- p -

• p1_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p1_deriv() : core::scoring::constraints::AngleConstraint
• p1_theta_deriv() : core::scoring::constraints::AngleConstraint
• p2_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p2_deriv() : core::scoring::constraints::AngleConstraint
• P_AA() : core::scoring::P_AA
• P_AA_energy() : core::scoring::P_AA
• P_AA_Energy() : core::scoring::methods::P_AA_Energy
• P_AA_initialize() : core::scoring::P_AA
• P_AA_pp_Energy() : core::scoring::methods::P_AA_pp_Energy
• P_AA_pp_energy() : core::scoring::P_AA
• p_atom_index() : core::chemical::rna::RNA_ResidueType
• p_value() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• packable() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• PackDaemon() : protocols::pack_daemon::PackDaemon
• packed_residues() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_rotamer_2_regular_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• packed_rotno() : core::pack::dunbrack::PackedDunbrackRotamer< S, P >
• packed_rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_sorted_rotno() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• PackedDunbrackRotamer() : core::pack::dunbrack::PackedDunbrackRotamer< S, P >
• packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• PackerEnergyAdd() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergyMultiply() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergySubtract() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerNeighborGraphFilter() : protocols::simple_filters::PackerNeighborGraphFilter
• packertask() : protocols::flxbb::DesignTask
• PackerTask_() : core::pack::task::PackerTask_
• packing_interaction_cutoff() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy
• packing_shell() : protocols::simple_filters::RelativePoseFilter
• PackingScore() : core::scoring::packstat::PackingScore
• PackingScoreResData() : core::scoring::packstat::PackingScoreResData
• PackingState() : protocols::multistate_design::PackingState
• PackRotamersMover() : protocols::simple_moves::PackRotamersMover
• PackRotamersMoverLazy() : protocols::simple_moves::PackRotamersMoverLazy
• PackRotamersMoverPartGreedy() : protocols::enzdes::PackRotamersMoverPartGreedy
• PackstatCalculator() : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• PackStatEnergy() : core::scoring::methods::PackStatEnergy
• PackStatFilter() : protocols::simple_filters::PackStatFilter
• PackStatMover() : protocols::analysis::PackStatMover
• pages() : core::fragment::picking_old::concepts::Book< Pages >
• pair_dp() : core::scoring::SecondaryStructurePotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• pair_energy_H() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::TableLookupEvaluator , core::scoring::etable::BaseEtableEnergy< Derived >
• pair_energy_H_() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::BaseEtableEnergy< Derived >
• pair_list() : protocols::scoring::Interface
• pair_overlap_tolerance() : protocols::match::BumpGrid
• pair_sets_with_positions() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• pair_term_energy() : core::scoring::PairEPotential
• pair_term_energy_and_deriv() : core::scoring::PairEPotential
• pair_term_energy_exists() : core::scoring::PairEPotential
• pair_with_scaffold() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet
• paired() : core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , protocols::dna::DnaPosition
• PairEnergy() : core::scoring::methods::PairEnergy
• PairEPotential() : core::scoring::PairEPotential
• PairFeatures() : protocols::features::PairFeatures
• PairFeaturesCreator() : protocols::features::PairFeaturesCreator
• pairing() : protocols::abinitio::PairingStatEntry
• Pairing() : core::scoring::dssp::Pairing
• PairingLibrary() : protocols::jumping::PairingLibrary
• pairings() : protocols::abinitio::Templates
• pairings_size() : protocols::jumping::MembraneJump
• PairingStatEntry() : protocols::abinitio::PairingStatEntry
• PairingStatistics() : protocols::abinitio::PairingStatistics
• PairingTemplate() : protocols::jumping::PairingTemplate
• pairs() : core::sequence::PairScoringScheme
• PairScoringScheme() : core::sequence::PairScoringScheme
• PalesEvaluator() : protocols::simple_filters::PalesEvaluator
• PalesEvaluatorCreator() : protocols::simple_filters::PalesEvaluatorCreator
• parallel() : protocols::design_opt::PointMutationCalculator , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover
• ParallelBetaPairingPreferenceFilter() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• ParallelTempering() : protocols::canonical_sampling::ParallelTempering
• param() : core::scoring::packing::HolesParamsRes
• param1() : protocols::branch_angle::BranchAngleOptimizer
• param2() : protocols::branch_angle::BranchAngleOptimizer
• param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• parameter_set4final() : protocols::hybridization::TMalign
• parameter_set4scale() : protocols::hybridization::TMalign
• parameter_set4search() : protocols::hybridization::TMalign
• parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• params_database_tag() : core::scoring::hbonds::HBondOptions
• parent() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• parent_id() : core::optimization::DOF_DataPoint
• parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• ParetoOptMutationMover() : protocols::design_opt::ParetoOptMutationMover
• parse() : core::io::pdb::PDB_DReader
• parse_atom_pair_constraint() : core::scoring::constraints::ConstraintIO
• parse_body_line() : core::pack::task::ResfileContents
• parse_cache_size_tag_item() : protocols::features::ReportToDB
• parse_chain_endings() : core::io::silent::BinaryProteinSilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parse_chi_and_bb() : protocols::simple_moves::MinMover
• parse_command_line() : protocols::frag_picker::FragmentPicker
• parse_configuration_options() : protocols::loops::JSONFormattedLoopsFileReader
• parse_coordinate_constraint() : core::scoring::constraints::ConstraintIO
• parse_def() : core::pack::task::operation::TaskOperation , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::ReadResfile , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::LigInterfaceEnergyFilter , protocols::filters::Filter , protocols::inputter::InputterStream , 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_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::TaskAwareMinMover , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::SelectBySASAOperation
• parse_def_opts() : protocols::simple_moves::MinMover
• parse_disulf_file() : core::io::raw_data::DisulfideFile
• parse_dof_task_type() : protocols::simple_moves::MinMover
• parse_dof_tasks() : protocols::simple_moves::MinMover
• parse_energies() : core::io::silent::SilentStruct
• parse_files() : core::scoring::orbitals::OrbitalsLookup
• parse_format_string() : protocols::outputter::FormatStringOutputter
• parse_header_line() : core::pack::task::ResfileContents
• parse_heterogen_name_for_carbohydrate_residues() : core::io::pdb::FileData
• parse_in_progress() : core::io::pdb::HeaderInformation
• 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_mol_data() : core::chemical::sdf::MolData
• parse_mol_file() : core::chemical::sdf::MolFileParser
