Here is a list of all class members with links to the classes they belong to:

- p -

• p : protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• p1 : protocols::environment::claims::JumpElement
• p2 : protocols::environment::claims::JumpElement
• p_cond_ : protocols::moves::WhileMover
• p_value() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• pack_all_side_chains() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_all_side_chains_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler , protocols::stepwise::modeler::packer::StepWisePacker
• pack_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• pack_full_repack_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::relax::ClassicRelax
• pack_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_missing_sidechains() : protocols::hybridization::MRMover
• pack_o2prime_hydrogens() : protocols::stepwise::modeler::packer::StepWisePacker
• pack_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_rotamers_ : protocols::abinitio::ClassicAbinitio
• pack_rotamers_fullatom_ : protocols::surface_docking::SurfaceDockingProtocol
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• pack_scorefxn_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel , protocols::stepwise::legacy::modeler::protein::StepWiseProteinModeler , protocols::stepwise::legacy::modeler::StepWiseLegacyConnectionSampler , protocols::stepwise::modeler::StepWiseModeler , protocols::ub_e2c::ubi_e2c_modeler
• pack_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• pack_separated_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• pack_task_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_together_ : protocols::features::InterfaceFeatures
• pack_virtual_o2prime_hydrogen_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pack_weights() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• pack_weights_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• PACKABLE : protocols::flxbb::LayerDesignOperation
• packable() : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• packable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• PackDaemon() : protocols::pack_daemon::PackDaemon
• packed_residues() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_residues_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packer() : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_ : protocols::antibody_legacy::GraftMover , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker , protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_pose_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_task_ : protocols::simple_moves::CoupledMover
• 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
• PackerNeighborGraphFilter() : protocols::simple_filters::PackerNeighborGraphFilter
• PackerTask : protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::SetCatalyticResPackBehavior
• packertask() : protocols::flxbb::DesignTask
• PackerTask : 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::BoltzmannRotamerMover , 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::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerizeMover , 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::BoltzmannRotamerMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::RotamerizeMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• packing_angle_enum_to_string() : protocols::antibody::AntibodyEnumManager
• packing_angle_numbering_ : protocols::antibody::AntibodyInfo
• packing_angle_residues_ : protocols::antibody::AntibodyInfo
• packing_angle_string_to_enum() : protocols::antibody::AntibodyEnumManager
• packing_angle_to_enum_ : protocols::antibody::AntibodyEnumManager
• packing_angle_to_string_ : protocols::antibody::AntibodyEnumManager
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_shell() : protocols::simple_filters::RelativePoseFilter
• packing_shell_ : protocols::simple_filters::RelativePoseFilter
• PackingState() : protocols::multistate_design::PackingState
• packonly_after_graft_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol
• PackRotamersMover() : protocols::simple_moves::PackRotamersMover
• PackRotamersMoverLazy() : protocols::simple_moves::PackRotamersMoverLazy
• PackRotamersMoverPartGreedy() : protocols::enzdes::PackRotamersMoverPartGreedy
• PackScreener() : protocols::stepwise::screener::PackScreener
• packstat : protocols::analysis::InterfaceData
• packstat_pdb_ : protocols::analysis::PackStatMover
• PackstatCalculator() : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• PackStatFilter() : protocols::simple_filters::PackStatFilter
• PackStatMover() : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• pair_dp() : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• pair_list() : protocols::scoring::Interface
• pair_list_ : protocols::scoring::Interface
• pair_overlap_tolerance() : protocols::match::BumpGrid
• pair_permit_overlap_ : protocols::match::BumpGrid
• pair_sets_with_positions() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• pair_vector_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• pair_with_scaffold() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• paired() : protocols::dna::DnaPosition
• paired_ : protocols::dna::DnaPosition
• PairFeatures() : protocols::features::PairFeatures
• PairFeaturesCreator() : protocols::features::PairFeaturesCreator
• pairing() : protocols::abinitio::PairingStatEntry
• pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• PairingLibrary() : protocols::jumping::PairingLibrary
• Pairings : protocols::abinitio::AlternativePairings
• pairings() : protocols::abinitio::Templates
• pairings_ : protocols::abinitio::AlternativePairings , protocols::abinitio::Templates , protocols::jumping::DisulfPairingLibrary , protocols::jumping::MembraneJump , protocols::jumping::PairingLibrary , protocols::jumping::SheetBuilder , protocols::topology_broker::TemplateJumpClaimer
• pairings_file_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• pairings_size() : protocols::jumping::MembraneJump
• pairings_size_ : protocols::jumping::MembraneJump
• PairingStatEntry() : protocols::abinitio::PairingStatEntry
• PairingStatistics() : protocols::abinitio::PairingStatistics
• PairingTemplate() : protocols::jumping::PairingTemplate
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• PairList : protocols::sparta::PDB
• PalesEvaluator() : protocols::simple_filters::PalesEvaluator
• PalesEvaluatorCreator() : protocols::simple_filters::PalesEvaluatorCreator
• parallel() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• parallel_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator
• ParallelBetaPairingPreferenceFilter() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• ParallelTempering() : protocols::canonical_sampling::ParallelTempering
• param1() : protocols::branch_angle::BranchAngleOptimizer , protocols::relax::RelaxScriptCommand
• param2() : protocols::branch_angle::BranchAngleOptimizer , protocols::relax::RelaxScriptCommand
• param3 : protocols::relax::RelaxScriptCommand
• param4 : protocols::relax::RelaxScriptCommand
• param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_index_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_type_ : protocols::simple_filters::RepeatParameterFilter
• parameter_set4final() : protocols::hybridization::TMalign
• parameter_set4scale() : protocols::hybridization::TMalign
• parameter_set4search() : protocols::hybridization::TMalign
• parameter_tag_ : protocols::qsar::scoring_grid::LigandPropertyScore
• Parameters : 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
• parameters_index() : protocols::helical_bundle::PerturbBundleHelix
• parameters_index_ : protocols::helical_bundle::PerturbBundleHelix
• parameters_set_index() : protocols::helical_bundle::PerturbBundleHelix
• parameters_set_index_ : protocols::helical_bundle::PerturbBundleHelix
• ParametersOP : 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 : 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
• ParametersSetOP : 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_derivs_to_vars() : protocols::helical_bundle::FitSimpleHelixMultiFunc
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• paratope : protocols::antibody::ParatopeMetric< T >
• paratope_cdrs_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover , protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_charge_ : protocols::antibody::AntibodyFeatures
• paratope_cst_mover_ : protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_epitope_cst_mover_ : protocols::antibody::design::AntibodyGraftDesignMover , protocols::antibody::design::AntibodySeqDesignMover
• paratope_heavy : protocols::antibody::ParatopeMetric< T >
• paratope_light : protocols::antibody::ParatopeMetric< T >
• paratope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• paratope_residues_from_cdrs() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• paratope_sasa_ : protocols::antibody::AntibodyFeatures
• ParatopeEpitopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover
• ParatopeMetric() : protocols::antibody::ParatopeMetric< T >
• ParatopeSiteConstraintMover() : protocols::antibody::constraints::ParatopeSiteConstraintMover
• 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::JumpingFoldConstraints , protocols::abinitio::JumpingFoldConstraintsWrapper , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , 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 , 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 >
• 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::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
• Parent : protocols::moves::MoveMapMover , protocols::moves::MoverApplyingMover
• parent : protocols::moves::MoverRegistrator< T >
• Parent : protocols::moves::ReplicaExchangeMC
• parent : protocols::multistate_design::PosType
• Parent : protocols::noesy_assign::EXCN_NoesyAssign , 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::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::pockets::SmallMol , 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::MutationsFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::TaskAwareScoreTypeFilter
• Parent : protocols::simple_moves::FragmentMover , protocols::simple_moves::LoggedFragmentMover
• parent : protocols::simple_moves::MembraneTopology
• Parent : protocols::simple_moves::MinMover
• parent : 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::AddGood2BPairEnergyRotamers , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , 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::RestrictToLoops , 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 , protocols::topology_broker::TMHTopologySamplerClaimer
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• parent_name_ : protocols::loop_modeling::LoopMover
• parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• ParentOP : protocols::abinitio::abscript::JumpSampleData , protocols::environment::AutoCutData
• ParetoOptMutationMover() : protocols::design_opt::ParetoOptMutationMover
• parin_favorite_output() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• parin_favorite_output_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• parse_batch_description_tag_item() : protocols::features::ReportToDB
• parse_batch_id_tag_item() : protocols::features::ReportToDB
• parse_batch_name_tag_item() : protocols::features::ReportToDB
• parse_cache_size_tag_item() : protocols::features::ReportToDB
• parse_cdr_design_option() : protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_general_option() : protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_graft_option() : protocols::antibody::design::CDRGraftDesignOptionsParser
• parse_cdr_option() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_cdr_set_option() : protocols::antibody::CDRSetOptionsParser
• parse_chi_and_bb() : protocols::simple_moves::MinMover
• parse_command_line() : protocols::frag_picker::FragmentPicker
• parse_configuration_options() : protocols::loops::JSONFormattedLoopsFileReader
• parse_ctrl_str() : protocols::environment::claims::EnvClaim
• parse_ddG_task_operations() : protocols::simple_filters::TaskAwareAlaScan
• parse_def() : protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::LigInterfaceEnergyFilter , protocols::filters::Filter , protocols::inputter::InputterStream , protocols::matdes::BuildingBlockInterfaceOperation , protocols::matdes::InterfacePackingFilter , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SymUnsatHbondFilter , protocols::moves::Mover , protocols::nonlocal::SingleFragmentMover , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::relax::FastRelax , protocols::simple_filters::DdgFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareAlaScan , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::MinMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::StoreTaskMover
• parse_def_opts() : protocols::simple_moves::MinMover
• parse_default_and_user_options() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_dof_task_type() : protocols::simple_moves::MinMover
• parse_dof_tasks() : protocols::simple_moves::MinMover
• parse_error_ : protocols::metal_interface::ZincSiteFinder
• parse_format_string() : protocols::outputter::FormatStringOutputter
• parse_job_tag() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_jobs_table_tag() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_jobs_tags() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_json_formatted_data() : protocols::loops::JSONFormattedLoopsFileReader
• parse_json_residue_info() : protocols::loops::JSONFormattedLoopsFileReader
• parse_jump_def() : protocols::abinitio::LoopJumpFoldCst
• parse_loop_tag() : protocols::loops::loops_definers::LoopsExplicitDefiner
• parse_lsm_spec() : protocols::hotspot_hashing::LSMSearchPattern
• parse_movemap() : protocols::md::CartesianMD
• parse_my_string_arguments_and_cast_to_globalPrivateSpaceVariables() : protocols::motif_grafting::movers::MotifGraftMover
• parse_my_tag() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::AbscriptMover , protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::FragmentJumpCM , protocols::abinitio::abscript::RigidChunkCM , protocols::abinitio::abscript::StructPerturberCM , protocols::abinitio::DomainAssembly , protocols::analysis::InterfaceAnalyzerMover , protocols::antibody::AntibodyFeatures , protocols::antibody::clusters::CDRClusterFeatures , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::BiasEnergy , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , 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::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::PartialThreadingMover , protocols::contact_map::ContactMap , protocols::cryst::FitBfactorsMover , protocols::cryst::LoadDensityMapMover , protocols::cryst::RecomputeDensityMapMover , protocols::cryst::SetCrystWeightMover , protocols::cryst::SetRefinementOptionsMover , protocols::cryst::TagPoseWithRefinementStatsMover , protocols::cryst::UpdateSolventMover , protocols::cyclic_peptide::CreateAngleConstraint , protocols::cyclic_peptide::CreateDistanceConstraint , protocols::cyclic_peptide::CreateTorsionConstraint , protocols::cyclic_peptide::DeclareBond , protocols::cyclic_peptide::PeptideStubMover , protocols::denovo_design::filters::ExposedHydrophobicsFilter , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::electron_density::BfactorFittingMover , protocols::electron_density::DensityMorphingMover , protocols::electron_density::ReportFSC , protocols::electron_density::ScaleMapIntensities , protocols::electron_density::SetupForDensityScoringMover , protocols::environment::claims::EnvLabelSelector , protocols::environment::CoMTrackerCM , protocols::environment::EnvMover , protocols::environment::ScriptCM , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::EnzScoreFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::RemoveLigandFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::ResidueConformerFilter , protocols::features::AtomAtomPairFeatures , protocols::features::FeaturesReporter , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::HelixCapFeatures , protocols::features::InterfaceFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ProteinRMSDNoSuperpositionFeatures , protocols::features::ReportToDB , protocols::features::ResidueGridScoresFeatures , protocols::features::ResidueScoresFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::ScreeningFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::strand_assembly::SandwichFeatures , protocols::features::StructureScoresFeatures , protocols::features::TaskOperationFeatures , protocols::features::TotalScoreFeatures , protocols::features::TrajectoryReportToDB , protocols::features::UnrecognizedAtomFeatures , protocols::features::WaterFeatures , protocols::filters::CalculatorFilter , protocols::filters::CombinedFilter , protocols::filters::CompoundFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::HeavyAtomFilter , protocols::filters::IfThenFilter , protocols::filters::MoveBeforeFilter , protocols::filters::ReplicateFilter , protocols::filters::StochasticFilter , protocols::filters::TimeFilter , 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::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::SheetConstraintsRCG , protocols::flexpep_docking::FlexPepDockingProtocol , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::InverseRotamersRCG , protocols::forge::constraints::InvrotTreeRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelConstraintGenerator , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::grafting::AnchoredGraftMover , protocols::grafting::simple_movers::DeleteRegionMover , protocols::grafting::simple_movers::InsertPoseIntoPoseMover , protocols::grafting::simple_movers::KeepRegionMover , protocols::grafting::simple_movers::ReplaceRegionMover , protocols::helical_bundle::MakeBundle , protocols::helical_bundle::PerturbBundle , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::hybridization::CartesianHybridize , protocols::hybridization::CartesianSampler , protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetupMover , protocols::idealize::IdealizeMover , protocols::indexed_structure_store::filters::FragmentLookupFilter , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , protocols::ligand_docking::ComputeLigandRDF , protocols::ligand_docking::FinalMinimizer , protocols::ligand_docking::GrowLigand , protocols::ligand_docking::HBondAcceptorFilter , protocols::ligand_docking::HBondDonorFilter , protocols::ligand_docking::HeavyAtomFilter , protocols::ligand_docking::HighResDocker , protocols::ligand_docking::InterfaceBuilder , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::LigandArea , protocols::ligand_docking::LigandDesign , protocols::ligand_docking::MinimizeBackbone , protocols::ligand_docking::MolarMassFilter , protocols::ligand_docking::MolecularMassFilter , protocols::ligand_docking::MoveMapBuilder , protocols::ligand_docking::RandomConformers , protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryHbondFunction , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFChargeFunction , protocols::ligand_docking::rdf::RDFElecFunction , protocols::ligand_docking::rdf::RDFEtableFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::ligand_docking::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_build::LoopmodelWrapper , protocols::loop_modeling::LoopBuilder , protocols::loop_modeling::LoopModeler , protocols::loop_modeling::LoopMover , protocols::loop_modeling::LoopProtocol , protocols::loop_modeling::refiners::MinimizationRefiner , protocols::loop_modeling::refiners::RepackingRefiner , protocols::loop_modeling::refiners::RotamerTrialsRefiner , protocols::loop_modeling::utilities::PrepareForFullatom , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashLibraryOptions , protocols::loophash::LoopHashMoverWrapper , protocols::loops::FoldTreeFromLoops , protocols::loops::loop_closure::ccd::CCDLoopClosureMover , protocols::loops::loop_closure::ccd::RamaCheckBase , protocols::loops::loop_mover::LoopCM , protocols::loops::loop_mover::refine::LoopMover_Refine_CCD , protocols::loops::loops_definers::LoopsDatabaseDefiner , protocols::loops::loops_definers::LoopsDefiner , protocols::loops::loops_definers::LoopsExplicitDefiner , protocols::loops::loops_definers::LoopsFileDefiner , protocols::loops::LoopsFileOptions , protocols::match::MatcherMover , protocols::matdes::ClashCheckFilter , protocols::matdes::ExtractSubposeMover , protocols::matdes::GetRBDOFValues , protocols::matdes::InterfacePackingFilter , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::OligomericAverageDegreeFilter , protocols::matdes::SchemePlaceMotifsMover , protocols::matdes::SymDofMover , protocols::matdes::SymUnsatHbondFilter , protocols::md::CartesianMD , protocols::membrane::AddMembraneMover , protocols::membrane::FlipMover , protocols::membrane::io::LipoFileOptions , protocols::membrane::io::SpanFileOptions , protocols::membrane::MembranePositionFromTopologyMover , protocols::membrane::RotationMover , protocols::membrane::SetMembraneCenterMover , protocols::membrane::SetMembraneNormalMover , protocols::membrane::SetMembranePositionMover , protocols::membrane::symmetry::SetupForMembraneSymmetry , protocols::membrane::TransformIntoMembraneMover , protocols::membrane::TranslationMover , protocols::membrane::TranslationRotationMover , protocols::membrane::visualize::VisualizeMembraneMover , protocols::motif_grafting::movers::MotifGraftMover , protocols::moves::DsspMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::MonteCarloUtil , protocols::moves::Mover , protocols::moves::PyMolMover , protocols::moves::RampingMover , protocols::moves::RandomMover , protocols::moves::StructureRestrictor , protocols::moves::TrialMover , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopCreatorMover , protocols::ncbb::oop::OopDockDesignProtocol , protocols::nonlocal::SingleFragmentMover , protocols::normalmode::NormalModeMinimizer , protocols::pb_potential::SetupPoissonBoltzmannPotential , protocols::pose_reporters::EnergyReporter , protocols::pose_reporters::FilterReporter , protocols::pose_reporters::RMSDReporter , protocols::pose_selectors::ClusterPoseSelector , protocols::pose_selectors::Filter , protocols::pose_selectors::LogicalSelector , protocols::pose_selectors::TopNByProperty , protocols::protein_interface_design::filters::AtomicContactCountFilter , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::ClashWithTargetFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::FNatFilter , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::IRmsdFilter , protocols::protein_interface_design::filters::LRmsdFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::RmsdSimpleFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::SSamountFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::AddChainBreak , protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BestHotspotCstMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::DisulfideMover , protocols::protein_interface_design::movers::DockAndRetrieveSidechains , protocols::protein_interface_design::movers::DockWithHotspotMover , protocols::protein_interface_design::movers::FavorNativeResiduePreCycle , protocols::protein_interface_design::movers::FavorNonNativeResiduePreCycle , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::movers::HotspotHasherMover , protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::movers::LoopFinder , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopOver , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::PatchdockTransform , protocols::protein_interface_design::movers::PeptideStapleDesignMover , protocols::protein_interface_design::movers::PlacementAuctionMover , protocols::protein_interface_design::movers::PlacementMinimizationMover , protocols::protein_interface_design::movers::PlaceOnLoop , protocols::protein_interface_design::movers::PlaceSimultaneouslyMover , protocols::protein_interface_design::movers::PlaceStubMover , protocols::protein_interface_design::movers::PrepackMover , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetAtomTree , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SetupHotspotConstraintsLoopsMover , protocols::protein_interface_design::movers::SetupHotspotConstraintsMover , protocols::protein_interface_design::movers::ShoveResidueMover , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TopologyBrokerMover , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::movers::VLB , protocols::qsar::qsarMover , protocols::qsar::RenderGridsToKinemage , protocols::qsar::scoring_grid::AtrGrid , protocols::qsar::scoring_grid::ChargeGrid , protocols::qsar::scoring_grid::ClassicGrid , protocols::qsar::scoring_grid::ConstantScoreBase , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridInitMover , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::LigandPropertyScore , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::ShapeGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::rbsegment_relax::IdealizeHelicesMover , protocols::rbsegment_relax::MakeStarTopologyMover , protocols::rbsegment_relax::OptimizeThreadingMover , protocols::relax::AtomCoordinateCstMover , protocols::relax::FastRelax , protocols::relax::membrane::MPFastRelaxMover , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::RollMover , protocols::rigid::UniformRigidBodyCM , protocols::rigid::UniformRigidBodyMover , protocols::rosetta_scripts::AdditionalOutputWrapper , protocols::rosetta_scripts::MultipleOutputWrapper , protocols::rosetta_scripts::MultiplePoseMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::PosePropertyReporter , protocols::rosetta_scripts::PoseSelector , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::AveragePathLengthFilter , protocols::simple_filters::BuriedRegionsFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::DisulfideEntropyFilter , protocols::simple_filters::DomainInterfaceFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::GeometryFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::MotifScoreFilter , protocols::simple_filters::MultipleSigmoids , protocols::simple_filters::MutationsFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NetChargeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NMerSVMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseComment , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::RepeatParameterFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::SavePoseConstraintToFileFilter , protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SSMotifFinder , protocols::simple_filters::StemFinder , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TaskAwareAlaScan , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_filters::TaskAwareScoreTypeFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_filters::TotalSasaFilter , protocols::simple_moves::AddChainMover , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::AddJobPairData , protocols::simple_moves::AlignChainMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::BoltzmannRotamerMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::ContingentAcceptMover , protocols::simple_moves::CoupledMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::FavorSymmetricSequence , protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloReset , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MSDMover , protocols::simple_moves::MutateResidue , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PackRotamersMoverLazy , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::PSSM2BfactorMover , protocols::simple_moves::RandomOmegaFlipMover , protocols::simple_moves::RandomTorsionMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RepeatPropagationMover , protocols::simple_moves::ReportEffectivePKA , protocols::simple_moves::ResetBaselineMover , protocols::simple_moves::ResidueTypeConstraintMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::ShortBackrubMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::symmetry::TaskAwareSymMinMover , protocols::simple_moves::TaskAwareMinMover , protocols::simple_moves::Tumble , protocols::simple_moves::VirtualRootMover , protocols::stepwise::modeler::options::StepWiseBasicModelerOptions , protocols::stepwise::modeler::options::StepWiseModelerOptions , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions , protocols::stepwise::options::StepWiseBasicOptions , protocols::surface_docking::SurfaceVectorOptions , protocols::symmetric_docking::SymDockProtocol , protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover , protocols::symmetric_docking::SymFoldandDockRbTrialMover , protocols::symmetric_docking::SymFoldandDockSlideTrialMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::task_operations::StoreCombinedStoredTasksMover , protocols::toolbox::task_operations::StoreCompoundTaskMover , protocols::toolbox::task_operations::StoreTaskMover
• parse_options() : protocols::antibody::CDRSetOptionsParser , protocols::antibody::design::CDRGraftDesignOptionsParser , protocols::antibody::design::CDRSeqDesignOptionsParser
• parse_options_name_and_value() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_opts() : protocols::md::CartesianMD , protocols::simple_moves::MinMover
• parse_output_mode() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_place_probe_tag() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_protocol_id_tag_item() : protocols::features::ReportToDB
• parse_protocol_tag() : protocols::rosetta_scripts::RosettaScriptsParser
• parse_quota_command_line() : protocols::frag_picker::FragmentPicker
• parse_region_string() : protocols::contact_map::ContactMap
• parse_relevant_residues_mode_tag_item() : protocols::features::ReportToDB
• parse_remove_xray_virt_tag_item() : protocols::features::ReportToDB
• parse_resfile() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• parse_resfiles() : protocols::simple_moves::FindConsensusSequence , protocols::simple_moves::MSDMover
• parse_schfile() : protocols::md::MDBase
• parse_score_function() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover
• parse_stage_id() : protocols::abinitio::abscript::AbscriptMover
• parse_startfrom_file() : protocols::ligand_docking::StartFrom
• parse_state() : protocols::moves::Mover
• parse_stride_tag_item() : protocols::features::TrajectoryReportToDB
• parse_subtag() : protocols::environment::EnvMover
• parse_subtags() : protocols::abinitio::abscript::AbscriptMover
• parse_tag() : 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::RemodelRotamerLinks , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::jd2::parser::FragmentReader , protocols::matdes::BuildingBlockInterfaceOperation , protocols::toolbox::task_operations::AlignedThreadOperation , protocols::toolbox::task_operations::CrystalContactsOperation , protocols::toolbox::task_operations::DatabaseThread , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::DsspDesignOperation , protocols::toolbox::task_operations::ImportUnboundRotamersOperation , protocols::toolbox::task_operations::InteractingRotamerExplosion , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::LinkResidues , protocols::toolbox::task_operations::ModifyAnnealer , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinCore , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictNonSurfaceToRepackingOperation , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoops , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , protocols::toolbox::task_operations::RestrictToTerminiOperation , protocols::toolbox::task_operations::RetrieveStoredTaskOperation , protocols::toolbox::task_operations::SelectByDeltaScoreOperation , protocols::toolbox::task_operations::SelectByDensityFitOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SelectResiduesWithinChainOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::SetIGTypeOperation , protocols::toolbox::task_operations::ThreadSequenceOperation
• parse_task_operations() : protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::TaskAwareMinMover
• parse_use_transactions_tag_item() : protocols::features::ReportToDB
• parsed_json_ : protocols::rpc::JSON_RPC
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• ParsedProtocol() : protocols::rosetta_scripts::ParsedProtocol
• ParsedProtocolOP : protocols::simple_moves::GenericMonteCarloMover
• parser() : protocols::jd2::JobDistributor
• parser_ : protocols::jd2::JobDistributor
• ParserJobInputter() : protocols::protein_interface_design::ParserJobInputter
• partial_state_assignment() : protocols::flexpack::interaction_graph::FlexbbNode
• partially_assign_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• PartialSecondarySimilarity() : protocols::frag_picker::scores::PartialSecondarySimilarity
• PartialThreadingMover() : protocols::comparative_modeling::PartialThreadingMover
• partition_ : protocols::hotspot_hashing::PartitionedSearchPattern
• partition_definition() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partition_definition_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partition_into_coordinates() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• partition_splits_a_fixed_domain() : protocols::stepwise::monte_carlo::SWA_MoveSelector
• PartitionAggregateFunction() : protocols::multistate_design::PartitionAggregateFunction< T >
• PartitionContactScreener() : protocols::stepwise::screener::PartitionContactScreener
• PartitionedSearchPattern() : protocols::hotspot_hashing::PartitionedSearchPattern
• partner() : protocols::docking::DockingEnsemble
• partner1() : protocols::contact_map::Contact
• partner1_ : protocols::contact_map::Contact
• partner2() : protocols::contact_map::Contact
• partner2_ : protocols::contact_map::Contact
• partner_ : protocols::docking::DockingEnsemble , protocols::farna::MultipleDomainMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::scoring::Interface
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking
• partners_ : protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_ : protocols::environment::DofUnlock
• pass_all_filters() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_all_pose_screens() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• pass_base_centroid_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• pass_clash_check() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pass_count() : protocols::stepwise::legacy::screener::RNA_LegacyNativeRMSD_Screener , protocols::stepwise::screener::NativeRMSD_Screener
• pass_count_ : protocols::stepwise::legacy::screener::RNA_LegacyNativeRMSD_Screener , protocols::stepwise::screener::NativeRMSD_Screener
• pass_FARFAR_no_auto_bulge_filter() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• pass_metropolis() : protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• pass_metropolis_multiple_nodes_changing() : protocols::flexpack::annealer::FlexbbSimAnnealer
• pass_screen_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_start_pose() : protocols::antibody::H3RefineCCD , protocols::antibody::RefineOneCDRLoop
• pass_the_loop() : protocols::antibody::H3PerturbCCD
• passed_automorphism() : protocols::motifs::MotifHit
• passed_automorphism_ : protocols::motifs::MotifHit
• passed_centroid_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_fullatom_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_highres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passed_lowres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passes_com_vector_criterion() : protocols::match::NumNeighborsMPM
• passes_etable_filter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• passes_fast_scan() : protocols::farna::RNA_LoopCloser
• passes_filter() : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchCollisionFilter , protocols::match::output::MatchFilter , protocols::match::output::StateAccumulatingMatchFilter , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::topology_broker::TopologyClaimer
• passes_filters() : protocols::match::output::MatchProcessor
• passes_hardsphere_filter() : protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• passport() : protocols::environment::ClaimingMover
• passport_updated() : protocols::abinitio::abscript::AbscriptLoopCloserCM , protocols::abinitio::abscript::FragmentCM , protocols::abinitio::abscript::RigidChunkCM , protocols::environment::ClaimingMover , protocols::environment::CoMTrackerCM , protocols::environment::ScriptCM , protocols::loops::loop_mover::LoopCM , protocols::rigid::UniformRigidBodyCM
• passports_ : protocols::environment::ClaimingMover
• PassportStack : protocols::environment::ClaimingMover
• patch_scores_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• patchdock_entry_num() : protocols::protein_interface_design::PatchdockReader
• patchdock_entry_num_ : protocols::protein_interface_design::PatchdockReader
• patchdock_fname() : protocols::protein_interface_design::PatchdockReader
• patchdock_fname_ : protocols::protein_interface_design::PatchdockReader
• PatchdockReader() : protocols::protein_interface_design::PatchdockReader
• PatchdockReaderOP : protocols::protein_interface_design::movers::PatchdockTransform
• PatchdockTransform() : protocols::protein_interface_design::movers::PatchdockTransform
• PatchOperation() : protocols::canonical_sampling::PatchOperation
• path : protocols::hybridization::TMalign , protocols::motifs::Motif
• path_ : protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter , protocols::motifs::Motif
• path_tightness() : protocols::simple_filters::AveragePathLengthFilter
• path_tightness_ : protocols::simple_filters::AveragePathLengthFilter
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• pb_cached_data_ : protocols::simple_moves::ddG
• pb_enabled_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• PBP_clustering_at_chain_closure() : protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• PBP_clustering_at_chain_closure_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• pca_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::PcaEvaluator
• PcaEvaluator() : protocols::abinitio::PcaEvaluator
• PCluster() : protocols::pockets::PCluster
• PClusterSet : protocols::pockets::PCluster , protocols::pockets::PClusterSet
• pconf_creation() : protocols::environment::Environment
• pconf_destruction() : protocols::environment::Environment
• pconfs_ : protocols::environment::Environment
• pcs_d_ : protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• pcs_d_c_ : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• PCS_data() : protocols::scoring::methods::pcs::PCS_data
• PCS_data_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PCS_data_from_pose() : 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
• PCS_data_input() : protocols::scoring::methods::pcs::PCS_data_input
• PCS_data_input_manager() : protocols::scoring::methods::pcs::PCS_data_input_manager
• PCS_data_input_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_manager_Ts1
• PCS_data_input_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2
• PCS_data_input_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_manager_Ts3
• PCS_data_input_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_manager_Ts4
• PCS_data_input_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1
• PCS_data_input_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2
• PCS_data_input_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3
• PCS_data_input_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• PCS_data_line_all_ : protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_data_line_all_spin_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• PCS_data_per_lanthanides() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• PCS_data_per_lanthanides_all_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• PCS_data_per_lanthanides_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_per_lanthanides_Ts1
• PCS_data_per_lanthanides_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2
• PCS_data_per_lanthanides_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_per_lanthanides_Ts3
• PCS_data_per_lanthanides_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_per_lanthanides_Ts4
• PCS_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_data_Ts1
• PCS_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_data_Ts2
• PCS_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_data_Ts3
• PCS_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• pcs_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PCS_Energy() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_Energy_parameters_manager() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• PCS_Energy_parameters_manager_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1
• PCS_Energy_parameters_manager_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2
• PCS_Energy_parameters_manager_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3
• PCS_Energy_parameters_manager_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• PCS_Energy_Ts1() : protocols::scoring::methods::pcsTs1::PCS_Energy_Ts1
• PCS_Energy_Ts2() : protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2
• PCS_Energy_Ts3() : protocols::scoring::methods::pcsTs3::PCS_Energy_Ts3
• PCS_Energy_Ts4() : protocols::scoring::methods::pcsTs4::PCS_Energy_Ts4
• PCS_experimental() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_experimental_ : protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_file_data() : protocols::scoring::methods::pcs::PCS_file_data
• PCS_file_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1
• PCS_file_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2
• PCS_file_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3
• PCS_file_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_filename_and_data_ : protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• PCS_FragDistance() : protocols::frag_picker::scores::PCS_FragDistance
• PCS_line_data() : protocols::scoring::methods::pcs::PCS_line_data
• PCS_line_data_Ts1() : protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1
• PCS_line_data_Ts2() : protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2
• PCS_line_data_Ts3() : protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3
• PCS_line_data_Ts4() : protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_multi_data_from_noone() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_multi_data_from_pose() : protocols::scoring::methods::pcs2::PcsEnergy
• PCS_tensor() : protocols::scoring::methods::pcs::PCS_tensor
• PCS_tensor_Ts1() : protocols::scoring::methods::pcsTs1::PCS_tensor_Ts1
• PCS_tensor_Ts2() : protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2
• PCS_tensor_Ts3() : protocols::scoring::methods::pcsTs3::PCS_tensor_Ts3
• PCS_tensor_Ts4() : protocols::scoring::methods::pcsTs4::PCS_tensor_Ts4
• PCS_tolerance() : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• PCS_tolerance_ : protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• pcs_weight_ : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• pcs_weight_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• PcsDataCenter() : protocols::scoring::methods::pcs2::PcsDataCenter
