- p -

• p : protocols::environment::claims::CutBiasElement , protocols::environment::claims::CutElement , protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• p0_ : protocols::features::helixAssembly::HelicalFragment
• P0_ : protocols::simple_moves::PeriodicBoxMover
• p0_E_ : core::scoring::P_AA_ss
• p0_H_ : core::scoring::P_AA_ss
• p0_L_ : core::scoring::P_AA_ss
• p1 : protocols::environment::claims::JumpElement
• p1_ : protocols::features::helixAssembly::HelicalFragment
• p2 : protocols::environment::claims::JumpElement
• p_ : core::optimization::Particle , core::scoring::fiber_diffraction::FiberDiffractionEnergy , core::scoring::fiber_diffraction::FiberDiffractionEnergyDens
• P_aa1 : core::scoring::motif::RPM_FilterStats
• P_aa2 : core::scoring::motif::RPM_FilterStats
• p_aa_ : core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy
• P_AA_ : core::scoring::P_AA
• p_aa_ : core::scoring::ScoringManager
• p_AA_ABEGO3_ : core::scoring::P_AA_ABEGO3
• P_AA_n_ : core::scoring::P_AA
• P_AA_pp_ : core::scoring::P_AA
• P_AA_pp_energy_splines_ : core::scoring::P_AA
• P_AA_ss_ : core::scoring::methods::P_AA_ss_Energy
• p_aa_ss_ : core::scoring::ScoringManager
• P_AA_SS_burial_ : protocols::simple_moves::StructProfileMover
• p_atom_index_ : core::chemical::rna::RNA_Info
• p_cond_ : protocols::moves::WhileMover
• P_coorderr : core::scoring::motif::RPM_FilterStats
• p_DMS_ : core::scoring::rna::data::RNA_DMS_Potential
• P_dssp1 : core::scoring::motif::RPM_FilterStats
• P_dssp2 : core::scoring::motif::RPM_FilterStats
• p_E_ : core::scoring::P_AA_ss
• P_faatr : core::scoring::motif::RPM_FilterStats
• P_faatr_or_hb : core::scoring::motif::RPM_FilterStats
• P_faatr_or_hbbb : core::scoring::motif::RPM_FilterStats
• p_H_ : core::scoring::P_AA_ss
• P_hb_bb : core::scoring::motif::RPM_FilterStats
• P_hb_bb_sc : core::scoring::motif::RPM_FilterStats
• P_hb_sc : core::scoring::motif::RPM_FilterStats
• p_L_ : core::scoring::P_AA_ss
• P_lig : core::scoring::motif::RPM_FilterStats
• p_max_ : core::optimization::ParticleSwarmMinimizer
• P_max_seqsep : core::scoring::motif::RPM_FilterStats
• P_maxdist2 : core::scoring::motif::RPM_FilterStats
• p_min_ : core::optimization::ParticleSwarmMinimizer
• P_mindist2 : core::scoring::motif::RPM_FilterStats
• p_model_ : core::scoring::rna::data::RNA_DMS_Potential
• P_no_hb_bb : core::scoring::motif::RPM_FilterStats
• P_nodisulf : core::scoring::motif::RPM_FilterStats
• P_noloops : core::scoring::motif::RPM_FilterStats
• P_not_restype : core::scoring::motif::RPM_FilterStats
• P_not_restype_one : core::scoring::motif::RPM_FilterStats
• P_occupancy : core::scoring::motif::RPM_FilterStats
• P_oneloop : core::scoring::motif::RPM_FilterStats
• P_pdb : core::scoring::motif::RPM_FilterStats
• P_randomize_ : protocols::ligand_docking::ga_ligand_dock::EntropyEstimator
• p_range_ : core::optimization::ParticleSwarmMinimizer
• P_restype : core::scoring::motif::RPM_FilterStats
• P_restype1 : core::scoring::motif::RPM_FilterStats
• P_restype2 : core::scoring::motif::RPM_FilterStats
• P_restype_one : core::scoring::motif::RPM_FilterStats
• P_score : core::scoring::motif::RPM_FilterStats
• P_seqsep : core::scoring::motif::RPM_FilterStats
• P_ss1 : core::scoring::motif::RPM_FilterStats
• P_ss2 : core::scoring::motif::RPM_FilterStats
• P_type_BB_BB : core::scoring::motif::RPM_FilterStats
• P_type_BB_PH : core::scoring::motif::RPM_FilterStats
• P_type_BB_PO : core::scoring::motif::RPM_FilterStats
• P_type_PH_PO : core::scoring::motif::RPM_FilterStats
• P_type_SC_BB : core::scoring::motif::RPM_FilterStats
• P_type_SC_PH : core::scoring::motif::RPM_FilterStats
• P_type_SC_PO : core::scoring::motif::RPM_FilterStats
• P_type_SC_SC : core::scoring::motif::RPM_FilterStats
• P_uniformfrag : core::scoring::motif::RPM_FilterStats
• paa_abego3_ : core::scoring::methods::Abego , core::scoring::ScoringManager
• pack_ : protocols::cryst::DockLatticeMover , protocols::residue_optimization::MetapatchEnumeration
• pack_all_side_chains_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_and_minimize_linker_and_sidechains_ : protocols::cyclic_peptide::CrosslinkerMover
• pack_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• pack_distance_ : protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::CreateGlycanSequonMover , protocols::carbohydrates::GlycanSampler
• pack_full_repack_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler , protocols::relax::ClassicRelax
• pack_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_min_ : protocols::switches::GraftSwitchMover
• pack_min_cycles_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
• pack_neighbors_ : protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::CreateGlycanSequonMover , protocols::simple_moves::SimpleThreadingMover , protocols::switches::GraftSwitchMover
• pack_o2prime_hydrogens_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_phosphate_penalty_ : core::scoring::methods::FreeDOF_Options
• pack_protein_side_chains_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions , protocols::stepwise::modeler::packer::StepWisePacker , protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_residue_ : core::pack::task::PackerTask_
• pack_rotamers_ : protocols::abinitio::ClassicAbinitio
• pack_rotamers_fullatom_ : protocols::surface_docking::SurfaceDockingProtocol
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• pack_rounds_ : protocols::analysis::InterfaceAnalyzerMover , protocols::calc_taskop_movers::CreateSequenceMotifMover , protocols::carbohydrates::CreateGlycanSequonMover , protocols::simple_moves::SimpleThreadingMover
• pack_scorefxn_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::LHRepulsiveRamp , protocols::antibody::LHRepulsiveRampLegacy , protocols::antibody::RefineBetaBarrel , protocols::stepwise::modeler::StepWiseModeler , protocols::ub_e2c::ubi_e2c_modeler
• pack_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• pack_separated_ : protocols::analysis::InterfaceAnalyzerMover , protocols::features::InterfaceFeatures
• pack_sfxn_ : protocols::relax::LocalRelax
• pack_shell_ : protocols::antibody::design::MutateFrameworkForCluster
• pack_task_ : protocols::stepwise::modeler::packer::StepWisePacker
• pack_time_ : protocols::ligand_docking::ga_ligand_dock::GridScorer
• pack_together_ : protocols::features::InterfaceFeatures
• pack_virtual_o2prime_hydrogen_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pack_weights_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• packable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter , protocols::simple_filters::MutationsFilter , protocols::simple_filters::ResidueCountFilter
• packcycles : protocols::ligand_docking::ga_ligand_dock::GADockStageParams
• packed_residues_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_rotno_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_2_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_rotwell_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• packed_rotno_conversion_data_current_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packer_ : protocols::antibody_legacy::GraftMover , protocols::carbohydrates::GlycanSampler , protocols::recon_design::FindConsensusSequence , protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_cycles_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GridScorer
• packer_neighbor_graph_ : core::optimization::SingleResidueMultifunc , protocols::hbnet::HBNet
• packer_palette_ : core::pack::task::PackerTask_ , core::pack::task::ResidueLevelTask_ , core::pack::task::TaskFactory
• packer_palette_creator_map_ : core::pack::palette::PackerPaletteFactory
• packer_pose_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• packer_problem_file_data_ : protocols::quantum_annealing::ExternalPackerResultLoader
• packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , protocols::simple_moves::CoupledMover
• packing_angle_degrees_ : protocols::legacy_sewing::Model
• packing_angle_numbering_ : protocols::antibody::AntibodyInfo
• packing_angle_residues_ : protocols::antibody::AntibodyInfo
• packing_angle_to_enum_ : protocols::antibody::AntibodyEnumManager
• packing_angle_to_string_ : protocols::antibody::AntibodyEnumManager
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_operation_ : protocols::backrub::BackrubProtocol
• packing_range_ : protocols::pose_creation::MergePDBMover
• packing_shell_ : protocols::calc_taskop_filters::RelativePoseFilter
• packonly_after_graft_ : protocols::antibody::AntibodyModelerProtocol , protocols::antibody::GraftCDRLoopsProtocol
• packrotamersmover_ : protocols::backrub::BackrubProtocol
• packstat : protocols::analysis::InterfaceData
• packstat_pdb_ : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• pad : core::scoring::mhc_epitope_energy::MHCEpitopeEnergy
• padding_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid , protocols::ligand_docking::ga_ligand_dock::GALigandDock
• pages_ : core::fragment::picking_old::concepts::Book< Pages >
• pair_ : core::scoring::SmoothEnvPairPotential
• pair_and_func_map_ : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• pair_bin_lower_bounds_ : core::scoring::dna::DNA_EnvPairPotential
• pair_corr_ : core::scoring::PairEPotential
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• pair_list_ : protocols::scoring::Interface
• pair_lists_vec_ : protocols::hbnet::HBNetStapleInterface
• pair_log_ : core::scoring::EnvPairPotential
• pair_map_ : core::scoring::custom_pair_distance::PairFuncMap
• 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_stats_ : core::scoring::dna::DNA_EnvPairPotential
• pair_to_data_map_ : core::scoring::epr_deer::DEERDataCache
• pair_vector_ : protocols::task_operations::RestrictInterGroupVectorOperation
• paircover : core::scoring::motif::MotifHits
• pairE_potential_ : core::scoring::ScoringManager
• paired_ : protocols::dna::DnaPosition
• pairing1 : core::scoring::dssp::StrandPairing
• pairing2 : core::scoring::dssp::StrandPairing
• pairings_ : core::scoring::dssp::StrandPairingSet , protocols::abinitio::AlternativePairings , protocols::abinitio::Templates , protocols::denovo_design::architects::CompoundArchitect , protocols::denovo_design::components::StructureData , 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
• pairs_ : core::sequence::PairScoringScheme , protocols::denovo_design::components::SolutionPredicate , protocols::fold_from_loops::movers::SplitAndMixPoseMover
• pairs_aligned : protocols::indexed_structure_store::search::PairQuerySummaryStatistics
• pairs_considered : protocols::indexed_structure_store::search::PairQuerySummaryStatistics
• pairsplines_ : core::scoring::CenRotEnvPairPotential
• PARALLEL : core::scoring::dssp::Pairing
• parallel_ : protocols::denovo_design::components::HelixPairing , protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::PointMutationCalculator , protocols::matdes::MatDesGreedyOptMutationMover , protocols::matdes::MatDesPointMutationCalculator , protocols::splice::AlignEndsMover
• parallel_weight_ : core::scoring::SecondaryStructureWeights
• parallelcount_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower , protocols::loop_grower::LoopPartialSolutionStore