• parse_my_tag() : protocols::docking::TemperedDocking , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::electron_density::SetupForDensityScoringMover , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::enzdes::AddOrRemoveMatchCsts , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::enzdes::BackboneSampler , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::enzdes::PredesignPerturbMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::enzdes::LigDSasaFilter , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::enzdes::LigBurialFilter , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::enzdes::LigInterfaceEnergyFilter , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MutateResidue , protocols::enzdes::EnzScoreFilter , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::enzdes::DiffAtomSasaFilter , protocols::simple_moves::PackRotamersMoverLazy , protocols::simple_moves::PDBReloadMover , protocols::enzdes::RepackWithoutLigandFilter , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::enzdes::EnzdesScorefileFilter , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::enzdes::EnzRepackMinimize , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::features::AtomAtomPairFeatures , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::features::FeaturesReporter , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::features::HBondFeatures , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SuperimposeMover , protocols::features::HBondParameterFeatures , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::features::helixAssembly::HelixBundleFeatures , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::features::LoopAnchorFeatures , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::features::ProteinRMSDFeatures , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::features::ReportToDB , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::features::ResidueGridScoresFeatures , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::features::ResidueScoresFeatures , protocols::features::ResidueTotalScoresFeatures , protocols::features::RotamerBoltzmannWeightFeatures , protocols::features::RotamerRecoveryFeatures , protocols::features::ScoreFunctionFeatures , protocols::features::SecondaryStructureSegmentFeatures , protocols::features::SmotifFeatures , protocols::features::StructureScoresFeatures , protocols::features::UnrecognizedAtomFeatures , protocols::filters::StochasticFilter , protocols::filters::CompoundFilter , protocols::filters::CombinedFilter , protocols::filters::MoveBeforeFilter , protocols::filters::IfThenFilter , protocols::filters::CalculatorFilter , protocols::filters::ContingentFilter , protocols::filters::Filter , protocols::filters::HeavyAtomFilter , protocols::filters::ReplicateFilter , 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::SecondaryStructureFilter , 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::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::forge::remodel::ResidueVicinityRCG , protocols::hotspot_hashing::movers::PlaceSurfaceProbe , protocols::hybridization::CartesianSampler , protocols::hybridization::HybridizeProtocol , protocols::idealize::IdealizeMover , protocols::ligand_docking::AddHydrogens , protocols::ligand_docking::AtomCountFilter , protocols::ligand_docking::ChainExistsFilter , protocols::ligand_docking::CompleteConnectionsFilter , protocols::ligand_docking::CompoundTranslate , 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::Rotate , protocols::ligand_docking::Rotates , protocols::ligand_docking::SlideTogether , protocols::ligand_docking::StartFrom , protocols::ligand_docking::Transform , protocols::ligand_docking::Translate , protocols::loophash::LoopHashDiversifier , protocols::loophash::LoopHashMoverWrapper , protocols::loops::FoldTreeFromLoops , 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::moves::DsspMover , protocols::moves::IfMover , protocols::moves::IteratedConvergenceMover , protocols::moves::Mover , protocols::moves::RandomMover , protocols::moves::RampingMover , protocols::moves::StructureRestrictor , protocols::moves::MonteCarloUtil , protocols::moves::TrialMover , protocols::nonlocal::SingleFragmentMover , protocols::pb_potential::SetupPoissonBoltzmannPotential , 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::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter , protocols::protein_interface_design::filters::InterfaceHolesFilter , protocols::protein_interface_design::filters::RelativeSegmentFilter , protocols::protein_interface_design::filters::RmsdFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , 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::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::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::Splice , protocols::protein_interface_design::movers::SubroutineMover , protocols::protein_interface_design::movers::TaskAwareCsts , 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 , core::chemical::ResidueLoaderOptions , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridInitMover , core::conformation::symmetry::SymmDataOptions , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , core::import_pose::ImportPoseOptions , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::SingleGrid , core::io::pdb::FileDataOptions , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , core::io::pdb::PDB_DReaderOptions , protocols::qsar::scoring_grid::VdwGrid , protocols::relax::FastRelax , core::io::silent::SilentFileOptions , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RollMover , core::scoring::electron_density::ElectronDensityOptions , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::abinitio::DomainAssembly , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::analysis::InterfaceAnalyzerMover , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::backrub::BackrubMover , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::backrub::BackrubSidechainMover , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SeedFoldTree , protocols::canonical_sampling::HamiltonianExchange , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::canonical_sampling::MetricRecorder , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::canonical_sampling::MetropolisHastingsMover , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::canonical_sampling::ParallelTempering , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::canonical_sampling::SimulatedTempering , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::canonical_sampling::TemperingBase , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::canonical_sampling::TrajectoryRecorder , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::canonical_sampling::TrialCounterObserver , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::comparative_modeling::LoopRelaxMover , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseInfoFilter , protocols::comparative_modeling::PartialThreadingMover , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::contact_map::ContactMap , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::design_opt::GreedyOptMutationMover , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::design_opt::ParetoOptMutationMover , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::dna::DesignProteinBackboneAroundDNA , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::dna::DnaInterfaceMinMover , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::dna::DnaInterfaceMultiStateDesign , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::dna::DnaInterfacePacker , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::dna::SeparateDnaFromNonDna , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::docking::DockingInitialPerturbation , protocols::simple_moves::BackboneMover , protocols::simple_moves::ClearConstraintsMover , protocols::docking::DockingProtocol , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstraintSetMover , protocols::docking::DockSetupMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG
• parse_name_tag_item() : protocols::features::ReportToDB
• parse_options_name_and_value() : protocols::jd2::JD2ResourceManagerJobInputter
• parse_opts() : protocols::simple_moves::MinMover
• parse_output_mode() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_PDBnum_icode() : core::pack::task::ResfileContents
• parse_place_probe_tag() : protocols::hotspot_hashing::movers::PlaceProbeMover
• parse_protocol_id_tag_item() : protocols::features::ReportToDB
• parse_quota_command_line() : protocols::frag_picker::FragmentPicker
• parse_region_string() : protocols::contact_map::ContactMap
• parse_remove_xray_virt_tag_item() : protocols::features::ReportToDB
• parse_resid() : core::pack::task::ResfileContents
• parse_residue() : core::scoring::constraints::ConstraintIO
• parse_sample_source_tag_item() : protocols::features::ReportToDB
• parse_score_function() : protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RepackSidechainsMover
• parse_startfrom_file() : protocols::ligand_docking::StartFrom
• parse_state() : protocols::moves::Mover
• parse_sub_filters_tag() : core::pack::task::operation::ResFilterComposition
