmentInsert , protocols::forge::build::Bridge , protocols::forge::build::SegmentSwap , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::RelativeConnectRight , protocols::forge::build::GrowRight
• PosList : core::fragment::NonContinuousFrame
• PosType : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• PrecomputedPairEnergiesInteractionGraph : protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::simple_moves::GreenPacker
• Probabilities : protocols::nonlocal::BiasedFragmentMover , protocols::medal::MedalMover
• Probability_AA : core::scoring::P_AA
• Probability_AA_n : core::scoring::P_AA
• Probability_AA_pp : core::scoring::P_AA
• ProjectionVector : protocols::evaluation::PCA