- p -

• p : protocols::forge::build::CountFromLeft , protocols::sic_dock::Rose
• p_ : core::optimization::Particle
• p_aa_ : core::scoring::methods::P_AA_Energy , core::scoring::methods::P_AA_pp_Energy , core::scoring::ScoringManager
• P_AA_ : core::scoring::P_AA
• P_AA_n_ : core::scoring::P_AA
• P_AA_pp_ : core::scoring::P_AA
• P_AA_pp_energy_splines_ : core::scoring::P_AA
• p_atom_index_ : core::chemical::rna::RNA_ResidueType
• p_CoM : core::scoring::electron_density::ElectronDensity
• p_cond_ : protocols::moves::WhileMover
• p_extent : core::scoring::electron_density::ElectronDensity
• p_grid : core::scoring::electron_density::ElectronDensity
• p_max_ : core::optimization::ParticleSwarmMinimizer
• p_min_ : core::optimization::ParticleSwarmMinimizer
• p_o : core::scoring::electron_density::ElectronDensity
• p_origin : core::scoring::electron_density::ElectronDensity
• p_range_ : core::optimization::ParticleSwarmMinimizer
• p_sumC : core::scoring::electron_density::ElectronDensity
• p_sumC2 : core::scoring::electron_density::ElectronDensity
• p_sumCO : core::scoring::electron_density::ElectronDensity
• p_sumO : core::scoring::electron_density::ElectronDensity
• p_sumO2 : core::scoring::electron_density::ElectronDensity
• p_vol : core::scoring::electron_density::ElectronDensity
• pack_at_neighbors_only_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• pack_cst_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler
• pack_full_repack_ : protocols::relax::ClassicRelax
• pack_input_ : protocols::analysis::InterfaceAnalyzerMover
• pack_interface_repack_ : protocols::symmetric_docking::SymDockingHiRes
• pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
• pack_operations_ : protocols::docking::DockingEnsemble , protocols::docking::DockingEnsemblePrepackProtocol , protocols::docking::DockingPrepackProtocol
• pack_region_ala_pose_ : protocols::enzdes::EnzdesFlexBBProtocol
• pack_residue_ : core::pack::task::PackerTask_
• pack_rottrial_ : protocols::relax::ClassicRelax , protocols::symmetric_docking::SymDockingHiRes
• pack_scorefxn_ : protocols::ub_e2c::ubi_e2c_modeler , protocols::antibody2::AntibodyModelerProtocol , protocols::antibody2::LHRepulsiveRamp , protocols::antibody2::LHRepulsiveRampLegacy , protocols::antibody2::RefineBetaBarrel
• pack_scrfxn_ : protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover
• pack_separated_ : protocols::analysis::InterfaceAnalyzerMover
• pack_task_ : protocols::swa::protein::StepWiseProteinPacker , protocols::swa::protein::StepWiseProteinResidueSampler
• packable_ : protocols::protein_interface_design::filters::DesignableResiduesFilter
• packed_residues_ : protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• packed_rotno_ : core::pack::dunbrack::PackedDunbrackRotamer< S, P > , core::pack::dunbrack::BBDepNRChiSample< P >
• packed_rotno_2_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_rotwell_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• packed_rotno_conversion_data_current_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
• packer_ : protocols::antibody::GraftMover
• packer_neighbor_graph_ : core::optimization::SingleResidueMultifunc
• packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• packing_angle_residues_ : protocols::antibody2::AntibodyInfo
• packing_isolated_to_active_loops_ : protocols::loops::loop_mover::refine::LoopMover_Refine_CCD
• packing_shell_ : protocols::simple_filters::RelativePoseFilter
• packonly_after_graft_ : protocols::antibody2::GraftCDRLoopsProtocol
• packstat_pdb_ : protocols::analysis::PackStatMover
• packtask_ : protocols::seeded_abinitio::SeedSetupMover
• pages_ : core::fragment::picking_old::concepts::Book< Pages >
• pair_ : core::scoring::SmoothEnvPairPotential
• pair_and_func_map_ : core::scoring::custom_pair_distance::FullatomCustomPairDistanceEnergy
• pair_corr_ : core::scoring::PairEPotential
• pair_dis_ : protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD
• pair_list_ : protocols::scoring::Interface
• pair_log_ : core::scoring::EnvPairPotential
• 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_vector_ : protocols::toolbox::task_operations::RestrictInterGroupVectorOperation
• pairE_potential_ : core::scoring::ScoringManager
• paired_ : protocols::dna::DnaPosition
• pairing1 : core::scoring::dssp::StrandPairing
• pairing2 : core::scoring::dssp::StrandPairing
• pairing_dists_ : protocols::coarse_rna::CoarseRNA_DeNovoProtocol
• pairings_ : core::scoring::dssp::StrandPairingSet , protocols::abinitio::AlternativePairings , protocols::abinitio::Templates , protocols::jumping::DisulfPairingLibrary , protocols::jumping::MembraneJump , protocols::jumping::PairingLibrary , protocols::jumping::SheetBuilder , protocols::topology_broker::TemplateJumpClaimer
• pairings_file_ : protocols::hybridization::FoldTreeHybridize , protocols::hybridization::HybridizeProtocol
• pairings_size_ : protocols::jumping::MembraneJump
• pairs_ : core::sequence::PairScoringScheme
• PARALLEL : core::scoring::dssp::Pairing
• parallel_ : protocols::design_opt::GreedyOptMutationMover , protocols::design_opt::ParetoOptMutationMover , protocols::design_opt::PointMutationCalculator
• parallel_weight_ : core::scoring::SecondaryStructureWeights
• param1 : protocols::relax::RelaxScriptCommand
• param2 : protocols::relax::RelaxScriptCommand