• parse_tag() : core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ChainIs , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::RestrictToInterface , core::pack::task::operation::TaskOperation , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::PreventRepacking , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraChiCutoff , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::SetCatalyticResPackBehavior , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::AddRigidBodyLigandConfs , protocols::enzdes::AddLigandMotifRotamers , protocols::flxbb::LayerDesignOperation , protocols::forge::remodel::RemodelRotamerLinks , protocols::hotspot_hashing::AddSearchPatternRotSetOp , protocols::jd2::parser::FragmentReader , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , 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::RestrictIdentitiesAtAlignedPositionsOperation , 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::RestrictToTerminiOperation , protocols::toolbox::task_operations::SelectBySASAOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , 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
• ParseAtom() : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::V2Parser , core::chemical::sdf::V3Parser
• ParseAtomTypeData() : core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser
• ParseBond() : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::V2Parser , core::chemical::sdf::V3Parser
• ParsedProtocol() : protocols::rosetta_scripts::ParsedProtocol
• parser() : protocols::jd2::JobDistributor
• ParserJobInputter() : protocols::protein_interface_design::ParserJobInputter
• ParseTable() : core::chemical::sdf::CtabBase , core::chemical::sdf::ctabV2000Parser , core::chemical::sdf::ctabV3000Parser , core::chemical::sdf::V2Parser , core::chemical::sdf::V3Parser
• partial_assign_relaxed_state() : core::pack::interaction_graph::FASTERNode
• partial_assign_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• partial_assign_state_with_lowest_one_body_energy() : core::pack::interaction_graph::FASTERNode
• 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
• Particle() : core::optimization::Particle
• ParticleSwarmMinimizer() : core::optimization::ParticleSwarmMinimizer
• partition_by_jump() : core::kinematics::FoldTree
• partition_by_residue() : core::kinematics::FoldTree
• partition_definition() : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• partition_into_coordinates() : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• PartitionAggregateFunction() : protocols::multistate_design::PartitionAggregateFunction< T >
• PartitionedSearchPattern() : protocols::hotspot_hashing::PartitionedSearchPattern
• partner() : protocols::docking::DockingEnsemble
• partner1() : protocols::contact_map::Contact
• partner2() : protocols::contact_map::Contact
• partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking
• pass_all_filters() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_all_pose_screens() : protocols::swa::rna::StepWiseRNA_Minimizer
• pass_FARFAR_no_auto_bulge_filter() : protocols::swa::rna::StepWiseRNA_Clusterer
• pass_metropolis() : core::pack::annealer::SimAnnealerBase , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::simple_moves::sidechain_moves::SidechainMCMover
• pass_metropolis_multiple_nodes_changing() : protocols::flexpack::annealer::FlexbbSimAnnealer
• pass_start_pose() : protocols::antibody2::H3RefineCCD , protocols::antibody2::RefineOneCDRLoop
• pass_the_loop() : protocols::antibody2::H3PerturbCCD
• passed_automorphism() : protocols::motifs::MotifHit
• passes_com_vector_criterion() : protocols::match::NumNeighborsMPM
• passes_etable_filter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• passes_fast_scan() : protocols::rna::RNA_LoopCloser
• passes_filter() : protocols::match::output::LimitHitsPerRotamerFilter , protocols::match::output::MatchFilter , protocols::match::output::StateAccumulatingMatchFilter , protocols::match::output::MatchCollisionFilter , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::swa::PoseFilter , protocols::swa::PoseFilter_RMSD_Screen , protocols::topology_broker::TopologyClaimer
• passes_filters() : protocols::match::output::MatchProcessor
• passes_hardsphere_filter() : protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter
• patch_str() : core::sequence::AnnotatedSequence
• PatchdockReader() : protocols::protein_interface_design::PatchdockReader
• PatchOperation() : protocols::canonical_sampling::PatchOperation
• path() : protocols::motifs::Motif
• path_dist() : core::scoring::AtomNeighbor
• path_distance() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::count_pair::CountPairGeneric
• path_distance_OK() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distances() : core::chemical::ResidueType , core::conformation::Residue
• PattersonCorrEnergy() : core::scoring::electron_density::PattersonCorrEnergy
• pb_bound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_unbound_tag() : core::scoring::methods::EnergyMethodOptions
• pbest() : core::optimization::Particle
• PBLifetimeCache() : core::scoring::methods::PBLifetimeCache
• PcaEvaluator() : protocols::abinitio::PcaEvaluator
• PCluster() : protocols::pockets::PCluster
• PClusterSet() : protocols::pockets::PClusterSet
• PCS_data() : protocols::scoring::methods::pcs::PCS_data
• PCS_data_from_pose() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_data_input() : protocols::scoring::methods::pcs::PCS_data_input
• PCS_data_input_manager() : protocols::scoring::methods::pcs::PCS_data_input_manager
• PCS_data_per_lanthanides() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• PCS_Energy() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_Energy_parameters_manager() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• PCS_experimental() : protocols::scoring::methods::pcs::PCS_line_data
• PCS_file_data() : protocols::scoring::methods::pcs::PCS_file_data
• PCS_FragDistance() : protocols::frag_picker::scores::PCS_FragDistance
• PCS_line_data() : protocols::scoring::methods::pcs::PCS_line_data
• 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_tolerance() : protocols::scoring::methods::pcs::PCS_line_data
• 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
• PcsInputCenterManager() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile() : protocols::scoring::methods::pcs2::PcsInputFile
• PcsInputLine() : protocols::scoring::methods::pcs2::PcsInputLine
• PcsTensor() : protocols::scoring::methods::pcs2::PcsTensor
• pd_edge_table_all_zeros() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• PDB() : protocols::sparta::PDB
• pdb2pose() : core::pose::PDBInfo
• pdb_chain() : protocols::pmut_scan::MutationData
• PDB_DReaderOptions() : core::io::pdb::PDB_DReaderOptions
• pdb_info() : core::pose::Pose
• pdb_name() : protocols::simple_filters::RelativePoseFilter
• pdb_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_profile() : protocols::protein_interface_design::movers::SpliceSegment
• PdbDataFeatures() : protocols::features::PdbDataFeatures
• PdbDataFeaturesCreator() : protocols::features::PdbDataFeaturesCreator
• PDBDumpMover() : protocols::moves::PDBDumpMover
• pdbid() : core::fragment::FragData , core::fragment::AnnotatedFragData
• PDBInfo() : core::pose::PDBInfo
• PDBInputter() : protocols::inputter::PDBInputter
• PDBJobInputter() : protocols::jd2::PDBJobInputter
• PDBJobOutputter() : protocols::jd2::PDBJobOutputter
• pdbname() : protocols::dna::DnaInterfacePacker
• pdboutput() : protocols::dna::DnaInterfacePacker
• PDBOutput() : protocols::dna::PDBOutput
• PDBOutputter() : protocols::outputter::PDBOutputter
• pdbpos() : core::fragment::FragData , core::fragment::AnnotatedFragData
• PDBPoseInputStream() : core::import_pose::pose_stream::PDBPoseInputStream
• PDBPoseMap() : core::pose::PDBPoseMap
• PDBReloadMover() : protocols::simple_moves::PDBReloadMover
• PDBSilentStruct() : core::import_pose::PDBSilentStruct
• PDBSilentStructCreator() : core::import_pose::PDBSilentStructCreator
• 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
• PDEdge() : core::pack::interaction_graph::PDEdge
• PDInteractionGraph() : core::pack::interaction_graph::PDInteractionGraph
• PDNode() : core::pack::interaction_graph::PDNode
• peak_id() : protocols::noesy_assign::CrossPeak
• peak_volume() : protocols::noesy_assign::PeakAssignment
• PeakAssignment() : protocols::noesy_assign::PeakAssignment
• PeakAssignmentParameters() : protocols::noesy_assign::PeakAssignmentParameters
• PeakAssignmentResidueMap() : 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
• 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() : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_random_loop_model() : protocols::flexpep_docking::FlexPepDockingProtocol
• PeptideBondedEnergyContainer() : core::scoring::PeptideBondedEnergyContainer
• PeptideBondedNeighborConstIterator() : core::scoring::PeptideBondedNeighborConstIterator
• PeptideBondedNeighborIterator() : core::scoring::PeptideBondedNeighborIterator
• PeptideBondEnergy() : core::scoring::methods::PeptideBondEnergy
• PeptideStapleDesignMover() : protocols::protein_interface_design::movers::PeptideStapleDesignMover
• PeptideStapleMover() : protocols::simple_moves::PeptideStapleMover
• per_constraint_build_points() : protocols::match::Matcher
• perform_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_local_refinement() : protocols::hotspot_hashing::movers::PlaceProbeMover
• perform_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• performing_pure_insertion() : protocols::forge::build::SegmentInsert
• period() : core::scoring::methods::CartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::BBDepCartBondedParameters
• periodic_range() : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• PeriodicBoundFunc() : core::scoring::constraints::PeriodicBoundFunc
• PeriodicFunc() : core::scoring::constraints::PeriodicFunc
• periodicity() : core::scoring::dna::TorsionFourierComponent , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permitted_overlap() : protocols::match::MatcherTask
• PerNativeRRReporterHuman() : protocols::rotamer_recovery::PerNativeRRReporterHuman
• PerSphereAccumulator() : core::scoring::packstat::PerSphereAccumulator
• perturb() : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel
• perturb_anchor() : protocols::anchored_design::AnchoredDesignMover
• perturb_backbone_for_test() : protocols::grafting::GraftMoverBase
• perturb_chain() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• perturb_chi() : protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_dBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_rot_within_well() : protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_sBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_weights() : core::scoring::ScoreFunction
• PerturbChiSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• perturber() : protocols::docking::DockingProtocol
• 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::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TabooSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber
• PerturbRotamerSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• phase() : core::scoring::dna::TorsionFourierComponent
• pHEnergy() : core::scoring::methods::pHEnergy
• Phi() : protocols::frag_picker::scores::Phi
• phi() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::protein_interface_design::movers::BBDofs , protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet
• phi_max() : core::util::ABEGO
• phi_min() : core::util::ABEGO
• PhiPsiRmsd() : protocols::frag_picker::scores::PhiPsiRmsd
• PhiPsiSquareWell() : protocols::frag_picker::scores::PhiPsiSquareWell
• PhiPsiTalosIO() : protocols::frag_picker::PhiPsiTalosIO
• pick_a_rotamer() : core::pack::annealer::RotamerAssigningAnnealer , protocols::flexpack::annealer::FlexbbSimAnnealer
• pick_a_rotamer_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• pick_a_rotamer_for_sBR() : core::pack::annealer::FASTERAnnealer
• pick_all_fragments() : protocols::forge::components::VarLengthBuild
• pick_baserotamer_from_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• pick_candidates() : protocols::frag_picker::FragmentPicker
• pick_chunk_candidates() : protocols::frag_picker::FragmentPicker
• pick_fragment_library() : protocols::rna::FullAtomRNA_Fragments , protocols::rna::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_random_chunk() : protocols::hybridization::ChunkTrialMover
• pick_random_fragment() : protocols::coarse_rna::CoarseRNA_Fragments , protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• pick_random_template() : protocols::hybridization::ChunkTrialMover
• pick_rotamer_for_node() : core::pack::annealer::FASTERAnnealer
• pick_starting_template() : protocols::hybridization::HybridizeProtocol
• pipemap() : protocols::wum2::WorkUnit_ElScripts
• PiPiCalculator() : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pivot_atoms() : protocols::backrub::BackrubMover
• pivot_range_randomly() : protocols::simple_moves::BBGaussianMover
• pivot_residues() : protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover
• place() : core::conformation::Residue
• place_adducts() : core::chemical::ResidueTypeSet
• place_atom() : protocols::motifs::Motif
• place_atom_() : protocols::motifs::Motif
• place_atoms() : protocols::motifs::Motif
• place_atoms_() : protocols::motifs::Motif
• place_c() : protocols::kinmatch::FunGroupTK , protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_d() : protocols::kinmatch::FunGroupTK , protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_h() : protocols::kinmatch::BruteFunGroupTK , protocols::kinmatch::FunGroupTK , protocols::kinmatch::KinFunGroupTK
• place_residue() : protocols::motifs::Motif
• place_residue_() : protocols::motifs::Motif
• place_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• place_stubs() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• PlaceFragments() : protocols::seeded_abinitio::PlaceFragments
• placeholder_info() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue() : core::scoring::GenBornPoseInfo , core::scoring::FACTSPoseInfo
• 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
• PlainPdbJobDistributor() : protocols::jobdist::PlainPdbJobDistributor
• PlainRawJobDistributor() : protocols::jobdist::PlainRawJobDistributor
• PlainSilentFileJobDistributor() : protocols::jobdist::PlainSilentFileJobDistributor
• PlanePointIntersection() : protocols::surface_docking::SurfaceParameters
• Pleating() : core::scoring::dssp::Pairing
• pleats1() : 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
• PocketConstraint() : protocols::pockets::PocketConstraint
• PocketConstraintCreator() : protocols::pockets::PocketConstraintCreator
• PocketGrid() : protocols::pockets::PocketGrid
• Point() : core::scoring::packstat::Point
• point_for_nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• point_graph() : core::scoring::Energies
• PointGraphEdgeData() : core::conformation::PointGraphEdgeData
• PointGraphVertexData() : core::conformation::PointGraphVertexData
• PointMutationCalculator() : protocols::design_opt::PointMutationCalculator
• PointMutScanDriver() : protocols::pmut_scan::PointMutScanDriver
• PointPair() : core::scoring::packstat::PointPair
• points_for_nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• PoissonBoltzmannEnergy() : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannPotential() : core::scoring::PoissonBoltzmannPotential
• polar_energy_pack_corrector() : core::scoring::FACTSPotential
• polarF2BR() : core::scoring::FACTSResidueInfo
• polarF2d() : core::scoring::FACTSResidueInfo
• Policy() : protocols::nonlocal::Policy
• poly_ala() : protocols::protein_interface_design::movers::Splice
• polyAla() : protocols::flexpep_docking::FlexPepDockingProtocol
• polymer_direction() : core::kinematics::Edge
• polymeric_oriented_sequence_distance() : core::conformation::Residue
• polymeric_sequence_distance() : core::conformation::Residue
• Polynomial_1d() : core::scoring::hbonds::Polynomial_1d
• Pool_ConvergenceCheck() : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
• Pool_Evaluator() : protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• pool_exists() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Pool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• PoolData() : protocols::canonical_sampling::mc_convergence_checks::PoolData
• PoolEvaluatorCreator() : protocols::simple_filters::PoolEvaluatorCreator
• pop() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , core::graph::NegSpaceElement< T >
• 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_front() : protocols::wum2::WUQueue
• pop_mutation() : protocols::pmut_scan::Mutant
• pop_next() : protocols::wum::WorkUnitQueue
• popular_bin() : protocols::noesy_assign::FragsToAtomDist::DistanceRecord
• populate_all_cdrs() : protocols::antibody::Antibody
• populate_batch_list_from_cmd() : protocols::jd2::JobDistributor
• population() : protocols::genetic_algorithm::GeneticAlgorithm
• pore_radius() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pos() : core::fragment::NonContinuousFrame , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::topology_broker::DofClaim , protocols::topology_broker::SequenceClaim , protocols::topology_broker::BBClaim , protocols::topology_broker::JumpClaim , protocols::topology_broker::RootClaim , protocols::topology_broker::CutClaim , core::fragment::NonContinuousFrame
• Pos1() : core::scoring::dssp::Pairing
• Pos2() : core::scoring::dssp::Pairing
• pos2select() : protocols::flxbb::LayerDesignOperation
• pose() : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::multistate_design::SingleState , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::sic_dock::Rose , protocols::simple_filters::RelativePoseFilter
• Pose() : core::pose::Pose
• pose() : protocols::pockets::PlaidFingerprint , core::pose::datacache::CacheablePoseRawPtr , core::fragment::picking_old::vall::eval::EnergyEval
• pose2pdb() : core::pose::PDBInfo
• pose_coords_are_same() : protocols::design_opt::GreedyOptMutationMover
• pose_from_job() : protocols::comparative_modeling::GenericJobInputter , protocols::comparative_modeling::ThreadingJobInputter , protocols::enzdes::EnzdesJobInputter , protocols::jd2::AtomTreeDiffJobInputter , protocols::jd2::BatchJobInputter , protocols::jd2::JD2ResourceManagerJobInputter , protocols::jd2::LazySilentFileJobInputter , protocols::jd2::PDBJobInputter , protocols::jd2::PoseInputStreamJobInputter , protocols::protein_interface_design::ParserJobInputter , protocols::jd2::SilentFileJobInputter , protocols::jd2::JobInputter , protocols::features::DatabaseJobInputter
• pose_has_chainbreak() : protocols::swa::protein::StepWiseProteinPoseMinimizer
• pose_index() : protocols::loops::ResidueIndexDescription
• pose_input_stream() : protocols::swa::InputStreamWithResidueInfo
• pose_name() : protocols::moves::StructureRestrictor
• pose_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numbered() : protocols::loops::ResidueIndexDescription
• pose_raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• pose_res_no() : core::scoring::constraints::FabConstraint
• pose_resnum() : protocols::pmut_scan::MutationData
• pose_right() : protocols::forge::build::ConnectRight
• Pose_selection_by_full_score() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• PoseBalls() : core::scoring::packing::PoseBalls
• PoseBallsLite() : core::scoring::packing::PoseBallsLite
• PoseCommentsFeatures() : protocols::features::PoseCommentsFeatures
• PoseCommentsFeaturesCreator() : protocols::features::PoseCommentsFeaturesCreator
• PoseCondition() : protocols::moves::PoseCondition
• PoseConformationFeatures() : protocols::features::PoseConformationFeatures
• PoseConformationFeaturesCreator() : protocols::features::PoseConformationFeaturesCreator
• PoseEvaluator() : protocols::evaluation::PoseEvaluator
• PoseFilter() : protocols::swa::PoseFilter
• PoseFilter_RMSD_Screen() : protocols::swa::PoseFilter_RMSD_Screen
• PoseFoundResiduesCombination() : protocols::enzdes::PoseFoundResiduesCombination
• PoseFromPDBLoader() : core::import_pose::PoseFromPDBLoader
• PoseInfoFilter() : protocols::simple_filters::PoseInfoFilter
• PoseInputStream() : core::import_pose::pose_stream::PoseInputStream
• PoseInputStreamJobInputter() : protocols::jd2::PoseInputStreamJobInputter
• PoseInserter() : protocols::match::output::PoseInserter
• PoseMatchOutputWriter() : protocols::match::output::PoseMatchOutputWriter
• PoseMetricCalculator() : core::pose::metrics::PoseMetricCalculator
• PoseMetricContainer() : core::pose::metrics::PoseMetricContainer
• PoseMetricEvaluator() : protocols::simple_filters::PoseMetricEvaluator< T >
• PoseNumberedLoopFileReader() : protocols::loops::PoseNumberedLoopFileReader
• PoseOutputStream() : core::import_pose::pose_stream::PoseOutputStream
• poses_from_cmd_line() : protocols::comparative_modeling::AlignmentClustering
• position() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::scoring::rna::RNA_Datum , protocols::optimize_weights::PNatAAOptEPositionData , core::kinematics::tree::Atom_
• position_ala_ddG() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_data_begin() : protocols::optimize_weights::OptEData
• position_data_end() : protocols::optimize_weights::OptEData
• position_index() : core::fragment::picking_old::vall::VallResidue , 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
• PositionConservedResiduesStore() : core::pose::datacache::PositionConservedResiduesStore
• PositionDdGInfo() : core::io::PositionDdGInfo::PositionDdGInfo
• positions() : protocols::dna::DnaChains , protocols::enzdes::EnzdesFlexibleRegion , protocols::forge::build::BuildManager
• PositionType() : protocols::dna::PositionType
• positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• post_catalog_op() : core::fragment::picking_old::vall::eval::VallFragmentEval
• post_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• post_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• post_packing() : protocols::dna::DnaInterfacePacker
• post_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• PostDockAssemblyScorer() : protocols::domain_assembly::PostDockAssemblyScorer
• PosType() : protocols::multistate_design::PosType
• potential_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• PowExpression() : protocols::pack_daemon::PowExpression
• PQR() : core::scoring::PQR
• pre_align() : protocols::constraints_additional::BindingSiteConstraint
• pre_catalog_op() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• pre_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• pre_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• pre_nresidue_change() : core::conformation::Conformation
• pre_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• pre_scoring() : protocols::flexpack::OtherContextScoreFunction
• preallocate() : core::fragment::picking_old::vall::VallLibrarian
• precalc_etable_coefficients() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• precision() : core::io::silent::SilentStruct
• precompute_all_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_energies() : protocols::flexpack::rotamer_set::FlexbbRotamerSets
• precompute_transforms() : protocols::toolbox::match_enzdes_util::ExternalGeomSampler
• precompute_two_body_energies() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• precompute_unweighted_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• PrecomputedPairEnergiesEdge() : core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• PrecomputedPairEnergiesInteractionGraph() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• PrecomputedPairEnergiesNode() : core::pack::interaction_graph::PrecomputedPairEnergiesNode
• PredesignPerturbMover() : protocols::enzdes::PredesignPerturbMover
• Predicate() : core::scoring::Predicate
• predict_H3_base_type() : protocols::antibody2::AntibodyInfo
• predict_n_matches_for_hit_subsets() : protocols::match::Matcher
• PredictedBurialEvaluator() : protocols::simple_filters::PredictedBurialEvaluator
• PredictedBurialFnEvaluatorCreator() : protocols::simple_filters::PredictedBurialFnEvaluatorCreator
• 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::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::build::SegmentInsert
• prefix() : protocols::match::output::PDBWriter
• prep_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• prep_for_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• prep_grid() : protocols::match::downstream::ActiveSiteGrid
• prepack_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• PrepackMover() : protocols::protein_interface_design::movers::PrepackMover
• prepare_constraints_energy_container() : core::scoring::constraints::ConstraintsEnergy
• 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_FASTER() : core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph
• prepare_for_hit_generation() : protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• 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_new_residue_type() : core::pack::rotamer_set::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• prepare_for_output_writing() : protocols::match::output::OutputWriter , protocols::match::output::PDBWriter , protocols::match::output::CloudPDBWriter
