- 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
• PackerTask : protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelRotamerLinks , protocols::motifs::LigandMotifSearch , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• PackerTaskCOP : 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_Layer , protocols::flxbb::DesignTask_Normal , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::scoring::Interface , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• Pairings : protocols::abinitio::AlternativePairings
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• PairList : protocols::sparta::PDB
• Parent : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::JumpSampleData , 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::JumpingFoldConstraints , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::MpiHamiltonianExchange , protocols::canonical_sampling::MpiParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , 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::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::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 >
• Parent : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::MPIMultiCommJobDistributor
• parent : protocols::jd2::parser::DataLoaderRegistrator< T >
• Parent : protocols::jd2::parser::FragmentReader
• parent : protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor , protocols::ligand_docking::rdf::RDFFunctionRegistrator< T >
• Parent : protocols::loops::EXCN_Loop_not_closed , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure , protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• parent : 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 , 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::md::MDBase , protocols::moves::MoverRegistrator< T >
• Parent : protocols::moves::ReplicaExchangeMC
• parent : protocols::multistate_design::PosType
• Parent : protocols::noesy_assign::EXCN_NoesyAssign , protocols::noesy_assign::FloatingResonance
• 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::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::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::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::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::rosetta_scripts::PosePropertyReporterRegistrator< T > , protocols::rosetta_scripts::PoseSelectorRegistrator< T > , protocols::rotamer_recovery::RotamerRecoveryRegistrator< T > , 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::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreCutoffFilter
• Parent : 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 , protocols::simple_moves::WobbleMover
• parent : protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InterfaceTaskOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , protocols::toolbox::task_operations::RestrictChainToRepackingOperation
• Parent : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• parent : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToCDRH3Loop , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToMoveMapChiOperation , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• 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::EXCN_FailedBroking , protocols::topology_broker::EXCN_FilterFailed , protocols::topology_broker::EXCN_Input , protocols::topology_broker::EXCN_TopologyBroker , 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
• ParentOP : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• ParsedProtocolOP : protocols::simple_moves::GenericMonteCarloMover
• PassportStack : protocols::environment::ClaimingMover
• PatchdockReaderOP : protocols::protein_interface_design::movers::PatchdockTransform
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• PerResidueAAProbSet : protocols::antibody::design::ResidueProbDesignOperation
• Pointer : protocols::jd2::utility::pointer::access_ptr< T >
• pointer : protocols::jd2::utility::pointer::access_ptr< T >
• Pointer : protocols::jd2::utility::RawType< T > , protocols::jd2::utility::RawType< T & > , protocols::jd2::utility::RawType< T * >
• pointer : 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 : protocols::boinc::BoincCurrentPoseObserver , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::constraints_additional::SequenceCouplingConstraint , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::SetCatalyticResPackBehavior , protocols::filters::FilterFactory , 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::SheetTopologyFilter , 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::NatbiasSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintsRCG , 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::ConstraintFileRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelGlobalFrame , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::idealize::IdealizeMover , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::jd2::Parser , protocols::loophash::FastGapMover , protocols::match::output::PoseInserter , protocols::metal_interface::MatchGrafter , protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::nonlocal::SingleFragmentMover , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::DockDesignFilterFactory , 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::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporterFactory , protocols::rosetta_scripts::PoseSelectorFactory , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , 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
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMetricCalculatorOP : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• PoseOP : protocols::dna::PDBOutput , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::forge::remodel::RemodelLoopMover , 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::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::symmetry::DetectSymmetry
• PoseOPs : protocols::comparative_modeling::ThreadingJobInputter
• PosePropertyReporterMap : protocols::rosetta_scripts::PosePropertyReporterFactory
• Poses : protocols::comparative_modeling::MultiThreadingMover
• PoseSelectorMap : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSP : protocols::simple_moves::O2M_MutateMover
• PoseVector : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator
• 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
• PosType : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• PrecomputedPairEnergiesInteractionGraph : protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::simple_moves::GreenPacker
• PreparerSet : protocols::abinitio::abscript::AbscriptStageMover
• Probabilities : protocols::medal::MedalMover , protocols::nonlocal::BiasedFragmentMover
• ProjectionVector : protocols::evaluation::PCA