• param3 : protocols::relax::RelaxScriptCommand
• param4 : 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_TE : core::scoring::GenBornPotential
• Param_TF : core::scoring::GenBornPotential
• Param_TG : core::scoring::GenBornPotential
• Param_TH : core::scoring::GenBornPotential
• Param_THH : core::scoring::GenBornPotential
• ParamB : core::scoring::GenBornPotential
• ParamD : core::scoring::GenBornPotential
• ParamG : core::scoring::GenBornPotential
• ParamS : core::scoring::GenBornPotential
• params_ : core::scoring::packing::HolesEnergyRes , core::scoring::packing::HolesParamsRes
• params_database_tag_ : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• params_file : protocols::flexpep_docking::FlexPepDockingFlags
• parent : core::graph::DS_Node , core::kinematics::Node
• parent_ : core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• parent_atom_ : core::chemical::AddConnect
• parent_entities_ : protocols::genetic_algorithm::GeneticAlgorithm
• parent_id_ : core::optimization::DOF_DataPoint
• parent_node_ : protocols::toolbox::match_enzdes_util::InvrotTreeNodeBase
• parent_remarks_map_ : core::io::silent::SilentStruct
• parent_tags_map_ : protocols::swa::rna::StepWiseRNA_Clusterer
• parents_ : core::chemical::ResidueType
• parin_favorite_output_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer , protocols::swa::rna::StepWiseRNA_ResidueSampler , protocols::swa::StepWisePoseSetup
• parsed_string_for_resfile : protocols::forge::remodel::RemodelData
• parser_ : protocols::jd2::JobDistributor
• 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
• partition_ : protocols::hotspot_hashing::PartitionedSearchPattern
• partition_definition_ : protocols::coarse_rna::CoarseRNA_LoopCloser , protocols::swa::rna::StepWiseRNA_JobParameters , protocols::swa::StepWiseJobParameters
• 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::MultipleDomainMover , protocols::scoring::Interface
• partner_ids_ : protocols::noesy_assign::FloatingResonance
• partners_ : protocols::dna::DNAParameters , protocols::docking::DockingHighRes , protocols::docking::DockingProtocol , protocols::docking::DockSetupMover , protocols::docking::TemperedDocking , protocols::protein_interface_design::filters::HbondsToResidueFilter
• pass_base_centroid_screen : protocols::swa::rna::SillyCountStruct
• pass_screen_struct_pair_ : protocols::swa::rna::StepWiseRNA_CombineLongLoopFilterer
• 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
• patch_scores_ : protocols::toolbox::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
• path : protocols::hybridization::TMalign
• path_ : core::chemical::NCAARotLibPath , protocols::jd2::FileSystemJobDistributor , protocols::jd2::PDBJobOutputter , protocols::motifs::Motif , protocols::rna::RNA_IdealCoord
• path_dist_ : core::scoring::AtomNeighbor
• path_dist_cutoff_ : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distance_ : core::chemical::ResidueType
• path_distances_to_connection_points_ : core::scoring::etable::etrie::GenericResidueConnectionData
• path_dists_ : core::scoring::etable::count_pair::CountPairIntraRes< CrossoverBehavior > , core::scoring::etable::count_pair::CountPairIntraResC3 , core::scoring::etable::count_pair::CountPairIntraResC4
• path_to_torsion_files_ : core::scoring::rna::RNA_TorsionPotential
• pAtoms : core::scoring::sc::_PROBE
• pattern_ : protocols::hotspot_hashing::AddSearchPatternRotSetOp
• PattersonB : core::scoring::electron_density::ElectronDensity
• PattersonEpsilon : core::scoring::electron_density::ElectronDensity
• PattersonMaxR : core::scoring::electron_density::ElectronDensity
• PattersonMinR : core::scoring::electron_density::ElectronDensity
• pb_bound_tag_ : core::scoring::methods::EnergyMethodOptions
• pb_by_state_ : core::scoring::methods::PBLifetimeCache
• pb_cached_data_ : protocols::simple_moves::ddG
• pb_enabled_ : protocols::simple_filters::DdgFilter , protocols::simple_moves::ddG
• pb_lengths_ : core::scoring::etable::count_pair::CountPairGeneric
• PB_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::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• pca_ : protocols::abinitio::PcaEvaluator , protocols::abinitio::AbrelaxApplication
• Pcalc : core::scoring::electron_density::ElectronDensity
• pcc_structure : core::scoring::electron_density::PattersonCorrEnergy
• pcs_d_ : protocols::scoring::methods::pcs::TensorsOptimizer
• pcs_d_c_ : protocols::scoring::methods::pcs2::TensorsOptimizer , protocols::scoring::methods::pcs2::TensorsOptimizerFix , protocols::scoring::methods::pcs2::TensorsOptimizerSvd
• PCS_data_all_ : protocols::scoring::methods::pcs2::PcsDataCenterManager , protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton
• PCS_data_line_all_ : protocols::scoring::methods::pcs::PCS_file_data
• PCS_data_line_all_spin_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• PCS_data_per_lanthanides_all_ : protocols::scoring::methods::pcs::PCS_data , protocols::scoring::methods::pcs2::PcsDataCenter
• pcs_e_p_all_ : protocols::scoring::methods::pcs2::PcsEnergyParameterManager
• PCS_experimental_ : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs2::PcsInputLine
• PCS_filename_and_data_ : protocols::scoring::methods::pcs::PCS_data_input
• PCS_tolerance_ : protocols::scoring::methods::pcs::PCS_line_data , protocols::scoring::methods::pcs2::PcsInputLine