• prepare_for_perturbation() : core::pack::interaction_graph::FASTERNode
• prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• prepare_for_scoring() : core::scoring::NeighborList
• prepare_for_simulated_annealing() : core::pack::interaction_graph::LinearMemNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::DoubleLazyNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::HPatchEdge< V, E, G > , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::BackgroundNode< V, E, G >
• prepare_for_simulated_annealing_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• prepare_ghost_pose() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• prepare_hashing_packer_task_() : protocols::hotspot_hashing::HotspotStubSet
• prepare_loop_in_stage3() : protocols::abinitio::KinematicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::MembraneAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints
• prepare_loop_in_stage4() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::JumpingFoldConstraints
• prepare_neighbor_graphs() : core::scoring::Energies
• prepare_otf_graph() : core::pack::rotamer_set::RotamerSets
• prepare_pose() : protocols::constraints_additional::ConstraintEvaluator
• prepare_pose_for_sampling() : protocols::abinitio::KinematicControl
• prepare_push_back() : protocols::toolbox::DecoySetEvaluation
• prepare_rotamers_for_packing() : core::scoring::methods::PairEnergy , core::scoring::methods::FACTSEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::GenBornEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::orbitals::OrbitalsScore , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::LK_BallEnergy , core::scoring::ScoreFunction
• prepare_scoring() : protocols::noesy_assign::DistanceScoreMover
• prepare_send_new_coords() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• prepare_sets_for_packing() : core::pack::rotamer_set::RotamerSets
• prepare_simulation() : protocols::canonical_sampling::MetropolisHastingsMover
• prepare_stage1() : protocols::abinitio::KinematicAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::MembraneAbinitio , protocols::abinitio::JumpingFoldConstraints
• prepare_stage2() : protocols::abinitio::MembraneAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::KinematicAbinitio
• prepare_stage3() : protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio
• prepare_stage4() : protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FoldConstraints
• prepare_stage5() : protocols::abinitio::ClassicAbinitio
• prepare_symm_otf_interaction_graph() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• prepare_to_note_hits_for_completed_round() : protocols::match::OccupiedSpaceHash
• prepend_output_name() : protocols::canonical_sampling::MetricRecorder
• prepend_polymer_residue_before_seqpos() : core::pose::Pose , core::conformation::Conformation
• prepend_res() : core::pose::PDBInfo
• prepend_residues() : protocols::swa::protein::StepWiseProteinPoseSetup
• PrependMainchainAtom() : core::chemical::PrependMainchainAtom
• preprocess_data() : core::scoring::ResidualDipolarCoupling
• preprocess_pose() : core::import_pose::pose_stream::PoseInputStream
• preserve_buried_contacts() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta() : core::pack::task::ResidueLevelTask_ , core::pack::task::ResidueLevelTask
• preserve_detailed_balance() : protocols::rigid::RigidBodyMover , protocols::backrub::BackrubMover , protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::BackboneMover , protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header() : core::io::pdb::FileDataOptions
• presetClass() : protocols::sparta::GDB
• pretty_print() : core::scoring::mm::MMBondAngleLibrary , core::coarse::Translator , core::coarse::RuleSet , core::coarse::Rule , core::coarse::TranslatorSet , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary
• preturb_rot_and_dunbrack_eval() : protocols::simple_moves::sidechain_moves::SidechainMover
• prevent_repacking() : protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , core::pack::task::ResidueLevelTask , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , core::pack::task::ResidueLevelTask_ , protocols::simple_moves::DesignRepackMover
• PreventChainFromRepackingOperation() : protocols::toolbox::task_operations::PreventChainFromRepackingOperation
• PreventResiduesFromRepackingOperation() : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation
• previous() : core::graph::EdgeListElement
• previous_child() : core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• previous_floating_base_chain_closure() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• previous_round_geometry_still_matchable() : protocols::match::OccupiedSpaceHash
• previous_sibling() : core::kinematics::tree::Atom_ , core::kinematics::tree::Atom
• previously_builded_res_clash_filter() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_contact_filter() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• previously_builded_res_VDW_filter() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• principal_component() : protocols::features::helixAssembly::HelicalFragment
• print() : core::scoring::hackelec::ElecAtom , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::dna::DnaChains , core::scoring::hackelec::ElecAtom , core::scoring::etable::etrie::TrieCountPairAll , core::pose::metrics::EnergyDependentCalculator , core::pack::interaction_graph::PDNode , core::chemical::sdf::MolData , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::StructureDependentCalculator , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator , core::scoring::EMapVector , core::scoring::etable::etrie::CountPairData_1_2 , protocols::moves::PyMolMover , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::MinimizationNode , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , protocols::flexpack::interaction_graph::FlexbbNode , protocols::frags::TorsionFragmentLibrary , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::loophash::BackboneSegment , protocols::motifs::Motif , protocols::moves::MoverStatistics , protocols::rbsegment_relax::RBSegmentMover , protocols::toolbox::pose_metric_calculators::ChargeCalculator , core::chemical::AtomType , core::chemical::Atom , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::PiPiCalculator , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , protocols::wum::SilentStructStore , protocols::wum2::WorkUnit , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::wum::WorkUnitBase , protocols::toolbox::pose_metric_calculators::SurfaceCalculator , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , core::pack::interaction_graph::SymmLinearMemNode , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , core::pose::metrics::PoseMetricContainer , protocols::toolbox::pose_metric_calculators::HPatchCalculator , protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , core::scoring::EnergyNode , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::scoring::Interface , protocols::pockets::PocketGrid , protocols::motifs::Motif , protocols::match::downstream::AtomAngleSecMatchRPE , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::flexpack::interaction_graph::OTFFlexbbNode , core::scoring::trie::TrieNode< AT, CPDATA > , protocols::jd2::ScoreMap , protocols::frag_picker::nonlocal::NonlocalPair , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::fldsgn::NcontactsCalculator , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::MembraneTopology , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::etable::etrie::CountPairDataGeneric , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairData_1_1 , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::DensePDNode , core::graph::Node , core::chemical::Orbital
• print_address() : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_all_bond_lengths() : core::chemical::IdealBondLengthSet
• print_all_types() : core::chemical::CSDAtomTypeSet , core::chemical::ElementSet , core::chemical::MMAtomTypeSet
• print_allowed_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• print_alt_energies() : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• print_bit_string() : core::pack::interaction_graph::RotamerDotsCache
• print_bondangles() : core::chemical::ResidueType
• print_cache() : protocols::genetic_algorithm::GeneticAlgorithm