• param1 : protocols::denovo_design::movers::RelaxScriptCommand , protocols::relax::RelaxScriptCommand
• param2 : protocols::denovo_design::movers::RelaxScriptCommand , protocols::relax::RelaxScriptCommand
• param3 : protocols::denovo_design::movers::RelaxScriptCommand , protocols::relax::RelaxScriptCommand
• param4 : protocols::denovo_design::movers::RelaxScriptCommand , protocols::relax::RelaxScriptCommand
• param_cache_ : protocols::toolbox::match_enzdes_util::EnzdesCstCache
• 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_type_ : protocols::simple_filters::RepeatParameterFilter
• ParamB : core::scoring::GenBornPotential
• ParamD : core::scoring::GenBornPotential
• parameter_description_ : core::conformation::parametric::Parameter
• parameter_list_ : core::conformation::parametric::Parameters
• parameter_name_ : core::conformation::parametric::Parameter
• parameter_tag_ : protocols::qsar::scoring_grid::LigandPropertyScore
• parameter_type_ : core::conformation::parametric::Parameter
• parameter_units_ : core::conformation::parametric::Parameter
• parameter_values_as_res_lists_ : core::pose::full_model_info::FullModelParameters
• parameter_values_at_res_ : core::pose::full_model_info::FullModelParameters
• parametercheck_ : protocols::loop_grower::FragmentExtension , protocols::loop_grower::LoopGrower
• parameters_ : core::conformation::parametric::ParametersSet , core::conformation::parametric::ParametrizationCalculator , protocols::helical_bundle_predict::HBPHelix
• parameters_index_ : protocols::helical_bundle::PerturbBundleHelix
• parameters_set_ : core::conformation::Conformation
• parameters_set_index_ : protocols::helical_bundle::PerturbBundleHelix
• ParamG : core::scoring::GenBornPotential
• ParamS : core::scoring::GenBornPotential
• params_ : core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::packing::HolesEnergyRes , core::scoring::packing::HolesParamsRes , protocols::mpi_refinement::Scheduler , protocols::recces::RECCES_Mover
• params_database_tag_ : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• params_files_ : protocols::jd2::ScreeningJobInputter
• params_vec : protocols::relax::RelaxScriptCommand
• paratope : protocols::antibody::ParatopeMetric< T >
• paratope_cdrs_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::design::AntibodyDesignMover
• paratope_charge_ : protocols::antibody::AntibodyFeatures
• paratope_cst_mover_ : protocols::antibody::design::AntibodyDesignMover
• paratope_epitope_cst_mover_ : protocols::antibody::design::AntibodyDesignMover
• paratope_heavy : protocols::antibody::ParatopeMetric< T >
• paratope_light : protocols::antibody::ParatopeMetric< T >
• paratope_residues_ : protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover , protocols::antibody::constraints::ParatopeSiteConstraintMover
• paratope_sasa_ : protocols::antibody::AntibodyFeatures
• parent : core::kinematics::Node , protocols::legacy_sewing::LegacyReadRepeatNativeRotamersFile , protocols::pockets::SmallMol
• parent_ : core::environment::FoldTreeSketch::Node , core::kinematics::tree::Atom_ , core::optimization::DOF_Node , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , protocols::jd3::JGResultNode , protocols::protein_interface_design::movers::CoordinateConstraintStack
• parent_atom_ : core::chemical::AddConnect
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithmBase
• parent_full_model_parameters_ : core::pose::full_model_info::FullModelParameters
• parent_id_ : core::optimization::DOF_DataPoint
• parent_name_ : protocols::loop_modeling::LoopMover
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_remarks_map_ : core::io::silent::SilentStruct
• parent_residue_ : core::conformation::carbohydrates::GlycanNode
• parent_residue_type_ : core::chemical::ResidueProperties
• parent_segments_ : protocols::legacy_sewing::SewSegment
• parent_tags_map_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• parents_ : protocols::jd3::JGJobNode
• parin_favorite_output_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions , protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• parse_error_ : protocols::metal_interface::ZincSiteFinder
• parsed_atoms_ : protocols::constraint_generator::DihedralConstraintGenerator
• parsed_custom_torsion_ : protocols::constraint_generator::DihedralConstraintGenerator
• parsed_json_ : protocols::rpc::JSON_RPC
• parsed_position_ : protocols::simple_moves::SimpleThreadingMover
• parsed_positions_ : core::select::residue_selector::GlycanResidueSelector , protocols::carbohydrates::GlycanSampler , protocols::carbohydrates::SimpleGlycosylateMover
• parsed_resnums_ : protocols::constraint_generator::DihedralConstraintGenerator
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• parser_ : protocols::jd2::JobDistributor , protocols::rosetta_scripts::RosettaScriptsJobQueen
• partial_charge_ : core::chemical::ResidueType , core::chemical::sdf::MolFileIOAtom
• partial_hydrate_dew_ : protocols::hydrate::Hydrate
• 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_solvated_ : core::scoring::sc::ElectrostaticComplementarityCalculator , core::simple_metrics::composite_metrics::ElectrostaticComplementarityMetric
• partition_ : protocols::hotspot_hashing::PartitionedSearchPattern
• partition_cache_ : core::scoring::rna::RNA_PartitionEnergy
• partition_definition_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser , protocols::stepwise::modeler::rna::o2prime::O2PrimePacker , protocols::stepwise::modeler::working_parameters::StepWiseBasicWorkingParameters
• partner1_ : 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::denovo::coarse::MultipleDomainMover , protocols::scoring::Interface , protocols::sewing::data_storage::SmartAssembly
• partner_contact : protocols::sewing::data_storage::ContactDescription
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partner_ligand : protocols::sewing::data_storage::LigandDescription
• partner_ligand_ : protocols::sewing::data_storage::LigandResidue
• partner_ligands_ : protocols::sewing::data_storage::SmartAssembly
• partner_pdb_ : protocols::sewing::movers::AppendAssemblyMover
• partner_pose_ : protocols::legacy_sewing::Assembly , protocols::legacy_sewing::LegacyAppendAssemblyMover
• partner_residue_ : protocols::sewing::scoring::TerminusMotifScorer
• partner_resnum_ : protocols::sewing::requirements::ClashRequirement
• partners_ : core::scoring::PDvertex , core::scoring::power_diagram::PDvertex , protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::EllipsoidalRandomizationMover , protocols::docking::membrane::MPFindInterfaceMover , protocols::docking::membrane::QuickRelaxPartnersSeparately , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToAtomFilter , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_ : protocols::environment::DofUnlock , protocols::environment::EXCN_Env_Security_Exception
• pass_base_centroid_screen : protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct
• pass_count_ : protocols::stepwise::screener::AlignRMSD_Screener
• pass_screen_struct_pair_ : protocols::stepwise::modeler::rna::StepWiseRNA_CombineLongLoopFilterer
• pass_throughs_ : core::chemical::ResidueTypeSetCache
• 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
• passports_ : protocols::environment::ClientMover
• passthrough_ : protocols::electron_density::DockIntoDensityMover
• patch_map_ : core::chemical::ResidueTypeSet
• patch_name : core::chemical::carbohydrates::SugarModificationsNomenclatureTableRow
• patch_names_ : core::chemical::ResidueTypeFinder
• patch_scores_ : protocols::pose_metric_calculators::HPatchCalculator
• patcharea_to_score_ : core::pack::interaction_graph::SurfacePotential
• patchdock_entry_num_ : protocols::protein_interface_design::PatchdockReader
• patchdock_fname_ : protocols::protein_interface_design::PatchdockReader
• patches_ : core::chemical::ResidueTypeSet
• path : protocols::network::NetworkQueue::ServerAddress
• path_ : core::chemical::NCAARotLibPath , core::pose::rna::RNA_IdealCoord , protocols::features::DatabaseJobOutputter , protocols::hybridization::TMalign , protocols::jd2::FileSystemJobDistributor , protocols::jd2::wwPDBJobOutputter , protocols::legacy_sewing::Assembly , protocols::motifs::Motif
• path_dist_ : core::scoring::AtomNeighbor , core::scoring::SmallAtNb
• path_dist_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distance_ : core::chemical::ResidueType , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• path_distances_to_connection_points_ : core::scoring::etable::etrie::GenericResidueConnectionData
• path_dists_ : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior >
• path_tightness_ : protocols::simple_filters::AveragePathLengthFilter
• path_to_parameter_files_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• path_to_torsion_files_ : core::scoring::rna::RNA_TorsionPotential
• pAtoms : core::scoring::sc::_PROBE
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• pb_bound_tag_ : core::scoring::methods::EnergyMethodOptions
• pb_by_state_ : core::scoring::methods::PBLifetimeCache
• pb_cached_data_ : protocols::simple_ddg::ddG
• pb_enabled_ : protocols::simple_ddg::ddG , protocols::simple_ddg::DdgFilter
• pb_lengths_ : core::scoring::etable::count_pair::CountPairGeneric
• PB_potential_ : core::scoring::ScoringManager
• pb_unbound_tag_ : core::scoring::methods::EnergyMethodOptions
• pbe_mode : core::scoring::APBSConfig::I_PARAM
• pbest_ : core::optimization::Particle
• PBP_clustering_at_chain_closure_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::modeler::options::StepWiseRNA_ModelerOptions
• pca_ : protocols::abinitio::AbrelaxApplication , protocols::abinitio::PcaEvaluator
• pconfs_ : protocols::environment::Environment
• pcs_calc_ : core::scoring::nmr::pcs::PCSSingle
• pcs_d_ : protocols::scoring::methods::pcs::TensorsOptimizer , protocols::scoring::methods::pcsTs1::TensorsOptimizer_Ts1 , protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2 , protocols::scoring::methods::pcsTs3::TensorsOptimizer_Ts3 , protocols::scoring::methods::pcsTs4::TensorsOptimizer_Ts4
• pcs_d_c_ : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• pcs_data_ : protocols::nmr::pcs::PCSLigandTransformMover::LMMinPCSDataRef , protocols::nmr::pcs::PCSLigandTransformMover
• PCS_data_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• pcs_data_file_ : protocols::nmr::pcs::PCSLigandTransformMover
• pcs_data_initialized_ : protocols::qsar::scoring_grid::PCSMultiGrid
• PCS_data_line_all_ : protocols::scoring::methods::pcs::PCS_file_data , protocols::scoring::methods::pcsTs1::PCS_file_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_file_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_file_data_Ts4
• PCS_data_line_all_spin_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• PCS_data_per_lanthanides_all_ : protocols::scoring::methods::pcs2::PcsDataCenter , protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcsTs1::PCS_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_Ts4
• pcs_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• pcs_err_ : core::scoring::nmr::pcs::PCSSingle
• pcs_exp_ : core::scoring::nmr::pcs::PCSSingle
• PCS_experimental_ : protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• pcs_file_ : protocols::qsar::scoring_grid::PCSSingleGrid
• PCS_filename_and_data_ : protocols::scoring::methods::pcs::PCS_data_input , protocols::scoring::methods::pcsTs1::PCS_data_input_Ts1 , protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 , protocols::scoring::methods::pcsTs3::PCS_data_input_Ts3 , protocols::scoring::methods::pcsTs4::PCS_data_input_Ts4
• pcs_grid_vector_ : protocols::qsar::scoring_grid::PCSMultiGrid
• pcs_input_file_ : protocols::qsar::scoring_grid::PCSMultiGrid
• pcs_multiset_vec_ : core::scoring::nmr::pcs::PCSData
• pcs_single_vec_ : core::scoring::nmr::pcs::PCSSingleSet
• pcs_single_weights_ : core::scoring::nmr::pcs::PCSSingleSet
• pcs_singleset_vec_ : core::scoring::nmr::pcs::PCSMultiSet
• pcs_tensor_diagonalized_ : core::scoring::nmr::pcs::PCSTensor
• pcs_tensor_in_arbitrary_frame_ : core::scoring::nmr::pcs::PCSTensor
• pcs_tensor_in_pas_ : core::scoring::nmr::pcs::PCSTensor
• pcs_tensor_reconfigured_ : core::scoring::nmr::pcs::PCSTensor
• PCS_tolerance_ : protocols::scoring::methods::pcs2::PcsInputLine , protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcsTs1::PCS_line_data_Ts1 , protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 , protocols::scoring::methods::pcsTs3::PCS_line_data_Ts3 , protocols::scoring::methods::pcsTs4::PCS_line_data_Ts4
• pcs_values_ : core::scoring::nmr::pcs::PCSSingleSet , protocols::qsar::scoring_grid::PCSSingleGrid
• pcs_weight_ : protocols::scoring::methods::pcs2::PcsEnergyParameter , protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcsTs1::PCS_Energy_parameters_manager_Ts1 , protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 , protocols::scoring::methods::pcsTs3::PCS_Energy_parameters_manager_Ts3 , protocols::scoring::methods::pcsTs4::PCS_Energy_parameters_manager_Ts4
• pcs_weight_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• pcs_weight_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController , protocols::topology_broker::PseudocontactShiftEnergyController_Ts1 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts2 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts3 , protocols::topology_broker::PseudocontactShiftEnergyController_Ts4
• PcsInputCenter_all_ : protocols::scoring::methods::pcs2::PcsInputCenterManager
• PcsInputFile_all_ : protocols::scoring::methods::pcs2::PcsInputCenter
• PcsInputLine_all_ : protocols::scoring::methods::pcs2::PcsInputFile
• pcut_ : protocols::hybridization::DDomainParse , protocols::hybridization::HybridizeProtocol
• pd_ : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::SASAPotential
• pd_reader_ : protocols::protein_interface_design::movers::PatchdockTransform
• pdamp_ : core::scoring::MultipoleParameter
• pdb : protocols::antibody::CDRDBPose , protocols::antibody::CDRDBSequence
• pdb2pose_ : core::pose::PDBInfo , core::pose::PDBPoseMap
• pdb2pose_noSegmentIDs_ : core::pose::PDBPoseMap
• Pdb4LetName_ : protocols::splice::Splice
• pdb_ : core::scoring::motif::ResPairMotif
• pdb_author_ : core::io::StructFileRepOptions
• pdb_cache_ : protocols::pose_creation::MakeJunctionsMover
• pdb_cache_bool_ : protocols::pose_creation::MakeJunctionsMover
• pdb_cache_max_size_ : protocols::pose_creation::MakeJunctionsMover
• pdb_code_ : protocols::legacy_sewing::Model
• pdb_codes_ : core::io::sequence_comparation::DesignContrast
• pdb_comments_ : core::io::StructFileRep , core::io::StructFileRepOptions
• pdb_components_directory_ : core::chemical::GlobalResidueTypeSet
• pdb_components_overrides_ : core::chemical::GlobalResidueTypeSet
• pdb_conformers : protocols::sewing::data_storage::LigandDescription
• pdb_conformers_string : protocols::sewing::data_storage::LigandDescription
• pdb_contains_target_ : protocols::seeded_abinitio::SeedFoldTree
• pdb_count_ : protocols::fold_from_loops::movers::ResidueLabelsToPymolSelectionMover
• pdb_data_features_ : protocols::features::ProteinSilentReport
• PDB_DIR : protocols::sparta::Sparta::SpartaLib
• pdb_end_ : protocols::antibody::clusters::CDRCluster
• pdb_end_insertion_code_ : protocols::antibody::clusters::CDRCluster
• 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::pack::annealer::SequenceSymmetricAnnealer , core::pose::Pose , protocols::antibody::snugdock::SnugDockProtocol , protocols::fold_from_loops::movers::SavePDBInfoMover
• pdb_lines_ : core::import_pose::PDBSilentStruct
• pdb_list_ : protocols::mean_field::GenMeanFieldMover
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• pdb_name_list : protocols::splice::RotLibOut
• pdb_names_ : protocols::splice::BBMatching , protocols::splice::RotLibdb
• pdb_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbered_h3_loop_end : protocols::task_operations::RestrictToCDRH3Loop
• pdb_numbered_h3_loop_start : protocols::task_operations::RestrictToCDRH3Loop
• pdb_numbering_ : protocols::score_filters::ScoreCutoffFilter
• pdb_parents_ : core::io::StructFileRepOptions
• pdb_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• pdb_position_ : protocols::antibody::design::MutantPosition
• pdb_prefix_ : protocols::helical_bundle::BackboneGridSampler , protocols::helical_bundle::BundleGridSampler
• pdb_residues_ : protocols::antibody::design::ResnumFromStringsWithRangesSelector
• pdb_resnum_ : protocols::pmut_scan::MutationData
• pdb_rotamers_file_ : core::chemical::rotamers::PDBRotamerLibrarySpecification
• pdb_segments_ : protocols::sewing::data_storage::SmartAssembly , protocols::sewing::hashing::AlignmentGenerator , protocols::sewing::hashing::BasisMapGenerator , protocols::sewing::hashing::EdgeMapGenerator , protocols::sewing::hashing::Hasher , protocols::splice::Splice , protocols::splice::SpliceManager
• pdb_seqpos : protocols::simple_filters::nmer_svm_res_data
• pdb_source_ : protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::SandwichFragment , protocols::features::strand_assembly::StrandFragment
• pdb_start : protocols::forge::remodel::RemodelData
• pdb_start_ : protocols::antibody::clusters::CDRCluster
• pdb_start_insertion_code_ : protocols::antibody::clusters::CDRCluster
• pdb_stop : protocols::forge::remodel::RemodelData
• pdb_to_H3_seq_map_ : protocols::splice::Splice , protocols::splice::SpliceOut
• pdb_to_next_allowed_partners_ : protocols::splice::BBMatching
• pdb_to_prev_allowed_partners_ : protocols::splice::BBMatching
• pdb_to_profile_map_ : protocols::splice::RotLibdb , protocols::splice::SpliceSegment
• pdbContent : protocols::pockets::SmallMol
• pdbdata_string_ : protocols::rpc::JSON_RPC
• PDBfileName : protocols::sparta::PDB
• pdbid_ : core::fragment::AnnotatedFragData , protocols::simple_filters::ResidueDepthFilter
• pdbinfo_labels_ : core::io::silent::SilentStruct
• pdblistfilename_ : protocols::cluster::calibur::PreloadedPDB
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbn : protocols::constel::ResMut
• pdbname_ : protocols::dna::DnaInterfacePacker , protocols::metal_interface::AddZincSiteConstraints , protocols::simple_filters::SSMotifFinder
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• pdbpos : protocols::dna::DnaDesignDef
• PDBs_ : protocols::cluster::calibur::Clustering
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• pdie : core::scoring::APBSConfig::R_PARAM
• pdime : core::scoring::APBSConfig
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• penalties_ : core::scoring::aa_repeat_energy::AARepeatEnergy , core::scoring::netcharge_energy::NetChargeEnergySetup
• 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 , protocols::simple_moves::FavorSymmetricSequence
• penalty_at_1M_ : core::scoring::methods::IntermolEnergy
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• penalty_res_ : protocols::rbsegment_relax::SequenceShiftMover
• penalty_wtd_ : protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep1 : core::io::CisPeptideInformation
• pep2 : core::io::CisPeptideInformation
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_lengths_ : protocols::peptide_deriver::PeptideDeriverFilter
• pep_next_ : core::environment::FoldTreeSketch::Node
• pep_prev_ : core::environment::FoldTreeSketch::Node
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• pep_start : protocols::peptide_deriver::DerivedPeptideEntry
• PEPTIDE : core::kinematics::Edge
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_num_ : protocols::simple_moves::DisulfideInsertionMover
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_length_ : core::scoring::mhc_epitope_energy::MHCEpitopePredictor
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• PEPTIDE_NEUTRAL_PHI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• PEPTIDE_NEUTRAL_PSI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_stub_mover_ : protocols::helical_bundle::BackboneGridSampler
• peptide_stub_mover_initialized_ : protocols::helical_bundle::BackboneGridSampler
• peptoid_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• peptoid_is_achiral_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• PEPTOID_NEUTRAL_OMG : core::pack::dunbrack::SingleResidueDunbrackLibrary
• PEPTOID_NEUTRAL_PHI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• PEPTOID_NEUTRAL_PSI : core::pack::dunbrack::SingleResidueDunbrackLibrary
• per_atom_lipid_accessibility_ : core::conformation::membrane::ImplicitLipidInfo , protocols::membrane::MPLipidAccessibility
• per_chain_renumbering_ : core::io::StructFileRepOptions
• 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_node_rotamer_sets_ : core::pack::interaction_graph::ResidueArrayAnnealingEvaluator
• per_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_data_ : protocols::analysis::InterfaceAnalyzerMover
• per_residue_ddg_ : protocols::simple_ddg::ddG
• per_residue_real_data_ : core::simple_metrics::SimpleMetricStruct
• per_residue_real_output_ : core::simple_metrics::SimpleMetricStruct
• per_residue_string_data_ : core::simple_metrics::SimpleMetricStruct
• per_residue_string_output_ : core::simple_metrics::SimpleMetricStruct
• percent_hbond_capacity : protocols::hbnet::HBondNetStruct
• perform_ABOXYZ_bin_analysis_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• perform_filters_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_minimizer_run_ : protocols::rna::denovo::movers::RNA_Minimizer
• perform_score_diff_cut_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer
• performs_major_reaction_only_ : protocols::enzymatic_movers::EnzymaticMover
• period_ : core::chemical::Element , core::scoring::methods::BBIndepCartBondedParameters
• periodic_mover_ : protocols::monte_carlo::GenericSimulatedAnnealer
• periodicity_ : core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::dna::TorsionFourierComponent , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::claims::JumpClaim
• permitted_overlap_ : protocols::match::MatcherTask
• permutations_ : protocols::denovo_design::architects::BetaSheetArchitect , protocols::denovo_design::components::StructureDataPerturber
• perres_excls_ : core::scoring::GenBondedExclInfo
• PerResidueRealMetric : core::simple_metrics::MetricKey
• PerResidueStringMetric : core::simple_metrics::MetricKey
• perrsd_dens_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_geometry_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_nbrdens_ : protocols::hybridization::FragmentBiasAssigner
• perrsd_rama_ : protocols::hybridization::FragmentBiasAssigner
• pert_dock_rot_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_dock_trans_mag_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_mc_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_num_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_num_rep_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_shear_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_E_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_H_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_L_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_pep_small_temp_ : protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pert_size_ : protocols::minimization_packing::PertMinMover
• pertinent_property_ : core::chemical::Metapatch
• pertscale_ : protocols::normalmode::NormalModeRelaxMover
• perturb_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::StartStructClaimer
• perturb_amplitude_ : core::import_pose::RNA_HelixAssembler
• perturb_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_chi_ : protocols::cryst::DockLatticeMover
• perturb_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_sequence_ : protocols::loop_modeler::perturbers::LoopHashPerturber
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• perturbation_magnitude_ : core::conformation::parametric::RealValuedParameter , protocols::simple_moves::SetTorsion
• perturbation_set_ : core::conformation::parametric::RealValuedParameter
• perturbation_type_ : core::conformation::parametric::RealValuedParameter , protocols::simple_moves::SetTorsion
• perturbed_ : core::pack::interaction_graph::FASTERNode
• perturbed_angles_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_lengths_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_res_ : protocols::hybridization::BackboneTorsionPerturbation , protocols::hybridization::BackboneTorsionSampler
• perturbed_sequence_ : protocols::kinematic_closure::ClosureProblem
• perturbed_torsions_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureProblem
• perturbed_two_body_energies_ : core::pack::interaction_graph::FASTERNode
• perturber_ : protocols::coupled_moves::CoupledMovesProtocol , protocols::denovo_design::movers::BuildDeNovoBackboneMover , protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover , protocols::simple_moves::CoupledMover
• perturberlist_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• perturbers_ : protocols::denovo_design::components::CompoundPerturber , protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover , protocols::kinematic_closure::perturbers::PerturberSet
• pfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• pfront_poses_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_ranks_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pfront_poses_filter_vals_ : protocols::design_opt::GreedyOptMutationMover , protocols::matdes::MatDesGreedyOptMutationMover
• pg : protocols::pockets::PocketExemplarMultifunc
• pH_ : core::scoring::methods::pHEnergy
• pH_His_ : protocols::hbnet::HBNetStapleInterface
• pH_mode_ : core::pack::palette::PackerPalette
• phase_ : core::scoring::dna::TorsionFourierComponent
• pheight_ : core::scoring::atomic_depth::AtomicDepth
• phenix_home_ : core::scoring::cryst::PhenixInterface
• phi : core::fragment::torsions , protocols::indexed_structure_store::ResidueBackboneEntry , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::minimization_packing::MinimalRotamer , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum
• phi_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::MutableICoorRecord , core::chemical::orbitals::ICoorOrbitalData , core::chemical::SetICoor , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::kinematics::tree::BondedAtom , core::scoring::motif::Xfres , core::scoring::power_diagram::SAnode , core::scoring::SAnode , protocols::backbone_moves::local_backbone_mover::Residue , protocols::denovo_design::components::ResidueDihedrals , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loop_grower::ResTorsions , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pose_length_moves::InsertResMover , protocols::splice::BBDofs
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• phi_bin_width_ : protocols::qsar::scoring_grid::ShapeGrid
• phi_max_ : core::sequence::ABEGO
• phi_min_ : core::sequence::ABEGO
• phi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• phi_psi_bins_above_thold_ : core::scoring::Ramachandran
• phi_sampler_mover_ : protocols::carbohydrates::LinkageConformerMover
• PHIPSI_BINRANGE : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary
• phis : protocols::antibody::clusters::ClusterData
• phithetascore_ : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• phore_dcut_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phore_match_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phores_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• phosphate_move_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• phosphate_move_list_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sample_pose_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• phosphate_sampler_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker , protocols::stepwise::screener::PhosphateScreener
• phosphate_sampler_for_restoration_ : protocols::stepwise::screener::PhosphateScreener
• phosphate_scorefxn_ : protocols::stepwise::modeler::packer::StepWiseMasterPacker
• phosphate_takeoff_donor_distance_cutoff2_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• physical_cut_ : protocols::environment::claims::JumpClaim
• physical_pose_clash_dist_cutoff_ : protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker
• pi_charge_to_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_contribution_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_orbitals_binding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_pi_total_ : protocols::pose_metric_calculators::PiPiCalculator
• pick_again_ : core::pack::annealer::SmartFixbbSimAnnealer
• pick_boundary_ : core::select::util::SelectResiduesByLayer
• pick_core_ : core::select::util::SelectResiduesByLayer
• pick_objfunction_ : protocols::mpi_refinement::Scheduler
• pick_strategy_ : protocols::mpi_refinement::Scheduler
• pick_surface_ : core::select::util::SelectResiduesByLayer
• picking_rounds_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::task_operations::MutationSetDesignOperation , protocols::task_operations::ResidueProbDesignOperation
• piece_ : protocols::grafting::GraftMoverBase
• piece_properties_ : protocols::fold_from_loops::utils::Nub
• pieces_ : protocols::fold_from_loops::utils::Nub
• pig_ : protocols::mean_field::MeanField
• pitch_copying_mode_ : protocols::helical_bundle::parameters::OmegaBundleParameter
• pivot1_ : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• pivot2_ : protocols::backbone_moves::local_backbone_mover::FreePeptide , protocols::backbone_moves::local_backbone_mover::LocalBackboneMover
• pivot_1_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_1_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_2_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_atmname_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_3_rsd_ : protocols::generalized_kinematic_closure::GeneralizedKIC
• pivot_atoms_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• pivot_ids_ : protocols::stepwise::sampler::rna::RNA_KinematicCloser
• pivot_picker_ : protocols::kinematic_closure::BalancedKicMover , protocols::kinematic_closure::KicMover
• pivot_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• pivot_residue_selector_ : protocols::backrub::BackrubMover
• pivot_residues_ : protocols::backrub::BackrubMover , protocols::backrub::BackrubProtocol
• pivot_to_scratch_res_ : protocols::rna::denovo::coarse::CoarseRNA_LoopCloser
• pivot_torsions1_ : protocols::backbone_moves::local_backbone_mover::GapCloser
• pivot_torsions2_ : protocols::backbone_moves::local_backbone_mover::GapCloser
• pivots_ : protocols::kinematic_closure::ClosureProblem
• pivots_residue_selector_ : protocols::backrub::BackrubProtocol
• pjn_job_ind_begin_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::PreliminaryLarvalJobTracker
• pjn_job_ind_end_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::PreliminaryLarvalJobTracker
• pjn_max_nstruct_ : protocols::jd3::standard::PreliminaryLarvalJobTracker
• pjns_requiring_resources_ : protocols::rosetta_scripts::RosettaScriptsJobQueen
• place_peptide : protocols::flexpep_docking::FlexPepDockingFlags
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• placeholder_info_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_residue_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo , core::scoring::MultipoleElecPoseInfo , core::scoring::VdWTinkerPoseInfo
• placeholder_seqs_ : protocols::frag_picker::FragmentScoreFilter
• plain_text : protocols::sparta::GDB
• plane_tolerance_ : protocols::symmetry::DetectSymmetry
• pleating1 : core::scoring::dssp::StrandPairing
• pleating_ : core::scoring::dssp::Pairing
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• plength_ : core::scoring::atomic_depth::AtomicDepth
• pmax_ : core::scoring::atomic_depth::AtomicDepth
• pmin_ : core::scoring::atomic_depth::AtomicDepth
• pml_file_written : protocols::hbnet::HBondNetStruct
• pmut : protocols::ligand_docking::ga_ligand_dock::GADockStageParams
• pmut_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• pnear_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_PNearToArbitraryStateSummary
• pocket_CoM_ : protocols::pockets::NonPlaidFingerprint
• pocketgrid_ : protocols::pockets::PocketConstraint
• pocketGrid_dim_ : protocols::pockets::FingerprintBase
• pocketGrid_mid_ : protocols::pockets::FingerprintBase
• pocketGrid_spacing_ : protocols::pockets::FingerprintBase
• pockets_ : protocols::pockets::PocketGrid
• point : core::scoring::sc::_PROBE
• point_ : protocols::match::VoxelSetIterator
• point_graph : core::conformation::AddEdgeVisitor< Vertex, Edge >
• point_graph_ : core::scoring::Energies
• point_inside_ : protocols::splice::FindEndpointsOperation
• point_radius_ : protocols::electron_density::DockIntoDensityMover
• points_ : core::scoring::func::FourPointsFunc , protocols::pockets::CCluster , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• points_defined_ : protocols::electron_density::DockIntoDensityMover
• 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
• points_to_search_ : protocols::electron_density::DockIntoDensityMover
• poisson_boltzmann_potential_ : core::scoring::methods::PoissonBoltzmannEnergy
• polar_ : core::pack::task::operation::ResidueTypeFilter , protocols::simple_filters::InterfaceSasaFilter , protocols::simple_filters::TotalSasaFilter
• polar_charge_cutoff_ : core::scoring::sasa::SasaCalc
• polar_expansion_radius_ : core::pack::interaction_graph::RotamerDotsRadiusData , protocols::vardist_solaccess::VarSolDistSasaCalculator , protocols::vardist_solaccess::VarSolDRotamerDots
• polar_gap_ : protocols::task_operations::CrystalContactsOperation
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_sasa_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_SASASummary
• polar_sc_atoms_not_satisfied_by_background_ : core::scoring::hbonds::graph::HBondNode
• polar_scale_ : protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• polarity_ : core::scoring::MultipoleParameter
• polarity_avg0 : core::scoring::sc::ElectrostaticComplementarityResults
• polarity_avg1 : core::scoring::sc::ElectrostaticComplementarityResults
• polarity_mag_avg0 : core::scoring::sc::ElectrostaticComplementarityResults
• polarity_mag_avg1 : core::scoring::sc::ElectrostaticComplementarityResults
• polars : protocols::sic_dock::BuriedPolarScore
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• poly_ala_ : protocols::splice::Splice
• polymer_type_ : protocols::make_rot_lib::MakeRotLibOptionsData
• polys_ : protocols::sasa_scores::PPoly
• pool : protocols::ligand_docking::ga_ligand_dock::GADockStageParams
• pool_ : protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD , protocols::canonical_sampling::mc_convergence_checks::PoolData
• pool_cache_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• pool_name_ : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaPool
• pool_names_ : protocols::frag_picker::quota::QuotaConfig
• pool_rms_ : protocols::canonical_sampling::CanonicalSamplingMover
• pool_weights_ : protocols::frag_picker::quota::QuotaConfig
• pop_from_ss_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• population : core::chemical::carbohydrates::LinkageConformerData
• population_based_conformer_sampling_ : protocols::carbohydrates::GlycanSampler
• population_size_ : protocols::evolution::EvolutionaryDynamicsMover
• population_weight_ : protocols::cluster::ClusterBase
• pore_center_x_ : core::conformation::membrane::AqueousPoreParameters
• pore_center_y_ : core::conformation::membrane::AqueousPoreParameters
• pore_major_radius_ : core::conformation::membrane::AqueousPoreParameters
• pore_minor_radius_ : core::conformation::membrane::AqueousPoreParameters
• pore_params_ : core::conformation::membrane::ImplicitLipidInfo
• pore_radius_ : core::select::util::SelectResiduesByLayer
• pore_rotation_angle_ : core::conformation::membrane::AqueousPoreParameters
• pore_transition_steepness_ : core::conformation::membrane::ImplicitLipidInfo
• port : protocols::network::NetworkQueue::ServerAddress
• pos : protocols::electron_density::ScoredPoint , protocols::environment::EnvClaimBroker::BrokeredJumpData
• pos1 : protocols::jumping::DisulfPairing
• pos1_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , protocols::environment::claims::JumpClaim
• pos2 : protocols::jumping::DisulfPairing
• pos2_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator , protocols::environment::claims::JumpClaim
• pos_ : core::fragment::NonContinuousFrame , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::PolymerBondedNeighborConstIterator , core::scoring::PolymerBondedNeighborIterator , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK , protocols::mean_field::AAProb , protocols::mean_field::RotProb
• 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::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
• pos_list_ : protocols::idealize::IdealizeMover
• pos_map_ : core::sequence::AnnotatedSequence
• pos_singular_bound_ : core::kinematics::jacobian::ModuleType1
• pose : core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::ReweightData , core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent , protocols::antibody::CDRDBPose , protocols::canonical_sampling::DbTrajectoryRecorder::Frame , protocols::cartesian::MolecularDynamics , protocols::environment::EnvClaimBroker::BrokerResult , protocols::multistage_rosetta_scripts::PoseForPoseID , protocols::network::NetworkQueue::WorkUnit , protocols::pose_creation::SliceToMiniProteinMover::Chunk , protocols::trajectory::DbTrajectoryWriter::Frame
• pose0_ : protocols::md::MDBase , protocols::mpi_refinement::MPI_Refinement , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc
• pose1_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery , protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose2_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery , protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore , protocols::sic_dock::scores::MotifHashRigidScore
• pose_ : core::fragment::picking_old::vall::eval::EnergyEval , core::import_pose::PoseResource , core::import_pose::RNA_DeNovoSetup , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pack::scmin::SCMinMultifunc , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::ObserverCache , core::scoring::packstat::MultiProbePoseAccumulator , protocols::abinitio::Template , protocols::calc_taskop_filters::RelativePoseFilter , protocols::electron_density::BfactorMultifunc , protocols::electron_density::RefinementResult , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::helical_bundle::FitSimpleHelixMultiFunc , protocols::helical_bundle_predict::HelicalBundlePredictApplication , protocols::hotspot_hashing::HotspotStub , protocols::hotspot_hashing::HotspotStubSet , protocols::jd2::InnerJob , protocols::jd3::chunk_library::ChunkLibraryJobResult , protocols::jd3::chunk_library::MoverAndChunkLibraryJob , protocols::jd3::job_results::PoseJobResult , protocols::jd3::jobs::MoverJob , protocols::kinmatch::FunGroupTK , protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc , protocols::ligand_docking::rdf::RDFBinaryOrbitalFunction , protocols::ligand_docking::rdf::RDFOrbitalFunction , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::multistage_rosetta_scripts::MRSJob , protocols::ncbb::SecStructMinimizeMultiFunc , protocols::normalmode::NormalModeMultifunc , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::residue_optimization::MetapatchEnumeration , protocols::rna::denovo::movers::RNA_DeNovoProtocolMover , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::scores::TrisBpyScore , protocols::simple_moves::AlignChainMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::legacy::screener::SimpleRMSD_Screener , protocols::stepwise::screener::PartitionContactScreener , protocols::stepwise::screener::PoseSelectionScreener , protocols::stepwise::screener::SampleApplier , protocols::stepwise::screener::Scorer , protocols::stepwise::screener::TagDefinition
• pose_aligner_ : protocols::rna::AlignmentEnergy , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::screener::AlignRMSD_Screener
• pose_at_origin_ : protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler
• pose_atom : protocols::constraint_generator::AtomPairConstraintGenerator::MappedAtom
• pose_build_resids_ : protocols::match::Matcher
• pose_by_state_ : core::scoring::methods::PBLifetimeCache
• pose_cache_real_data_ : core::io::StructFileRep
• pose_cache_string_data_ : core::io::StructFileRep
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• pose_copy_ : protocols::dna::PDBOutput
• pose_count_ : protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• pose_cys_pos_ : protocols::splice::SpliceInAntibody , protocols::splice::SpliceOutAntibody
• pose_data_uptodate_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• pose_deviation_tolerance_ : core::scoring::methods::PoissonBoltzmannEnergy
• pose_end_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_energy_ : protocols::cyclic_peptide_predict::HierarchicalHybridJD_JobResultsSummary
• pose_fold_tree_ : protocols::rna::denovo::movers::RNA_HelixMover
• pose_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_free_ : protocols::stepwise::modeler::rna::phosphate::PhosphateMover
• pose_from_res_ : protocols::splice::SpliceManager
• pose_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_id : protocols::multistage_rosetta_scripts::PoseForPoseID
• pose_id_ : protocols::jd3::deallocation::InputPoseDeallocationMessage , protocols::jd3::pose_inputters::PoseInputSource
• pose_idx_ : protocols::electron_density::RBfitResult
• pose_index_ : core::pose::ResidueIndexDescriptionPoseNum
• pose_infos_ : protocols::ligand_docking::ProtLigEnsemble
• pose_init_ : protocols::stepwise::modeler::packer::StepWisePacker
• pose_input_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_input_stream_ : protocols::stepwise::modeler::protein::InputStreamWithResidueInfo
• pose_inputter : protocols::jd3::standard::PreliminaryLarvalJob
• pose_inputter_creator_map_ : protocols::jd3::pose_inputters::PoseInputterFactory
• pose_intensities_ : core::scoring::saxs::SAXSEnergy
• pose_is_proper : core::scoring::electron_density::ElecDensAllAtomCenEnergy , core::scoring::electron_density::ElecDensCenEnergy , core::scoring::electron_density::ElecDensEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• pose_is_set_ : protocols::rna::denovo::movers::RNA_HelixMover
• pose_length_ : protocols::denovo_design::components::StructureData
• pose_list : protocols::stepwise::modeler::rna::sugar::SugarModeling
• pose_list_ : protocols::rna::movers::RNA_DeNovoOptimizer , protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer , protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSelection , protocols::stepwise::legacy::screener::SimplePoseSelection , protocols::stepwise::modeler::align::StepWiseClusterer , protocols::stepwise::modeler::StepWiseConnectionSampler , protocols::stepwise::modeler::StepWiseMinimizer , protocols::stepwise::modeler::StepWiseModeler , protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler , protocols::stepwise::sampler::copy_dofs::ResidueAlternativeSet
• pose_minobj_ : protocols::md::MDBase
• pose_name : core::pose::rna::VDW_RepScreenInfo
• pose_name_ : protocols::fold_from_loops::NubInitioMover , protocols::pose_length_moves::NearNativeLoopCloser
• pose_native_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_output_cache_ : protocols::rosetta_scripts::MultiplePoseMover
• pose_output_list_ : protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer , protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased
• pose_output_specification_for_job_result_id_ : protocols::multistage_rosetta_scripts::MRSJobQueen
• pose_outputter_creator_map_ : protocols::jd3::pose_outputters::PoseOutputterFactory
• pose_outputter_map_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• pose_outputters_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• pose_p_ : protocols::multistate_design::SingleState
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_ptr_ : core::pose::metrics::PoseMetricContainer
• pose_ref_ : protocols::simple_moves::CombinePoseMover
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right_ : protocols::forge::build::ConnectRight
• pose_secstruct_ : core::select::residue_selector::SecondaryStructureSelector , protocols::task_operations::DsspDesignOperation
• pose_segment_dssp_ : protocols::sewing::movers::AppendAssemblyMover
• pose_segment_ends : protocols::sewing::hashing::AlignmentFGMSettings
• pose_segment_ends_ : protocols::legacy_sewing::LegacyAppendAssemblyMover
• pose_segment_ends_string_ : protocols::sewing::movers::AppendAssemblyMover
• pose_segment_starts : protocols::sewing::hashing::AlignmentFGMSettings
• pose_segment_starts_ : protocols::legacy_sewing::LegacyAppendAssemblyMover
• pose_segment_starts_string_ : protocols::sewing::movers::AppendAssemblyMover
• pose_sequence_ : core::scoring::electron_density_atomwise::PoseSequence , protocols::task_operations::ConservativeDesignOperation
• pose_setup_complete_ : core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid
• pose_start_ : protocols::protein_interface_design::filters::ClashWithTargetFilter
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_string_ : protocols::simple_moves::CopyDofMover
• pose_tag_ : protocols::jd3::pose_outputters::ScoreFileOutputSpecification , protocols::jd3::pose_outputters::SilentFilePoseOutputSpecification , protocols::simple_moves::CombinePoseMover
• pose_temps_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• pose_to_local_numbers_ : core::environment::SequenceAnnotation
• pose_to_res_ : protocols::splice::SpliceManager
• pose_to_rinfo_ : core::io::pose_from_sfr::PoseFromSFRBuilder
• pose_with_original_HO2prime_torsion_ : protocols::stepwise::modeler::rna::o2prime::O2PrimePacker
• pose_with_original_phosphates_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• pose_with_original_terminal_phosphates_ : protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler
• poselist : protocols::cluster::GatherPosesMover
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• poseOP : protocols::pose_length_moves::Chain
• poses_ : core::pack::rotamer_set::UnboundRotamersOperation , protocols::abinitio::StructureStore , protocols::docking::membrane::MPDockingSetupMover , protocols::filters::VectorPoseFilter , protocols::hybridization::DomainAssembly , protocols::mean_field::GenMeanFieldMover , protocols::mean_field::MeanField , protocols::moves::VectorPoseMover , protocols::mpi_refinement::StructAvrgMover , protocols::simple_filters::StructuralSimilarityEvaluator , protocols::splice::SampleRotamersFromPDB_RotamerSetOperation
• poses_input_ : protocols::rosetta_scripts::MultiplePoseMover
• poses_output_ : protocols::rosetta_scripts::MultiplePoseMover
• poseselector_creator_map_ : protocols::rosetta_scripts::PoseSelectorFactory
• posesOutputed_ : protocols::pose_length_moves::InsertResMover
• posestart_ : protocols::denovo_design::components::Segment
• posesToOutput_ : protocols::pose_length_moves::InsertResMover
• position : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , core::scoring::lkball::ScoredBridgingWater , protocols::cartesian::CartesianAtom , protocols::dna::PositionType , protocols::hotspot_hashing::VectorPair
• position_ : core::chemical::sdf::MolFileIOAtom , core::chemical::Selector_UPPER_ATOM , core::environment::LocalPosition , core::kinematics::tree::Atom_ , core::pose::rna::RNA_Datum , core::pose::rna::RNA_Reactivity , core::scoring::methods::D2H_SA_Energy , core::scoring::motif::Xfrag , protocols::optimize_weights::PNatAAOptEPositionData , protocols::topology_broker::claims::CutClaim
• position_above_surface_ : protocols::surface_docking::SurfaceDockingProtocol
• position_ddGs_ : protocols::task_operations::RestrictConservedLowDdgOperation
• position_in_motif_ : core::select::residue_selector::ResidueInSequenceMotifSelector
• position_index_ : core::fragment::picking_old::vall::VallResidue
• positions_ : core::select::residue_selector::GlycanPositionSelector , protocols::analysis::LoopAnalyzerMover , protocols::carbohydrates::SimpleGlycosylateMover , protocols::dna::DnaChains , protocols::environment::claims::EnvLabelSelector , protocols::enzdes::EnzdesFlexibleRegion , protocols::loop_grower::LoopPartialSolution , protocols::score_filters::ScoreCutoffFilter , protocols::task_operations::ConservativeDesignOperation
• positions_as_start_of_sequon_ : protocols::carbohydrates::CreateGlycanSequonMover
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• positive_scores_are_better_ : protocols::multistage_rosetta_scripts::MRSJob
• possible_coordinations_ : protocols::sewing::hashing::LigandBindingResPlacer
• possible_hbond_acceptors_ : protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker
• possible_mutants : protocols::simple_filters::SecretionPredictionFilter::tm_region
• possible_working_res_1 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::stepwise::modeler::rna::InternalWorkingResidueParameter
• possibleLoops_ : protocols::pose_length_moves::NearNativeLoopCloser
• post_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_mover_ : protocols::recon_design::MSDMover
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• post_trans_ : protocols::electron_density::RBfitResult
• postfold_movers_ : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• potential_ : core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::loop_graph::evaluator::SixDTransRotPotentialEvaluator , core::scoring::methods::CenHBEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::CenRotEnvEnergy , core::scoring::methods::CenRotPairEnergy , core::scoring::methods::dfire::DFIRE_Potential , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::DNA_DihedralEnergy , core::scoring::methods::DNA_EnvPairEnergy , core::scoring::methods::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::GenericBondedEnergy , core::scoring::methods::HydroxylTorsionEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MembraneEnvEnergy , core::scoring::methods::MembraneEnvPenalties , 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::MultipoleElecEnergy , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::PointWaterEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::RamaPreProEnergy , core::scoring::methods::SASAEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::VdWTinkerEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::PoissonBoltzmannPotential , core::scoring::rna::RNP_LowResEnergy , core::scoring::rna::RNP_LowResPairDistEnergy , core::scoring::rna::RNP_LowResStackEnergy , protocols::protein_interface_design::filters::DisulfideFilter , protocols::protein_interface_design::movers::DisulfideMover
• potential_energy_ : protocols::md::MDBase
• potential_ids_ : core::scoring::PointWaterPotential
• potential_is_loaded_ : core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::dfire::DFIRE_Potential
• potential_vect_ : core::scoring::func::SplineFunc
• potential_vect_size_ : core::scoring::func::SplineFunc
• power_ : core::scoring::func::CircularPowerFunc , core::scoring::PDvertex , core::scoring::power_diagram::PDvertex
• power_mode_ : core::pack::annealer::SequenceSymmetricAnnealer
• ppi_packer_weight_ : protocols::pack_interface::ProteinProteinInterfaceUpweighter
• ppk_only : protocols::flexpep_docking::FlexPepDockingFlags
• pqr : core::scoring::APBSWrapper
• pqr_filename_ : core::scoring::PoissonBoltzmannPotential
• pr_idx_ : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• pre_calc_ : core::scoring::nmr::pre::PRESingle
• pre_chitip_transforms_ : protocols::match::upstream::UpstreamResTypeGeometry
• pre_cyc_pose : protocols::peptide_deriver::CyclizedPeptideInfo
• pre_data_ : protocols::nmr::pre::PREMover
• pre_data_file_ : protocols::nmr::pre::PREMover
• pre_err_ : core::scoring::nmr::pre::PRESingle
• pre_exp_ : core::scoring::nmr::pre::PRESingle
• pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_loaded_data_ : protocols::antibody::task_operations::AddCDRProfileSetsOperation , protocols::antibody::task_operations::AddCDRProfilesOperation
• pre_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody::snugdock::SnugDock
• pre_multiset_vec_ : core::scoring::nmr::pre::PREData
• pre_pre_ligand_atom_id_ : protocols::metal_interface::MetalSiteResidue
• pre_scoring_filter_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_filter_exists_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_mover_ : protocols::helical_bundle::BackboneGridSampler
• pre_scoring_mover_exists_ : protocols::helical_bundle::BackboneGridSampler
• pre_selection_filter_ : protocols::helical_bundle::BundleGridSampler
• pre_selection_filter_exists_ : protocols::helical_bundle::BundleGridSampler
• pre_selection_mover_ : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• pre_selection_mover_exists_ : protocols::generalized_kinematic_closure::GeneralizedKIC , protocols::helical_bundle::BundleGridSampler
• pre_single_vec_ : core::scoring::nmr::pre::PRESingleSet
• pre_single_weights_ : core::scoring::nmr::pre::PREMultiSet
• pre_singleset_vec_ : core::scoring::nmr::pre::PREMultiSet
• pre_talaris2013_geometries : core::init::pre_talaris_2013_behavior_settings
• pre_trans_ : protocols::electron_density::RBfitResult
• pre_type_ : core::scoring::nmr::pre::PRESingle
• pre_values_ : core::scoring::nmr::pre::PREMultiSet
• preallocate_ : core::fragment::picking_old::vall::VallLibrarian
• preapply_ : protocols::monte_carlo::GenericMonteCarloMover
• precalculated_bb_bb_energy_ : core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• precision_ : core::io::silent::SilentStruct , protocols::frag_picker::scores::FragmentScoreManager , protocols::rotamer_recovery::RRReporterHuman
• precompute_ : protocols::task_operations::SetIGTypeOperation
• precompute_ig_ : core::pack::task::PackerTask_
• precomputed_library_mover_ : protocols::stepwise::modeler::StepWiseModeler
• pred_ : core::scoring::ExcludedResPredicate , core::scoring::ResRangePredicate , core::scoring::SelectedResPredicate
• pred_aa_matrix_ : protocols::mean_field::GenMeanFieldMover
• pred_burial_ : core::scoring::methods::BurialEnergy
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_name_ : core::scoring::mhc_epitope_energy::MHCEpitopePredictorExternal
• pred_ss : core::io::external::PsiPredResult
• pred_ss_ : protocols::medal::MedalExchangeMover , protocols::star::Extender , protocols::star::StarAbinitio
• predefined_torsions_ : protocols::loops::loop_closure::kinematic_closure::TorsionRestrictedKinematicPerturber
• predefined_window_start_ : protocols::simple_moves::ClassicFragmentMover
• predicted_burial_ : protocols::simple_filters::PredictedBurialEvaluator
• predicted_H3_base_type_ : protocols::antibody::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• prediction_name_ : protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• predictor_ : core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup
• pref_ref_use_first_few_decoys : protocols::cluster::calibur::Clustering
• pref_use_scud : protocols::cluster::calibur::Clustering
• pref_use_sig : protocols::cluster::calibur::Clustering
• prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• preference_type : core::scoring::carbohydrates::OmegaPreferenceSamplingData
• preferred_alias_ : core::chemical::AddAtomAlias
• preferred_contact_angle : protocols::sewing::hashing::IdealContact
• preferred_dihedral_1 : protocols::sewing::hashing::IdealContact
• preferred_dihedral_2 : protocols::sewing::hashing::IdealContact
• preferred_distance : protocols::sewing::hashing::IdealContact
• preferred_properties_ : core::chemical::ResidueTypeFinder
• preferred_root_res_ : core::import_pose::FullModelPoseBuilder
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• prefix_ : core::select::residue_selector::DensityFitResidueSelector , protocols::analysis::simple_metrics::RunSimpleMetricsMover , protocols::constraint_movers::CstInfoMover , protocols::features::SimpleMetricFeatures , protocols::fold_from_loops::NubInitioMover , protocols::forge::remodel::RemodelMover::instruction_flags , protocols::frag_picker::FragmentPicker , protocols::jd2::JobOutputter , protocols::ligand_docking::InterfaceScoreCalculator , protocols::ligand_docking::WriteLigandMolFile , protocols::loop_modeling::utilities::TrajectoryLogger , protocols::match::output::PDBWriter , protocols::matdes::ExtractSubposeMover , protocols::membrane::benchmark::SampleTiltAngles , protocols::peptide_deriver::PeptideDeriverBasicStreamOutputter , protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter , protocols::simple_moves::DumpSingleResidueRotamers , protocols::simple_moves::WriteFiltersToPose
• prefix_each_output_pdb_ : protocols::recces::options::RECCES_Options
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• prefix_len : core::kinematics::Node
• prefold_movers_ : protocols::denovo_design::movers::BuildDeNovoBackboneMover
• prelim_job_tracker_ : protocols::jd3::standard::StandardJobQueen
• preliminary_job_node_ : protocols::jd3::standard::StandardInnerLarvalJob
• preliminary_job_node_inds_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::PreliminaryLarvalJobTracker
• preliminary_job_nodes_assigned_ : protocols::jd3::standard::PreliminaryLarvalJobTracker
• preliminary_job_nodes_complete_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen
• preliminary_larval_jobs_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• preliminary_larval_jobs_determined_ : protocols::jd3::chunk_library::ChunkLibraryJobQueen , protocols::jd3::full_model::FullModelJobQueen , protocols::jd3::standard::StandardJobQueen
• preloadedPDB : protocols::cluster::calibur::SimPDB
• preloadPDB : protocols::cluster::calibur::SimPDB
• premin_ligand_ : protocols::ligand_docking::ga_ligand_dock::GALigandDock
• preminimize_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• prepack_ : protocols::stepwise::modeler::options::StepWiseProteinModelerOptions
• prepack_full_repack_ : protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• prepack_res_was_inputted_ : protocols::stepwise::modeler::StepWiseModeler
• prepacked_ : protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler
• prepare_for_centroid_ : protocols::loop_modeler::LoopModeler
• prepare_for_fullatom_ : protocols::loop_modeler::LoopModeler
• prepared_for_simA_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G > , core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >
• prepared_for_simulated_annealing_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• preparers_ : protocols::abinitio::abscript::AbscriptStageMover
• preped_for_sim_annealing_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• prepend_ : protocols::denovo_design::movers::ExtendChainMover
• prepend_n_residues_ : protocols::ncbb::oop::OopCreatorMover
• prepend_output_name_ : protocols::canonical_sampling::MetricRecorder
• prepro_file_ : core::chemical::RamaPreproFilename
• prepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• preprocessing_script_version_ : protocols::antibody::GraftOneCDRLoop
• prerelax_ : protocols::energy_based_clustering::EnergyBasedClusteringOptions
• presample_added_residue_ : protocols::stepwise::monte_carlo::mover::AddMover
• presample_by_swa_ : protocols::stepwise::monte_carlo::mover::AddMover
• preserve_atom_coords_ : protocols::simple_moves::MutateResidue
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta_ : core::pack::task::ResidueLevelTask_
• preserve_crystinfo_ : core::io::StructFileRepOptions
• preserve_datacache_ : protocols::symmetry::SetupForSymmetryMover
• preserve_detailed_balance_ : protocols::backrub::BackrubMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::BBGaussianMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header_ : core::io::StructFileRepOptions
• preserve_whole_input_tag_ : protocols::jobdist::BasicJob
• prev_state_hash_ : protocols::pack_daemon::PackDaemon
• PREV_Tab : protocols::sparta::Sparta::SpartaLib
• prevburied : core::scoring::sc::MolecularSurfaceCalculator
• prevent_design_file_read_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• prevent_pruning_ : core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty
• prevent_repacking_ : protocols::calc_taskop_movers::DesignRepackMover , protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::task_operations::RestrictIdentitiesOperation , protocols::task_operations::RestrictNativeResiduesOperation
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous_ : protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_hash_value_ : core::scoring::methods::LinearChainbreakEnergy
• previous_mover_ : protocols::rosetta_scripts::MultiplePoseMover
• previous_sequence_ : protocols::docking::DockingProtocol , protocols::docking::TemperedDocking
• previous_tree_ : protocols::nonlocal::SingleFragmentMover
• previous_vertex1 : protocols::viewer::GraphicsState
• previous_vertex2 : protocols::viewer::GraphicsState
• previous_width_vector : protocols::viewer::GraphicsState
• previous_working_pack_res_ : protocols::stepwise::modeler::packer::StepWisePacker
• previously_completed_jobs_ : protocols::jd3::JobTracker
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• prevp : core::scoring::sc::MolecularSurfaceCalculator
• primary_atom_id_ : core::scoring::constraints::BackboneStubConstraint
• primary_backbone_target_ : core::scoring::constraints::BackboneStubConstraint
• primary_cdrs_ : protocols::antibody::design::AntibodyDesignMover
• primary_output_index : protocols::jd3::JobOutputIndex
• primary_outputter_ : protocols::jd3::output::StandardResultOutputter
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_after_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_C_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_seq_distance_cutoff_for_beta_sheet_capping_before_N_term_capping_ : protocols::features::strand_assembly::SandwichFeatures
• primary_sidechain_target_ : core::scoring::constraints::BackboneStubConstraint
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• print_all_score_headers_ : core::io::silent::SilentFileOptions
• print_out_info_to_pdb_ : protocols::frag_picker::FragmentScoreFilter , protocols::simple_filters::BuriedUnsatHbondFilter
• print_splines_ : protocols::simple_filters::ResidueLipophilicityFilter
• print_statw_interval_ : protocols::wum::MPI_WorkUnitManager
• print_tracer_info_ : protocols::antibody::design::AntibodyDesignMover
• prior_probs_ : core::sequence::ProfSimScoringScheme
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod , protocols::topology_broker::claims::SequenceClaim , protocols::topology_broker::SequenceClaimer
• pro_cd_cprev_n_ca_interres_improper_params_ : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index_ : core::scoring::methods::ResidueCartBondedParameters
• pro_nv_ : core::scoring::methods::CartesianBondedEnergy
• prob : protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer
• prob_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• prob_accum : protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer
• prob_buried_ : core::pack::dunbrack::RotamerLibrary
• prob_buried_semi_ : core::pack::dunbrack::RotamerLibrary
• prob_cutoff_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• PROB_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_larger_current_ : protocols::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_nonburied_ : core::pack::dunbrack::RotamerLibrary
• prob_nonburied_semi_ : core::pack::dunbrack::RotamerLibrary
• prob_profile_ : core::scoring::methods::ProQ_Energy
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_set_ : protocols::antibody::task_operations::AddCDRProfilesOperation , protocols::task_operations::ResidueProbDesignOperation
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_table_ : protocols::docking::ConformerSwitchMover
• prob_terminus_ramapert_ : protocols::mpi_refinement::MPI_Refine_Master
• prob_to_accumulate_buried_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_to_accumulate_nonburied_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_uniform_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_withinrot_ : protocols::simple_moves::sidechain_moves::SidechainMover
• probA_ : core::scoring::packstat::PackingScore
• probabilities : core::scoring::carbohydrates::CHIDihedralSamplingData , core::scoring::carbohydrates::OmegaPreferenceSamplingData
• probabilities_ : core::chemical::mainchain_potential::MainchainScoreTable , core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser , protocols::pose_metric_calculators::RotamerBoltzCalculator
• probability : core::pack::dunbrack::ChiSet
• probability_ : core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::ProbSortClass , protocols::make_rot_lib::RotData , protocols::mean_field::AAProb , protocols::mean_field::RotProb
• probability_matrix_ : core::scoring::bin_transitions::BinTransitionData
• probability_rigid_ : protocols::simple_moves::PeriodicBoxMover
• probB_ : core::scoring::packstat::PackingScore
• probe_atom_type_ : protocols::qsar::scoring_grid::SolvationGrid
• probe_rad_ : protocols::pockets::PocketGrid
• probe_radii : core::scoring::packstat::SasaOptions
• probe_radius_ : core::pack::interaction_graph::RotamerDots , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::scoring::sasa::SasaCalc , core::scoring::sasa::SasaMethod , protocols::simple_filters::BuriedUnsatHbondFilter , protocols::simple_filters::TaskAwareSASAFilter , protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator , protocols::task_operations::SelectBySASAOperation , protocols::vardist_solaccess::VarSolDistSasaCalculator
• probe_radius_apo_ : protocols::simple_filters::BuriedUnsatHbondFilter
• probe_scorefxn_ : core::scoring::rna::data::RNA_DMS_Potential
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• proberadius_ : core::scoring::atomic_depth::AtomicDepth
• probes : core::scoring::sc::MolecularSurfaceCalculator
• problem_ : protocols::kinematic_closure::ClosureProblem::Memento , protocols::kinematic_closure::ClosureSolution
• problem_was_loaded_ : protocols::quantum_annealing::ExternalPackerResultLoader
• probs_ : protocols::frag_picker::LAMBEGO_IO , protocols::frag_picker::TorsionBinIO , protocols::nonlocal::SingleFragmentMover
• proc_id_ : protocols::jobdist::BaseJobDistributor
• process_termination_ : protocols::mpi_refinement::MPI_Refine_Emperor
• 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::DoubleLazyNode , core::pack::interaction_graph::LazyNode
• profile_ : core::fragment::picking_old::vall::VallResidue , core::scoring::mhc_epitope_energy::AlleleMatrix , core::sequence::SequenceProfile , protocols::frag_picker::VallResidue
• profile_config_ : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• profile_picking_rounds_ : protocols::antibody::design::AntibodySeqDesignTFCreator
• profile_save_filename_ : protocols::simple_moves::StructProfileMover
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_sets_task_ : protocols::antibody::task_operations::AddCDRProfilesOperation
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_weight_away_from_interface_ : protocols::splice::Splice , protocols::splice::SpliceManager
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• progress_ : protocols::canonical_sampling::ProgressBarObserver
• progress_file_ : protocols::monte_carlo::GenericMonteCarloMover
• progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
• prohibit_D_at_negative_phi_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• prohibit_L_at_positive_phi_ : protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication
• prohibit_single_residue_loops_ : protocols::loops::LoopFromFileData
• prohibited_properties_i_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_properties_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_res_identities_i_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_res_identities_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• prohibited_types_ : core::chemical::ResidueTypeSetCache
• project_pref_bg_ : protocols::boinc::Boinc
• 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
• proline_corrections_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• proline_N_is_lk_nonpolar : core::scoring::etable::EtableOptions
• proline_N_is_lk_nonpolar_ : core::scoring::etable::Etable
• prop_dir_ : protocols::dna_dock::PropagateClashCheckFilter
• propeller_ : protocols::dna::DNABasepair
• properties_ : core::chemical::Atom , core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::ResidueTypeBase , core::chemical::ResidueTypeFinder , core::chemical::Selector_PROPERTY , core::pack::task::operation::ProhibitResidueProperties , core::pack::task::operation::RestrictToResidueProperties , core::scoring::hbonds::graph::AtomInfo , core::select::residue_selector::ResiduePropertySelector , protocols::ligand_docking::ga_ligand_dock::ConstraintInfo
• properties_i_ : core::scoring::bin_transitions::BinTransitionData
• properties_iplus1_ : core::scoring::bin_transitions::BinTransitionData
• property_ : core::chemical::AddProperty , core::chemical::DeleteProperty , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::PROPERTY
• property_deviation_ranges_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_enum_ : core::chemical::AddProperty
• property_name_ : core::chemical::DeleteProperty
• property_penalties_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_penalty_fracts_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_sets_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_tailfunctions_ : core::scoring::aa_composition_energy::AACompositionEnergySetup
• property_to_string_map_ : core::chemical::AtomPropertiesManager
• proposal_density_ratio_ : protocols::stepwise::monte_carlo::mover::StepWiseMasterMover
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposal_probabilities_ : protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector
• proposed_energy_ : core::pack::interaction_graph::SimpleEdge
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• propred_ : core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix
• props_ : protocols::ligand_docking::ga_ligand_dock::Pharmacophore
• ProQ_potential_ : core::scoring::ScoringManager
• prot_factor_ : core::scoring::methods::HRF_MSLabelingEnergy
• protchimutWidth_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• protein_ : protocols::membrane::MPMutateRelaxMover
• protein_atom : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_charge : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_coords : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_id : protocols::ligand_docking::rdf::AtomPairData
• protein_atom_type : protocols::ligand_docking::rdf::AtomPairData
• protein_atoms_ : core::scoring::rna::RNP_LowResPairDistPotential
• protein_atr_rep_screening_pose_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_CA_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• protein_ccd_closer_ : protocols::stepwise::modeler::StepWiseMinimizer
• protein_ccd_closers_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_ccd_poses_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_connection_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_cutpoints_closed_ : protocols::stepwise::modeler::StepWiseConnectionSampler
• protein_dielectric_ : core::scoring::methods::EnergyMethodOptions
• protein_family_ : protocols::splice::Splice
• protein_family_to_database_ : protocols::splice::Splice , protocols::splice::SpliceOut
• protein_file_name_ : protocols::cluster::calibur::SimPDB
• protein_flexibility_ : protocols::hydrate::Hydrate
• protein_gaussian_variance_per_residue_ : core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator
• protein_interface_design_ : protocols::task_operations::SeqprofConsensusOperation
• protein_mass_ : core::scoring::nmr::pre::PREMultiSet
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_pack_all_ : core::import_pose::options::RNA_MinimizerOptions
• protein_packing_ : core::import_pose::options::RNA_MinimizerOptions
• protein_packing_distance_ : core::import_pose::options::RNA_MinimizerOptions
• protein_positions_ : protocols::motifs::LigandMotifSearch , protocols::motifs::MotifSearch
• protein_prepack_ : protocols::stepwise::monte_carlo::options::StepWiseMonteCarloOptions
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_rots_ : protocols::simple_moves::WaterRotsDB
• protein_sc_pack_cutoff_ : protocols::rna::denovo::movers::RNP_HighResMover
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobInputter , protocols::features::DatabaseJobOutputter
• protein_spins_ : core::scoring::nmr::pcs::PCSSingle , core::scoring::nmr::pre::PRESingle
• proteinchis_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• proteinrestypes_ : protocols::ligand_docking::ga_ligand_dock::LigandConformer
• protocol_ : protocols::features::RotamerRecoveryFeatures , protocols::ligand_docking::ga_ligand_dock::GALigandDock , protocols::ligand_docking::ga_ligand_dock::GAOptimizer , protocols::ligand_docking::LigandDockProtocol , protocols::loop_modeling::LoopProtocol , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::rotamer_recovery::RotamerRecovery
• protocol_features_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_id_ : protocols::features::ProteinSilentReport , protocols::features::ReportToDB
• protocol_name_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_params_ : protocols::rotamer_recovery::RRReporterHuman , protocols::rotamer_recovery::RRReporterSQLite
• protocol_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• protocols_ : protocols::multistage_rosetta_scripts::MRSJob
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_chi_extra_samples_ : core::chemical::MutableChiRecord , core::chemical::ResidueType
• proton_chi_samples_ : core::chemical::MutableChiRecord , core::chemical::ResidueType
• proton_chis_ : core::chemical::ResidueType
• proton_indices_ : core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list_ : protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters
• protons_ : protocols::simple_filters::AtomicContactFilter
• proxnc_ : protocols::constel::FilterByProxTerm
• prune_cavity_burial_probe_radii : core::scoring::packstat::SasaOptions
• prune_max_delta : core::scoring::packstat::SasaOptions
• prune_max_iters : core::scoring::packstat::SasaOptions
• prv_eqxyz_ : protocols::md::MDBase
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pseudo_bonds_ : core::conformation::PseudoBondCollection
• pseudobonds_ : core::conformation::Residue
• pseudocount : protocols::indexed_structure_store::SegmentSequenceProfileConfig
• pseudorotation_ : protocols::dna::DNABase
• psi : core::fragment::torsions , protocols::indexed_structure_store::ResidueBackboneEntry , protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::pockets::spherical_coor_triplet , protocols::pockets::triplet_and_originnum
• psi_ : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::scoring::motif::Xfres , protocols::backbone_moves::local_backbone_mover::Residue , protocols::denovo_design::components::ResidueDihedrals , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loop_grower::ResTorsions , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::membrane::benchmark::MakeCanonicalHelix , protocols::optimize_weights::PNatRotOptEPositionData , protocols::pose_length_moves::InsertResMover , protocols::splice::BBDofs
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover , protocols::simple_moves::triazolamer::TriazolamerMover
• psi_max_ : core::sequence::ABEGO
• psi_min_ : core::sequence::ABEGO
• psi_offsets_ : protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup , protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger
• psi_sampler_mover_ : protocols::carbohydrates::LinkageConformerMover
• psipred2_confidence : core::io::external::PsiPredResult
• psipred_ : protocols::frag_picker::FragmentScoreFilter
• psipred_interface_ : protocols::denovo_design::filters::SSPredictionFilter , protocols::simple_moves::WriteSSEMover
• psipred_output_ : core::io::external::PsiPredInterface
• psipred_prob : core::io::external::PsiPredResult
• psis : protocols::antibody::clusters::ClusterData
• psn : protocols::constel::ResMut
• pssm_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• pssm_data_ : protocols::optimize_weights::IterativeOptEDriver , protocols::protein_interface_design::ReportPSSMDifferences
• pssm_output_order : protocols::indexed_structure_store::movers::SegmentSequenceProfileMover
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• ptask_ : protocols::calc_taskop_movers::ConsensusDesignMover , protocols::enzdes::RepackLigandSiteWithoutLigandMover
• ptask_p_ : protocols::multistate_design::PackingState
• ptr_ : core::scoring::BondOrderParser
• ptran_ : core::scoring::atomic_depth::AtomicDepth
• pts_ : core::scoring::SecondaryStructurePotential , protocols::cluster::APCluster
• pucker_flip_rate_ : protocols::recces::sampler::rna::MC_RNA_Suite
• pucker_state_ : protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler , protocols::stepwise::sampler::rna::RNA_KIC_Sampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_ : protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler , protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler
• pucker_states_lower_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• pucker_states_upper_ : protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler
• put_intra_into_total_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• put_jump_stub_intra_residue : protocols::environment::EnvClaimBroker::BrokeredJumpData
• pwater_ref_wt_ : core::scoring::methods::PointWaterEnergy
• pwater_water_bonus_ : core::scoring::methods::PointWaterEnergy
• pwater_water_bonus_width_ : core::scoring::methods::PointWaterEnergy
• pwidth_ : core::scoring::atomic_depth::AtomicDepth
• pwp_ : core::scoring::ScoringManager
• pymol_ : protocols::moves::PyMOLObserver , protocols::ncbb::NcbbDockDesignProtocol , protocols::ncbb::oop::OopDockDesignProtocol
• pymol_mover_ : protocols::docking::DockingLowRes , protocols::symmetric_docking::SymDockingLowRes
• pymol_movie_ : protocols::carbohydrates::GlycanSampler
• pymol_name_ : protocols::moves::PyMOLMover
• pymol_sel_hbond_unsat : protocols::analysis::InterfaceData
• pymol_sel_interface : protocols::analysis::InterfaceData
• pymol_sel_packing : protocols::analysis::InterfaceData