• pcs_weight_ : protocols::scoring::methods::pcs::PCS_Energy_parameters_manager , protocols::scoring::methods::pcs2::PcsEnergyParameter
• pcs_weight_stage1_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage2_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage3_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• pcs_weight_stage4_ : protocols::scoring::methods::pcs2::PcsGridSearchParameter , protocols::topology_broker::PseudocontactShiftEnergyController
• 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
• pdb2pose_ : core::pose::PDBInfo , core::pose::PDBPoseMap
• pdb_codes_ : core::io::sequence_comparation::DesignContrast
• pdb_contains_target_ : protocols::seeded_abinitio::SeedFoldTree
• pdb_data_features_ : protocols::features::ProteinSilentReport
• PDB_DIR : protocols::sparta::Sparta::SpartaLib
• pdb_file_names_ : core::io::sequence_comparation::DesignContrast , protocols::pmut_scan::PointMutScanDriver
• pdb_filenames_ : protocols::docking::DockingEnsemble
• pdb_hash_ : protocols::frag_picker::PdbIdChunkFilter
• pdb_id : protocols::loophash::BBExtraData
• pdb_info_ : core::pose::Pose
• pdb_lines_ : core::import_pose::PDBSilentStruct
• pdb_name_ : protocols::pack_daemon::StructureFileNames
• pdb_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pdb_numbered_h3_loop_end : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_numbered_h3_loop_start : protocols::toolbox::task_operations::RestrictToCDRH3Loop
• pdb_pose_map_ : protocols::pack_daemon::EntityCorrespondence
• PDB_Records_ : core::io::pdb::Field
• pdb_resnum_ : protocols::pmut_scan::MutationData
• pdb_segments_ : protocols::protein_interface_design::movers::Splice
• pdb_source_ : protocols::features::helixAssembly::HelicalFragment , protocols::features::strand_assembly::StrandFragment
• pdb_start : protocols::forge::remodel::RemodelData
• pdb_stop : protocols::forge::remodel::RemodelData
• pdb_to_profile_map_ : protocols::protein_interface_design::movers::SpliceSegment
• PDBfileName : protocols::sparta::PDB
• pdbid_ : core::fragment::AnnotatedFragData
• pdbListName : protocols::sparta::Sparta::SpartaLib
• pdbname_ : protocols::dna::DnaInterfacePacker
• pdbno_ : protocols::pockets::PocketGrid
• pdboutput_ : protocols::dna::DnaInterfacePacker , protocols::motifs::MotifDnaPacker
• pdbpos : protocols::dna::DnaDesignDef
• pdbs_this_round_ : protocols::optimize_weights::IterativeOptEDriver
• pdf_ : protocols::nonlocal::BiasedFragmentMover
• pdie : core::scoring::APBSConfig::R_PARAM
• pdime : core::scoring::APBSConfig
• PDL : protocols::swa::rna::FloatingBaseChainClosureJobParameter
• peak_id_ : protocols::noesy_assign::CrossPeak
• peak_violation_counts_ : protocols::noesy_assign::DistanceScoreMover
• peaks_ : protocols::noesy_assign::CrossPeakList , protocols::noesy_assign::PeakCalibrator
• PENALTY : protocols::frag_picker::scores::ProlinePhiScore , protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::SequenceIdentity
• penalty_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• penalty_factor_ : protocols::simple_filters::ResidueIEFilter
• pending_notifications_ : protocols::jd2::archive::MPIArchiveJobDistributor
• pep_fold_only : protocols::flexpep_docking::FlexPepDockingFlags
• pep_refine : protocols::flexpep_docking::FlexPepDockingFlags
• PEPTIDE : core::kinematics::Edge
• peptide_anchors : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_chain_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_cuts : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_first_res_ : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_loop_model : protocols::flexpep_docking::FlexPepDockingFlags
• peptide_nres_ : protocols::flexpep_docking::FlexPepDockingFlags
• per_constraint_build_points_ : protocols::match::Matcher
• per_cst_build_resids_ : protocols::match::Matcher
• per_cst_pose_build_resids_ : protocols::match::MatcherTask
• per_native_recovery_ : protocols::rotamer_recovery::RRReporterHuman
• per_res_atom_ind_ : protocols::match::output::UpstreamDownstreamCollisionFilter
• per_residue_ddg_ : protocols::simple_moves::ddG
• per_residue_energy_ : protocols::analysis::InterfaceAnalyzerMover
• perform_electron_density_screen_ : protocols::swa::rna::StepWiseRNA_Minimizer
• perform_filters_ : protocols::swa::rna::StepWiseRNA_Clusterer
• perform_minimize_ : protocols::swa::rna::StepWiseRNA_Minimizer
• perform_minimizer_run_ : protocols::rna::RNA_Minimizer
• perform_o2star_pack_ : protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• perform_score_diff_cut_ : protocols::swa::rna::StepWiseRNA_Clusterer
• perform_VDW_rep_screen_ : protocols::swa::rna::StepWiseRNA_Clusterer
• period_ : core::scoring::methods::BBIndepCartBondedParameters
• periodicity_ : core::scoring::constraints::PeriodicBoundFunc , core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::dna::TorsionFourierComponent , protocols::match::downstream::AtomDihedralSecMatchRPE , protocols::toolbox::match_enzdes_util::GeomSampleInfo
• permanent_ : protocols::topology_broker::JumpClaim
• permitted_overlap_ : protocols::match::MatcherTask
• perturb_ : protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::topology_broker::CoordConstraintClaimer , protocols::topology_broker::StartStructClaimer
• perturb_amplitude_ : protocols::rna::RNA_HelixAssembler
• perturb_CCD_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_cycles_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_KIC_off_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_show_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_start_structures_ : protocols::abinitio::IterativeFullatom
• perturb_temp_ : protocols::anchored_design::AnchoredPerturbMover
• perturb_torsion_ : protocols::swa::protein::StepWiseProteinLoopBridger
• perturb_torsion_ids_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• perturbed_ : core::pack::interaction_graph::FASTERNode
• perturbed_two_body_energies_ : core::pack::interaction_graph::FASTERNode
• perturber_ : protocols::docking::DockingProtocol , protocols::loops::loop_closure::kinematic_closure::KinematicMover
• pfp_ : protocols::pockets::DarcParticleSwarmMinimizer , protocols::pockets::FingerprintMultifunc
• pfront_poses_ : protocols::design_opt::GreedyOptMutationMover
• pfront_poses_filter_ranks_ : protocols::design_opt::GreedyOptMutationMover
• pfront_poses_filter_vals_ : protocols::design_opt::GreedyOptMutationMover
• pH_ : core::scoring::methods::pHEnergy
• phase_ : core::scoring::dna::TorsionFourierComponent
• phi : protocols::jumping::DisulfTemplate , protocols::jumping::PairingTemplate , protocols::pockets::spherical_coor_triplet , protocols::simple_moves::MinimalRotamer
• phi_ : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::chemical::AddConnect , core::chemical::SetICoor , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::kinematics::tree::BondedAtom , protocols::fldsgn::topology::DimerPairing , protocols::frag_picker::DiversifyDihedralsSelector , protocols::frag_picker::VallResidue , protocols::frags::RMSVallData , protocols::frags::VallData , protocols::loophash::BackboneSegment , protocols::MakeRotLib::RotData , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::optimize_weights::PNatRotOptEPositionData , protocols::protein_interface_design::movers::BBDofs , protocols::swa::MainChainTorsionSet , protocols::swa::protein::MainChainTorsionSet
• phi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• phi_max_ : core::util::ABEGO
• phi_mean_ : core::pack::dunbrack::CoarseRotamer
• phi_min_ : core::util::ABEGO
• phi_offsets_ : protocols::swa::protein::StepWiseProteinLoopBridger , protocols::swa::StepWisePoseSetup
• phi_sdev_ : core::pack::dunbrack::CoarseRotamer
• PHIPSI_BINRANGE : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
• phithetascore_ : protocols::fldsgn::potentials::sspot::HSPairPotential , protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential , protocols::fldsgn::potentials::sspot::SSPairPotential
• physical_pose_clash_dist_cutoff_ : protocols::swa::rna::StepWiseRNA_VDW_Bin_Screener
• pi_pi_total_ : protocols::toolbox::pose_metric_calculators::PiPiCalculator
• pick_boundary_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pick_core_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pick_surface_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• piece_ : protocols::grafting::GraftMoverBase
• pipemap_ : protocols::wum2::WorkUnit_ElScripts
• pivot_atoms_ : protocols::backrub::BackrubMover
• pivot_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• pivot_residues_ : protocols::backrub::BackrubMover
• pivot_to_scratch_res_ : protocols::coarse_rna::CoarseRNA_LoopCloser
• place_scaffold_ : protocols::protein_interface_design::movers::PlaceStubMover
• placed_stubs_ : protocols::protein_interface_design::movers::PlaceStubMover
• placeholder_info_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• plain_text : protocols::sparta::GDB
• plane_tolerance_ : protocols::simple_moves::symmetry::DetectSymmetry
• pleat_weird : core::scoring::dssp::StrandPairing
• pleating1 : core::scoring::dssp::StrandPairing
• pleating_ : core::scoring::dssp::Pairing
• pleats1_ : protocols::fldsgn::topology::StrandPairing
• pleats2_ : protocols::fldsgn::topology::StrandPairing
• po_bar : core::scoring::electron_density::ElectronDensity
• pocketgrid_ : protocols::pockets::PocketConstraint
• 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
• points_ : core::scoring::constraints::FourPointsFunc , protocols::pockets::PCluster , protocols::scoring::ImplicitFastClashCheck , protocols::sic_dock::CBScore
• points_for_nonchitip_atoms_ : protocols::match::upstream::UpstreamResTypeGeometry
• points_in_D3_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• points_in_global_orintation_frame_ : protocols::toolbox::match_enzdes_util::LigandConformer
• poisson_boltzmann_potential_ : core::scoring::methods::PoissonBoltzmannEnergy
• polar_ : core::pack::task::operation::ResidueTypeFilter , protocols::simple_filters::InterfaceSasaFilter
• polar_expansion_radius_ : core::pack::interaction_graph::RotamerDots
• polar_max : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_min : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polar_rotation_sampling : protocols::hotspot_hashing::SphericalRotationSearchPattern
• polarF2BR_ : core::scoring::FACTSResidueInfo
• polarF2d_ : core::scoring::FACTSResidueInfo
• polars : protocols::sic_dock::BuriedPolarScore
• policy_ : protocols::nonlocal::BiasedFragmentMover , protocols::nonlocal::SingleFragmentMover
• poly_A_seq_ : protocols::frag_picker::VallProvider
• poly_ala_ : protocols::protein_interface_design::movers::Splice
• polys_ : protocols::sasa_scores::PPoly
• pool_ : protocols::canonical_sampling::mc_convergence_checks::PoolData , protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
• pool_cache_ : protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel
• pool_defs_ : protocols::frag_picker::quota::ABEGO_SS_Config
• pool_master_node_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• pool_name_ : protocols::frag_picker::FragmentCandidate , protocols::frag_picker::quota::QuotaPool
• pool_names_ : protocols::frag_picker::quota::QuotaConfig
• pool_npes_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD
• pool_rank_ : protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD
• pool_rms_ : protocols::canonical_sampling::CanonicalSamplingMover , protocols::moves::CanonicalSamplingMover
• pool_size_ : protocols::canonical_sampling::mc_convergence_checks::MPIBPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD , protocols::canonical_sampling::mc_convergence_checks::MPIPool_RMSD
• pool_weights_ : protocols::frag_picker::quota::QuotaConfig
• pop_from_ss_ : protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover , protocols::dna::DnaInterfaceMultiStateDesign
• pop_size_ : protocols::dna::DnaInterfaceMultiStateDesign , protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover
• population_weight_ : protocols::cluster::ClusterBase
• pore_radius_ : protocols::toolbox::SelectResiduesByLayer , protocols::toolbox::task_operations::LayerOperations
• pos1 : protocols::jumping::DisulfPairing , protocols::rna::RNA_Pairing
• pos1_ : core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , protocols::topology_broker::JumpClaim , protocols::topology_broker::CutClaim , protocols::topology_broker::RootClaim
• pos2 : protocols::jumping::DisulfPairing , protocols::rna::RNA_Pairing
• pos2_ : core::scoring::dssp::Pairing , core::scoring::DenseNeighborIterator , core::scoring::DenseNeighborConstIterator , core::scoring::OneToAllNeighborIterator , core::scoring::OneToAllNeighborConstIterator , protocols::topology_broker::JumpClaim
• pos_ : protocols::topology_broker::BBClaim , core::fragment::NonContinuousFrame , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::PeptideBondedNeighborIterator , core::scoring::PeptideBondedNeighborConstIterator , protocols::forge::build::GrowLeft , protocols::forge::build::GrowRight , protocols::kinmatch::FunGroupTK , protocols::topology_broker::SequenceClaim
• pos_in_bg_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_bg_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_edge_vector_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_fc_nodes_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G >
• pos_in_nodes_edge_list_ : core::graph::Edge , core::pack::interaction_graph::EdgeBase
• pos_in_nodes_edge_vector_ : core::pack::interaction_graph::EdgeBase
• pos_in_owners_edge_list_ : core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase , core::graph::Edge
• pos_list_ : protocols::idealize::IdealizeMover , protocols::simple_moves::BackboneMover
• pos_map_ : core::sequence::AnnotatedSequence
• pose : core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent , protocols::cartesian::MolecularDynamics
• pose1_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore
• pose2_ : protocols::hybridization::DomainAssembly , protocols::sic_dock::LinkerScore
• pose_ : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , core::optimization::symmetry::SymMinimizerMap , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::OnTheFlyInteractionGraph , core::pack::interaction_graph::SimpleInteractionGraph , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SymmOnTheFlyInteractionGraph , core::pack::scmin::CartSCMinMultifunc , core::pose::datacache::CacheablePoseRawPtr , core::pose::datacache::ObserverCache , core::scoring::packstat::MultiProbePoseAccumulator , protocols::flexpack::interaction_graph::OTFFlexbbEdge , protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph , protocols::hotspot_hashing::HotspotStub , protocols::jd2::InnerJob , protocols::kinmatch::FunGroupTK , protocols::LoopRebuild , protocols::match::output::PoseInserter , protocols::pack_daemon::EntityCorrespondence , protocols::pack_daemon::PackDaemon , protocols::pack_daemon::QuickRepacker , protocols::pockets::PlaidFingerprint , protocols::scoring::ImplicitFastClashCheck , protocols::simple_filters::RelativePoseFilter , protocols::swa::rna::StepWiseRNA_RotamerGenerator_Wrapper , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::abinitio::Template , protocols::pack_daemon::BasicSimAnnealerRepacker , protocols::hotspot_hashing::HotspotStubSet , core::pack::scmin::SCMinMultifunc , core::optimization::symmetry::SymAtomTreeMultifunc
• pose_build_resids_ : protocols::match::Matcher
• pose_by_state_ : core::scoring::methods::PBLifetimeCache
• pose_chemical_checksum_ : core::scoring::constraints::NamedAtomPairConstraint
• pose_comments_features_ : protocols::features::ProteinSilentReport
• pose_conformation_features_ : protocols::features::ProteinSilentReport
• pose_copy_ : protocols::dna::PDBOutput
• pose_count_ : protocols::swa::protein::StepWiseProteinCCD_Closer , protocols::swa::protein::StepWiseProteinLoopBridger
• pose_data_list_ : protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler , protocols::swa::rna::StepWiseRNA_Minimizer , protocols::swa::rna::StepWiseRNA_ResidueSampler
• pose_data_uptodate_ : protocols::toolbox::match_enzdes_util::EnzCstTemplateResCache
• pose_filter_ : protocols::swa::protein::StepWiseProteinPacker
• pose_frag_moves_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_has_resolved_loop_indices_ : protocols::loops::GuardedLoopsFromFile
• pose_index_ : protocols::loops::ResidueIndexDescription
• pose_init_ : protocols::swa::protein::StepWiseProteinPacker
• pose_input_stream_ : protocols::swa::InputStreamWithResidueInfo
• 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::FastDensEnergy , core::scoring::electron_density::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• pose_list_ : protocols::swa::protein::StepWiseProteinPoseMinimizer
• pose_name : protocols::swa::rna::VDW_RepScreeninfo
• pose_numb_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• pose_numbered_ : protocols::loops::ResidueIndexDescription
• pose_OP : protocols::swa::rna::pose_data_struct2 , protocols::swa::rna::FB_Pose_Data
• pose_output_list_ : protocols::swa::rna::StepWiseRNA_Clusterer , protocols::swa::StepWiseClusterer
• pose_p_ : protocols::multistate_design::SingleState
• pose_pddf_ : protocols::scoring::methods::saxs::PDDFEnergy
• pose_prepack_ : protocols::swa::protein::StepWiseProteinResidueSampler
• pose_ptr_ : core::pose::metrics::PoseMetricContainer
• pose_relax_ : protocols::forge::remodel::RemodelMover::instruction_flags
• pose_resnum_ : protocols::pmut_scan::MutationData
• pose_right_ : protocols::forge::build::ConnectRight
• pose_store_ : protocols::forge::remodel::RemodelAccumulator
• pose_to_native_map_ : protocols::swa::rna::StepWiseRNA_Minimizer
• poselist : protocols::cluster::GatherPosesMover
• posename_ : protocols::analysis::InterfaceAnalyzerMover
• posename_base_ : protocols::analysis::InterfaceAnalyzerMover
• poses_ : protocols::abinitio::StructureStore , core::pack::rotamer_set::UnboundRotamersOperation , protocols::hybridization::DomainAssembly , protocols::simple_filters::StructuralSimilarityEvaluator
• position : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent , protocols::cartesian::CartesianAtom , protocols::dna::PositionType , protocols::hotspot_hashing::VectorPair
• position_ : protocols::optimize_weights::PNatAAOptEPositionData , core::scoring::rna::RNA_Datum , core::kinematics::tree::Atom_
• position_ddGs_ : protocols::toolbox::task_operations::RestrictConservedLowDdgOperation
• position_index_ : protocols::frag_picker::VallResidue , core::fragment::picking_old::vall::VallResidue
• positions_ : protocols::enzdes::EnzdesFlexibleRegion , protocols::analysis::LoopAnalyzerMover , protocols::dna::DnaChains , protocols::simple_filters::ScoreCutoffFilter
• positions_to_replace_ : protocols::enzdes::PredesignPerturbMover
• positive_filters_ : protocols::protein_interface_design::filters::BoltzmannFilter
• positive_scores_ : protocols::jd2::archive::NormalizedEvaluatedArchive
• possible_pairing_sets_ : protocols::rna::RNA_StructureParameters
• possible_working_res_1 : protocols::swa::rna::InternalWorkingResidueParameter
• possible_working_res_2 : protocols::swa::rna::InternalWorkingResidueParameter
• post_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• post_placement_sdev_ : protocols::protein_interface_design::movers::PlaceStubMover
• potential_ : core::scoring::methods::dfire::DFIRE_Potential , core::scoring::methods::DNA_BaseEnergy , core::scoring::methods::CenHBEnergy , core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::methods::MembraneEnvPenalties , core::scoring::methods::MembraneEnvEnergy , core::scoring::dna::DNAChiEnergy , core::scoring::methods::CenPairEnergy , core::scoring::methods::DirectReadoutEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::MembraneCenPairEnergy , core::scoring::methods::MMBondAngleEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::MMTorsionEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::WaterAdductHBondEnergy , protocols::scoring::methods::InterchainEnvEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::methods::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::MembraneCbetaEnergy , core::scoring::methods::MembraneLipo , core::scoring::methods::OmegaTetherEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::MMLJEnergyIntra , core::scoring::PoissonBoltzmannPotential , protocols::protein_interface_design::filters::DisulfideFilter , protocols::scoring::methods::InterchainPairEnergy , core::scoring::methods::MMBondLengthEnergy , core::scoring::methods::SmoothEnvEnergy , protocols::protein_interface_design::movers::DisulfideMover , core::scoring::methods::RamachandranEnergy
• potential_is_loaded_ : core::scoring::methods::dfire::DFIRE_Energy , core::scoring::methods::dfire::DFIRE_Potential
• potential_starting_positions_ : protocols::ligand_docking::StartFrom
• potential_vect_ : core::scoring::constraints::SplineFunc
• potential_vect_size_ : core::scoring::constraints::SplineFunc
• power_ : core::scoring::constraints::CircularPowerFunc
• 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_loop_closure_protocol_ : protocols::abinitio::AbrelaxMover
• pre_minimization_ : protocols::antibody2::SnugDock
• preallocate_ : core::fragment::picking_old::vall::VallLibrarian
• preapply_ : protocols::simple_moves::GenericMonteCarloMover
• precision_ : protocols::frag_picker::scores::FragmentScoreManager , core::io::silent::SilentStruct , protocols::rotamer_recovery::RRReporterHuman
• pred_ : core::scoring::ResRangePredicate , core::scoring::SelectedResPredicate , core::scoring::ExcludedResPredicate
• pred_burial_ : core::scoring::methods::BurialEnergy
• PRED_DIR : protocols::sparta::Sparta::SpartaLib
• pred_ss_ : protocols::star::Extender , protocols::medal::MedalExchangeMover , 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::antibody2::AntibodyInfo
• predicted_sa_norm_ : protocols::frag_picker::scores::SolventAccessibility
• prediction_ : protocols::frag_picker::quota::TorsionBinPool
• prediction_name_ : protocols::frag_picker::scores::SecondaryIdentity , protocols::frag_picker::scores::PartialSecondarySimilarity , protocols::frag_picker::scores::RamaScore , protocols::frag_picker::scores::SecondarySimilarity , protocols::frag_picker::scores::TalosSSSimilarity
• prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• prefilter_scorefxn_ : protocols::loophash::LoopHashMoverWrapper
• prefix_ : protocols::forge::remodel::RemodelMover::instruction_flags , protocols::frag_picker::FragmentPicker , protocols::match::output::PDBWriter
• PREFIX_FINAL : protocols::nonlocal::StarTreeBuilder
• PREFIX_INITIAL : protocols::nonlocal::StarTreeBuilder
• prefix_len : core::kinematics::Node
• prepack_full_repack_ : protocols::docking::DockingPrepackProtocol , protocols::docking::DockingEnsemblePrepackProtocol
• prepack_only_ : protocols::docking::DockTaskFactory
• prepared_for_simA_ : core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G >
• prepared_for_simulated_annealing_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• preped_for_sim_annealing_ : core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::LinearMemEdge
• prepend_output_name_ : protocols::canonical_sampling::MetricRecorder
• prepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• presample_added_residue_ : protocols::swa::monte_carlo::RNA_AddMover
• preserve_buried_contacts_ : protocols::toolbox::match_enzdes_util::EnzdesLoopInfo
• preserve_c_beta_ : core::pack::task::ResidueLevelTask_
• preserve_detailed_balance_ : protocols::backrub::BackrubMover , protocols::simple_moves::sidechain_moves::SidechainMover , protocols::simple_moves::BackboneMover , protocols::simple_moves::sidechain_moves::SidechainMoverBase
• preserve_header_ : core::io::pdb::FileDataOptions
• 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_repacking_ : protocols::toolbox::task_operations::RestrictIdentitiesAtAlignedPositionsOperation , protocols::toolbox::task_operations::RestrictNativeResiduesOperation , protocols::simple_moves::DesignRepackMover
• prevFileName : protocols::sparta::Sparta::SpartaLib
• previous_ : core::graph::EdgeListElement , protocols::simple_moves::sidechain_moves::SidechainMCMover
• previous_coordinate_constraints_ : protocols::protein_interface_design::movers::PlaceStubMover
• previous_hash_value_ : core::scoring::methods::LinearChainbreakEnergy
• previous_sequence_ : protocols::docking::TemperedDocking , protocols::docking::DockingProtocol
• previous_tree_ : protocols::nonlocal::SingleFragmentMover
• previous_vertex1 : protocols::viewer::GraphicsState
• previous_vertex2 : protocols::viewer::GraphicsState
• previous_width_vector : protocols::viewer::GraphicsState
• previously_grown_ : protocols::seeded_abinitio::SwapSegment
• prevp : core::scoring::sc::MolecularSurfaceCalculator
• principal_component_ : protocols::features::helixAssembly::HelicalFragment
• print_statw_interval_ : protocols::wum::MPI_WorkUnitManager
• prior_probs_ : core::sequence::ProfSimScoringScheme
• prioritize_ : protocols::wum2::WorkUnit
• priority_ : protocols::frag_picker::scores::FragmentScoringMethod
• prob_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBIndNRChiSample< P >
• prob_larger_current_ : protocols::toolbox::task_operations::SeqprofConsensusOperation
• prob_level_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_random_pert_to_current_ : protocols::simple_moves::sidechain_moves::SidechainMover
• prob_sigmoid_m_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_tau_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_sigmoid_w_ : protocols::noesy_assign::PeakAssignmentParameters
• prob_table_ : protocols::docking::ConformerSwitchMover
• 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
• probability : core::pack::dunbrack::ChiSet
• probability_ : protocols::MakeRotLib::RotData , core::pack::dunbrack::ProbSortClass , core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::CoarseRotamer
• 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::pose::metrics::simple_calculators::SasaCalculator , protocols::toolbox::task_operations::SelectBySASAOperation , core::pack::interaction_graph::RotamerDots
• probe_specificity_ : protocols::dna::DnaInterfacePacker
• probes : core::scoring::sc::MolecularSurfaceCalculator
• probs_ : protocols::frag_picker::LAMBEGO_IO , protocols::nonlocal::SingleFragmentMover , protocols::frag_picker::TorsionBinIO
• proc_id_ : protocols::jobdist::BaseJobDistributor
• processed_ : protocols::cluster::GatherPosesMover , protocols::cluster::AssignToClustersMover
• procorr_alt_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_curr_conf_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procorr_energies_ : protocols::flexpack::interaction_graph::OTFFlexbbEdge
• procrastinated_ : core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::DoubleLazyNode
• profile_ : core::fragment::picking_old::vall::VallResidue , protocols::frag_picker::VallResidue , core::sequence::SequenceProfile , core::sequence::CacheableSequenceProfile
• profile_scoring_ : protocols::frag_picker::scores::ProfileScore
• profile_struct_ : protocols::frag_picker::VallResidue
• profile_weight_away_from_interface_ : protocols::protein_interface_design::movers::Splice
• profile_wgt_ : protocols::simple_moves::SequenceProfileMover
• progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
• prohibit_single_residue_loops_ : protocols::loops::LoopsFileOptions , protocols::loops::LoopFromFileData
• 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::SymmOnTheFlyEdge , core::pack::interaction_graph::OnTheFlyEdge
• propeller_ : protocols::dna::DNABasepair
• properties_ : core::chemical::Selector_PROPERTY , core::chemical::ResidueType
• property_ : core::chemical::AddProperty , core::pack::task::operation::ResidueHasProperty , core::chemical::DeleteProperty
• proposal_hists_ : protocols::backrub::BackrubSidechainMover
• proposed_energy_ : core::pack::interaction_graph::SimpleEdge
• proposed_since_last_batch_ : protocols::jd2::archive::ArchiveBase
• protein_CA_stddev_Ang_ : protocols::ligand_docking::LigandDockProtocol
• protein_neighbors_ : protocols::dna::DnaInterfaceFinder
• protein_positions_ : protocols::motifs::MotifSearch , protocols::motifs::LigandMotifSearch
• protein_residue_conformation_features_ : protocols::features::ProteinSilentReport
• protein_scan_ : protocols::dna::DnaInterfacePacker
• protein_silent_report_ : protocols::features::DatabaseJobOutputter , protocols::features::DatabaseJobInputter
• protocol_ : protocols::features::RotamerRecoveryFeatures , protocols::protein_interface_design::movers::LoopMoverFromCommandLine , protocols::protein_interface_design::movers::LoopRemodel , protocols::ligand_docking::LigandDockProtocol , 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::RRReporterSQLite , protocols::rotamer_recovery::RRReporterHuman
• protocol_types_ : protocols::rotamer_recovery::RotamerRecoveryFactory
• proton1_ : protocols::noesy_assign::CrossPeak
• proton2_ : protocols::noesy_assign::CrossPeak
• proton_atom_name_ : protocols::noesy_assign::CrossPeakInfo
• proton_chi_extra_samples_ : core::chemical::ResidueType
• proton_chi_samples_ : core::chemical::ResidueType
• proton_chis_ : core::chemical::ResidueType
• proton_tolerance_ : protocols::noesy_assign::CrossPeakInfo
• protonated_H1_adenosine_list_ : protocols::swa::rna::StepWiseRNA_JobParameters
• protons_ : protocols::simple_filters::AtomicContactFilter
• prune_cavity_burial_probe_radii : core::scoring::packstat::SasaOptions
• prune_max_delta : core::scoring::packstat::SasaOptions
• prune_max_iters : core::scoring::packstat::SasaOptions
• pSer2Asp_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pSer2Glu_centroid : protocols::flexpep_docking::FlexPepDockingFlags
• pseudo_bonds_ : core::conformation::PseudoBondCollection
• pseudobonds_ : core::conformation::Residue
• pseudorotation_ : protocols::dna::DNABase
• psi : protocols::jumping::PairingTemplate , protocols::jumping::DisulfTemplate , protocols::pockets::spherical_coor_triplet
• psi_ : protocols::MakeRotLib::RotData , protocols::swa::MainChainTorsionSet , core::io::raw_data::DecoyStruct , core::fragment::picking_old::vall::VallResidue , protocols::frags::VallData , protocols::frag_picker::VallResidue , protocols::optimize_weights::PNatRotOptEPositionData , core::io::silent::ProteinSilentStruct_Template< T > , protocols::loophash::BackboneSegment , protocols::match::upstream::ProteinBackboneBuildPoint , protocols::swa::protein::MainChainTorsionSet , protocols::frags::RMSVallData , protocols::frag_picker::DiversifyDihedralsSelector , protocols::protein_interface_design::movers::BBDofs
• psi_angle_ : protocols::rigid::RigidBodyRandomizeMover , protocols::simple_moves::oop::OopMover
• psi_max_ : core::util::ABEGO
• psi_min_ : core::util::ABEGO
• psi_offsets_ : protocols::swa::StepWisePoseSetup , protocols::swa::protein::StepWiseProteinLoopBridger
• pssm_ : protocols::protein_interface_design::movers::InterfaceRecapitulationMover
• pssm_data_ : protocols::protein_interface_design::ReportPSSMDifferences , protocols::optimize_weights::IterativeOptEDriver
• pssm_probabilities_ : protocols::optimize_weights::PSSMOptEPositionData
• ptask_ : protocols::enzdes::RepackLigandSiteWithoutLigandMover , protocols::simple_moves::ConsensusDesignMover
• ptask_p_ : protocols::multistate_design::PackingState
• pts_ : core::scoring::SecondaryStructurePotential , protocols::cluster::APCluster
• pucker1_specified_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pucker2_specified_ : protocols::swa::rna::StepWiseRNA_RotamerGenerator
• pucker_ID_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_ID_old_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_state_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pucker_state_list_ : protocols::swa::rna::StepWiseRNA_Base_Sugar_Rotamer
• pure_large_frags_ : protocols::abinitio::JumpingFoldConstraints
• pymol_ : protocols::moves::PyMolObserver
• pymol_sel_hbond_unsat_ : protocols::analysis::InterfaceAnalyzerMover
• pymol_sel_interface_ : protocols::analysis::InterfaceAnalyzerMover
• pymol_sel_packing_ : protocols::analysis::InterfaceAnalyzerMover