• print_cluster_assignment() : protocols::cluster::ClusterBase , protocols::toolbox::ClusterBase
• print_cluster_PDBs() : protocols::cluster::ClusterBase
• print_clusters_silentfile() : protocols::cluster::ClusterBase
• print_comments() : core::io::silent::SilentStruct
• print_conformation() : core::io::silent::ScoreFileSilentStruct , core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::ScoreStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::SilentStruct , core::io::raw_data::RawStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• print_current_energy() : core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::LinearMemEdge
• print_current_state_assignment() : core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph
• print_debug() : protocols::abinitio::MembraneAbinitio
• print_dihedrals() : core::chemical::ResidueType
• print_dofs() : protocols::optimize_weights::WrapperOptEMultifunc
• print_dot_bit_string() : core::pack::interaction_graph::InvRotamerDots
• 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::GeneticAlgorithm
• print_grid_param() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• print_header() : core::io::silent::RNA_SilentStruct , core::io::silent::BinaryProteinSilentStruct , core::import_pose::PDBSilentStruct , core::io::raw_data::RawStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::SilentStruct
• print_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• print_info() : core::scoring::rna::Base_pair
• print_internal_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::DoubleLazyNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DoubleDensePDNode
• print_internal_energies_for_current_state_assignment() : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• print_library() : protocols::loophash::MPI_LoopHashRefine
• print_metric() : core::pose::Pose
• print_mutation_data() : protocols::pmut_scan::MutationData
• print_pack_report() : protocols::vip::VIP_Mover
• print_parent_remarks() : core::io::silent::SilentStruct
• print_particles() : core::optimization::ParticleSwarmMinimizer
• print_peak_info() : protocols::noesy_assign::CrossPeak
• print_population() : protocols::genetic_algorithm::GeneticAlgorithm
• print_pretty_path_distances() : core::chemical::ResidueType
• 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::quota::QuotaCollector , protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::GrabAllCollector
• print_residue_info() : core::coarse::CoarseEtable
• print_rot_vec() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• print_score() : protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData
• print_score_functions() : core::scoring::disulfides::FullatomDisulfidePotential
• print_score_header() : core::io::silent::SilentStruct
• print_scores() : core::io::raw_data::RawStruct , core::io::silent::SilentStruct
• print_sequence() : protocols::frag_picker::PhiPsiTalosIO , protocols::frag_picker::CSTalosIO
• print_stats() : protocols::wum::MPI_WorkUnitManager , protocols::loophash::MPI_LoopHashRefine
• print_stats_auto() : protocols::wum::MPI_WorkUnitManager
• print_summary() : protocols::toolbox::ClusterBase , protocols::cluster::ClusterBase
• print_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• print_tag() : protocols::swa::protein::StepWiseProteinPacker
• print_timing_stats() : protocols::wum::MPI_WorkUnitManager
• print_to_file() : protocols::pockets::FingerprintBase
• print_to_pdb() : protocols::pockets::FingerprintBase
• print_torsion_info() : core::scoring::rna::RNA_TorsionPotential
• print_verbose_ddgs() : protocols::ddg::ddGMover
• print_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• print_vertices() : core::pack::interaction_graph::InteractionGraphBase , core::graph::Graph
• PrintErrorAndQuit() : protocols::hybridization::TMalign
• printGrishinFormat() : core::sequence::SequenceAlignment
• prioritize() : protocols::wum2::WorkUnit
• prob_random_pert_current() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::backrub::BackrubSidechainMover
• prob_sum_of_gaussians() : core::scoring::constraints::SOGFunc_Impl
• prob_to_accumulate() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_buried() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_nonburied() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::backrub::BackrubSidechainMover
• probA() : core::scoring::packstat::PackingScore
• probabilistically_commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• probability() : protocols::frag_picker::quota::ABEGO_SS_Config , core::pack::dunbrack::DunbrackRotamerSampleData , protocols::noesy_assign::CrossPeak
• probability_limit() : protocols::match::upstream::BuildSet
• probability_to_accumulate_while_building_rotamers() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• probB() : core::scoring::packstat::PackingScore
• probe_radius() : protocols::match::BumpGrid
• 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
• process_discard_entity_message() : protocols::pack_daemon::DaemonSet
• process_energy_change() : core::pose::metrics::PoseMetricContainer
• 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::output::WriteUpstreamHitKinemage , protocols::match::upstream::UpstreamResidueProcessor , protocols::match::output::UpstreamHitCacher , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::PoseInserter
• process_inbound_wus() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::wum::MPI_WorkUnitManager_Slave , protocols::wum::MPI_WorkUnitManager
• process_inbound_wus_master() : protocols::wum::MPI_Relax
• process_incoming_msgs() : protocols::wum::MPI_WorkUnitManager
• process_input_file() : protocols::rna::RNA_ChunkLibrary
• process_input_line_tokens() : protocols::toolbox::match_enzdes_util::ResInteractions
• process_insert_design_string() : protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR
• process_match() : protocols::match::output::MatchOutputter , protocols::match::output::MatchProcessor , protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter , protocols::match::output::MatchConsolidator
• 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_message() : protocols::jd2::MPIFileBufJobDistributor , protocols::jd2::archive::MPIArchiveJobDistributor
• process_motifs() : protocols::simple_filters::SymmetricMotifFilter
• process_NPD_PROPERTY_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_outbound_wus() : protocols::loophash::MPI_LoopHashRefine_Master , protocols::wum::MPI_WorkUnitManager , protocols::wum::MPI_WorkUnitManager_Slave , protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::loophash::MPI_LoopHashRefine_Emperor
• process_outbound_wus_master() : protocols::wum::MPI_Relax
• process_pdb_header() : protocols::toolbox::match_enzdes_util::EnzConstraintIO
• 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_rotamers() : protocols::optimize_weights::PNatAAOptEPositionData
• process_SCALAR_EXPRESSION_line() : protocols::pack_daemon::DynamicAggregateFunction
• process_score() : protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::DDGBindOptEData
• 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_structure_change() : core::pose::metrics::PoseMetricContainer
• 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::GatherPosesMover , protocols::cluster::AssignToClustersMover
• ProcessorFactory() : protocols::match::output::ProcessorFactory
• ProClosureEnergy() : core::scoring::methods::ProClosureEnergy
• prof_row() : core::sequence::SequenceProfile , protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO , core::sequence::SequenceProfile
• profile() : protocols::frag_picker::VallResidue , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue , core::sequence::CacheableSequenceProfile
• profile_mapping() : core::scoring::constraints::SequenceProfileConstraint
• profile_struct() : protocols::frag_picker::VallResidue
• profile_weight_away_from_interface() : protocols::protein_interface_design::movers::Splice
• 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
• ProfSimScoringScheme() : core::sequence::ProfSimScoringScheme
• prohibit_single_residue_loops() : protocols::loops::LoopsFileOptions , protocols::loops::LoopFromFileData
• project_deltaE_for_substitution() : core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::LinearMemNode , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::LazyNode
• project_deltaE_for_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_point_to_3d() : protocols::match::OccupiedSpaceHash
• project_surface_deltaE() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• ProlineFixMover() : protocols::simple_moves::ProlineFixMover
• ProlinePhiScore() : protocols::frag_picker::scores::ProlinePhiScore
• promote_sameresidue_nonjump_child() : core::kinematics::AtomTree
• propagate_best_from_previous_generation() : protocols::genetic_algorithm::GeneticAlgorithm
• propeller() : protocols::dna::DNABasepair
• properties() : core::chemical::ResidueType
• property() : core::pack::task::operation::ResidueHasProperty
• proposal_density() : protocols::simple_moves::sidechain_moves::SidechainMover
• proposed_one_body_energy() : core::pack::interaction_graph::SimpleNode
• proposed_since_last_batch() : protocols::jd2::archive::ArchiveBase
• protein_calculate() : protocols::scoring::Interface
• 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_neighbors() : protocols::dna::DnaInterfaceFinder
• protein_position_equal_within() : core::scoring::methods::PoissonBoltzmannEnergy
• protein_positions() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_scan() : protocols::dna::DnaInterfacePacker
• ProteinBackboneAtomAtomPairFeatures() : protocols::features::ProteinBackboneAtomAtomPairFeatures
• ProteinBackboneAtomAtomPairFeaturesCreator() : protocols::features::ProteinBackboneAtomAtomPairFeaturesCreator
• ProteinBackboneBuildPoint() : protocols::match::upstream::ProteinBackboneBuildPoint
• ProteinBackboneTorsionAngleFeatures() : protocols::features::ProteinBackboneTorsionAngleFeatures
• ProteinBackboneTorsionAngleFeaturesCreator() : protocols::features::ProteinBackboneTorsionAngleFeaturesCreator
• ProteinBondGeometryFeatures() : protocols::features::ProteinBondGeometryFeatures
• ProteinBondGeometryFeaturesCreator() : protocols::features::ProteinBondGeometryFeaturesCreator
• ProteinCore() : protocols::toolbox::task_operations::ProteinCore
• ProteinInterfaceDesignOperation() : protocols::toolbox::task_operations::ProteinInterfaceDesignOperation
• ProteinInterfaceMultiStateDesignMover() : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• ProteinLigandInterfaceUpweighter() : protocols::enzdes::ProteinLigandInterfaceUpweighter
• ProteinResidueConformationFeatures() : protocols::features::ProteinResidueConformationFeatures
• ProteinResidueConformationFeaturesCreator() : protocols::features::ProteinResidueConformationFeaturesCreator
• ProteinRMSDFeatures() : protocols::features::ProteinRMSDFeatures
• ProteinRMSDFeaturesCreator() : protocols::features::ProteinRMSDFeaturesCreator
• ProteinSilentReport() : protocols::features::ProteinSilentReport
• ProteinSilentStruct_SinglePrecCreator() : core::io::silent::ProteinSilentStruct_SinglePrecCreator
• ProteinSilentStruct_Template() : core::io::silent::ProteinSilentStruct_Template< T >
• ProteinSilentStructCreator() : core::io::silent::ProteinSilentStructCreator
• ProteinUpstreamBuilder() : protocols::match::upstream::ProteinUpstreamBuilder
• Protocol() : protocols::abinitio::Protocol
• ProtocolFeatures() : protocols::features::ProtocolFeatures
• ProtocolFeaturesCreator() : protocols::features::ProtocolFeaturesCreator
• proton() : protocols::noesy_assign::CrossPeak
• proton_chi_2_chi() : core::chemical::ResidueType
• proton_chi_extra_samples() : core::chemical::ResidueType
• proton_chi_samples() : core::chemical::ResidueType
• proton_index() : protocols::noesy_assign::MethylNames
• proton_tolerance() : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• provide_stored_derivatives() : core::optimization::ArmijoLineMinimization , core::optimization::StrongWolfeLineMinimization , core::optimization::LineMinimizationAlgorithm
• PseudoBond() : core::conformation::PseudoBond
• PseudoBondCollection() : core::conformation::PseudoBondCollection
• pseudobonds() : core::conformation::Residue
• PseudocontactShiftEnergyController() : protocols::topology_broker::PseudocontactShiftEnergyController
• pseudorotation() : protocols::dna::DNABase
• psi() : core::pose::Pose , protocols::frags::VallData , protocols::protein_interface_design::movers::BBDofs , protocols::match::upstream::ProteinBackboneBuildPoint , core::fragment::picking_old::vall::VallResidue , protocols::swa::protein::MainChainTorsionSet , protocols::optimize_weights::PNatRotOptEPositionData , protocols::loophash::BackboneSegment , core::io::silent::ProteinSilentStruct_Template< T > , protocols::swa::MainChainTorsionSet , core::io::raw_data::DecoyStruct , protocols::frag_picker::VallResidue , core::io::raw_data::DecoyStruct
• Psi() : protocols::frag_picker::scores::Psi
• psi() : core::io::silent::ProteinSilentStruct_Template< T > , protocols::optimize_weights::PNatRotOptEPositionData , protocols::frags::RMSVallData , protocols::frag_picker::VallResidue , protocols::frag_picker::PhiPsiTalosIO , protocols::swa::protein::MainChainTorsionSet , protocols::swa::MainChainTorsionSet , core::fragment::picking_old::vall::VallResidue , protocols::protein_interface_design::movers::BBDofs , protocols::match::upstream::ProteinBackboneBuildPoint
• psi_max() : core::util::ABEGO
• psi_min() : core::util::ABEGO
• pssm_() : protocols::protein_interface_design::ReportPSSMDifferences
• PSSMOptEPositionData() : protocols::optimize_weights::PSSMOptEPositionData
• ptask() : protocols::multistate_design::PackingState
• pucker_state() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pulldomain() : protocols::hybridization::DDomainParse
• push() : protocols::frag_picker::quota::ABEGO_SS_Pool , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• push_back() : core::pack::task::TaskFactory , protocols::cluster::Cluster , protocols::moves::MonteCarlo , protocols::wum::WorkUnitQueue , protocols::toolbox::DecoySetEvaluation , protocols::frag_picker::VallChunk , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::coarse_rna::SourcePositions , protocols::cluster::GatherPosesMover , protocols::fldsgn::topology::HSSTripletSet , core::conformation::PseudoBondCollection , protocols::loops::Loops , core::id::SequenceMapping , protocols::loops::LoopsFileData , core::conformation::symmetry::VirtualCoordinates , core::pack::task::TaskFactory , core::pack::dunbrack::CoarseRotamerSet , protocols::wum2::WUQueue , protocols::fldsgn::topology::HelixPairingSet , protocols::wum2::WUQueue , protocols::fldsgn::topology::StrandPairingSet , core::scoring::dssp::StrandPairingSet , protocols::frag_picker::VallProvider , core::io::silent::SilentFileData , core::graph::EdgeList , protocols::fldsgn::topology::SheetSet , protocols::protein_interface_design::movers::ResidueBBDofs
• 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_back_origin() : core::conformation::symmetry::VirtualCoordinates
• push_back_rotamer() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• push_back_x() : core::conformation::symmetry::VirtualCoordinates
• push_back_y() : core::conformation::symmetry::VirtualCoordinates
• push_front() : core::graph::EdgeList , protocols::wum::WorkUnitQueue , protocols::wum2::WUQueue , protocols::cluster::Cluster
• 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::rna::RNA_HelixAssembler
• put_jump_stubs_intra_residue() : core::kinematics::FoldTree
• PValuedFragmentScoreManager() : protocols::frag_picker::scores::PValuedFragmentScoreManager
• Py_defines_intrares_energy() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• Py_eval_dof_derivative() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• Py_eval_intrares_energy() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• Py_indicate_required_context_graphs() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• Py_residue_energy() : core::scoring::methods::PyContextIndependentOneBodyEnergy
• Py_residue_pair_energy() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• PyContextIndependentOneBodyEnergy() : core::scoring::methods::PyContextIndependentOneBodyEnergy
• PyContextIndependentTwoBodyEnergy() : core::scoring::methods::PyContextIndependentTwoBodyEnergy
• PyEnergyMethodRegistrator() : core::scoring::methods::PyEnergyMethodRegistrator
• pymol() : protocols::moves::PyMolObserver
• PyMolMover() : protocols::moves::PyMolMover
• PyMolObserver() : protocols::moves::PyMolObserver
• pythag() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl