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

- p -

• p : protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• 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_ : core::optimization::Particle
• P_AA() : core::scoring::P_AA
• p_aa_ : core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::ScoringManager
• P_AA_ : core::scoring::P_AA
• P_AA_Energy() : core::scoring::methods::P_AA_Energy
• P_AA_energy() : core::scoring::P_AA
• P_AA_initialize() : core::scoring::P_AA
• P_AA_n_ : core::scoring::P_AA
• P_AA_pp_ : core::scoring::P_AA
• P_AA_pp_Energy() : core::scoring::methods::P_AA_pp_Energy
• P_AA_pp_energy() : core::scoring::P_AA
• P_AA_pp_energy_splines_ : core::scoring::P_AA
• p_atom_index() : core::chemical::rna::RNA_ResidueType
• p_atom_index_ : core::chemical::rna::RNA_ResidueType
• p_CoM : core::scoring::electron_density::ElectronDensity
• p_cond_ : protocols::moves::WhileMover
• p_extent : core::scoring::electron_density::ElectronDensity
• p_grid : core::scoring::electron_density::ElectronDensity
• p_max_ : core::optimization::ParticleSwarmMinimizer
• p_min_ : core::optimization::ParticleSwarmMinimizer
• p_o : core::scoring::electron_density::ElectronDensity
• p_origin : core::scoring::electron_density::ElectronDensity
• p_range_ : core::optimization::ParticleSwarmMinimizer
• p_sumC : core::scoring::electron_density::ElectronDensity
• p_sumC2 : core::scoring::electron_density::ElectronDensity
• p_sumCO : core::scoring::electron_density::ElectronDensity
• p_sumO : core::scoring::electron_density::ElectronDensity
• p_sumO2 : core::scoring::electron_density::ElectronDensity
• p_value() : protocols::frag_picker::scores::AdaptiveScoreHistogram
• p_vol : core::scoring::electron_density::ElectronDensity
• pack_at_neighbors_only_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• pack_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• pack_full_repack_ : protocols::relax::ClassicRelax
• pack_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• pack_residue_ : core::pack::task::PackerTask_
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• pack_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::RefineBetaBarrel
• pack_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• pack_separated_ : protocols::analysis::InterfaceAnalyzerMover
• pack_task_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• packable() : protocols::protein_interface_design::filters::DesignableResiduesFilter
• 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_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_ : core::pack::dunbrack::PackedDunbrackRotamer< S, P > , core::pack::dunbrack::BBDepNRChiSample< P >
• packed_rotno_2_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_rotwell_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_sorted_rotno() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• packed_rotno_conversion_data_current_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• PackedDunbrackRotamer() : core::pack::dunbrack::PackedDunbrackRotamer< S, P >
• packer_ : protocols::antibody::GraftMover
• packer_neighbor_graph_ : core::optimization::SingleResidueMultifunc
• packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• PackerEnergy : protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::rotamer_set::FlexbbRotamerSets
• 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::simple_moves::GenericMonteCarloMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation
• packertask() : protocols::flxbb::DesignTask
• PackerTask : core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OptCysHG , core::pack::task::operation::OptH , 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::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelRotamerLinks , protocols::motifs::LigandMotifSearch , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet
• PackerTask_() : core::pack::task::PackerTask_
• PackerTaskCOP : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::RotamerSubsets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::PDBOutput , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::FlxbbDesignPack , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation
• PackerTaskOP : protocols::enzdes::PackRotamersMoverPartGreedy , protocols::flxbb::DesignTask , protocols::flxbb::DesignTask_Normal , protocols::flxbb::DesignTask_Layer , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::DaemonSet , protocols::pack_daemon::QuickRepacker , protocols::scoring::Interface , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::GreenPacker , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover
• packing_angle_residues_ : protocols::antibody2::AntibodyInfo
• packing_interaction_cutoff() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_shell() : protocols::simple_filters::RelativePoseFilter
• packing_shell_ : protocols::simple_filters::RelativePoseFilter
• PackingScore() : core::scoring::packstat::PackingScore
• PackingScoreResData() : core::scoring::packstat::PackingScoreResData
• PackingState() : protocols::multistate_design::PackingState
• packonly_after_graft_ : protocols::antibody2::GraftCDRLoopsProtocol
• PackRotamersMover() : protocols::simple_moves::PackRotamersMover
• PackRotamersMoverLazy() : protocols::simple_moves::PackRotamersMoverLazy
• PackRotamersMoverPartGreedy() : protocols::enzdes::PackRotamersMoverPartGreedy
• packstat_pdb_ : protocols::analysis::PackStatMover
• PackstatCalculator() : protocols::toolbox::pose_metric_calculators::PackstatCalculator
• PackStatEnergy() : core::scoring::methods::PackStatEnergy
• PackStatFilter() : protocols::simple_filters::PackStatFilter
• PackStatMover() : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• Page : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::VallResidues
• PageConstIterator : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::scores::VallFragmentScore , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• PageIterator : core::fragment::picking_old::concepts::Book< Pages > , core::fragment::picking_old::concepts::Extent< PageIterator > , core::fragment::picking_old::concepts::Librarian< Bookmark, ExtentEvaluator, ExtentGenerator, Library > , core::fragment::picking_old::vall::gen::LengthGen , core::fragment::picking_old::vall::gen::SecStructGen , core::fragment::picking_old::vall::gen::VallFragmentGen , core::fragment::picking_old::vall::VallLibrarian , core::fragment::picking_old::vall::VallSection
• pages() : core::fragment::picking_old::concepts::Book< Pages >
• pages_ : core::fragment::picking_old::concepts::Book< Pages >
• pair_ : core::scoring::SmoothEnvPairPotential
• pair_and_func_map_ : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• pair_corr_ : core::scoring::PairEPotential
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• 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_list_ : protocols::scoring::Interface
• pair_log_ : core::scoring::EnvPairPotential
• pair_overlap_tolerance() : protocols::match::BumpGrid
• pair_permit_overlap_ : protocols::match::BumpGrid
• pair_score_bin_base_ : core::scoring::PairEPotential
• pair_score_bin_range_ : core::scoring::PairEPotential
• pair_score_cb_thresh_ : core::scoring::PairEPotential
• pair_score_min_sep_ : core::scoring::PairEPotential
• pair_set_ : core::scoring::dssp::Dssp
• 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_vector_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• pair_with_scaffold() : protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::hotspot_hashing::HotspotStub
• pairE_potential_ : core::scoring::ScoringManager
• paired() : core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet , protocols::dna::DnaPosition
• paired_ : protocols::dna::DnaPosition
• PairEnergy() : core::scoring::methods::PairEnergy
• PairEPotential() : core::scoring::PairEPotential
• PairFeatures() : protocols::features::PairFeatures
• PairFeaturesCreator() : protocols::features::PairFeaturesCreator
• PairFuncMap : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• pairing() : protocols::abinitio::PairingStatEntry
• Pairing() : core::scoring::dssp::Pairing
• pairing1 : core::scoring::dssp::StrandPairing
• pairing2 : core::scoring::dssp::StrandPairing
• pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• PairingLibrary() : protocols::jumping::PairingLibrary
• pairings() : protocols::abinitio::Templates
• Pairings : protocols::abinitio::AlternativePairings
• pairings_ : core::scoring::dssp::StrandPairingSet , protocols::abinitio::AlternativePairings , protocols::abinitio::Templates , protocols::jumping::DisulfPairingLibrary , protocols::jumping::MembraneJump , protocols::jumping::PairingLibrary , protocols::jumping::SheetBuilder , protocols::topology_broker::TemplateJumpClaimer
• pairings_file_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• pairings_size() : protocols::jumping::MembraneJump
• pairings_size_ : protocols::jumping::MembraneJump
• PairingStatEntry() : protocols::abinitio::PairingStatEntry
• PairingStatistics() : protocols::abinitio::PairingStatistics
• PairingTemplate() : protocols::jumping::PairingTemplate
• PairingTemplateList : protocols::jumping::PairingLibrary
• PairingTemplateMap : protocols::jumping::PairingLibrary
• pairs() : core::sequence::PairScoringScheme
• pairs_ : core::sequence::PairScoringScheme
• PairScoringScheme() : core::sequence::PairScoringScheme
• PalesEvaluator() : protocols::simple_filters::PalesEvaluator
• PalesEvaluatorCreator() : protocols::simple_filters::PalesEvaluatorCreator
• parallel() : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator
• PARALLEL : core::scoring::dssp::Pairing
• parallel_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator
• parallel_weight_ : core::scoring::SecondaryStructureWeights
• ParallelBetaPairingPreferenceFilter() : protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter
• ParallelTempering() : protocols::canonical_sampling::ParallelTempering
• param() : core::scoring::packing::HolesParamsRes
• param1 : protocols::relax::RelaxScriptCommand , protocols::branch_angle::BranchAngleOptimizer
• param2 : protocols::relax::RelaxScriptCommand , protocols::branch_angle::BranchAngleOptimizer
• param3 : protocols::relax::RelaxScriptCommand
• param4 : protocols::relax::RelaxScriptCommand
• param_cache() : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• param_index() : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_index_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateRes
• param_set_ : core::scoring::methods::MMBondAngleEnergy
• Param_TA : core::scoring::GenBornPotential
• Param_TB : core::scoring::GenBornPotential
• Param_TC : core::scoring::GenBornPotential
• Param_TD : core::scoring::GenBornPotential
• Param_TDD : core::scoring::GenBornPotential
• Param_TE : core::scoring::GenBornPotential
• Param_TF : core::scoring::GenBornPotential
• Param_TG : core::scoring::GenBornPotential
• Param_TH : core::scoring::GenBornPotential
• Param_THH : core::scoring::GenBornPotential
• ParamB : core::scoring::GenBornPotential
• ParamD : core::scoring::GenBornPotential
• parameter_set4final() : protocols::hybridization::TMalign
• parameter_set4scale() : protocols::hybridization::TMalign
• parameter_set4search() : protocols::hybridization::TMalign
• parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• ParamG : core::scoring::GenBornPotential
• Params : core::scoring::dna::DNA_BasePotential
• ParamS : core::scoring::GenBornPotential
• params_ : core::scoring::packing::HolesEnergyRes , core::scoring::packing::HolesParamsRes
• params_database_tag() : core::scoring::hbonds::HBondOptions
• params_database_tag_ : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• parent : core::scoring::methods::LinearChainbreakEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::LK_CosThetaEnergy , core::scoring::methods::LK_hack , core::scoring::methods::LongRangeTwoBodyEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvSmoothEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::NMerPSSMEnergy , core::scoring::methods::NMerRefEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::OneBodyEnergy , core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::methods::PackStatEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PeptideBondEnergy , core::scoring::methods::pHEnergy , core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::ProClosureEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::ReferenceEnergy , core::scoring::methods::ReferenceEnergyNoncanonical , core::scoring::methods::ResidualDipolarCouplingEnergy , core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl , core::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , core::scoring::methods::RG_Energy_Fast , core::scoring::methods::RMS_Energy , core::scoring::methods::SA_Energy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SequenceDependentRefEnergy , core::scoring::methods::ShortRangeTwoBodyEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::SuckerEnergy , core::scoring::methods::SymmetricLigandEnergy , core::scoring::methods::TwoBodyEnergy , core::scoring::methods::UnfoldedStateEnergy , core::scoring::methods::VDW_Energy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::methods::WaterAdductIntraEnergy , core::scoring::methods::WholeStructureEnergy , core::scoring::methods::YHHPlanarityEnergy , core::scoring::MinimizationNode , core::scoring::MinimizationEdge , core::scoring::MinimizationGraph , core::scoring::MinScoreScoreFunction , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::ResidueNblistData , core::scoring::ResiduePairNeighborList , core::scoring::rna::RNA_BulgeEnergy , core::scoring::rna::RNA_FullAtomVDW_BasePhosphate , core::scoring::rna::RNA_SugarCloseEnergy , core::scoring::solid_surface::SurfaceEnergies , core::scoring::symmetry::SymmetricScoreFunction , core::scoring::TenANeighborNode , core::scoring::TenANeighborEdge , core::scoring::TenANeighborGraph , core::scoring::TwelveANeighborNode , core::scoring::TwelveANeighborEdge , core::scoring::TwelveANeighborGraph , core::sequence::SequenceRegistrator< T > , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::enzdes::EnzdesJobOutputter , protocols::enzdes::ModifyStoredRBConfs , protocols::enzdes::GenerateStoredRBConfs , protocols::enzdes::ApplyRandomStoredRBConf , protocols::enzdes::MinimizeStoredRBConfs , protocols::enzdes::DiversifyStoredRBConfs , protocols::evaluation::EvaluatorRegistrator< T > , protocols::features::DatabaseJobOutputter , protocols::features::FeaturesReporterRegistrator< T > , protocols::filters::ContingentFilter , protocols::filters::FilterRegistrator< T > , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::flexpack::annealer::FlexbbSimAnnealer , protocols::flexpack::interaction_graph::FlexbbNode , protocols::flexpack::interaction_graph::FlexbbEdge , protocols::flexpack::interaction_graph::FlexbbInteractionGraph , protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbNode , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::OtherContextScoreFunction , protocols::flexpack::rotamer_set::FlexbbRotamerSet , protocols::flxbb::LayerDesignOperation , protocols::genetic_algorithm::EntityElement , protocols::genetic_algorithm::EntityElementRegistrator< T > , protocols::hotspot_hashing::SearchPatternRotSetOp , protocols::jd2::FileJobOutputter , protocols::jd2::JobInputterRegistrator< T > , protocols::jd2::JobOutputterRegistrator< T > , protocols::jd2::parser::DataLoaderRegistrator< T > , protocols::jd2::PDBJobOutputter , protocols::jd2::SilentFileJobOutputter , protocols::jobdist::AtomTreeDiffJobDistributor , protocols::jobdist::PlainPdbJobDistributor , protocols::jobdist::PlainRawJobDistributor , protocols::jobdist::PlainSilentFileJobDistributor , protocols::loops::loop_closure::kinematic_closure::TorsionSamplingKinematicPerturber , protocols::loops::loop_closure::kinematic_closure::VicinitySamplingKinematicPerturber , 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 , protocols::loops::loops_definers::LoopsDefinerRegistrator< T > , protocols::match::BumpGrid , protocols::match::downstream::ActiveSiteGrid , protocols::match::downstream::ClassicMatchAlgorithm , protocols::match::downstream::DownstreamBuilder , protocols::match::downstream::LigandConformerBuilder , protocols::match::downstream::RigidLigandBuilder , protocols::match::downstream::SecondaryMatcherToDownstreamResidue , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::output::CloudPDBWriter , protocols::match::output::PoseMatchOutputWriter , protocols::match::output::SameSequenceAndDSPositionGrouper , protocols::match::output::UpstreamCollisionFilter , protocols::match::output::UpstreamDownstreamCollisionFilter , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::match::upstream::OriginalBackboneBuildPoint , protocols::match::upstream::BuildSet , protocols::moves::MoverRegistrator< T > , protocols::multistate_design::PosType , protocols::optimize_weights::ScaleAnnealerTemperatureOperation , protocols::optimize_weights::PSSMOptEPositionData , protocols::pack_daemon::VectorExpression , protocols::pack_daemon::VariableVectorExpression , protocols::pack_daemon::IterativeVectorExpression , protocols::pack_daemon::VectorFunction , protocols::pack_daemon::VectorFunction2 , protocols::pack_daemon::VMax , protocols::pack_daemon::VMin , protocols::pack_daemon::VMaxBy , protocols::pack_daemon::VMinBy , protocols::pack_daemon::PowExpression , protocols::pack_daemon::ExpExpression , protocols::pack_daemon::LnExpression , protocols::pack_daemon::InSetExpression , protocols::pack_daemon::SurrogateVariableExpression , protocols::pack_daemon::VectorExpressionCreator , protocols::pack_daemon::DynamicAggregateFunction , protocols::pack_daemon::EntityFuncExpressionCreator , protocols::pack_daemon::EntityFunc , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::MultistateAggregateFunction , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::RotamerSubsetRepacker , protocols::pack_daemon::DenseIGRepacker , protocols::pack_daemon::DoubleDenseIGRepacker , protocols::pack_daemon::FASTER_IG_Repacker , protocols::protein_interface_design::filters::AverageDegreeFilter , protocols::protein_interface_design::filters::BindingStrainFilter , protocols::protein_interface_design::filters::BoltzmannFilter , protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::filters::FilterScanFilter , protocols::protein_interface_design::filters::SequenceRecoveryFilter , protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter , protocols::protein_interface_design::filters::StubScoreFilter , protocols::protein_interface_design::filters::Torsion , protocols::protein_interface_design::movers::DisulfideMover , protocols::qsar::scoring_grid::GridRegistrator< T > , protocols::relax::ClassicRelax , protocols::relax::MiniRelax , protocols::relax::RelaxProtocolBase , protocols::rigid::RigidBodyMover , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rigid::RigidBodySpinMover , protocols::rigid::RigidBodyDeterministicSpinMover , protocols::rigid::RigidBodyTransMover , protocols::rigid::UniformSphereTransMover , protocols::rigid::RigidBodyDofRandomizeMover , protocols::rigid::RigidBodyDofSeqRandomizeMover , protocols::rigid::RigidBodyDofTransMover , protocols::rigid::RigidBodyDofSeqTransMover , protocols::rigid::RigidBodyDofRandomTransMover , protocols::rigid::RigidBodyDofPerturbMover , protocols::rigid::RigidBodyDofSeqPerturbMover , protocols::rotamer_recovery::RotamerRecoveryRegistrator< T > , protocols::scoring::methods::EnsembleEnergy , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , protocols::scoring::methods::pcs::PCS_Energy , protocols::scoring::methods::pcs2::PcsEnergy , protocols::scoring::methods::ResidualDipolarCouplingEnergyRigidSegments , protocols::scoring::methods::SpecialRotamerEnergy , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RelativePoseFilter , core::conformation::RotamerSetBase , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ScoreCutoffFilter , core::graph::Graph , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MutateResidue , core::io::silent::SilentStructRegistrator< T > , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::SetChiMover , core::optimization::MinimizerMap , protocols::toolbox::match_enzdes_util::ExternalGeomSampler , protocols::toolbox::match_enzdes_util::LigandConformer , core::optimization::Multifunc , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , core::optimization::NumDerivCheckData , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::rotamer_set_operations::RigidBodyMoveBaseRSO , core::optimization::NumericalDerivCheckResult , protocols::toolbox::rotamer_set_operations::RigidBodyMoveRSO , protocols::toolbox::rotamer_set_operations::SpecialRotamerRSO , core::optimization::SingleResidueMultifunc , protocols::toolbox::task_operations::DesignAroundOperation , protocols::toolbox::task_operations::InterfaceTaskOperation , core::pack::annealer::FASTERAnnealer , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , core::pack::dunbrack::DunbrackEnergy , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::toolbox::task_operations::PreventChainFromRepackingOperation , core::pack::dunbrack::DunbrackRotamer< S, P > , protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation , protocols::toolbox::task_operations::ProteinInterfaceDesignOperation , core::pack::dunbrack::PackedDunbrackRotamer< S, P > , protocols::toolbox::task_operations::ReadResfileFromDB , protocols::toolbox::task_operations::RestrictByCalculatorsOperation , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T > , protocols::toolbox::task_operations::RestrictChainToRepackingOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , core::pack::dunbrack::BBDepSemiRotamericData< T > , protocols::toolbox::task_operations::RestrictInterGroupVectorOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , core::pack::dunbrack::BBIndSemiRotamericData< T > , protocols::toolbox::task_operations::RestrictOperationsBase , protocols::toolbox::task_operations::RestrictResiduesToRepackingOperation , core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T > , protocols::toolbox::task_operations::RestrictToAlignedSegmentsOperation , protocols::toolbox::task_operations::RestrictToCDRH3Loop , core::pack::interaction_graph::DoubleLazyInteractionGraph , protocols::toolbox::task_operations::DockingNoRepack1 , protocols::toolbox::task_operations::DockingNoRepack2 , core::pack::interaction_graph::FASTERNode , protocols::toolbox::task_operations::RestrictToInterface , protocols::toolbox::task_operations::RestrictToInterfaceOperation , core::pack::interaction_graph::FASTEREdge , protocols::toolbox::task_operations::RestrictToInterfaceVectorOperation , protocols::toolbox::task_operations::RestrictToLoopsAndNeighbors , core::pack::interaction_graph::FASTERInteractionGraph , protocols::toolbox::task_operations::RestrictToNeighborhoodOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , core::pack::interaction_graph::HPatchEnergy , protocols::toolbox::task_operations::ThreadSequenceOperation , core::graph::DS_Node , core::pack::interaction_graph::HPatchNode< V, E, G > , core::kinematics::Node , core::kinematics::tree::Atom , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::kinematics::tree::Atom , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::kinematics::tree::Atom_ , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• Parent : core::fragment::BBTorsionAndAnglesSRFD , core::fragment::BBTorsionSRFD
• parent : core::pack::interaction_graph::SurfaceEnergy
• Parent : core::fragment::ConstantLengthFragSet , core::fragment::FragCache< T >
• parent : core::pack::interaction_graph::SurfaceNode< V, E, G >
• Parent : core::fragment::FragStore< T > , core::fragment::AnnotatedFragData
• parent : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• Parent : core::fragment::FragSetCollection , core::fragment::NonContinuousFrame
• parent : core::pack::interaction_graph::SurfaceEdge< V, E, G >
• Parent : core::fragment::UpJumpSRFD , core::fragment::DownJumpSRFD
• parent : core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G >
• Parent : core::fragment::OrderedFragSet , core::fragment::SecstructSRFD
• parent : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• Parent : core::kinematics::EXCN_InvalidFoldTree , core::pose::datacache::SpecialSegmentsObserver
• parent : core::pack::rotamer_set::ContinuousRotamerSet
• Parent : protocols::abinitio::ClassicAbinitio , protocols::abinitio::ConstraintFragmentSampler
• parent : core::pack::rotamer_set::FixbbRotamerSets
• Parent : protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler
• parent : core::pack::rotamer_set::RotamerSet
• Parent : protocols::abinitio::HedgeArchive , protocols::abinitio::IterativeAbrelax
• parent : core::pack::task::operation::OperateOnCertainResidues
• Parent : protocols::abinitio::IterativeBase , protocols::abinitio::IterativeCentroid
• parent : core::pack::task::operation::ReplicateTask
• Parent : protocols::abinitio::IterativeFullatom , protocols::abinitio::JumpingFoldConstraints
• parent : core::pack::task::operation::ResFilterRegistrator< T >
• Parent : protocols::abinitio::KinematicAbinitio , protocols::abinitio::JumpingFoldConstraintsWrapper
• parent : core::pack::task::operation::ResFilterComposition
• Parent : protocols::abinitio::MembraneAbinitio , protocols::canonical_sampling::HamiltonianExchange
• parent : core::pack::task::operation::AnyResFilter
• Parent : protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder
• parent : core::pack::task::operation::AllResFilter
• Parent : protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder
• parent : core::pack::task::operation::NoResFilter
• Parent : protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase
• parent : core::pack::task::operation::ResidueTypeFilter
• Parent : protocols::constraints_additional::MaxSeqSepConstraintSet , protocols::evaluation::MetaPoseEvaluator
• parent : core::pack::task::operation::ResidueHasProperty
• Parent : protocols::fldsgn::topology::Strand , protocols::fldsgn::topology::Helix
• parent : core::pack::task::operation::ResidueLacksProperty
• Parent : protocols::fldsgn::topology::Loop , protocols::jd2::archive::EvaluatedArchive
• parent : core::pack::task::operation::ResidueName3Is
• Parent : protocols::jd2::archive::MPIArchiveJobDistributor , protocols::jd2::archive::NormalizedEvaluatedArchive
• parent : core::pack::task::operation::ResidueName3Isnt
• Parent : protocols::jd2::archive::VarianceStatisticsArchive , protocols::jd2::MPIFileBufJobDistributor
• parent : core::pack::task::operation::ResidueIndexIs
• Parent : protocols::jd2::MPIMultiCommJobDistributor , protocols::jd2::parser::FragmentReader
• parent : core::pack::task::operation::ResidueIndexIsnt
• Parent : protocols::loops::EXCN_Loop_not_closed , protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure
• parent : core::pack::task::operation::ResiduePDBIndexIs
• Parent : protocols::loops::loop_closure::ccd::ShortLoopClosure , protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure
• parent : core::pack::task::operation::ResiduePDBIndexIsnt
• Parent : protocols::match::output::PDBWriter , protocols::moves::ReplicaExchangeMC
• parent : core::pack::task::operation::ChainIs
• Parent : protocols::noesy_assign::EXCN_NoesyAssign , protocols::noesy_assign::FloatingResonance
• parent : core::pack::task::operation::ChainIsnt
• Parent : protocols::protein_interface_design::filters::StubScoreLoopsFilter , protocols::rigid::RigidBodyPerturbNoCenterMover
• parent : core::pack::task::operation::ResLvlTaskOperationRegistrator< T >
• Parent : protocols::simple_moves::LoggedFragmentMover , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover
• parent : core::pack::task::operation::RestrictToRepackingRLT
• Parent : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover
• parent : core::pack::task::operation::RestrictAbsentCanonicalAASRLT
• Parent : protocols::simple_moves::SmoothFragmentMover , protocols::simple_moves::WobbleMover
• parent : core::pack::task::operation::DisallowIfNonnativeRLT
• Parent : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation , protocols::topology_broker::AsymFoldandDockClaimer
• parent : core::pack::task::operation::PreventRepackingRLT
• Parent : protocols::topology_broker::ConstraintClaimer , protocols::topology_broker::CoordConstraintClaimer
• parent : core::pack::task::operation::AddBehaviorRLT
• Parent : protocols::topology_broker::DisulfJumpClaimer , protocols::topology_broker::EXCN_TopologyBroker
• parent : core::pack::task::operation::DockingNoRepack1
• Parent : protocols::topology_broker::EXCN_Input , protocols::topology_broker::EXCN_FailedBroking
• parent : core::pack::task::operation::DockingNoRepack2
• Parent : protocols::topology_broker::EXCN_FilterFailed , protocols::topology_broker::FibrilModelingClaimer
• parent : core::pack::task::operation::RestrictToInterface
• Parent : protocols::topology_broker::FoldandDockClaimer , protocols::topology_broker::FragmentClaimer
• parent : core::pack::task::operation::TaskOperationRegistrator< T >
• Parent : protocols::topology_broker::JumpClaimer , protocols::topology_broker::MembraneTopologyClaimer
• parent : core::pack::task::operation::RestrictToRepacking
• Parent : protocols::topology_broker::PcsEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController
• parent : core::pack::task::operation::RestrictResidueToRepacking
• Parent : protocols::topology_broker::RigidChunkClaimer , protocols::topology_broker::SequenceClaimer
• parent : core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::InitializeExtraRotsFromCommandline , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::SetRotamerCouplings , core::pack::task::operation::SetRotamerLinks , core::pack::task::operation::AppendRotamer , core::pack::task::operation::AppendRotamerSet , core::pack::task::operation::AppendResidueRotamerSet , core::pack::task::operation::PreserveCBeta , core::pack::task::operation::PreventRepacking , core::pack::task::operation::RestrictYSDesign , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraChiCutoff , core::pack::task::TaskFactory , core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::ConstraintRegistrator< T > , core::scoring::constraints::ConstraintNode , core::scoring::constraints::ConstraintEdge , core::scoring::constraints::ConstraintGraph , core::scoring::constraints::FourPointsFunc , core::scoring::ContextGraph , core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::dna::DNAChiEnergy , core::scoring::dna::DNATorsionEnergy , core::scoring::DockingScoreFunction , core::scoring::EnergyNode , core::scoring::EnergyEdge , core::scoring::EnergyGraph , core::scoring::etable::WholeWholeEnergyInvoker< Evaluator > , core::scoring::etable::SC_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_Whole_EnergyInvoker< Evaluator > , core::scoring::etable::BB_BB_EnergyInvoker< Evaluator > , core::scoring::etable::SC_SC_EnergyInvoker< Evaluator > , core::scoring::etable::CoarseEtableEnergy , core::scoring::etable::count_pair::CountPair1B< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairAll , core::scoring::etable::count_pair::CountPairCrossover3 , core::scoring::etable::count_pair::CountPairCrossover4 , core::scoring::etable::count_pair::CountPairGeneric , core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4 , core::scoring::etable::count_pair::CountPairNone , core::scoring::etable::TableLookupEtableEnergy , core::scoring::etable::AnalyticEtableEnergy , core::scoring::etable::etrie::EtableAtom , core::scoring::hackelec::ElecAtom , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::methods::CartesianBondedEnergy , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::ChainbreakEnergy , core::scoring::methods::ChemicalShiftAnisotropyEnergy , core::scoring::methods::ContactOrderEnergy , core::scoring::methods::ContextDependentLRTwoBodyEnergy , core::scoring::methods::ContextDependentOneBodyEnergy , core::scoring::methods::ContextDependentTwoBodyEnergy , core::scoring::methods::ContextIndependentLRTwoBodyEnergy , core::scoring::methods::ContextIndependentOneBodyEnergy , core::scoring::methods::ContextIndependentTwoBodyEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::DipolarCouplingEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DistanceChainbreakEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::EnergyMethodRegistrator< T > , core::scoring::methods::EnvEnergy , core::scoring::methods::EnvSmoothEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GaussianOverlapEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::HybridVDW_Energy
• parent_ : core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• parent_atom_ : core::chemical::AddConnect
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithm
• parent_id() : core::optimization::DOF_DataPoint
• parent_id_ : core::optimization::DOF_DataPoint
• parent_node() : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_remarks_map_ : core::io::silent::SilentStruct
• parent_tags_map_ : protocols::swa::rna::StepWiseRNA_Clusterer
• parents_ : core::chemical::ResidueType
• ParetoOptMutationMover() : protocols::design_opt::ParetoOptMutationMover
• parin_favorite_output_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup
• 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::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 , protocols::qsar::scoring_grid::GridBase , protocols::qsar::scoring_grid::GridInitMover , protocols::qsar::scoring_grid::HbaGrid , protocols::qsar::scoring_grid::HbdGrid , protocols::qsar::scoring_grid::RepGrid , protocols::qsar::scoring_grid::SingleGrid , protocols::qsar::scoring_grid::SolvationGrid , protocols::qsar::scoring_grid::SolvationMetaGrid , protocols::qsar::scoring_grid::VdwGrid , protocols::relax::FastRelax , protocols::rigid::RigidBodyPerturbNoCenterMover , protocols::rigid::RollMover , protocols::rosetta_scripts::ParsedProtocol , protocols::rosetta_scripts::SavePoseMover , protocols::rotamer_recovery::RotamerRecoveryMover , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CloseFold , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::DefineMovableLoops , protocols::seeded_abinitio::GrowPeptides , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SeedFoldTree , protocols::seeded_abinitio::SeedSetupMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::seeded_abinitio::SwapSegment , protocols::simple_filters::AlaScan , protocols::simple_filters::AtomicContactFilter , protocols::simple_filters::AtomicDistanceFilter , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::ConservedPosMutationFilter , protocols::simple_filters::ConstraintScoreCutoffFilter , protocols::simple_filters::DdgFilter , protocols::simple_filters::DeltaFilter , protocols::simple_filters::EnergyPerResidueFilter , protocols::simple_filters::ExpiryFilter , protocols::simple_filters::FileExistFilter , protocols::simple_filters::FileRemoveFilter , protocols::simple_filters::HolesFilter , protocols::simple_filters::InterfaceBindingEnergyDensityFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::NeighborTypeFilter , protocols::simple_filters::NMerPSSMEnergyFilter , protocols::simple_filters::NonSequentialNeighborsFilter , protocols::simple_filters::Operator , protocols::simple_filters::PackStatFilter , protocols::simple_filters::PoseInfoFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::RelativePoseFilter , protocols::simple_filters::ReportFilter , protocols::simple_filters::ResidueBurialFilter , protocols::simple_filters::ResidueCountFilter , protocols::simple_filters::ResidueDistanceFilter , protocols::simple_filters::ResidueIEFilter , protocols::simple_filters::ResidueSetChainEnergyFilter , protocols::simple_filters::ResiduesInInterfaceFilter , protocols::simple_filters::RotamerBoltzmannWeight , protocols::simple_filters::ScoreCutoffFilter , protocols::simple_filters::ScoreTypeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_filters::SidechainRmsdFilter , protocols::simple_filters::Sigmoid , protocols::simple_filters::SymmetricMotifFilter , protocols::simple_filters::TerminusDistanceFilter , protocols::simple_moves::AddConstraintsToCurrentConformationMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::ClearConstraintsMover , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ConstraintSetMover , protocols::simple_moves::CutChainMover , protocols::simple_moves::ddG , protocols::simple_moves::DesignRepackMover , protocols::simple_moves::DumpPdb , protocols::simple_moves::ExtendedPoseMover , protocols::simple_moves::FavorSequenceProfile , protocols::simple_moves::ForceDisulfidesMover , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::LoadPDBMover , protocols::simple_moves::LoadUnboundRotMover , protocols::simple_moves::MakePolyXMover , protocols::simple_moves::MembraneTopology , protocols::simple_moves::MinMover , protocols::simple_moves::MinPackMover , protocols::simple_moves::ModifyVariantTypeMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::MutateResidue , protocols::simple_moves::O2M_MutateMover , protocols::simple_moves::PackRotamersMover , protocols::simple_moves::PackRotamersMoverLazy , protocols::simple_moves::PDBReloadMover , protocols::simple_moves::RepackSidechainsMover , protocols::simple_moves::RotamerTrialsMinMover , protocols::simple_moves::RotamerTrialsMover , protocols::simple_moves::ScoreMover , protocols::simple_moves::SequenceProfileMover , protocols::simple_moves::SetTorsion , protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover , protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover , protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover , protocols::simple_moves::sidechain_moves::SetChiMover , protocols::simple_moves::sidechain_moves::SidechainMCMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::simple_moves::SuperimposeMover , protocols::simple_moves::SwitchChainOrderMover , protocols::simple_moves::SwitchResidueTypeSetMover , protocols::simple_moves::symmetry::DetectSymmetry , protocols::simple_moves::symmetry::SetupForSymmetryMover , protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover , protocols::simple_moves::symmetry::ExtractAsymmetricPoseMover , protocols::simple_moves::symmetry::SetupNCSMover , protocols::simple_moves::symmetry::SymMinMover , protocols::simple_moves::symmetry::SymPackRotamersMover , protocols::simple_moves::symmetry::SymRotamerTrialsMover , protocols::simple_moves::TaskAwareMinMover , protocols::toolbox::pose_metric_calculators::FragQualCalculator , core::chemical::ResidueLoaderOptions , core::conformation::symmetry::SymmDataOptions , core::import_pose::ImportPoseOptions , core::io::pdb::FileDataOptions , core::io::pdb::PDB_DReaderOptions , core::io::silent::SilentFileOptions , core::scoring::electron_density::ElectronDensityOptions , protocols::abinitio::DomainAssembly , protocols::analysis::InterfaceAnalyzerMover , protocols::backrub::BackrubMover , protocols::backrub::BackrubSidechainMover , protocols::canonical_sampling::HamiltonianExchange , protocols::canonical_sampling::MetricRecorder , protocols::canonical_sampling::MetropolisHastingsMover , protocols::canonical_sampling::ParallelTempering , protocols::canonical_sampling::PDBTrajectoryRecorder , protocols::canonical_sampling::SidechainMetropolisHastingsMover , protocols::canonical_sampling::SilentTrajectoryRecorder , protocols::canonical_sampling::SimulatedTempering , protocols::canonical_sampling::TemperingBase , protocols::canonical_sampling::TrajectoryRecorder , protocols::canonical_sampling::TrialCounterObserver , protocols::comparative_modeling::LoopRelaxMover , protocols::comparative_modeling::PartialThreadingMover , protocols::contact_map::ContactMap , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::dna::DesignProteinBackboneAroundDNA , protocols::dna::DnaInterfaceMinMover , protocols::dna::DnaInterfaceMultiStateDesign , protocols::dna::DnaInterfacePacker , protocols::dna::SeparateDnaFromNonDna , protocols::docking::DockingInitialPerturbation , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::electron_density::SetupForDensityScoringMover , protocols::enzdes::AddOrRemoveMatchCsts , protocols::enzdes::BackboneSampler , protocols::enzdes::PredesignPerturbMover , protocols::enzdes::LigDSasaFilter , protocols::enzdes::LigBurialFilter , protocols::enzdes::LigInterfaceEnergyFilter , protocols::enzdes::EnzScoreFilter , protocols::enzdes::DiffAtomSasaFilter , protocols::enzdes::RepackWithoutLigandFilter , protocols::enzdes::EnzdesScorefileFilter , protocols::enzdes::EnzRepackMinimize , protocols::enzdes::PackRotamersMoverPartGreedy , protocols::features::AtomAtomPairFeatures , protocols::features::FeaturesReporter , protocols::features::HBondFeatures , protocols::features::HBondParameterFeatures , protocols::features::helixAssembly::HelixBundleFeatures , protocols::features::LoopAnchorFeatures , protocols::features::ProteinRMSDFeatures , protocols::features::ReportToDB , protocols::features::ResidueGridScoresFeatures , 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
• 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
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• ParsedProtocol() : protocols::rosetta_scripts::ParsedProtocol
• parser() : protocols::jd2::JobDistributor
• 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
• partial_state_assignment_ : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• 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_ : protocols::hotspot_hashing::PartitionedSearchPattern
• 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_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
• partner1_ : protocols::contact_map::Contact
• partner2() : protocols::contact_map::Contact
• partner2_ : protocols::contact_map::Contact
• partner_ : core::scoring::dna::BasePartner , protocols::docking::DockingEnsemble , protocols::rigid::RigidBodyPerturbMover , protocols::rigid::RigidBodyRandomizeMover , protocols::rna::MultipleDomainMover , protocols::scoring::Interface
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partners() : protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking
• partners_ : protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_all_filters() : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_all_pose_screens() : protocols::swa::rna::StepWiseRNA_Minimizer
• pass_base_centroid_screen : protocols::swa::rna::SillyCountStruct
• 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_screen_struct_pair_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_start_pose() : protocols::antibody2::H3RefineCCD , protocols::antibody2::RefineOneCDRLoop
• pass_the_loop() : protocols::antibody2::H3PerturbCCD
• passed_automorphism() : protocols::motifs::MotifHit
• passed_automorphism_ : protocols::motifs::MotifHit
• passed_centroid_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_fullatom_filter_ : protocols::ub_e2c::ubi_e2c_modeler
• passed_highres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passed_lowres_filter_ : protocols::symmetric_docking::SymDockProtocol
• passes_com_vector_criterion() : protocols::match::NumNeighborsMPM
• passes_etable_filter() : protocols::match::output::UpstreamDownstreamCollisionFilter
• passes_fast_scan() : protocols::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_scores_ : protocols::toolbox::pose_metric_calculators::HPatchCalculator
• patch_str() : core::sequence::AnnotatedSequence
• patcharea_to_score_ : core::pack::interaction_graph::SurfacePotential
• patchdock_entry_num_ : protocols::protein_interface_design::PatchdockReader
• patchdock_fname_ : protocols::protein_interface_design::PatchdockReader
• PatchdockReader() : protocols::protein_interface_design::PatchdockReader
• PatchOperation() : protocols::canonical_sampling::PatchOperation
• path : protocols::hybridization::TMalign , protocols::motifs::Motif
• path_ : core::chemical::NCAARotLibPath , protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter , protocols::motifs::Motif , protocols::rna::RNA_IdealCoord
• path_dist() : core::scoring::AtomNeighbor
• path_dist_ : core::scoring::AtomNeighbor
• path_dist_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distance() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::count_pair::CountPairGeneric
• path_distance_ : core::chemical::ResidueType
• path_distance_OK() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distances() : core::chemical::ResidueType , core::conformation::Residue
• path_distances_to_connection_points_ : core::scoring::etable::etrie::GenericResidueConnectionData
• path_dists_ : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4
• path_to_torsion_files_ : core::scoring::rna::RNA_TorsionPotential
• pAtoms : core::scoring::sc::_PROBE
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• PattersonB : core::scoring::electron_density::ElectronDensity
• PattersonCorrEnergy() : core::scoring::electron_density::PattersonCorrEnergy
• PattersonEpsilon : core::scoring::electron_density::ElectronDensity
• PattersonMaxR : core::scoring::electron_density::ElectronDensity
• PattersonMinR : core::scoring::electron_density::ElectronDensity
• pb_bound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_bound_tag_ : core::scoring::methods::EnergyMethodOptions
• pb_by_state_ : core::scoring::methods::PBLifetimeCache
• pb_cached_data_ : protocols::simple_moves::ddG
• pb_enabled_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• pb_lengths_ : core::scoring::etable::count_pair::CountPairGeneric
• PB_LIFETIME_CACHE : core::pose::datacache::CacheableDataType
• PB_potential_ : core::scoring::ScoringManager
• pb_unbound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_unbound_tag_ : core::scoring::methods::EnergyMethodOptions
• pbe_mode : core::scoring::APBSConfig::I_PARAM
• pbest() : core::optimization::Particle
• pbest_ : core::optimization::Particle
• PBIter : core::conformation::PseudoBondCollection
• PBLifetimeCache : core::scoring::methods::PoissonBoltzmannEnergy , core::scoring::methods::PBLifetimeCache
• PBLifetimeCacheOP : core::scoring::methods::PoissonBoltzmannEnergy
• PBP_clustering_at_chain_closure_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• pca_ : protocols::abinitio::PcaEvaluator , protocols::abinitio::AbrelaxApplication
• PcaEvaluator() : protocols::abinitio::PcaEvaluator
• Pcalc : core::scoring::electron_density::ElectronDensity
• pcc_structure : core::scoring::electron_density::PattersonCorrEnergy
• PCluster() : protocols::pockets::PCluster
• PClusterSet() : protocols::pockets::PClusterSet
• pcs_d_ : protocols::scoring::methods::pcs::TensorsOptimizer
• pcs_d_c_ : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• PCS_data() : protocols::scoring::methods::pcs::PCS_data
• PCS_data_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PCS_data_from_pose() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_data_input() : protocols::scoring::methods::pcs::PCS_data_input
• PCS_data_input_manager() : protocols::scoring::methods::pcs::PCS_data_input_manager
• PCS_data_line_all_ : protocols::scoring::methods::pcs::PCS_file_data
• PCS_data_line_all_spin_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• PCS_data_per_lanthanides() : protocols::scoring::methods::pcs::PCS_data_per_lanthanides
• PCS_data_per_lanthanides_all_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• pcs_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PCS_Energy() : protocols::scoring::methods::pcs::PCS_Energy
• PCS_Energy_parameters_manager() : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager
• PCS_experimental() : protocols::scoring::methods::pcs::PCS_line_data
• PCS_experimental_ : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs2::PcsInputLine
• PCS_file_data() : protocols::scoring::methods::pcs::PCS_file_data
• PCS_filename_and_data_ : protocols::scoring::methods::pcs::PCS_data_input
• 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
• PCS_tolerance_ : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs2::PcsInputLine
• pcs_weight_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• pcs_weight_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• PcsDataCenter() : protocols::scoring::methods::pcs2::PcsDataCenter
• PcsDataCenterManager() : protocols::scoring::methods::pcs2::PcsDataCenterManager
• PcsDataCenterManagerSingleton() : protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PcsDataLanthanide() : protocols::scoring::methods::pcs2::PcsDataLanthanide
• PcsEnergy() : protocols::scoring::methods::pcs2::PcsEnergy
• PcsEnergyController() : protocols::topology_broker::PcsEnergyController
• PcsEnergyParameter() : protocols::scoring::methods::pcs2::PcsEnergyParameter
• PcsEnergyParameterManager() : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PcsGridSearchParameter() : protocols::scoring::methods::pcs2::PcsGridSearchParameter
• PcsGridSearchParameterManager() : protocols::scoring::methods::pcs2::PcsGridSearchParameterManager
• PcsInputCenter() : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputCenter_all_ : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputCenterManager() : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile() : protocols::scoring::methods::pcs2::PcsInputFile
• PcsInputFile_all_ : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputLine() : protocols::scoring::methods::pcs2::PcsInputLine
• PcsInputLine_all_ : protocols::scoring::methods::pcs2::PcsInputFile
• PcsTensor() : protocols::scoring::methods::pcs2::PcsTensor
• pcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol
• pd_ : core::scoring::packstat::MultiProbePerSphereAccumulator
• 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::PDBPoseMap
• pdb2pose() : core::pose::PDBInfo
• pdb2pose_ : core::pose::PDBInfo , core::pose::PDBPoseMap
• pdb_chain() : protocols::pmut_scan::MutationData
• pdb_codes_ : core::io::sequence_comparation::DesignContrast
• pdb_contains_target_ : protocols::seeded_abinitio::SeedFoldTree
• pdb_data_features_ : protocols::features::ProteinSilentReport
• PDB_DIR : protocols::sparta::Sparta::SpartaLib
• PDB_DReaderOptions() : core::io::pdb::PDB_DReaderOptions
• pdb_file_names_ : core::io::sequence_comparation::DesignContrast , protocols::pmut_scan::PointMutScanDriver
• pdb_filenames_ : protocols::docking::DockingEnsemble
• pdb_hash_ : protocols::frag_picker::PdbIdChunkFilter
• pdb_id : protocols::loophash::BBExtraData
• pdb_info() : core::pose::Pose
• pdb_info_ : core::pose::Pose
• pdb_lines_ : core::import_pose::PDBSilentStruct
• pdb_name() : protocols::simple_filters::RelativePoseFilter
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• pdb_num : core::io::raw_data::DisulfideFile
• pdb_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbered_h3_loop_end : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbered_h3_loop_start : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• pdb_profile() : protocols::protein_interface_design::movers::SpliceSegment
• PDB_Records_ : core::io::pdb::Field
• pdb_resnum_ : protocols::pmut_scan::MutationData
• pdb_segments_ : protocols::protein_interface_design::movers::Splice
• pdb_source_ : protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::StrandFragment
• pdb_start : protocols::forge::remodel::RemodelData
• pdb_stop : protocols::forge::remodel::RemodelData
• pdb_to_profile_map_ : protocols::protein_interface_design::movers::SpliceSegment
• PdbDataFeatures() : protocols::features::PdbDataFeatures
• PdbDataFeaturesCreator() : protocols::features::PdbDataFeaturesCreator
• PDBDumpMover() : protocols::moves::PDBDumpMover
• PDBfileName : protocols::sparta::PDB
• pdbid() : core::fragment::FragData , core::fragment::AnnotatedFragData
• pdbid_ : core::fragment::AnnotatedFragData
• PDBInfo() : core::pose::PDBInfo
• PDBInputter() : protocols::inputter::PDBInputter
• PDBJobInputter() : protocols::jd2::PDBJobInputter
• PDBJobOutputter() : protocols::jd2::PDBJobOutputter
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbname() : protocols::dna::DnaInterfacePacker
• pdbname_ : protocols::dna::DnaInterfacePacker
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput() : protocols::dna::DnaInterfacePacker
• PDBOutput() : protocols::dna::PDBOutput
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• PDBOutputter() : protocols::outputter::PDBOutputter
• pdbpos : protocols::dna::DnaDesignDef , core::fragment::FragData , core::fragment::AnnotatedFragData
• PDBPoseInputStream() : core::import_pose::pose_stream::PDBPoseInputStream
• PDBPoseMap() : core::pose::PDBPoseMap
• PDBReloadMover() : protocols::simple_moves::PDBReloadMover
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• 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
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• pdie : core::scoring::APBSConfig::R_PARAM
• pdime : core::scoring::APBSConfig
• PDInteractionGraph() : core::pack::interaction_graph::PDInteractionGraph
• PDL : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• PDNode() : core::pack::interaction_graph::PDNode
• peak_id() : protocols::noesy_assign::CrossPeak
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peak_volume() : protocols::noesy_assign::PeakAssignment
• PeakAssignment() : protocols::noesy_assign::PeakAssignment
• PeakAssignmentMap : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignmentParameters() : protocols::noesy_assign::PeakAssignmentParameters
• PeakAssignmentResidueMap() : protocols::noesy_assign::PeakAssignmentResidueMap
• PeakAssignments : protocols::noesy_assign::CrossPeak , protocols::noesy_assign::PeakAssignmentResidueMap
• PeakCalibrator() : protocols::noesy_assign::PeakCalibrator
• PeakCalibratorMap() : protocols::noesy_assign::PeakCalibratorMap
• PeakFileFormat() : protocols::noesy_assign::PeakFileFormat
• PeakFileFormat_Base() : protocols::noesy_assign::PeakFileFormat_Base
• PeakFileFormat_Sparky() : protocols::noesy_assign::PeakFileFormat_Sparky
• PeakFileFormat_xeasy() : protocols::noesy_assign::PeakFileFormat_xeasy
• PeakFileFormat_xpk() : protocols::noesy_assign::PeakFileFormat_xpk
• peaks() : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• PeakViolationCounts : protocols::noesy_assign::DistanceScoreMover
• peek_back() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• peek_front() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >
• PENALTY : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• penalty() : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• penalty_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• PEPTIDE : core::kinematics::Edge
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_last_res() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres() : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_random_loop_model() : protocols::flexpep_docking::FlexPepDockingProtocol
• 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
• per_constraint_build_points_ : protocols::match::Matcher
• per_cst_build_resids_ : protocols::match::Matcher
• per_cst_pose_build_resids_ : protocols::match::MatcherTask
• per_native_recovery_ : protocols::rotamer_recovery::RRReporterHuman
• per_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_ddg_ : protocols::simple_moves::ddG
• per_residue_energy_ : protocols::analysis::InterfaceAnalyzerMover
• perform_bump_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_electron_density_screen_ : protocols::swa::rna::StepWiseRNA_Minimizer
• perform_filters_ : protocols::swa::rna::StepWiseRNA_Clusterer
• perform_local_refinement() : protocols::hotspot_hashing::movers::PlaceProbeMover
• perform_minimize_ : protocols::swa::rna::StepWiseRNA_Minimizer
• perform_minimizer_run_ : protocols::rna::RNA_Minimizer
• perform_o2star_pack_ : protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• perform_rama_check() : protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perform_score_diff_cut_ : protocols::swa::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::swa::rna::StepWiseRNA_Clusterer
• performing_pure_insertion() : protocols::forge::build::SegmentInsert
• period() : core::scoring::methods::CartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::BBDepCartBondedParameters
• period_ : core::scoring::methods::BBIndepCartBondedParameters
• 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
• periodicity_ : core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::dna::TorsionFourierComponent , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::JumpClaim
• permitted_overlap() : protocols::match::MatcherTask
• 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_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::StartStructClaimer
• perturb_amplitude_ : protocols::rna::RNA_HelixAssembler
• perturb_anchor() : protocols::anchored_design::AnchoredDesignMover
• perturb_backbone_for_test() : protocols::grafting::GraftMoverBase
• perturb_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• 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_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_dBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_rot_within_well() : protocols::simple_moves::sidechain_moves::SidechainMover
• perturb_sBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion_ : protocols::swa::protein::StepWiseProteinLoopBridger
• perturb_torsion_ids_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• perturb_weights() : core::scoring::ScoreFunction
• PerturbChiSidechainMover() : protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover
• perturbed_ : core::pack::interaction_graph::FASTERNode
• perturbed_two_body_energies_ : core::pack::interaction_graph::FASTERNode
• perturber() : protocols::docking::DockingProtocol
• perturber_ : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• perturber_exhausted() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::TorsionSweepingKinematicPerturber
• perturber_type() : protocols::loops::loop_closure::kinematic_closure::KinematicPerturber , protocols::loops::loop_closure::kinematic_closure::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
• pfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• pfront_poses_ : protocols::design_opt::GreedyOptMutationMover
• pfront_poses_filter_ranks_ : protocols::design_opt::GreedyOptMutationMover
• pfront_poses_filter_vals_ : protocols::design_opt::GreedyOptMutationMover
• pH_ : core::scoring::methods::pHEnergy
• phase() : core::scoring::dna::TorsionFourierComponent
• phase_ : core::scoring::dna::TorsionFourierComponent
• pHEnergy() : core::scoring::methods::pHEnergy
• phi() : core::io::raw_data::DecoyStruct , protocols::swa::protein::MainChainTorsionSet , protocols::protein_interface_design::movers::BBDofs , protocols::frag_picker::VallResidue , core::pose::Pose
• Phi() : protocols::frag_picker::scores::Phi
• phi : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::pockets::spherical_coor_triplet , protocols::simple_moves::MinimalRotamer , 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 > , 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_ : protocols::protein_interface_design::movers::BBDofs , protocols::loophash::BackboneSegment , protocols::frag_picker::DiversifyDihedralsSelector , core::chemical::orbitals::ICoorOrbitalData , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::AddConnect , core::chemical::SetICoor , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::kinematics::tree::BondedAtom , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::MakeRotLib::RotData , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• phi_max() : core::util::ABEGO
• phi_max_ : core::util::ABEGO
• phi_mean_ : core::pack::dunbrack::CoarseRotamer
• phi_min() : core::util::ABEGO
• phi_min_ : core::util::ABEGO
• phi_offsets_ : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::StepWisePoseSetup
• phi_sdev_ : core::pack::dunbrack::CoarseRotamer
• PHIPSI_BINRANGE : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• PhiPsiRmsd() : protocols::frag_picker::scores::PhiPsiRmsd
• PhiPsiSquareWell() : protocols::frag_picker::scores::PhiPsiSquareWell
• PhiPsiTalosIO() : protocols::frag_picker::PhiPsiTalosIO
• phithetascore_ : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• physical_pose_clash_dist_cutoff_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• pi_pi_total_ : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• 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_boundary_ : protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::SelectResiduesByLayer
• pick_candidates() : protocols::frag_picker::FragmentPicker
• pick_chunk_candidates() : protocols::frag_picker::FragmentPicker
• pick_core_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pick_fragment_library() : protocols::rna::FullAtomRNA_Fragments , protocols::rna::RNA_Fragments
• pick_fragments() : protocols::forge::components::VarLengthBuild
• pick_frags() : protocols::abinitio::Templates
• pick_large_frags() : protocols::abinitio::Templates , protocols::abinitio::Template
• 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::rna::RNA_Fragments , 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
• pick_surface_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• piece_ : protocols::grafting::GraftMoverBase
• pipemap() : protocols::wum2::WorkUnit_ElScripts
• pipemap_ : protocols::wum2::WorkUnit_ElScripts
• PiPiCalculator() : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pivot_atoms() : protocols::backrub::BackrubMover
• pivot_atoms_ : protocols::backrub::BackrubMover
• pivot_range_randomly() : protocols::simple_moves::BBGaussianMover
• pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivot_residues() : protocols::backrub::BackrubSidechainMover , protocols::backrub::BackrubMover
• pivot_residues_ : protocols::backrub::BackrubMover
• pivot_to_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• 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::FunGroupTK , protocols::kinmatch::KinFunGroupTK , protocols::kinmatch::BruteFunGroupTK
• place_residue() : protocols::motifs::Motif
• place_residue_() : protocols::motifs::Motif
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• place_stub() : protocols::protein_interface_design::movers::PlaceStubMover
• place_stubs() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceFragments() : protocols::seeded_abinitio::PlaceFragments
• placeholder_info() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_info_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• PlacementAuctionMover() : protocols::protein_interface_design::movers::PlacementAuctionMover
• PlacementMinimizationMover() : protocols::protein_interface_design::movers::PlacementMinimizationMover
• PlaceOnLoop() : protocols::protein_interface_design::movers::PlaceOnLoop
• PlaceProbeMover() : protocols::hotspot_hashing::movers::PlaceProbeMover
• placeResidueAtTransform() : protocols::hotspot_hashing::StubGenerator
• placeResidueOnPose() : protocols::hotspot_hashing::StubGenerator
• PlaceSimultaneouslyMover() : protocols::protein_interface_design::movers::PlaceSimultaneouslyMover
• PlaceStubMover() : protocols::protein_interface_design::movers::PlaceStubMover
• PlaceSurfaceProbe() : protocols::hotspot_hashing::movers::PlaceSurfaceProbe
• PlaidFingerprint() : protocols::pockets::PlaidFingerprint
• plain_text : protocols::sparta::GDB
• PlainPdbJobDistributor() : protocols::jobdist::PlainPdbJobDistributor
• PlainRawJobDistributor() : protocols::jobdist::PlainRawJobDistributor
• PlainSilentFileJobDistributor() : protocols::jobdist::PlainSilentFileJobDistributor
• plane_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• PlanePointIntersection() : protocols::surface_docking::SurfaceParameters
• pleat_weird : core::scoring::dssp::StrandPairing
• Pleating() : core::scoring::dssp::Pairing
• pleating1 : core::scoring::dssp::StrandPairing
• pleating_ : core::scoring::dssp::Pairing
• pleats1() : protocols::fldsgn::topology::StrandPairing
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2() : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• pmatch() : protocols::noesy_assign::FloatingResonance , protocols::noesy_assign::Resonance
• PNatAAOptEPositionData() : protocols::optimize_weights::PNatAAOptEPositionData
• PNatAAOptERotamerData() : protocols::optimize_weights::PNatAAOptERotamerData
• PNatLigPoseOptEData() : protocols::optimize_weights::PNatLigPoseOptEData
• PNatRotOptEPositionData() : protocols::optimize_weights::PNatRotOptEPositionData
• PNatRotOptERotamerData() : protocols::optimize_weights::PNatRotOptERotamerData
• PNatStructureOptEData() : protocols::optimize_weights::PNatStructureOptEData
• po_bar : core::scoring::electron_density::ElectronDensity
• PO_BURIED : protocols::pockets::PocketGrid
• PO_EDGE : protocols::pockets::PocketGrid
• PO_SURF : protocols::pockets::PocketGrid
• POCKET : protocols::pockets::PocketGrid
• PocketConstraint() : protocols::pockets::PocketConstraint
• PocketConstraintCreator() : protocols::pockets::PocketConstraintCreator
• PocketGrid : protocols::pockets::PCluster , protocols::pockets::PClusterSet , protocols::pockets::PocketGrid
• pocketgrid_ : protocols::pockets::PocketConstraint
• pockets_ : protocols::pockets::PocketGrid
• point : core::scoring::sc::_PROBE
• Point() : core::scoring::packstat::Point
• point_ : protocols::match::VoxelSetIterator
• point_for_nonchitip_atom() : protocols::match::upstream::UpstreamResTypeGeometry
• point_graph() : core::scoring::Energies , core::conformation::AddEdgeVisitor< Vertex, Edge >
• point_graph_ : core::scoring::Energies
• pointer : core::io::silent::SilentFileData::iterator , core::io::silent::SilentFileData::const_iterator , protocols::toolbox::OP_const_iterator< const_iterator, SomeOP >
• PointGraphEdgeData() : core::conformation::PointGraphEdgeData
• PointGraphVertexData() : core::conformation::PointGraphVertexData
• PointMutationCalculator() : protocols::design_opt::PointMutationCalculator
• PointMutScanDriver : protocols::pmut_scan::MutationData , protocols::pmut_scan::Mutant , protocols::pmut_scan::PointMutScanDriver
• PointPair() : core::scoring::packstat::PointPair
• points_ : core::scoring::constraints::FourPointsFunc , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• points_for_nonchitip_atoms() : protocols::match::upstream::UpstreamResTypeGeometry
• points_for_nonchitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• points_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• points_in_global_orintation_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• poisson_boltzmann_potential_ : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannEnergy() : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannPotential() : core::scoring::PoissonBoltzmannPotential
• polar_ : core::pack::task::operation::ResidueTypeFilter , protocols::simple_filters::InterfaceSasaFilter
• polar_energy_pack_corrector() : core::scoring::FACTSPotential
• polar_expansion_radius_ : core::pack::interaction_graph::RotamerDots
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polarF2BR() : core::scoring::FACTSResidueInfo
• polarF2BR_ : core::scoring::FACTSResidueInfo
• polarF2d() : core::scoring::FACTSResidueInfo
• polarF2d_ : core::scoring::FACTSResidueInfo
• polars : protocols::sic_dock::BuriedPolarScore
• Policy() : protocols::nonlocal::Policy
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• poly_ala() : protocols::protein_interface_design::movers::Splice
• poly_ala_ : protocols::protein_interface_design::movers::Splice
• polyAla() : protocols::flexpep_docking::FlexPepDockingProtocol
• polymer_direction() : core::kinematics::Edge
• POLYMER_LOWER : core::chemical::ICoorAtomID
• POLYMER_UPPER : core::chemical::ICoorAtomID
• polymeric_oriented_sequence_distance() : core::conformation::Residue
• polymeric_sequence_distance() : core::conformation::Residue
• Polynomial_1d() : core::scoring::hbonds::Polynomial_1d
• polys_ : protocols::sasa_scores::PPoly
• pool_ : protocols::canonical_sampling::mc_convergence_checks::PoolData , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_cache_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• Pool_ConvergenceCheck() : protocols::canonical_sampling::mc_convergence_checks::Pool_ConvergenceCheck
• pool_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• Pool_Evaluator() : protocols::canonical_sampling::mc_convergence_checks::Pool_Evaluator
• pool_exists() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• pool_name_ : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaPool
• pool_names_ : protocols::frag_picker::quota::QuotaConfig
• pool_npes_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rank_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rms_ : protocols::moves::CanonicalSamplingMover , protocols::canonical_sampling::CanonicalSamplingMover
• Pool_RMSD() : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_size() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_size_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• pool_weights_ : protocols::frag_picker::quota::QuotaConfig
• PoolData() : protocols::canonical_sampling::mc_convergence_checks::PoolData
• PoolEvaluatorCreator() : protocols::simple_filters::PoolEvaluatorCreator
• pop() : core::graph::NegSpaceElement< T > , protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering >
• pop_all() : protocols::wum2::WUQueue
• pop_back() : protocols::evaluation::MetaPoseEvaluator , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pop_back_CA_xyz() : protocols::toolbox::DecoySetEvaluation
• pop_const_const_iter : protocols::genetic_algorithm::GeneticAlgorithm
• pop_const_iter : protocols::genetic_algorithm::GeneticAlgorithm
• pop_from_ss_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• pop_front() : protocols::wum2::WUQueue
• pop_iter : protocols::genetic_algorithm::GeneticAlgorithm
• pop_mutation() : protocols::pmut_scan::Mutant
• pop_next() : protocols::wum::WorkUnitQueue
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• 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
• population_weight_ : protocols::cluster::ClusterBase
• pore_radius() : protocols::flxbb::LayerDesignOperation , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pore_radius_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pos() : 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::CutClaim , protocols::topology_broker::RootClaim , core::fragment::NonContinuousFrame
• pos1 : protocols::jumping::DisulfPairing , protocols::rna::RNA_Pairing
• Pos1() : core::scoring::dssp::Pairing
• pos1_ : core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , protocols::topology_broker::JumpClaim , protocols::topology_broker::CutClaim , protocols::topology_broker::RootClaim , core::scoring::OneToAllNeighborIterator
• pos2 : protocols::jumping::DisulfPairing , protocols::rna::RNA_Pairing
• Pos2() : core::scoring::dssp::Pairing
• pos2_ : core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , protocols::topology_broker::JumpClaim , core::scoring::OneToAllNeighborIterator
• pos2select() : protocols::flxbb::LayerDesignOperation
• pos_ : core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK , protocols::topology_broker::SequenceClaim , protocols::topology_broker::BBClaim , core::fragment::NonContinuousFrame
• pos_in_bg_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_bg_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_nodes_edge_list_ : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• pos_in_nodes_edge_vector_ : core::pack::interaction_graph::EdgeBase
• pos_in_owners_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::graph::Edge
• pos_list_ : protocols::idealize::IdealizeMover , protocols::simple_moves::BackboneMover
• pos_map_ : core::sequence::AnnotatedSequence
• pose : core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent , protocols::cartesian::MolecularDynamics , core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pose::datacache::CacheablePoseRawPtr , protocols::multistate_design::SingleState , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::sic_dock::Rose , protocols::simple_filters::RelativePoseFilter
• Pose : core::fragment::IndependentBBTorsionSRFD , core::fragment::picking_old::vall::eval::EnergyEval , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::task::operation::NoRepackDisulfides , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OptH , core::pack::task::operation::ResFilter , core::pack::task::operation::TaskOperation , core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent , core::scoring::constraints::ConstraintSet , core::scoring::constraints::SequenceProfileConstraint , core::scoring::MinimizationEdge , core::scoring::OmegaTether , core::scoring::Ramachandran , core::util::ABEGOManager , protocols::boinc::BoincCurrentPoseObserver , protocols::constraints_additional::SequenceCoupling1BDConstraint , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::dna::PDBOutput , protocols::dna::RestrictDesignToProteinDNAInterface , protocols::dna::WatsonCrickRotamerCouplings , protocols::enzdes::BackboneSampler , protocols::enzdes::DetectProteinLigandInterface , protocols::enzdes::ProteinLigandInterfaceUpweighter , protocols::enzdes::AddRigidBodyLigandConfs , protocols::filters::FilterFactory , protocols::fldsgn::BluePrintBDR , protocols::fldsgn::CircularPermutation , 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::SheetTopologyFilter , protocols::fldsgn::MatchResidues , protocols::fldsgn::MatchResiduesMover , protocols::fldsgn::potentials::AACompositionEnergy , protocols::fldsgn::potentials::SetAACompositionPotential , protocols::fldsgn::potentials::SetSecStructEnergies , protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential , protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy , protocols::fldsgn::potentials::sspot::NatbiasSheetPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential , protocols::fldsgn::SheetConstraintsRCG , protocols::fldsgn::topology::BB_Pos , protocols::fldsgn::topology::SS_Info2 , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flexpack::rotamer_set::FlexbbRotamerSets , protocols::flxbb::DesignTask_Normal , protocols::flxbb::DesignTask_Layer , protocols::flxbb::FilterStructs , protocols::flxbb::FilterStructs_TotalCharge , protocols::flxbb::FlxbbDesign , protocols::flxbb::InterlockAroma , protocols::flxbb::LayerDesignOperation , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::BuildManager , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::forge::build::RelativeConnectRight , protocols::forge::build::SegmentRebuild , protocols::forge::build::SegmentSwap , protocols::forge::components::BDR , protocols::forge::constraints::ConstraintFileRCG , protocols::forge::constraints::NtoC_RCG , protocols::forge::constraints::RemoveCsts , protocols::forge::remodel::RemodelAccumulator , protocols::forge::remodel::RemodelDesignMover , protocols::forge::remodel::RemodelLoopMover , protocols::forge::remodel::RemodelMover , protocols::idealize::IdealizeMover , protocols::jd2::parser::BluePrint , protocols::jd2::parser::FragmentReader , protocols::loophash::FastGapMover , protocols::match::output::PoseInserter , protocols::motifs::LigandMotifSearch , protocols::moves::FilterMover , protocols::moves::MonteCarlo , protocols::moves::Mover , protocols::moves::MoverFactory , protocols::nonlocal::SingleFragmentMover , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::PackDaemon , protocols::protein_interface_design::ReportSequenceDifferences , protocols::protein_interface_design::FavorNativeResidue , protocols::protein_interface_design::FavorNonNativeResidue , protocols::protein_interface_design::movers::BackrubDDMover , protocols::protein_interface_design::movers::BuildAlaPose , protocols::protein_interface_design::movers::DesignMinimizeHbonds , protocols::protein_interface_design::movers::LoopLengthChange , protocols::protein_interface_design::movers::MapHotspot , protocols::protein_interface_design::movers::RandomMutation , protocols::protein_interface_design::movers::RepackMinimize , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::protein_interface_design::movers::SetTemperatureFactor , protocols::protein_interface_design::movers::SpinMover , protocols::protein_interface_design::movers::TaskAwareCsts , protocols::protein_interface_design::movers::TryRotamers , protocols::protein_interface_design::ReportPSSMDifferences , protocols::seeded_abinitio::CAcstGenerator , protocols::seeded_abinitio::CoordinateCst , protocols::seeded_abinitio::PlaceFragments , protocols::seeded_abinitio::SwapSegment , protocols::sic_dock::RigidScore , protocols::sic_dock::Rose , protocols::simple_filters::HolesFilter , protocols::simple_filters::PackStatFilter , protocols::simple_filters::RangeFilter , protocols::simple_filters::ShapeComplementarityFilter , protocols::simple_moves::ConsensusDesignMover , protocols::simple_moves::ddG , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::UserDefinedGroupDiscriminator , protocols::simple_moves::GreenPacker , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::rational_mc::RationalMonteCarlo , protocols::simple_moves::symmetry::DetectSymmetry , protocols::toolbox::pose_metric_calculators::FragQualCalculator , protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::JointSequenceOperation , protocols::toolbox::task_operations::LayerOperations , protocols::toolbox::task_operations::LimitAromaChi2_RotamerSetOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::SeqprofConsensusOperation , protocols::viewer::SilentObserver , core::pose::Pose , protocols::toolbox::task_operations::LimitAromaChi2Operation , protocols::simple_moves::MonteCarloTest , protocols::simple_moves::GroupDiscriminator , protocols::simple_moves::BBGaussianMover , protocols::seeded_abinitio::SegmentHybridizer , protocols::rosetta_scripts::ParsedProtocol , protocols::protein_interface_design::movers::Splice , protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover , protocols::protein_interface_design::DockDesignFilterFactory , protocols::pack_daemon::DaemonSet , protocols::motifs::MotifSearch , protocols::jd2::Parser , protocols::forge::remodel::RemodelRotamerLinks , protocols::forge::components::VarLengthBuild , protocols::forge::build::SegmentInsert , protocols::forge::build::ConnectRight , protocols::flxbb::FilterStructs_Packstat , protocols::flxbb::DesignTask , protocols::fldsgn::topology::Sheet , protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::NcontactsCalculator , protocols::fldsgn::filters::SecondaryStructureFilter , protocols::fldsgn::filters::CoreDunbrackFilter , protocols::enzdes::AddLigandMotifRotamers , protocols::enzdes::SetCatalyticResPackBehavior , protocols::constraints_additional::SequenceCouplingConstraint , core::scoring::Ramachandran2B , core::scoring::MinimizationNode , core::pack::task::operation::OptCysHG , core::pack::interaction_graph::OnTheFlyInteractionGraph
• pose() : protocols::simple_filters::RelativePoseFilter , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::optimization::CartesianMultifunc
• pose1_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore
• pose2_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore
• pose2pdb() : core::pose::PDBInfo
• pose_ : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pose::datacache::ObserverCache , core::scoring::packstat::MultiProbePoseAccumulator , protocols::abinitio::Template , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::kinmatch::FunGroupTK , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::scoring::ImplicitFastClashCheck , protocols::simple_filters::RelativePoseFilter , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper , protocols::pockets::PlaidFingerprint , protocols::pack_daemon::EntityCorrespondence , protocols::jd2::InnerJob , core::pose::datacache::CacheablePoseRawPtr , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::optimization::symmetry::SymMinimizerMap
• POSE_BEFORE_CAVITIES_ADDED : core::pose::datacache::CacheableDataType
• pose_build_resids_ : protocols::match::Matcher
• pose_by_state_ : core::scoring::methods::PBLifetimeCache
• pose_chemical_checksum_ : core::scoring::constraints::NamedAtomPairConstraint
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• pose_coords_are_same() : protocols::design_opt::GreedyOptMutationMover
• pose_copy_ : protocols::dna::PDBOutput
• pose_count_ : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger
• pose_data_list_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_Minimizer
• pose_data_uptodate_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• pose_filter_ : protocols::swa::protein::StepWiseProteinPacker
• pose_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• 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_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_index() : protocols::loops::ResidueIndexDescription
• pose_index_ : protocols::loops::ResidueIndexDescription
• pose_init_ : protocols::swa::protein::StepWiseProteinPacker
• pose_input_stream() : protocols::swa::InputStreamWithResidueInfo
• pose_input_stream_ : protocols::swa::InputStreamWithResidueInfo
• pose_intensities_ : core::scoring::saxs::SAXSEnergy
• pose_is_proper : core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy , core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::FastDensEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density::PattersonCorrEnergy
• pose_list_ : protocols::swa::protein::StepWiseProteinPoseMinimizer
• pose_name : protocols::swa::rna::VDW_RepScreeninfo , protocols::moves::StructureRestrictor
• pose_numb() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numbered() : protocols::loops::ResidueIndexDescription
• pose_numbered_ : protocols::loops::ResidueIndexDescription
• pose_OP : protocols::swa::rna::pose_data_struct2 , protocols::swa::rna::FB_Pose_Data
• pose_output_list_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• pose_p_ : protocols::multistate_design::SingleState
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_prepack_ : protocols::swa::protein::StepWiseProteinResidueSampler
• pose_ptr_ : core::pose::metrics::PoseMetricContainer
• pose_raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_res_no() : core::scoring::constraints::FabConstraint
• pose_resnum() : protocols::pmut_scan::MutationData
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right() : protocols::forge::build::ConnectRight
• pose_right_ : protocols::forge::build::ConnectRight
• Pose_selection_by_full_score() : protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_to_native_map_ : protocols::swa::rna::StepWiseRNA_Minimizer
• 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
• PoseCOP : protocols::dna::PDBOutput , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::sic_dock::Rose , protocols::moves::MonteCarlo , protocols::simple_moves::BBGaussianMover , protocols::moves::Mover , protocols::pack_daemon::PackDaemon , protocols::dna::RestrictDesignToProteinDNAInterface
• 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
• poselist : protocols::cluster::GatherPosesMover
• PoseMap : protocols::comparative_modeling::ThreadingJobInputter
• PoseMatchOutputWriter() : protocols::match::output::PoseMatchOutputWriter
• PoseMetricCalculator() : core::pose::metrics::PoseMetricCalculator
• PoseMetricCalculatorOP : protocols::fldsgn::NcontactsCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator
• PoseMetricContainer() : core::pose::metrics::PoseMetricContainer
• PoseMetricEvaluator() : protocols::simple_filters::PoseMetricEvaluator< T >
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• PoseNumberedLoopFileReader() : protocols::loops::PoseNumberedLoopFileReader
• PoseOP : protocols::simple_moves::symmetry::DetectSymmetry , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , protocols::fldsgn::BluePrintBDR , protocols::forge::remodel::RemodelLoopMover , protocols::pack_daemon::MultistateFitnessFunction , protocols::pack_daemon::DaemonSet , protocols::simple_moves::GenericMonteCarloMover , protocols::simple_moves::MonteCarloRecover , protocols::simple_moves::MonteCarloTest , protocols::pack_daemon::QuickRepacker , protocols::protein_interface_design::movers::SaveAndRetrieveSidechains , protocols::simple_moves::BBGaussianMover , protocols::pack_daemon::PackDaemon , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::flxbb::FilterStructs , protocols::moves::MonteCarlo , protocols::dna::PDBOutput , protocols::fldsgn::potentials::SetSecStructEnergies
• PoseOPs : protocols::comparative_modeling::ThreadingJobInputter
• PoseOutputStream() : core::import_pose::pose_stream::PoseOutputStream
• Poses : protocols::comparative_modeling::MultiThreadingMover
• poses_ : protocols::hybridization::DomainAssembly , core::pack::rotamer_set::UnboundRotamersOperation , protocols::abinitio::StructureStore , protocols::simple_filters::StructuralSimilarityEvaluator
• poses_from_cmd_line() : protocols::comparative_modeling::AlignmentClustering
• PoseSP : protocols::simple_moves::O2M_MutateMover
• PoseVector : protocols::noesy_assign::DistanceScoreMover , protocols::noesy_assign::StructureDependentPeakCalibrator
• position : protocols::dna::PositionType , core::conformation::signals::IdentityEvent , protocols::optimize_weights::PNatAAOptEPositionData , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , protocols::hotspot_hashing::VectorPair , core::kinematics::tree::Atom_ , core::conformation::signals::LengthEvent , protocols::cartesian::CartesianAtom , core::kinematics::tree::Atom , core::scoring::rna::RNA_Datum
• Position : core::kinematics::tree::Atom
• position_ : protocols::optimize_weights::PNatAAOptEPositionData , core::kinematics::tree::Atom_ , core::scoring::rna::RNA_Datum
• position_ala_ddG() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• POSITION_CONSERVED_RESIDUES : core::pose::datacache::CacheableDataType
• position_data_begin() : protocols::optimize_weights::OptEData
• position_data_end() : protocols::optimize_weights::OptEData
• position_ddGs_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_index() : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue
• position_index_ : protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue
• position_stub() : protocols::protein_interface_design::movers::PlaceOnLoop
• position_untouchable() : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_vector_setup() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• PositionConservedResiduesStore() : core::pose::datacache::PositionConservedResiduesStore
• PositionDdGInfo() : core::io::PositionDdGInfo::PositionDdGInfo
• PositionMap : core::sequence::AnnotatedSequence
• positions() : protocols::enzdes::EnzdesFlexibleRegion , protocols::forge::build::BuildManager
• Positions : protocols::forge::build::SegmentSwap , protocols::forge::build::GrowRight , protocols::forge::build::Bridge , protocols::forge::build::BuildInstruction , protocols::forge::build::GrowLeft , protocols::forge::build::SegmentRebuild , protocols::forge::components::VarLengthBuild
• positions() : protocols::dna::DnaChains
• Positions : protocols::forge::build::RelativeConnectRight , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentInsert
• positions() : protocols::dna::DnaChains
• Positions : protocols::forge::build::BuildManager
• positions_ : protocols::analysis::LoopAnalyzerMover , protocols::dna::DnaChains , protocols::enzdes::EnzdesFlexibleRegion , protocols::simple_filters::ScoreCutoffFilter
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• PositionType() : protocols::dna::PositionType
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• positive_states() : protocols::multistate_design::MultiStateFitnessFunction
• PosList : core::fragment::NonContinuousFrame
• possible_pairing_sets_ : protocols::rna::RNA_StructureParameters
• possible_working_res_1 : protocols::swa::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::swa::rna::InternalWorkingResidueParameter
• 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_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_packing() : protocols::dna::DnaInterfacePacker
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• post_process() : protocols::relax::WorkUnit_BatchRelax , protocols::relax::WorkUnit_BatchRelax_and_PostRescore
• PostDockAssemblyScorer() : protocols::domain_assembly::PostDockAssemblyScorer
• PosType() : protocols::multistate_design::PosType , protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• potential_ : protocols::protein_interface_design::movers::DisulfideMover , protocols::scoring::methods::InterchainEnvEnergy , protocols::scoring::methods::InterchainPairEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::RamachandranEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::CenHBEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::dfire::DFIRE_Potential , core::scoring::methods::EnvEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::PairEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::WaterAdductHBondEnergy , protocols::protein_interface_design::filters::DisulfideFilter , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::PoissonBoltzmannPotential
• potential_is_loaded_ : core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::dfire::DFIRE_Potential
• potential_starting_positions_ : protocols::ligand_docking::StartFrom
• potential_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• potential_vect_ : core::scoring::constraints::SplineFunc
• potential_vect_size_ : core::scoring::constraints::SplineFunc
• power_ : core::scoring::constraints::CircularPowerFunc
• PowExpression() : protocols::pack_daemon::PowExpression
• ppk_only : protocols::flexpep_docking::FlexPepDockingFlags
• pqr : core::scoring::APBSWrapper
• PQR() : core::scoring::PQR
• pqr_filename_ : core::scoring::PoissonBoltzmannPotential
• pr_idx_ : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• pre_align() : protocols::constraints_additional::BindingSiteConstraint
• pre_catalog_op() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::VallFragmentEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval
• pre_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• pre_loop_closure_protocol() : protocols::abinitio::AbrelaxMover
• pre_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody2::SnugDock
• pre_nresidue_change() : core::conformation::Conformation
• pre_process() : protocols::relax::WorkUnit_BatchRelax_and_PostRescore , protocols::relax::WorkUnit_BatchRelax
• pre_scoring() : protocols::flexpack::OtherContextScoreFunction
• preallocate() : core::fragment::picking_old::vall::VallLibrarian
• preallocate_ : core::fragment::picking_old::vall::VallLibrarian
• preapply_ : protocols::simple_moves::GenericMonteCarloMover
• precalc_etable_coefficients() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• precision() : core::io::silent::SilentStruct
• precision_ : protocols::frag_picker::scores::FragmentScoreManager , protocols::rotamer_recovery::RRReporterHuman , 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 , protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesInteractionGraphOP : protocols::simple_moves::GreenPacker
• PrecomputedPairEnergiesNode() : core::pack::interaction_graph::PrecomputedPairEnergiesNode
• pred_ : core::scoring::ResRangePredicate , core::scoring::ExcludedResPredicate , core::scoring::SelectedResPredicate
• pred_burial_ : core::scoring::methods::BurialEnergy
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_ss_ : protocols::star::StarAbinitio , protocols::star::Extender , protocols::medal::MedalExchangeMover
• predefined_torsions_ : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• PredesignPerturbMover() : protocols::enzdes::PredesignPerturbMover
• Predicate() : core::scoring::Predicate
• predict_H3_base_type() : protocols::antibody2::AntibodyInfo
• predict_n_matches_for_hit_subsets() : protocols::match::Matcher
• predicted_burial_ : protocols::simple_filters::PredictedBurialEvaluator
• predicted_H3_base_type_ : protocols::antibody2::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• PredictedBurialEvaluator() : protocols::simple_filters::PredictedBurialEvaluator
• PredictedBurialFnEvaluatorCreator() : protocols::simple_filters::PredictedBurialFnEvaluatorCreator
• prediction_ : protocols::frag_picker::quota::TorsionBinPool
• prediction_name_ : protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::RamaScore
• preexisting_positions() : protocols::forge::build::GrowLeft , protocols::forge::build::BuildManager , protocols::forge::build::SegmentRebuild , protocols::forge::build::BuildInstruction , protocols::forge::build::GrowRight , protocols::forge::build::SegmentInsert , protocols::forge::build::Bridge , protocols::forge::build::ConnectRight , protocols::forge::build::SegmentSwap
• prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• prefix() : protocols::match::output::PDBWriter
• prefix_ : protocols::match::output::PDBWriter , protocols::frag_picker::FragmentPicker , protocols::forge::remodel::RemodelMover::instruction_flags
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• prefix_len : core::kinematics::Node
• prep_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• prep_for_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• prep_grid() : protocols::match::downstream::ActiveSiteGrid
• prepack_full_repack_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• prepack_only() : protocols::flexpep_docking::FlexPepDockingProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• 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::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatcherToDownstreamResidue
• 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::CloudPDBWriter , protocols::match::output::OutputWriter , protocols::match::output::PDBWriter
• 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() : protocols::flexpack::interaction_graph::MinimalistFlexbbNode , protocols::flexpack::interaction_graph::MinimalistFlexbbEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::interaction_graph::SymmMinimalistInteractionGraph , protocols::flexpack::interaction_graph::OTFFlexbbEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• prepare_for_simulated_annealing_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::LazyEdge
• prepare_ghost_pose() : protocols::swa::protein::StepWiseProteinScreener , protocols::swa::StepWiseScreener
• prepare_hashing_packer_task_() : protocols::hotspot_hashing::HotspotStubSet
• prepare_loop_in_stage3() : protocols::abinitio::FragmentSampler , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::FoldConstraints , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::ClassicAbinitio
• prepare_loop_in_stage4() : protocols::abinitio::FoldConstraints , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::MembraneAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::ConstraintFragmentSampler
• 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::etable::BaseEtableEnergy< Derived > , core::scoring::ScoreFunction , core::scoring::hackelec::HackElecEnergyAroAro , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::hackelec::HackElecEnergy , core::scoring::hbonds::HBondEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::PairEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::HackElecEnergyAroAll , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hackelec::RNAHackElecEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::GenBornEnergy
• 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::FragmentSampler , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::KinematicAbinitio , protocols::abinitio::FoldConstraints , protocols::abinitio::ClassicAbinitio , protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::MembraneAbinitio
• prepare_stage2() : protocols::abinitio::JumpingFoldConstraints , protocols::abinitio::FoldConstraints , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , protocols::abinitio::ConstraintFragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio
• prepare_stage3() : protocols::abinitio::FragmentSampler , protocols::abinitio::ClassicAbinitio , protocols::abinitio::KinematicAbinitio , protocols::abinitio::MembraneAbinitio , protocols::abinitio::JumpingFoldConstraints
• prepare_stage4() : protocols::abinitio::ClassicAbinitio , protocols::abinitio::FragmentSampler , protocols::abinitio::MembraneAbinitio , 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
• prepared_for_simA_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• prepared_for_simulated_annealing_ : core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• preped_for_sim_annealing_ : core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::LinearMemEdge
• prepend_output_name() : protocols::canonical_sampling::MetricRecorder
• 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
• prepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• preprocess_data() : core::scoring::ResidualDipolarCoupling
• preprocess_pose() : core::import_pose::pose_stream::PoseInputStream
• presample_added_residue_ : protocols::swa::monte_carlo::RNA_AddMover
• preserve_buried_contacts() : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• preserve_c_beta_ : core::pack::task::ResidueLevelTask_
• preserve_detailed_balance() : protocols::backrub::BackrubSidechainMover , protocols::rigid::RigidBodyMover , protocols::canonical_sampling::ThermodynamicMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase , protocols::backrub::BackrubMover
• preserve_detailed_balance_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::backrub::BackrubMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header() : core::io::pdb::FileDataOptions
• preserve_header_ : core::io::pdb::FileDataOptions
• preserve_whole_input_tag_ : protocols::jobdist::BasicJob
• presetClass() : protocols::sparta::GDB
• pretty_print() : core::coarse::Rule , core::coarse::Translator , core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary , core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary , core::coarse::TranslatorSet , core::coarse::RuleSet
• preturb_rot_and_dunbrack_eval() : protocols::simple_moves::sidechain_moves::SidechainMover
• prev_state_hash_ : protocols::pack_daemon::PackDaemon
• PREV_Tab : protocols::sparta::Sparta::SpartaLib
• prevburied : core::scoring::sc::MolecularSurfaceCalculator
• prevent_repacking() : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , core::pack::task::ResidueLevelTask , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , core::pack::task::ResidueLevelTask_
• prevent_repacking_ : protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::simple_moves::DesignRepackMover , protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation
• PreventChainFromRepackingOperation() : protocols::toolbox::task_operations::PreventChainFromRepackingOperation
• PreventResiduesFromRepackingOperation() : protocols::toolbox::task_operations::PreventResiduesFromRepackingOperation
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous() : core::graph::EdgeListElement
• previous_ : core::graph::EdgeListElement , protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• previous_floating_base_chain_closure() : protocols::swa::rna::StepWiseRNA_ResidueSampler
• previous_hash_value_ : core::scoring::methods::LinearChainbreakEnergy
• previous_round_geometry_still_matchable() : protocols::match::OccupiedSpaceHash
• previous_sequence_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• previous_sibling() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_tree_ : protocols::nonlocal::SingleFragmentMover
• previous_vertex1 : protocols::viewer::GraphicsState
• previous_vertex2 : protocols::viewer::GraphicsState
• previous_width_vector : protocols::viewer::GraphicsState
• 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
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• prevp : core::scoring::sc::MolecularSurfaceCalculator
• principal_component() : protocols::features::helixAssembly::HelicalFragment
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• print() : protocols::loophash::BackboneSegment , core::pack::interaction_graph::SymmLinearMemNode , protocols::frag_picker::nonlocal::NonlocalPair , core::pack::interaction_graph::RotamerDotsCache , core::scoring::MembraneTopology , core::scoring::MinimizationNode , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::CountPairData_1_2 , core::pack::interaction_graph::LazyNode , core::scoring::hackelec::ElecAtom , protocols::toolbox::pose_metric_calculators::ChargeCalculator , core::scoring::etable::etrie::CountPairData_1_3 , protocols::match::downstream::AtomDihedralSecMatchRPE , core::scoring::trie::RotamerTrieBase , protocols::moves::MoverStatistics , protocols::moves::PyMolMover , protocols::frags::TorsionFragmentLibrary , core::pack::interaction_graph::DoubleDensePDNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pose::metrics::PoseMetricContainer , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::hbonds::hbtrie::HBAtom , core::pose::metrics::simple_calculators::SasaCalculator , core::scoring::etable::etrie::TrieCountPair1BC3 , core::pose::metrics::StructureDependentCalculator , core::scoring::etable::etrie::EtableAtom , protocols::fldsgn::NcontactsCalculator , core::chemical::Atom , protocols::flexpack::interaction_graph::OTFFlexbbNode , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::DotSphere , core::scoring::EnergyNode , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::hbonds::hbtrie::HBAtom , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::hackelec::ElecAtom , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::EMapVector , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::etable::etrie::CountPairData_1_1 , protocols::flexpack::interaction_graph::MinimalistFlexbbNode , core::scoring::etable::etrie::CountPairDataGeneric , protocols::scoring::Interface , protocols::toolbox::pose_metric_calculators::CatPiCalculator , protocols::toolbox::pose_metric_calculators::ClashCountCalculator , protocols::toolbox::pose_metric_calculators::HPatchCalculator , core::pack::interaction_graph::SymmMinimalistNode , protocols::toolbox::pose_metric_calculators::ResidueDecompositionCalculator , core::pose::metrics::EnergyDependentCalculator , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::DoubleLazyNode , core::chemical::AtomType , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::chemical::Orbital , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::BackgroundNode< V, E, G > , protocols::match::downstream::AtomGeometrySecMatchRPE , protocols::match::downstream::AtomDistanceSecMatchRPE , protocols::jd2::ScoreMap , protocols::rbsegment_relax::RBSegmentMover , protocols::motifs::Motif , protocols::match::downstream::AtomAngleSecMatchRPE , protocols::toolbox::pose_metric_calculators::PackstatCalculator , protocols::toolbox::pose_metric_calculators::FragQualCalculator , core::scoring::mm::mmtrie::MMEnergyTableAtom , protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator , core::scoring::trie::TrieNode< AT, CPDATA > , protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator , protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculator , protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculator , protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator , protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , core::pose::metrics::PoseMetricCalculator , core::pack::interaction_graph::SurfaceNode< V, E, G > , protocols::dna::DnaChains , protocols::motifs::Motif , protocols::toolbox::pose_metric_calculators::SurfaceCalculator , core::pack::interaction_graph::SimpleNode , protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator , core::pack::interaction_graph::HPatchNode< V, E, G > , protocols::wum::SilentStructStore , core::graph::Node , protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculator , protocols::pockets::PocketGrid , protocols::wum::WorkUnitBase , protocols::toolbox::pose_metric_calculators::SaltBridgeCalculator , core::scoring::etable::etrie::EtableAtom , core::chemical::sdf::MolData , protocols::wum2::WorkUnit , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator , core::pack::interaction_graph::FASTERNode , protocols::toolbox::pose_metric_calculators::PiPiCalculator
• print_address() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• print_addresses_at_level() : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• print_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::ProteinSilentStruct_Template< T > , core::io::silent::SilentStruct , core::io::raw_data::ScoreStruct , core::io::silent::BinaryRNASilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::import_pose::PDBSilentStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct
• print_current_energy() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmLinearMemEdge
• print_current_state_assignment() : core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::InteractionGraphBase
• 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::import_pose::PDBSilentStruct , core::io::raw_data::RawStruct , core::io::silent::BinaryRNASilentStruct , core::io::silent::SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::BinaryProteinSilentStruct , core::io::silent::RNA_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::DoubleDensePDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::LinearMemNode , protocols::flexpack::interaction_graph::FlexbbNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode
• 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::GrabAllCollector , protocols::frag_picker::quota::SecondaryStructurePool
• print_residue_info() : core::coarse::CoarseEtable
• print_rot_vec() : protocols::toolbox::pose_metric_calculators::RotamerRecovery
• print_score() : protocols::optimize_weights::PNatAAOptEPositionData , protocols::optimize_weights::OptEPositionData , protocols::optimize_weights::PSSMOptEPositionData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::PNatLigPoseOptEData , protocols::optimize_weights::PNatRotOptEPositionData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DGBindOptEData , protocols::optimize_weights::ConstraintedOptimizationWeightFunc
• 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_statw_interval_ : 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
• prior_probs_ : core::sequence::ProfSimScoringScheme
• prioritize() : protocols::wum2::WorkUnit
• prioritize_ : protocols::wum2::WorkUnit
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod
• prob_ : core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::BBDepNRChiSample< P >
• prob_larger_current_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_random_pert_current() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sum_of_gaussians() : core::scoring::constraints::SOGFunc_Impl
• prob_table_ : protocols::docking::ConformerSwitchMover
• prob_to_accumulate() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_buried() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_buried_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_nonburied() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_nonburied_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_uniform() : protocols::backrub::BackrubSidechainMover , protocols::simple_moves::sidechain_moves::SidechainMover
• prob_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot() : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::backrub::BackrubSidechainMover
• prob_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• probA() : core::scoring::packstat::PackingScore
• probA_ : core::scoring::packstat::PackingScore
• probabilistically_commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• Probabilities : protocols::medal::MedalMover , protocols::nonlocal::BiasedFragmentMover
• probability() : core::pack::dunbrack::DunbrackRotamerSampleData , protocols::noesy_assign::CrossPeak , core::pack::dunbrack::ChiSet , protocols::frag_picker::quota::ABEGO_SS_Config
• probability_ : core::pack::dunbrack::ProbSortClass , core::pack::dunbrack::DunbrackRotamerSampleData , protocols::MakeRotLib::RotData , core::pack::dunbrack::CoarseRotamer
• Probability_AA : core::scoring::P_AA
• Probability_AA_n : core::scoring::P_AA
• Probability_AA_pp : core::scoring::P_AA
• probability_limit() : protocols::match::upstream::BuildSet
• probability_to_accumulate_while_building_rotamers() : core::pack::dunbrack::SingleResidueDunbrackLibrary
• probB() : core::scoring::packstat::PackingScore
• probB_ : core::scoring::packstat::PackingScore
• Probe : protocols::hotspot_hashing::movers::PlaceProbeMover
• probe_atom_type_ : protocols::qsar::scoring_grid::SolvationGrid
• probe_rad_ : protocols::pockets::PocketGrid
• probe_radii : core::scoring::packstat::SasaOptions