• PcsDataCenterManager() : protocols::scoring::methods::pcs2::PcsDataCenterManager
• PcsDataCenterManagerSingleton() : protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PcsDataLanthanide() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• PcsEnergy() : protocols::scoring::methods::pcs2::PcsEnergy
• PcsEnergyController() : protocols::topology_broker::PcsEnergyController
• PcsEnergyParameter() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• PcsEnergyParameterManager() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PcsGridSearchParameter() : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• PcsGridSearchParameterManager() : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• PcsInputCenter() : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputCenter_all_ : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputCenterManager() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile() : protocols::scoring::methods::pcs2::PcsInputFile
• PcsInputFile_all_ : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputLine() : protocols::scoring::methods::pcs2::PcsInputLine
• PcsInputLine_all_ : protocols::scoring::methods::pcs2::PcsInputFile
• PcsTensor() : protocols::scoring::methods::pcs2::PcsTensor
• pcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• pd_reader() : protocols::protein_interface_design::movers::PatchdockTransform
• pd_reader_ : protocols::protein_interface_design::movers::PatchdockTransform
• pdb : protocols::antibody::CDRPose
• PDB() : protocols::sparta::PDB
• pdb_chain() : protocols::pmut_scan::MutationData
• pdb_contains_target_ : protocols::seeded_abinitio::SeedFoldTree
• pdb_data_features_ : protocols::features::ProteinSilentReport
• PDB_DIR : protocols::sparta::Sparta::SpartaLib
• pdb_end() : protocols::antibody::clusters::CDRCluster
• pdb_end_ : protocols::antibody::clusters::CDRCluster
• pdb_end_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_file_names_ : protocols::pmut_scan::PointMutScanDriver
• pdb_filenames_ : protocols::docking::DockingEnsemble
• pdb_hash_ : protocols::frag_picker::PdbIdChunkFilter
• pdb_id : protocols::loophash::BBExtraData
• pdb_name() : protocols::simple_filters::RelativePoseFilter
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• pdb_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbered_h3_loop_end : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbered_h3_loop_start : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbering_ : protocols::simple_filters::ScoreCutoffFilter
• pdb_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• pdb_resnum_ : protocols::pmut_scan::MutationData
• pdb_seqpos : protocols::simple_filters::nmer_svm_res_data
• pdb_source_ : protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment
• pdb_start() : protocols::antibody::clusters::CDRCluster , protocols::forge::remodel::RemodelData
• pdb_start_ : protocols::antibody::clusters::CDRCluster
• pdb_start_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_stop : protocols::forge::remodel::RemodelData
• pdbContent : protocols::pockets::SmallMol
• pdbdata_string_ : protocols::rpc::JSON_RPC
• PdbDataFeatures() : protocols::features::PdbDataFeatures
• PdbDataFeaturesCreator() : protocols::features::PdbDataFeaturesCreator
• PDBDumpMover() : protocols::moves::PDBDumpMover
• PDBfileName : protocols::sparta::PDB
• PDBInputter() : protocols::inputter::PDBInputter
• PDBJobInputter() : protocols::jd2::PDBJobInputter
• PDBJobOutputter() : protocols::jd2::PDBJobOutputter
• PDBLandmark() : protocols::antibody::PDBLandmark
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbname() : protocols::dna::DnaInterfacePacker , protocols::simple_filters::SSMotifFinder
• pdbname_ : protocols::dna::DnaInterfacePacker , protocols::metal_interface::AddZincSiteConstraints , protocols::simple_filters::SSMotifFinder
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput() : protocols::dna::DnaInterfacePacker
• PDBOutput() : protocols::dna::PDBOutput
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• PDBOutputter() : protocols::outputter::PDBOutputter
• pdbpos : protocols::dna::DnaDesignDef
• PDBReloadMover() : protocols::simple_moves::PDBReloadMover
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• PDBTrajectoryRecorder() : protocols::canonical_sampling::PDBTrajectoryRecorder
• PDBWriter() : protocols::match::output::PDBWriter
• PDDFEnergy() : protocols::scoring::methods::saxs::PDDFEnergy
• PDDFEnergyCreator() : protocols::scoring::methods::saxs::PDDFEnergyCreator
• PDDFScoreFilter() : protocols::simple_filters::PDDFScoreFilter
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• peak_id() : protocols::noesy_assign::CrossPeak
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peak_volume() : protocols::noesy_assign::PeakAssignment
• PeakAssignment() : protocols::noesy_assign::PeakAssignment
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignmentParameters() : protocols::noesy_assign::PeakAssignmentParameters
• PeakAssignmentResidueMap() : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakCalibrator() : protocols::noesy_assign::PeakCalibrator
• PeakCalibratorMap() : protocols::noesy_assign::PeakCalibratorMap
• PeakFileFormat() : protocols::noesy_assign::PeakFileFormat
• PeakFileFormat_Base() : protocols::noesy_assign::PeakFileFormat_Base
• PeakFileFormat_Sparky() : protocols::noesy_assign::PeakFileFormat_Sparky
• PeakFileFormat_xeasy() : protocols::noesy_assign::PeakFileFormat_xeasy
• PeakFileFormat_xpk() : protocols::noesy_assign::PeakFileFormat_xpk
• peaks() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• peek_back() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• peek_front() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• PENALTY : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• penalty_ : protocols::simple_moves::FavorSymmetricSequence
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• penalty_res_ : protocols::rbsegment_relax::SequenceShiftMover
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_random_loop_model() : protocols::flexpep_docking::FlexPepDockingProtocol
• PeptideStapleDesignMover() : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• PeptideStapleMover() : protocols::simple_moves::PeptideStapleMover
• PeptideStubMover() : protocols::cyclic_peptide::PeptideStubMover
• per_constraint_build_points() : protocols::match::Matcher
• per_constraint_build_points_ : protocols::match::Matcher
• per_cst_build_resids_ : protocols::match::Matcher
• per_cst_pose_build_resids_ : protocols::match::MatcherTask
• per_native_recovery_ : protocols::rotamer_recovery::RRReporterHuman
• per_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_data_ : protocols::analysis::InterfaceAnalyzerMover
• per_residue_ddg_ : protocols::simple_moves::ddG
• perform_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_electron_density_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• perform_filters_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_local_refinement() : protocols::hotspot_hashing::movers::PlaceProbeMover
• perform_minimizer_run_ : protocols::farna::RNA_Minimizer
• perform_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• performing_pure_insertion() : protocols::forge::build::SegmentInsert
• periodic_range() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• periodicity() : protocols::toolbox::match_enzdes_util::GeomSampleInfo
• periodicity_ : protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::claims::JumpClaim
• permitted_overlap() : protocols::match::MatcherTask
• permitted_overlap_ : protocols::match::MatcherTask
• permutate_n_vv_of_pairs() : protocols::motif_grafting::movers::MotifGraftMover
• PerNativeRRReporterHuman() : protocols::rotamer_recovery::PerNativeRRReporterHuman
• PerResidueAAProbSet : protocols::antibody::design::ResidueProbDesignOperation
• pert_dock_rot_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_dock_trans_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_num_rep_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• perturb() : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::kinematic_closure::perturbers::Perturber , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• perturb_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::StartStructClaimer
• perturb_amplitude_ : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• perturb_anchor() : protocols::anchored_design::AnchoredDesignMover
• perturb_angles() : protocols::kinematic_closure::ClosureProblem
• perturb_beta_residue() : protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber
• perturb_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_c_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_ca_c_n() : protocols::kinematic_closure::ClosureProblem
• perturb_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_chain() : protocols::loops::loop_closure::kinematic_closure::BaseTabooPerturber , protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• perturb_chi() : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_lengths() : protocols::kinematic_closure::ClosureProblem
• perturb_n_ca() : protocols::kinematic_closure::ClosureProblem
• perturb_n_ca_c() : protocols::kinematic_closure::ClosureProblem
• perturb_omega() : protocols::kinematic_closure::ClosureProblem
• perturb_phi() : protocols::kinematic_closure::ClosureProblem
• perturb_psi() : protocols::kinematic_closure::ClosureProblem
• perturb_rot_within_well() : protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_subset() : protocols::kinematic_closure::perturbers::BondAnglePerturber , protocols::kinematic_closure::perturbers::FragmentPerturber , protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::LogFilePerturber , protocols::kinematic_closure::perturbers::OmegaPerturber , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::Rama2bPerturber , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber
• perturb_subset_with_balance() : protocols::kinematic_closure::perturbers::IdealizeNonPhiPsi , protocols::kinematic_closure::perturbers::Perturber , protocols::kinematic_closure::perturbers::PerturberSet , protocols::kinematic_closure::perturbers::RamaPerturber , protocols::kinematic_closure::perturbers::UniformPerturber , protocols::kinematic_closure::perturbers::VicinityPerturber , protocols::kinematic_closure::perturbers::WalkingBondAnglePerturber , protocols::kinematic_closure::perturbers::WalkingPerturber
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• perturb_torsion_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• perturb_torsions() : protocols::kinematic_closure::ClosureProblem
• perturb_values() : protocols::helical_bundle::PerturbBundle
• perturb_with_balance() : protocols::kinematic_closure::perturbers::Perturber
• perturbable_ : protocols::helical_bundle::PerturbBundleOptions
• perturbation_magnitude() : protocols::helical_bundle::PerturbBundleOptions
• perturbation_magnitude_ : protocols::helical_bundle::PerturbBundleOptions
• perturbation_type() : protocols::helical_bundle::PerturbBundleOptions
• perturbation_type_ : protocols::helical_bundle::PerturbBundleOptions
• PerturbBundle() : protocols::helical_bundle::PerturbBundle
• PerturbBundleHelix() : protocols::helical_bundle::PerturbBundleHelix
• PerturbBundleOptions() : protocols::helical_bundle::PerturbBundleOptions
• PerturbChiSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• perturbed_angles_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_lengths_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_res_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• perturbed_torsions_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturber() : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_ : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_exhausted() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• perturber_type() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , 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::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber
• perturberlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• perturbers_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::perturbers::PerturberSet
• PerturberSet() : protocols::kinematic_closure::perturbers::PerturberSet
• PerturbRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• pfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• pfront_poses_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_ranks_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_vals_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pg : protocols::pockets::PocketExemplarMultifunc
• phi() : protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::PhiPsiTalosIO
• Phi() : protocols::frag_picker::scores::Phi
• phi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum , protocols::simple_moves::MinimalRotamer , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_ : protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::stepwise::modeler::protein::MainChainTorsionSet
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::hbs::HbsMover , protocols::simple_moves::oop::OopMover
• phi_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• phi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• phi_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• PhiPsiRmsd() : protocols::frag_picker::scores::PhiPsiRmsd
• PhiPsiSquareWell() : protocols::frag_picker::scores::PhiPsiSquareWell
• PhiPsiTalosIO() : protocols::frag_picker::PhiPsiTalosIO
• phis : protocols::antibody::clusters::ClusterData
• phithetascore_ : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• phosphate_move_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• phosphate_move_list() : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sample_pose_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sampler_ : protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::screener::PhosphateScreener
• phosphate_sampler_for_restoration_ : protocols::stepwise::screener::PhosphateScreener
• phosphate_scorefxn_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• phosphate_takeoff_donor_distance_cutoff2_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• PhosphateMove() : protocols::stepwise::modeler::rna::phosphate::PhosphateMove
• PhosphateMover() : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• PhosphateScreener() : protocols::stepwise::screener::PhosphateScreener
• physical() : protocols::environment::claims::JumpClaim
• physical_cut_ : protocols::environment::claims::JumpClaim
• physical_pose_clash_dist_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• pi_pi_total_ : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pick() : protocols::kinematic_closure::pivot_pickers::EndToEndPivots , protocols::kinematic_closure::pivot_pickers::FixedOffsetPivots , protocols::kinematic_closure::pivot_pickers::FixedPivots , protocols::kinematic_closure::pivot_pickers::LoopPivots , protocols::kinematic_closure::pivot_pickers::PivotPicker , protocols::kinematic_closure::pivot_pickers::StandardPivots
• pick_a_rotamer() : protocols::flexpack::annealer::FlexbbSimAnnealer
• pick_all_fragments() : protocols::forge::components::VarLengthBuild
• pick_and_apply() : protocols::kinematic_closure::solution_pickers::FilteredSolutions , protocols::kinematic_closure::solution_pickers::RandomSolutions , protocols::kinematic_closure::solution_pickers::SolutionPicker
• pick_boundary_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pick_candidates() : protocols::frag_picker::FragmentPicker
• pick_chunk_candidates() : protocols::frag_picker::FragmentPicker
• pick_core_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pick_fragment_library() : protocols::farna::FullAtomRNA_Fragments , protocols::farna::RNA_Fragments
• pick_fragments() : protocols::forge::components::VarLengthBuild
• pick_frags() : protocols::abinitio::Templates
• pick_large_frags() : protocols::abinitio::Template , protocols::abinitio::Templates
• pick_loop_frags() : protocols::protein_interface_design::movers::LoopRemodel
• pick_new_cutpoint() : protocols::anchored_design::AnchorMoversData
• pick_new_cutpoints() : protocols::anchored_design::AnchorMoversData
• pick_pivots() : protocols::generalized_kinematic_closure::GeneralizedKIC
• pick_random_chunk() : protocols::hybridization::ChunkTrialMover
• pick_random_fragment() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::farna::FullAtomRNA_Fragments , protocols::farna::RNA_Fragments
• pick_random_template() : protocols::hybridization::ChunkTrialMover
• pick_sequence_from_database() : protocols::toolbox::task_operations::DatabaseThread
• pick_solution() : protocols::kinematic_closure::BalancedKicMover
• pick_starting_template() : protocols::hybridization::HybridizeProtocol , protocols::hybridization::HybridizeSetup
• pick_surface_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• picking_rounds() : protocols::antibody::design::ResidueProbDesignOperation
• picking_rounds_ : protocols::antibody::design::ResidueProbDesignOperation
• piece() : protocols::grafting::GraftMoverBase
• piece_ : protocols::grafting::GraftMoverBase
• pipemap() : protocols::wum2::WorkUnit_ElScripts
• pipemap_ : protocols::wum2::WorkUnit_ElScripts
• PiPiCalculator() : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pivot_1_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_1_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_atoms() : protocols::backrub::BackrubMover , protocols::kinematic_closure::ClosureProblem
• pivot_atoms_ : protocols::backrub::BackrubMover
• pivot_loop() : protocols::kinematic_closure::ClosureProblem
• pivot_picker_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• pivot_range_randomly() : protocols::simple_moves::BBGaussianMover
• pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivot_residues() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::kinematic_closure::ClosureProblem
• pivot_residues_ : protocols::backrub::BackrubMover
• pivot_to_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivots_ : protocols::kinematic_closure::ClosureProblem
• place_atom() : protocols::motifs::Motif
• place_atom_() : protocols::motifs::Motif
• place_atoms() : protocols::motifs::Motif
• place_atoms_() : protocols::motifs::Motif
• place_c() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_d() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_h() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_origin_point() : protocols::pockets::NonPlaidFingerprint
• place_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• place_peptide_on_binding_site() : protocols::flexpep_docking::FlexPepDockingProtocol
• place_residue() : protocols::motifs::Motif
• place_residue_() : protocols::motifs::Motif
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• place_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• place_stubs() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceFragments() : protocols::seeded_abinitio::PlaceFragments
• PlacementAuctionMover() : protocols::protein_interface_design::movers::PlacementAuctionMover
• PlacementMinimizationMover() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• PlaceOnLoop() : protocols::protein_interface_design::movers::PlaceOnLoop
• PlaceProbeMover() : protocols::hotspot_hashing::movers::PlaceProbeMover
• placeResidueAtTransform() : protocols::hotspot_hashing::StubGenerator
• placeResidueOnPose() : protocols::hotspot_hashing::StubGenerator
• PlaceSimultaneouslyMover() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• PlaceStubMover() : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceSurfaceProbe() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• PlaidFingerprint() : protocols::pockets::PlaidFingerprint
• plain_text : protocols::sparta::GDB
• PlainPdbJobDistributor() : protocols::jobdist::PlainPdbJobDistributor
• PlainRawJobDistributor() : protocols::jobdist::PlainRawJobDistributor
• PlainSilentFileJobDistributor() : protocols::jobdist::PlainSilentFileJobDistributor
• plane_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• pleats1() : protocols::fldsgn::topology::StrandPairing
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2() : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• pmatch() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• PNatAAOptEPositionData() : protocols::optimize_weights::PNatAAOptEPositionData
• PNatAAOptERotamerData() : protocols::optimize_weights::PNatAAOptERotamerData
• PNatLigPoseOptEData() : protocols::optimize_weights::PNatLigPoseOptEData
• PNatRotOptEPositionData() : protocols::optimize_weights::PNatRotOptEPositionData
• PNatRotOptERotamerData() : protocols::optimize_weights::PNatRotOptERotamerData
• PNatStructureOptEData() : protocols::optimize_weights::PNatStructureOptEData
• PO_BURIED : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PO_EDGE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PO_SURF : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• POCKET : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• pocket_CoM_ : protocols::pockets::NonPlaidFingerprint
• PocketConstraint() : protocols::pockets::PocketConstraint
• PocketConstraintCreator() : protocols::pockets::PocketConstraintCreator
• PocketExemplarMultifunc() : protocols::pockets::PocketExemplarMultifunc
• PocketGrid : protocols::pockets::CCluster , protocols::pockets::CClusterSet , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• pocketgrid_ : protocols::pockets::PocketConstraint
• pocketGrid_dim_ : protocols::pockets::FingerprintBase
• pocketGrid_mid_ : protocols::pockets::FingerprintBase
• pocketGrid_spacing_ : protocols::pockets::FingerprintBase
• pockets_ : protocols::pockets::PocketGrid
• point_ : protocols::match::VoxelSetIterator
• point_for_nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• point_on_ellipsoid() : protocols::docking::EllipsoidalRandomizationMover
• pointer : protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• PointMutationCalculator() : protocols::design_opt::PointMutationCalculator
• PointMutScanDriver : protocols::pmut_scan::Mutant , protocols::pmut_scan::MutationData , protocols::pmut_scan::PointMutScanDriver
• points_ : protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• points_for_nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• points_for_nonchitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• points_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• points_in_global_orintation_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• polar_ : protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• polar_gap_ : protocols::toolbox::task_operations::CrystalContactsOperation
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• PolarHydrogenPacker() : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• polars : protocols::sic_dock::BuriedPolarScore
• Policy() : protocols::nonlocal::Policy
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• polyAla() : protocols::flexpep_docking::FlexPepDockingProtocol
• polymer_type_ : protocols::make_rot_lib::MakeRotLibOptionsData
• polys_ : protocols::sasa_scores::PPoly
• pool_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::mc_convergence_checks::PoolData
• pool_cache_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Pool_ConvergenceCheck() : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
• pool_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• Pool_Evaluator() : protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• pool_exists() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• pool_name_ : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaPool
• pool_names_ : protocols::frag_picker::quota::QuotaConfig
• pool_npes_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rank_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rms_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• Pool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_size_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• pool_weights_ : protocols::frag_picker::quota::QuotaConfig
• PoolData() : protocols::canonical_sampling::mc_convergence_checks::PoolData
• PoolEvaluatorCreator() : protocols::simple_filters::PoolEvaluatorCreator
• pop() : protocols::forge::remodel::RemodelAccumulator , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::pack_daemon::TopEntitySet
• pop_all() : protocols::wum2::WUQueue
• pop_back() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::evaluation::MetaPoseEvaluator
• pop_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• pop_const_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_const_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_from_ss_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• pop_front() : protocols::wum2::WUQueue
• pop_iter : protocols::genetic_algorithm::GeneticAlgorithmBase
• pop_mutation() : protocols::pmut_scan::Mutant
• pop_next() : protocols::wum::WorkUnitQueue
• pop_passport() : protocols::environment::ClaimingMover , protocols::environment::ProtectedConformation
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• popular_bin() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• populate_all_cdrs() : protocols::antibody_legacy::Antibody
• populate_batch_list_from_cmd() : protocols::jd2::JobDistributor
• population() : protocols::genetic_algorithm::GeneticAlgorithmBase
• population_weight_ : protocols::cluster::ClusterBase
• pore_radius() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pore_radius_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pos : protocols::environment::EnvClaimBroker::BrokeredJumpData , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight
• pos1() : protocols::environment::claims::JumpClaim , protocols::farna::RNA_Pairing , protocols::jumping::DisulfPairing
• pos1_ : protocols::environment::claims::JumpClaim , protocols::topology_broker::claims::LegacyRootClaim
• pos2() : protocols::environment::claims::JumpClaim , protocols::farna::RNA_Pairing , protocols::jumping::DisulfPairing
• pos2_ : protocols::environment::claims::JumpClaim
• pos2select() : protocols::flxbb::LayerDesignOperation
• pos_ : protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK
• pos_list_ : protocols::idealize::IdealizeMover , protocols::simple_moves::BackboneMover
• pose : protocols::antibody::CDRPose
• Pose : protocols::boinc::BoincCurrentPoseObserver
• pose : protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::cartesian::MolecularDynamics
• Pose : 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
• pose : protocols::environment::EnvClaimBroker::BrokerResult
• Pose : 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::SecondaryStructureHasResidueFilter , 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::indexed_structure_store::filters::FragmentLookupFilter , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::jd2::Parser , 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::motifs::LigandMotifSearch , protocols::motifs::MotifSearch , protocols::moves::FilterMover , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory
• pose() : protocols::multistate_design::SingleState
• Pose : protocols::nonlocal::SingleFragmentMover
• pose() : protocols::normalmode::NormalModeMultifunc
• Pose : protocols::pack_daemon::DaemonSet , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon
• pose() : protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint
• Pose : 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
• pose() : protocols::sic_dock::Rose
• Pose : protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterRepeatContactFilter , protocols::simple_filters::IntraRepeatContactFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter
• pose() : protocols::simple_filters::RelativePoseFilter
• Pose : protocols::simple_filters::SaveResfileToDiskFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::TaskAwareSASAFilter
• pose() : protocols::simple_moves::AlignChainMover
• Pose : 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
• pose() : protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet , protocols::stepwise::screener::SampleApplier
• Pose : 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
• pose : protocols::trajectory::DbTrajectoryWriter::Frame
• Pose : protocols::viewer::SilentObserver
• pose0_ : protocols::md::MDBase , protocols::normalmode::NormalModeMultifunc
• pose1_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose2_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose_ : protocols::abinitio::Template , protocols::electron_density::BfactorMultifunc , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::InnerJob , protocols::kinmatch::FunGroupTK , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_filters::RelativePoseFilter , protocols::simple_moves::AlignChainMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::stepwise::legacy::screener::RNA_LegacyPoseSelectionScreener , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::TagDefinition
• pose_aligner_ : protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::screener::NativeRMSD_Screener
• pose_at_origin() : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_build_resids_ : protocols::match::Matcher
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• pose_coords_are_same() : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pose_copy_ : protocols::dna::PDBOutput
• pose_count_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• pose_data_uptodate_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• pose_end_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_free_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pose_from_job() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::enzdes::EnzdesJobInputter , protocols::features::DatabaseJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::JobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::jd2::ScreeningJobInputter , protocols::jd2::SilentFileJobInputter , protocols::make_rot_lib::MakeRotLibJobInputter , protocols::protein_interface_design::ParserJobInputter
• pose_has_chainbreak() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer
• pose_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_index() : protocols::loops::ResidueIndexDescription
• pose_index_ : protocols::loops::ResidueIndexDescription
• pose_init_ : protocols::stepwise::modeler::packer::StepWisePacker
• pose_input_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_input_stream() : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_input_stream_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_list() : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::rna::sugar::SugarModeling , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_list_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker , protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::modeler::StepWiseLegacyConnectionSampler , protocols::stepwise::legacy::modeler::StepWiseLegacyMinimizer , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_minobj_ : protocols::md::MDBase
• pose_name() : protocols::moves::StructureRestrictor , protocols::stepwise::modeler::rna::checker::VDW_RepScreeninfo
• pose_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numbered() : protocols::loops::ResidueIndexDescription
• pose_numbered_ : protocols::loops::ResidueIndexDescription
• pose_output_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• pose_p_ : protocols::multistate_design::SingleState
• pose_passes_ss_length_check() : protocols::frags::TorsionFragmentMover
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_resnum() : protocols::pmut_scan::MutationData
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right() : protocols::forge::build::ConnectRight
• pose_right_ : protocols::forge::build::ConnectRight
• pose_screener_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker
• pose_selection_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler , protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::legacy::screener::RNA_LegacyPoseSelectionScreener
• pose_selection_by_full_score() : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection
• pose_sequence_ : protocols::antibody::design::ConservativeDesignOperation
• pose_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_string_ : protocols::simple_moves::CopyDofMover
• pose_to_native_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Minimizer
• pose_with_original_HO2prime_torsion_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pose_with_original_phosphates_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• pose_with_original_terminal_phosphates_ : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler
• poseBfacts2multivec() : protocols::electron_density::BfactorMultifunc
• PoseComment() : protocols::simple_filters::PoseComment
• PoseCommentsFeatures() : protocols::features::PoseCommentsFeatures
• PoseCommentsFeaturesCreator() : protocols::features::PoseCommentsFeaturesCreator
• PoseCondition() : protocols::moves::PoseCondition
• PoseConformationFeatures() : protocols::features::PoseConformationFeatures
• PoseConformationFeaturesCreator() : protocols::features::PoseConformationFeaturesCreator
• 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
• PoseEvaluator() : protocols::evaluation::PoseEvaluator
• PoseFoundResiduesCombination() : protocols::enzdes::PoseFoundResiduesCombination
• PoseInfoFilter() : protocols::simple_filters::PoseInfoFilter
• PoseInputStreamJobInputter() : protocols::jd2::PoseInputStreamJobInputter
• PoseInserter() : protocols::match::output::PoseInserter
• poselist : protocols::cluster::GatherPosesMover
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMatchOutputWriter() : protocols::match::output::PoseMatchOutputWriter
• PoseMetricCalculatorOP : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• PoseMetricEvaluator() : protocols::simple_filters::PoseMetricEvaluator< T >
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• PoseNumberedLoopFileReader() : protocols::loops::PoseNumberedLoopFileReader
• 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
• PosePropertyReporter() : protocols::rosetta_scripts::PosePropertyReporter
• PosePropertyReporterCreator() : protocols::rosetta_scripts::PosePropertyReporterCreator
• PosePropertyReporterFactory() : protocols::rosetta_scripts::PosePropertyReporterFactory
• PosePropertyReporterMap : protocols::rosetta_scripts::PosePropertyReporterFactory
• PosePropertyReporterRegistrator() : protocols::rosetta_scripts::PosePropertyReporterRegistrator< T >
• Poses : protocols::comparative_modeling::MultiThreadingMover
• poses_ : protocols::abinitio::StructureStore , protocols::docking::membrane::MPDockingSetupMover , protocols::hybridization::DomainAssembly , protocols::moves::VectorPoseMover , protocols::simple_filters::StructuralSimilarityEvaluator
• poses_from_cmd_line() : protocols::comparative_modeling::AlignmentClustering
• poses_input_ : protocols::rosetta_scripts::MultiplePoseMover
• poses_output_ : protocols::rosetta_scripts::MultiplePoseMover
• PoseSelectionScreener() : protocols::stepwise::screener::PoseSelectionScreener
• PoseSelector() : protocols::rosetta_scripts::PoseSelector
• poseselector_creator_map_ : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorCreator() : protocols::rosetta_scripts::PoseSelectorCreator
• PoseSelectorFactory() : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorMap : protocols::rosetta_scripts::PoseSelectorFactory
• PoseSelectorRegistrator() : protocols::rosetta_scripts::PoseSelectorRegistrator< T >
• PoseSP : protocols::simple_moves::O2M_MutateMover
• PoseVector : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator
• position : protocols::cartesian::CartesianAtom , protocols::dna::PositionType , protocols::hotspot_hashing::VectorPair , protocols::optimize_weights::PNatAAOptEPositionData
• position_ : protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::claims::CutClaim
• position_above_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• position_ala_ddG() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_data_begin() : protocols::optimize_weights::OptEData
• position_data_end() : protocols::optimize_weights::OptEData
• position_ddGs_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_index() : protocols::frag_picker::VallResidue
• position_index_ : protocols::frag_picker::VallResidue
• position_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• position_untouchable() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_vector_setup() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• positions() : protocols::dna::DnaChains , protocols::enzdes::EnzdesFlexibleRegion
• Positions : protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager
• positions() : protocols::forge::build::BuildManager
• Positions : 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
• positions_ : protocols::analysis::LoopAnalyzerMover , protocols::antibody::design::ConservativeDesignOperation , protocols::dna::DnaChains , protocols::environment::claims::EnvLabelSelector , protocols::enzdes::EnzdesFlexibleRegion , protocols::simple_filters::ScoreCutoffFilter
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• PositionType() : protocols::dna::PositionType
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• possible_hbond_acceptors_ : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• possible_working_res_1 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• post_graft_ensemble_output_ : protocols::antibody::design::AntibodyDesignMover
• post_graft_modeling_cycles_ : protocols::antibody::design::AntibodyGraftDesignMover
• post_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• post_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_packing() : protocols::dna::DnaInterfacePacker
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• post_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• PostDockAssemblyScorer() : protocols::domain_assembly::PostDockAssemblyScorer
• PosType : protocols::dna::DnaInterfaceMultiStateDesign , protocols::multistate_design::PosType , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• potential_ : protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::movers::DisulfideMover
• potential_energy_ : protocols::md::MDBase
• potential_starting_positions_ : protocols::ligand_docking::StartFrom
• PowExpression() : protocols::pack_daemon::PowExpression
• ppk_only : protocols::flexpep_docking::FlexPepDockingFlags
• pre_align() : protocols::constraints_additional::BindingSiteConstraint
• pre_compute_grid_points() : protocols::topology_broker::TMHTopologySamplerClaimer
• pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• pre_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody::SnugDock
• pre_pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::topology_broker::MembraneTopologyClaimer , protocols::topology_broker::TMHTopologySamplerClaimer , protocols::topology_broker::TopologyClaimer
• pre_scoring() : protocols::flexpack::OtherContextScoreFunction
• pre_selection_mover_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pre_selection_mover_exists_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• preamble() : protocols::ligand_docking::rdf::RDFBase , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFHbondFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction
• preapply() : protocols::simple_moves::GenericMonteCarloMover
• preapply_ : protocols::simple_moves::GenericMonteCarloMover
• precision_ : protocols::frag_picker::scores::FragmentScoreManager , protocols::rotamer_recovery::RRReporterHuman
• precompute_all_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_transforms() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• precomputed_library_mover() : protocols::stepwise::modeler::StepWiseModeler
• precomputed_library_mover_ : protocols::stepwise::modeler::StepWiseModeler
• PrecomputedLibraryMover() : protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover
• PrecomputedPairEnergiesInteractionGraph : protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::simple_moves::GreenPacker
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_ss_ : protocols::medal::MedalExchangeMover , protocols::star::Extender , protocols::star::StarAbinitio
• predefined_torsions_ : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• PredesignPerturbMover() : protocols::enzdes::PredesignPerturbMover
• predict_H3_base_type() : protocols::antibody::AntibodyInfo
• predict_n_matches_for_hit_subsets() : protocols::match::Matcher
• predict_pos_rd1() : protocols::ss_prediction::SS_predictor
• predict_pos_rd2() : protocols::ss_prediction::SS_predictor
• predict_rd1() : protocols::ss_prediction::SS_predictor
• predict_rd2() : protocols::ss_prediction::SS_predictor
• predict_ss() : protocols::ss_prediction::SS_predictor
• predicted_burial_ : protocols::simple_filters::PredictedBurialEvaluator
• predicted_H3_base_type_ : protocols::antibody::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• PredictedBurialEvaluator() : protocols::simple_filters::PredictedBurialEvaluator
• PredictedBurialFnEvaluatorCreator() : protocols::simple_filters::PredictedBurialFnEvaluatorCreator
• prediction_ : protocols::frag_picker::quota::TorsionBinPool
• prediction_name_ : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• preexisting_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::SegmentInsert , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• prefix() : protocols::match::output::PDBWriter
• prefix_ : protocols::forge::remodel::RemodelMover::instruction_flags , protocols::frag_picker::FragmentPicker , protocols::jd2::JobOutputter , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::WriteLigandMolFile , protocols::match::output::PDBWriter , protocols::matdes::ExtractSubposeMover
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• preminimize_pose() : protocols::stepwise::monte_carlo::StepWiseMonteCarlo
• prep_grid() : protocols::match::downstream::ActiveSiteGrid
• prepack() : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinMultiPosePacker , protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_full_repack_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• prepack_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• prepack_res_was_inputted_ : protocols::stepwise::modeler::StepWiseModeler
• prepacked_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• PrepackMover() : protocols::protein_interface_design::movers::PrepackMover
• prepare() : protocols::abinitio::abscript::ConstraintPreparer , protocols::abinitio::abscript::StagePreparer
• prepare_coord() : protocols::normalmode::NormalMode
• prepare_fold_tree_for_erraser() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• prepare_for_altbb_move_to_closest_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_altbb_move_to_state() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• prepare_for_centroid_ : protocols::loop_modeling::LoopModeler
• prepare_for_fullatom_ : protocols::loop_modeling::LoopModeler
• prepare_for_hit_generation() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_at_target_build_point() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_hit_generation_for_constraint() : protocols::match::Matcher
• prepare_for_hit_generation_for_geomcst() : protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• prepare_for_match_enumeration() : protocols::match::downstream::DownstreamAlgorithm , protocols::match::downstream::SecondaryMatcherToUpstreamResidue
• prepare_for_output_writing() : protocols::match::output::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• prepare_for_simulated_annealing() : protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge
• prepare_from_prior_sampled_sugar_jobs() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• prepare_from_prior_sampled_sugar_jobs_for_chain_break() : protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator
• prepare_ghost_pose() : protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler
• prepare_hashing_packer_task_() : protocols::hotspot_hashing::HotspotStubSet
• prepare_loop_in_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_loop_in_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_pose() : protocols::constraints_additional::ConstraintEvaluator
• prepare_pose_for_sampling() : protocols::abinitio::KinematicControl
• prepare_push_back() : protocols::toolbox::DecoySetEvaluation
• prepare_scoring() : protocols::noesy_assign::DistanceScoreMover
• prepare_send_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• prepare_simulation() : protocols::canonical_sampling::MetropolisHastingsMover
• prepare_stage1() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage2() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage3() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio
• prepare_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• prepare_stage5() : protocols::abinitio::ClassicAbinitio
• prepare_to_note_hits_for_completed_round() : protocols::match::OccupiedSpaceHash
• PrepareForCentroid() : protocols::loop_modeling::utilities::PrepareForCentroid
• PrepareForFullatom() : protocols::loop_modeling::utilities::PrepareForFullatom
• preparers_ : protocols::abinitio::abscript::AbscriptStageMover
• PreparerSet : protocols::abinitio::abscript::AbscriptStageMover
• prepend_Aform_residue() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• prepend_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• prepend_other_pose() : protocols::stepwise::monte_carlo::mover::AddMover
• prepend_output_name() : protocols::canonical_sampling::MetricRecorder
• prepend_output_name_ : protocols::canonical_sampling::MetricRecorder
• prepend_polymer_residue_before_seqpos() : protocols::environment::ProtectedConformation
• prepend_residue() : protocols::stepwise::monte_carlo::mover::AddMover
• preprocessing_script_version_ : protocols::antibody::GraftOneCDRLoop
• presample_added_residue_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_by_swa_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_virtual_sugars() : protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler , protocols::stepwise::modeler::StepWiseConnectionSampler
• preselection_mover_exists() : protocols::generalized_kinematic_closure::GeneralizedKIC
• preserve_buried_contacts() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_detailed_balance() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::ThermodynamicMover , protocols::kinematic_closure::BalancedKicMover , protocols::rigid::RigidBodyMover , protocols::rigid::UniformRigidBodyMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_detailed_balance_ : protocols::backrub::BackrubMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_whole_input_tag_ : protocols::jobdist::BasicJob
• presetClass() : protocols::sparta::GDB
• preturb_rot_and_dunbrack_eval() : protocols::simple_moves::sidechain_moves::SidechainMover
• prev_state_hash_ : protocols::pack_daemon::PackDaemon
• PREV_Tab : protocols::sparta::Sparta::SpartaLib
• prevent_repacking() : protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• prevent_repacking_ : protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictIdentitiesOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation
• PreventChainFromRepackingOperation() : protocols::toolbox::task_operations::PreventChainFromRepackingOperation
• PreventResiduesFromRepackingOperation() : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• previous_mover_ : protocols::rosetta_scripts::MultiplePoseMover
• previous_round_geometry_still_matchable() : protocols::match::OccupiedSpaceHash
• previous_sequence_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• previous_tree_ : protocols::nonlocal::SingleFragmentMover
• previous_vertex1 : protocols::viewer::GraphicsState
• previous_vertex2 : protocols::viewer::GraphicsState
• previous_width_vector : protocols::viewer::GraphicsState
• previous_working_pack_res() : protocols::stepwise::modeler::packer::StepWisePacker
• previous_working_pack_res_ : protocols::stepwise::modeler::packer::StepWisePacker
• previously_builded_res_clash_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_contact_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_VDW_filter() : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• principal_component() : protocols::features::helixAssembly::HelicalFragment
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• print() : protocols::dna::DnaChains , protocols::fldsgn::NcontactsCalculator , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::frag_picker::nonlocal::NonlocalPair , protocols::frags::TorsionFragmentLibrary , protocols::jd2::ScoreMap , protocols::loophash::BackboneSegment , protocols::match::downstream::AtomAngleSecMatchRPE , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::motifs::Motif , protocols::moves::MoverStatistics , protocols::moves::PyMolMover , protocols::pockets::PocketGrid , protocols::rbsegment_relax::RBSegmentMover , protocols::scoring::Interface , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ChargeCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::SurfaceCalculator , protocols::wum2::WorkUnit , protocols::wum::SilentStructStore , protocols::wum::WorkUnitBase
• print_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• print_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_alt_energies() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• print_avg_cluster_centroid_dist() : protocols::make_rot_lib::MakeRotLibMover
• print_cache() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_cluster_assignment() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• print_cluster_PDBs() : protocols::cluster::ClusterBase
• print_clusters_silentfile() : protocols::cluster::ClusterBase
• print_current_state_assignment() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
• print_debug() : protocols::abinitio::MembraneAbinitio
• print_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• print_dunbrack02_rotlib() : protocols::make_rot_lib::MakeRotLibMover
• print_energies() : protocols::optimize_weights::IterativeOptEDriver
• print_entity_history() : protocols::pack_daemon::PackDaemon
• print_fragment() : protocols::frag_picker::FragmentCandidate
• print_fragment_seq() : protocols::frag_picker::FragmentCandidate
• print_generation_statistics() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_grid_param() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• print_internal_energies() : protocols::flexpack::interaction_graph::FlexbbNode
• print_library() : protocols::loophash::MPI_LoopHashRefine
• print_mutation_data() : protocols::pmut_scan::MutationData
• print_ngb_mask() : protocols::neighbor::Neighborhood
• print_pack_report() : protocols::vip::VIP_Mover
• print_peak_info() : protocols::noesy_assign::CrossPeak
• print_population() : protocols::genetic_algorithm::GeneticAlgorithmBase
• print_pymol_selection_of_hbond_unsat() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_interface_residues() : protocols::analysis::InterfaceAnalyzerMover
• print_pymol_selection_of_packing() : protocols::analysis::InterfaceAnalyzerMover
• print_raw_numbers() : protocols::cluster::ClusterBase
• print_relax_report() : protocols::vip::VIP_Mover
• print_report() : protocols::frag_picker::BoundedCollector< StrictWeakOrdering > , protocols::frag_picker::CandidatesCollector , protocols::frag_picker::GrabAllCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaCollector , protocols::frag_picker::quota::SecondaryStructurePool
• print_rot_data() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_data_vec() : protocols::make_rot_lib::MakeRotLibMover
• print_rot_vec() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• print_score() : protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PSSMOptEPositionData
• print_sequence() : protocols::frag_picker::CSTalosIO , protocols::frag_picker::PhiPsiTalosIO
• print_stats() : protocols::loophash::MPI_LoopHashRefine , protocols::wum::MPI_WorkUnitManager
• print_stats_auto() : protocols::wum::MPI_WorkUnitManager
• print_statw_interval_ : protocols::wum::MPI_WorkUnitManager
• print_str_vec() : protocols::antibody::design::AntibodyGraftDesignMover
• print_string_to_PDBfile() : protocols::pockets::GenPharmacophore
• print_summary() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• print_timing_stats() : protocols::wum::MPI_WorkUnitManager
• print_to_file() : protocols::pockets::FingerprintBase
• print_to_oegrid() : protocols::pockets::ElectrostaticpotentialGrid
• print_to_pdb() : protocols::pockets::FingerprintBase
• print_tracer_info_ : protocols::antibody::design::AntibodyGraftDesignMover
• print_verbose_ddgs() : protocols::ddg::ddGMover
• printContent() : protocols::pockets::SmallMol
• printCoordinates() : protocols::pockets::SmallMol
• PrintErrorAndQuit() : protocols::hybridization::TMalign
• prioritize() : protocols::wum2::WorkUnit
• prioritize_ : protocols::wum2::WorkUnit
• priority() : protocols::topology_broker::claims::SequenceClaim
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::SequenceClaimer
• PrioSubtype : protocols::environment::claims::ClaimStrength
• prob_cutoff_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• prob_larger_current_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_set_ : protocols::antibody::design::ResidueProbDesignOperation
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_table_ : protocols::docking::ConformerSwitchMover
• prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• Probabilities : protocols::medal::MedalMover , protocols::nonlocal::BiasedFragmentMover
• probability() : protocols::frag_picker::quota::ABEGO_SS_Config , protocols::noesy_assign::CrossPeak
• probability_ : protocols::make_rot_lib::RotData
• probability_limit() : protocols::match::upstream::BuildSet
• Probe : protocols::hotspot_hashing::movers::PlaceProbeMover
• probe_atom_type_ : protocols::qsar::scoring_grid::SolvationGrid
• probe_rad_ : protocols::pockets::PocketGrid
• probe_radius() : protocols::match::BumpGrid , protocols::simple_filters::TaskAwareSASAFilter
• probe_radius_ : protocols::simple_filters::TaskAwareSASAFilter , protocols::toolbox::task_operations::SelectBySASAOperation
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• problem_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureSolution
• probs_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO , protocols::nonlocal::SingleFragmentMover
• proc_id_ : protocols::jobdist::BaseJobDistributor
• process_AA_SET_line() : protocols::pack_daemon::EntityFunc
• process_add_daemon_message() : protocols::pack_daemon::DaemonSet
• process_algorithm_info() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_continuous_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_data() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_decoy() : protocols::abinitio::AbrelaxApplication , protocols::features::strand_assembly::SandwichFeatures
• process_discard_entity_message() : protocols::pack_daemon::DaemonSet
• process_elements() : protocols::environment::EnvClaimBroker
• process_ENTITY_FUNCTION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_FITNESS_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_fragments() : protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure
• process_hit() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::PoseInserter , protocols::match::output::UpstreamHitCacher , protocols::match::output::WriteUpstreamHitKinemage , protocols::match::upstream::UpstreamResidueProcessor
• process_inbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_inbound_wus_master() : protocols::wum::MPI_Relax
• process_include_xml() : protocols::rosetta_scripts::RosettaScriptsParser
• process_includes() : protocols::rosetta_scripts::RosettaScriptsParser
• process_incoming_msgs() : protocols::wum::MPI_WorkUnitManager
• process_input_line_tokens() : protocols::toolbox::match_enzdes_util::ResInteractions
• process_insert_design_string() : protocols::forge::components::BDR , protocols::forge::remodel::RemodelMover
• process_match() : protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor
• process_match_list() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_matches() : protocols::match::Matcher
• process_matches_all_hit_combos_for_hit_subsets() : protocols::match::Matcher
• process_matches_main_loop_enumerating_all_hit_combos() : protocols::match::Matcher
• process_matches_where_one_geomcst_defines_downstream_location() : protocols::match::Matcher
• process_matching_exchange_requests() : protocols::canonical_sampling::AsyncMPITemperingBase
• process_message() : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::MPIFileBufJobDistributor
• process_motifs() : protocols::simple_filters::SymmetricMotifFilter
• process_NPD_PROPERTY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_outbound_wus() : protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave
• process_outbound_wus_master() : protocols::wum::MPI_Relax
• process_pdb_header() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• process_pose() : protocols::rosetta_scripts::MultiplePoseMover
• process_POSE_ENERGY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_POSE_ENERGY_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_pose_request_for_entity() : protocols::pack_daemon::DaemonSet
• process_poses() : protocols::rosetta_scripts::MultiplePoseMover
• process_rotamers() : protocols::optimize_weights::PNatAAOptEPositionData
• process_SCALAR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_score() : protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatStructureOptEData
• process_SCORE_line() : protocols::pack_daemon::EntityFunc
• process_SET_CONDITION_line() : protocols::pack_daemon::EntityFunc
• process_state_energy_evaluations_for_entity() : protocols::pack_daemon::DaemonSet
• process_STATE_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_STATE_VECTOR_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_SUB_EXPRESSION_line() : protocols::pack_daemon::EntityFunc
• process_VECTOR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_VECTOR_VARIABLE_line() : protocols::pack_daemon::DynamicAggregateFunction
• processed() : protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover
• processed_ : protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover
• ProcessorFactory() : protocols::match::output::ProcessorFactory
• procorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• prof_row() : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO
• profile() : protocols::frag_picker::VallResidue
• profile_ : protocols::frag_picker::VallResidue
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_struct() : protocols::frag_picker::VallResidue
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• ProfilerMover() : protocols::moves::ProfilerMover
• ProfileScore() : protocols::frag_picker::scores::ProfileScore
• ProfileScoreBlosum62() : protocols::frag_picker::scores::ProfileScoreBlosum62
• ProfileScoreDistWeight() : protocols::frag_picker::scores::ProfileScoreDistWeight
• ProfileScoreL1() : protocols::frag_picker::scores::ProfileScoreL1
• ProfileScoreStructL1() : protocols::frag_picker::scores::ProfileScoreStructL1
• ProfileScoreSubMatrix() : protocols::frag_picker::scores::ProfileScoreSubMatrix
• progress_ : protocols::canonical_sampling::ProgressBarObserver
• progress_file() : protocols::simple_moves::GenericMonteCarloMover
• progress_file_ : protocols::simple_moves::GenericMonteCarloMover
• ProgressBarObserver() : protocols::canonical_sampling::ProgressBarObserver
• prohibit_single_residue_loops() : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• prohibit_single_residue_loops_ : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• project_deltaE_for_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• project_point_to_3d() : protocols::match::OccupiedSpaceHash
• project_pref_max_cpu_run_time_ : protocols::boinc::Boinc
• project_pref_max_gfx_cpu_ : protocols::boinc::Boinc
• project_pref_max_gfx_fps_ : protocols::boinc::Boinc
• ProjectionVector : protocols::evaluation::PCA
• ProlineFixMover() : protocols::simple_moves::ProlineFixMover
• ProlinePhiScore() : protocols::frag_picker::scores::ProlinePhiScore
• propagate_best_from_previous_generation() : protocols::genetic_algorithm::GeneticAlgorithmBase
• propeller() : protocols::dna::DNABasepair
• propeller_ : protocols::dna::DNABasepair
• proposal_density() : protocols::simple_moves::sidechain_moves::SidechainMover
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposed_since_last_batch() : protocols::jd2::archive::ArchiveBase
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• ProtectedConformation() : protocols::environment::ProtectedConformation
• PROTEIN : protocols::pockets::ComparisonGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketGrid
• protein_atom : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_charge : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_coords : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_id : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_type : protocols::ligand_docking::rdf::AtomPairData
• protein_atr_rep_screening_pose_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_CA_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• protein_calculate() : protocols::scoring::Interface
• protein_ccd_closer_ : protocols::stepwise::modeler::StepWiseMinimizer
• protein_ccd_closers_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_ccd_poses_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_connection_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_cutpoints_closed_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler , protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_dna_motif() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_build_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_target_positions_JA() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_full_optimize() : protocols::stepwise::legacy::modeler::StepWiseLegacyMinimizer
• protein_full_optimize_ : protocols::stepwise::legacy::modeler::StepWiseLegacyMinimizer
• protein_interface_design() : protocols::toolbox::task_operations::SeqprofConsensusOperation
• protein_interface_design_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• protein_neighbors() : protocols::dna::DnaInterfaceFinder
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_positions() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_prepack() : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_prepack_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_protein_rdf() : protocols::ligand_docking::ComputeLigandRDF
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_scan() : protocols::dna::DnaInterfacePacker
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• ProteinAtrRepChecker() : protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker
• ProteinAtrRepScreener() : protocols::stepwise::legacy::screener::ProteinAtrRepScreener
• ProteinBackboneAtomAtomPairFeatures() : protocols::features::ProteinBackboneAtomAtomPairFeatures
• ProteinBackboneAtomAtomPairFeaturesCreator() : protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator
• ProteinBackboneBuildPoint() : protocols::match::upstream::ProteinBackboneBuildPoint
• ProteinBackboneTorsionAngleFeatures() : protocols::features::ProteinBackboneTorsionAngleFeatures
• ProteinBackboneTorsionAngleFeaturesCreator() : protocols::features::ProteinBackboneTorsionAngleFeaturesCreator
• ProteinBetaAntiParallelStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler
• ProteinBondGeometryFeatures() : protocols::features::ProteinBondGeometryFeatures
• ProteinBondGeometryFeaturesCreator() : protocols::features::ProteinBondGeometryFeaturesCreator
• ProteinCCD_ClosureScreener() : protocols::stepwise::screener::ProteinCCD_ClosureScreener
• ProteinCore() : protocols::toolbox::task_operations::ProteinCore
• ProteinFragmentStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler
• ProteinInterfaceDesignOperation() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• ProteinInterfaceMultiStateDesignMover() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• ProteinLigandInterfaceUpweighter() : protocols::enzdes::ProteinLigandInterfaceUpweighter
• ProteinMainChainStepWiseSampler() : protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler
• ProteinResidueConformationFeatures() : protocols::features::ProteinResidueConformationFeatures
• ProteinResidueConformationFeaturesCreator() : protocols::features::ProteinResidueConformationFeaturesCreator
• ProteinRMSDFeatures() : protocols::features::ProteinRMSDFeatures
• ProteinRMSDFeaturesCreator() : protocols::features::ProteinRMSDFeaturesCreator
• ProteinRMSDNoSuperpositionFeatures() : protocols::features::ProteinRMSDNoSuperpositionFeatures
• ProteinRMSDNoSuperpositionFeaturesCreator() : protocols::features::ProteinRMSDNoSuperpositionFeaturesCreator
• ProteinSideChainCopier() : protocols::stepwise::modeler::protein::ProteinSideChainCopier
• ProteinSilentReport() : protocols::features::ProteinSilentReport
• ProteinUpstreamBuilder() : protocols::match::upstream::ProteinUpstreamBuilder
• Protocol() : protocols::abinitio::Protocol
• protocol_ : protocols::features::RotamerRecoveryFeatures , protocols::ligand_docking::LigandDockProtocol , protocols::loop_modeling::LoopProtocol , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::rotamer_recovery::RotamerRecovery
• protocol_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_id_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_params_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• ProtocolFeatures() : protocols::features::ProtocolFeatures
• ProtocolFeaturesCreator() : protocols::features::ProtocolFeaturesCreator
• protocols::jd2::JobDistributor : protocols::jd2::InnerJob
• protocols::jd2::JobDistributorFactory : protocols::jd2::archive::MPIArchiveJobDistributor
• protocols::jd2::JobInputter : protocols::jd2::InnerJob
• protocols::jd2::Parser : protocols::jd2::InnerJob
• proton() : protocols::noesy_assign::CrossPeak
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_index() : protocols::noesy_assign::MethylNames
• proton_tolerance() : protocols::noesy_assign::CrossPeakInfo
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list() : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• protonated_H1_adenosine_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• ProtonResonance() : protocols::noesy_assign::ProtonResonance
• protons_ : protocols::simple_filters::AtomicContactFilter
• prune_extra_atoms() : protocols::generalized_kinematic_closure::GeneralizedKIC
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• PSEUDO_PROTEIN : protocols::pockets::ElectrostaticpotentialGrid
• PseudocontactShiftEnergyController() : protocols::topology_broker::PseudocontactShiftEnergyController
• PseudocontactShiftEnergyController_Ts1() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts1
• PseudocontactShiftEnergyController_Ts2() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts2
• PseudocontactShiftEnergyController_Ts3() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts3
• PseudocontactShiftEnergyController_Ts4() : protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pseudorotation() : protocols::dna::DNABase
• pseudorotation_ : protocols::dna::DNABase
• psi() : protocols::frag_picker::PhiPsiTalosIO
• Psi() : protocols::frag_picker::scores::Psi
• psi() : protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::kinematic_closure::ClosureProblem , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_ : protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::make_rot_lib::MakeRotLibJob , protocols::make_rot_lib::RotData , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::stepwise::modeler::protein::MainChainTorsionSet
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::hbs::HbsMover , protocols::simple_moves::oop::OopMover
• psi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• psi_range_ : protocols::make_rot_lib::MakeRotLibOptionsData
• psis : protocols::antibody::clusters::ClusterData
• PSP : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• PSSM2BfactorMover() : protocols::simple_moves::PSSM2BfactorMover
• pssm_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_data_ : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• PSSMOptEPositionData() : protocols::optimize_weights::PSSMOptEPositionData
• PSURFACE : protocols::pockets::ComparisonGrid , protocols::pockets::PocketGrid
• ptask() : protocols::multistate_design::PackingState
• ptask_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::simple_moves::ConsensusDesignMover
• ptask_p_ : protocols::multistate_design::PackingState
• pts_ : protocols::cluster::APCluster
• PtType : protocols::pockets::ComparisonGrid , protocols::pockets::ElectrostaticpotentialGrid , protocols::pockets::PocketGrid
• pucker() : protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_flip_rate_ : protocols::stepwise::sampler::rna::RNA_MC_Suite
• pucker_state() : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler
• pucker_state_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_ : protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• pucker_states_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• pulldomain() : protocols::hybridization::DDomainParse
• pure_large_frags_ : protocols::abinitio::JumpingFoldConstraints
• PURE_TOPO_RESAMPLING : protocols::abinitio::IterativeBase
• push() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool
• push_back() : protocols::cluster::Cluster , protocols::cluster::GatherPosesMover , protocols::coarse_rna::SourcePositions , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::fldsgn::topology::HSSTripletSet , protocols::fldsgn::topology::SheetSet , protocols::fldsgn::topology::StrandPairingSet , protocols::frag_picker::VallChunk , protocols::frag_picker::VallProvider , protocols::loops::Loops , protocols::loops::LoopsFileData , protocols::moves::MonteCarlo , protocols::toolbox::DecoySetEvaluation , protocols::wum2::WUQueue , protocols::wum::WorkUnitQueue
• push_back_and_finalize() : protocols::fldsgn::topology::StrandPairingSet
• push_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• push_back_CA_xyz_from_silent_file() : protocols::toolbox::DecoySetEvaluation
• push_front() : protocols::cluster::Cluster , protocols::wum2::WUQueue , protocols::wum::WorkUnitQueue
• push_passport() : protocols::environment::ClaimingMover , protocols::environment::ProtectedConformation
• push_the_limits() : protocols::frag_picker::quota::QuotaSelector
• push_the_limits_to_the_winner() : protocols::frag_picker::quota::QuotaSelector
• put_constraints_on_base_step() : protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler
• put_in_cutpoints() : protocols::stepwise::monte_carlo::mover::TransientCutpointHandler
• put_jump_stub_intra_residue : protocols::environment::EnvClaimBroker::BrokeredJumpData
• put_lock_on_silent_file() : protocols::stepwise::setup::StepWiseCSA_JobDistributor
• PValuedFragmentScoreManager() : protocols::frag_picker::scores::PValuedFragmentScoreManager
• pymol() : protocols::moves::PyMolObserver
• pymol_ : protocols::moves::PyMolObserver , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pymol_name() : protocols::moves::PyMolMover
• pymol_name_ : protocols::moves::PyMolMover
• pymol_sel_hbond_unsat : protocols::analysis::InterfaceData
• pymol_sel_interface : protocols::analysis::InterfaceData
• pymol_sel_packing : protocols::analysis::InterfaceData
• PyMolMover() : protocols::moves::PyMolMover
• PyMolObserver() : protocols::moves::PyMolObserver
• pythag() : protocols::normalmode::NormalMode