• probe_radius() : protocols::match::BumpGrid
• probe_radius_ : core::pack::interaction_graph::RotamerDots , protocols::toolbox::task_operations::SelectBySASAOperation , core::pose::metrics::simple_calculators::SasaCalculator
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• probes : core::scoring::sc::MolecularSurfaceCalculator
• probs_ : protocols::nonlocal::SingleFragmentMover , protocols::frag_picker::TorsionBinIO , protocols::frag_picker::LAMBEGO_IO
• proc_id_ : protocols::jobdist::BaseJobDistributor
• process_AA_SET_line() : protocols::pack_daemon::EntityFunc
• process_add_daemon_message() : protocols::pack_daemon::DaemonSet
• process_algorithm_info() : protocols::toolbox::match_enzdes_util::MatchConstraintFileInfo
• process_continuous_design_string() : protocols::forge::remodel::RemodelMover , protocols::forge::components::BDR
• 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::UpstreamHitCacher , protocols::match::downstream::SecondaryMatcherToUpstreamResidue , protocols::match::downstream::SecondaryMatchUpstreamResProcessor , protocols::match::upstream::UpstreamResidueProcessor , protocols::match::output::WriteUpstreamHitKinemage , protocols::match::output::PoseInserter
• process_inbound_wus() : protocols::wum::MPI_WorkUnitManager_Slave , protocols::wum::DatabaseQueryWorkUnitManager< T > , protocols::wum::MPI_WorkUnitManager , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::loophash::MPI_LoopHashRefine_Master
• 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::components::BDR , protocols::forge::remodel::RemodelMover
• process_match() : protocols::match::output::MatchProcessor , protocols::match::output::MatchOutputter , protocols::match::output::MatchConsolidator , protocols::match::output::MatchOutputter
• 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::DatabaseQueryWorkUnitManager< T > , protocols::wum::MPI_WorkUnitManager , protocols::loophash::MPI_LoopHashRefine_Emperor , protocols::wum::MPI_WorkUnitManager_Slave
• 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::PNatRotOptEPositionData , protocols::optimize_weights::DDGMutationOptEData , protocols::optimize_weights::DDGBindOptEData , protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData , protocols::optimize_weights::PNatStructureOptEData , protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData
• 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
• processed_ : protocols::cluster::AssignToClustersMover , protocols::cluster::GatherPosesMover
• ProcessorFactory() : protocols::match::output::ProcessorFactory
• ProClosureEnergy() : core::scoring::methods::ProClosureEnergy
• procorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procrastinated_ : core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DoubleLazyNode
• prof_row() : core::sequence::SequenceProfile , protocols::frag_picker::TorsionBinIO , core::sequence::SequenceProfile , protocols::frag_picker::LAMBEGO_IO
• profile() : core::sequence::CacheableSequenceProfile , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue , core::sequence::CacheableSequenceProfile , protocols::frag_picker::VallResidue , core::sequence::SequenceProfile , core::fragment::picking_old::vall::VallResidue
• profile_ : core::sequence::CacheableSequenceProfile , core::sequence::SequenceProfile , core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue
• profile_mapping() : core::scoring::constraints::SequenceProfileConstraint
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_struct() : protocols::frag_picker::VallResidue
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_weight_away_from_interface() : protocols::protein_interface_design::movers::Splice
• profile_weight_away_from_interface_ : protocols::protein_interface_design::movers::Splice
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• ProfilerMover() : protocols::moves::ProfilerMover
• ProfileScore() : protocols::frag_picker::scores::ProfileScore
• ProfileScoreBlosum62() : protocols::frag_picker::scores::ProfileScoreBlosum62
• ProfileScoreDistWeight() : protocols::frag_picker::scores::ProfileScoreDistWeight
• ProfileScoreL1() : protocols::frag_picker::scores::ProfileScoreL1
• ProfileScoreStructL1() : protocols::frag_picker::scores::ProfileScoreStructL1
• ProfileScoreSubMatrix() : protocols::frag_picker::scores::ProfileScoreSubMatrix
• ProfSimScoringScheme() : core::sequence::ProfSimScoringScheme
• progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
• prohibit_single_residue_loops() : protocols::loops::LoopsFileOptions , protocols::loops::LoopFromFileData
• prohibit_single_residue_loops_ : protocols::loops::LoopFromFileData , protocols::loops::LoopsFileOptions
• project_deltaE_for_substitution() : protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::DensePDNode , protocols::flexpack::interaction_graph::MinimalistFlexbbNode
• project_deltaE_for_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_point_to_3d() : protocols::match::OccupiedSpaceHash
• project_pref_max_cpu_run_time_ : protocols::boinc::Boinc
• project_pref_max_gfx_cpu_ : protocols::boinc::Boinc
• project_pref_max_gfx_fps_ : protocols::boinc::Boinc
• project_surface_deltaE() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• ProjectionVector : protocols::evaluation::PCA
• proline_corrections_ : core::pack::interaction_graph::SymmOnTheFlyEdge , core::pack::interaction_graph::OnTheFlyEdge
• 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
• propeller_ : protocols::dna::DNABasepair
• properties() : core::chemical::ResidueType
• properties_ : core::chemical::ResidueType , core::chemical::Selector_PROPERTY
• property() : core::pack::task::operation::ResidueHasProperty
• property_ : core::chemical::AddProperty , core::chemical::DeleteProperty , core::pack::task::operation::ResidueHasProperty
• proposal_density() : protocols::simple_moves::sidechain_moves::SidechainMover
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposed_energy_ : core::pack::interaction_graph::SimpleEdge
• proposed_one_body_energy() : core::pack::interaction_graph::SimpleNode
• proposed_since_last_batch() : protocols::jd2::archive::ArchiveBase
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• PROTEIN : protocols::pockets::PocketGrid
• protein_CA_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• protein_calculate() : protocols::scoring::Interface
• protein_dna_motif() : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_DNA_motif_build_positions_JA() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_DNA_motif_target_positions_JA() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_neighbors() : protocols::dna::DnaInterfaceFinder
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_position_equal_within() : core::scoring::methods::PoissonBoltzmannEnergy
• protein_positions() : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_positions_ : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_scan() : protocols::dna::DnaInterfacePacker
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobOutputter , protocols::features::DatabaseJobInputter
• 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
• protocol_ : protocols::rotamer_recovery::RotamerRecovery , protocols::ligand_docking::LigandDockProtocol , protocols::features::RotamerRecoveryFeatures , protocols::protein_interface_design::movers::LoopRemodel , protocols::protein_interface_design::movers::LoopMoverFromCommandLine
• protocol_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_id_ : protocols::features::ReportToDB , protocols::features::ProteinSilentReport
• protocol_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_params_ : protocols::rotamer_recovery::RRReporterSQLite , protocols::rotamer_recovery::RRReporterHuman
• protocol_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• ProtocolFeatures() : protocols::features::ProtocolFeatures
• ProtocolFeaturesCreator() : protocols::features::ProtocolFeaturesCreator
• protocols::jd2::JobDistributor : protocols::jd2::InnerJob
• protocols::jd2::JobDistributorFactory : protocols::jd2::archive::MPIArchiveJobDistributor
• protocols::jd2::JobInputter : protocols::jd2::InnerJob
• protocols::jd2::Parser : protocols::jd2::InnerJob
• proton() : protocols::noesy_assign::CrossPeak
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_chi_2_chi() : core::chemical::ResidueType
• proton_chi_extra_samples() : core::chemical::ResidueType
• proton_chi_extra_samples_ : core::chemical::ResidueType
• proton_chi_samples() : core::chemical::ResidueType
• proton_chi_samples_ : core::chemical::ResidueType
• proton_chis_ : core::chemical::ResidueType
• proton_index() : protocols::noesy_assign::MethylNames
• proton_tolerance() : protocols::noesy_assign::CrossPeakInfo
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list() : protocols::swa::rna::StepWiseRNA_JobParameters
• protonated_H1_adenosine_list_ : protocols::swa::rna::StepWiseRNA_JobParameters
• protons_ : protocols::simple_filters::AtomicContactFilter
• provide_stored_derivatives() : core::optimization::LineMinimizationAlgorithm , core::optimization::StrongWolfeLineMinimization , core::optimization::ArmijoLineMinimization
• prune_cavity_burial_probe_radii : core::scoring::packstat::SasaOptions
• prune_max_delta : core::scoring::packstat::SasaOptions
• prune_max_iters : core::scoring::packstat::SasaOptions
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pseudo_bonds_ : core::conformation::PseudoBondCollection
• PseudoBond() : core::conformation::PseudoBond
• PseudoBondCollection() : core::conformation::PseudoBondCollection
• pseudobonds() : core::conformation::Residue
• pseudobonds_ : core::conformation::Residue
• PSEUDOCONTACT_SHIFT_DATA : core::pose::datacache::CacheableDataType
• PSEUDOCONTACT_SHIFT_MULTI_DATA : core::pose::datacache::CacheableDataType
• PseudocontactShiftEnergyController() : protocols::topology_broker::PseudocontactShiftEnergyController
• pseudorotation() : protocols::dna::DNABase
• pseudorotation_ : protocols::dna::DNABase
• psi() : protocols::frag_picker::VallResidue , protocols::swa::MainChainTorsionSet , protocols::optimize_weights::PNatRotOptEPositionData , core::io::silent::ProteinSilentStruct_Template< T >
• Psi() : protocols::frag_picker::scores::Psi
• psi() : core::fragment::picking_old::vall::VallResidue , protocols::protein_interface_design::movers::BBDofs , protocols::swa::MainChainTorsionSet , core::fragment::picking_old::vall::VallResidue , protocols::pockets::spherical_coor_triplet , protocols::frag_picker::PhiPsiTalosIO , protocols::swa::protein::MainChainTorsionSet , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::jumping::PairingTemplate , protocols::jumping::DisulfTemplate , protocols::swa::protein::MainChainTorsionSet , protocols::frag_picker::VallResidue , core::pose::Pose , protocols::frags::VallData , core::io::silent::ProteinSilentStruct_Template< T > , protocols::protein_interface_design::movers::BBDofs , protocols::match::upstream::ProteinBackboneBuildPoint , core::io::raw_data::DecoyStruct , protocols::frags::RMSVallData
• psi_ : protocols::frag_picker::VallResidue , protocols::swa::MainChainTorsionSet , protocols::MakeRotLib::RotData , protocols::frag_picker::DiversifyDihedralsSelector , protocols::protein_interface_design::movers::BBDofs , core::io::silent::ProteinSilentStruct_Template< T > , protocols::optimize_weights::PNatRotOptEPositionData , protocols::swa::protein::MainChainTorsionSet , protocols::frags::RMSVallData , protocols::loophash::BackboneSegment , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , protocols::frags::VallData , protocols::match::upstream::ProteinBackboneBuildPoint
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• psi_max() : core::util::ABEGO
• psi_max_ : core::util::ABEGO
• psi_min() : core::util::ABEGO
• psi_min_ : core::util::ABEGO
• psi_offsets_ : protocols::swa::StepWisePoseSetup , protocols::swa::protein::StepWiseProteinLoopBridger
• PSP : protocols::pockets::PocketGrid
• pssm_() : protocols::protein_interface_design::ReportPSSMDifferences , protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• pssm_data_ : protocols::protein_interface_design::ReportPSSMDifferences , protocols::optimize_weights::IterativeOptEDriver
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• PSSMOptEPositionData() : protocols::optimize_weights::PSSMOptEPositionData
• PSURFACE : protocols::pockets::PocketGrid
• ptask() : protocols::multistate_design::PackingState
• ptask_ : protocols::simple_moves::ConsensusDesignMover , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• ptask_p_ : protocols::multistate_design::PackingState
• pts_ : protocols::cluster::APCluster , core::scoring::SecondaryStructurePotential
• PtType : protocols::pockets::PocketGrid
• pucker1_specified_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pucker2_specified_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pucker_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_ID_old_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_state() : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pucker_state_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_state_list_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pulldomain() : protocols::hybridization::DDomainParse
• pure_large_frags_ : protocols::abinitio::JumpingFoldConstraints
• PURE_TOPO_RESAMPLING : protocols::abinitio::IterativeBase
• push() : protocols::frag_picker::BoundedPriorityQueue< T, StrictWeakOrdering > , protocols::frag_picker::quota::QuotaPool , protocols::frag_picker::quota::SecondaryStructurePool , protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering > , protocols::frag_picker::quota::ABEGO_SS_Pool
• push_back() : protocols::wum2::WUQueue , core::pack::task::TaskFactory , protocols::wum2::WUQueue , protocols::frag_picker::VallChunk , protocols::moves::MonteCarlo , protocols::fldsgn::topology::SheetSet , core::io::silent::SilentFileData , protocols::frag_picker::VallProvider , protocols::coarse_rna::SourcePositions , core::id::SequenceMapping , protocols::fldsgn::topology::HSSTripletSet , core::scoring::dssp::StrandPairingSet , protocols::cluster::GatherPosesMover , protocols::wum::WorkUnitQueue , protocols::protein_interface_design::movers::ResidueBBDofs , protocols::fldsgn::topology::StrandPairingSet , core::pack::task::TaskFactory , protocols::loops::Loops , protocols::loops::LoopsFileData , protocols::toolbox::DecoySetEvaluation , protocols::loops::Loops , core::graph::EdgeList , core::pack::dunbrack::CoarseRotamerSet , core::conformation::PseudoBondCollection , core::conformation::symmetry::VirtualCoordinates , protocols::fldsgn::topology::BetaAlphaBetaMotifSet , protocols::fldsgn::topology::HelixPairingSet , protocols::cluster::Cluster
• 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::RotamerSubset , core::pack::rotamer_set::RotamerSet_
• push_back_x() : core::conformation::symmetry::VirtualCoordinates
• push_back_y() : core::conformation::symmetry::VirtualCoordinates
• push_front() : protocols::wum::WorkUnitQueue , core::graph::EdgeList , protocols::cluster::Cluster , protocols::wum2::WUQueue
• 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
• pymol_ : protocols::moves::PyMolObserver
• pymol_sel_hbond_unsat_ : protocols::analysis::InterfaceAnalyzerMover
• pymol_sel_interface_ : protocols::analysis::InterfaceAnalyzerMover
• pymol_sel_packing_ : protocols::analysis::InterfaceAnalyzerMover
• PyMolMover() : protocols::moves::PyMolMover
• PyMolObserver() : protocols::moves::PyMolObserver
• pythag() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl