- p -

• 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_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_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_extent : core::scoring::electron_density::ElectronDensity
• 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_grid : core::scoring::electron_density::ElectronDensity
• 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_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_o : core::scoring::electron_density::ElectronDensity
• P_occupancy : core::scoring::motif::RPM_FilterStats
• P_oneloop : core::scoring::motif::RPM_FilterStats
• p_origin : core::scoring::electron_density::ElectronDensity
• P_pdb : core::scoring::motif::RPM_FilterStats
• 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_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_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
• p_vol : core::scoring::electron_density::ElectronDensity
• paapp1_ : core::scoring::Rama2BOffset
• paapp2_ : core::scoring::Rama2BOffset
• pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
• pack_phosphate_penalty_ : core::scoring::methods::FreeDOF_Options
• pack_residue_ : core::pack::task::PackerTask_
• packed_rotno_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_2_rotno_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• packed_rotno_2_rotwell_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• packed_rotno_2_sorted_rotno_ : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• packed_rotno_conversion_data_current_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• packer_neighbor_graph_ : core::optimization::SingleResidueMultifunc
• packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::task::residue_selector::ClashBasedRepackShellSelector
• 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_log_ : core::scoring::EnvPairPotential
• 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
• paircover : core::scoring::motif::MotifHits
• pairE_potential_ : core::scoring::ScoringManager
• pairing1 : core::scoring::dssp::StrandPairing
• pairing2 : core::scoring::dssp::StrandPairing
• pairings_ : core::scoring::dssp::StrandPairingSet
• pairs_ : core::sequence::PairScoringScheme
• pairsplines_ : core::scoring::CenRotEnvPairPotential
• PARALLEL : core::scoring::dssp::Pairing
• parallel_weight_ : core::scoring::SecondaryStructureWeights
• 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
• ParamB : core::scoring::GenBornPotential
• ParamD : core::scoring::GenBornPotential
• parameter_values_as_res_lists_ : core::pose::full_model_info::FullModelParameters
• parameter_values_at_res_ : core::pose::full_model_info::FullModelParameters
• parameters_ : core::conformation::parametric::ParametersSet
• parameters_set_ : core::conformation::Conformation
• ParamG : core::scoring::GenBornPotential
• ParamS : core::scoring::GenBornPotential
• params_ : core::scoring::disulfides::FullatomDisulfidePotential , core::scoring::packing::HolesEnergyRes , core::scoring::packing::HolesParamsRes
• params_database_tag_ : core::scoring::hbonds::HBondDatabase , core::scoring::hbonds::HBondOptions
• parent : core::graph::DS_Node , core::kinematics::Node
• parent_ : core::environment::FoldTreeSketch::Node , core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• parent_atom_ : core::chemical::AddConnect
• parent_id_ : core::optimization::DOF_DataPoint
• parent_remarks_map_ : core::io::silent::SilentStruct
• partial_charge_ : core::chemical::sdf::MolFileIOAtom
• 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
• partner_ : core::scoring::dna::BasePartner
• patcharea_to_score_ : core::pack::interaction_graph::SurfacePotential
• path_ : core::chemical::NCAARotLibPath , core::pose::rna::RNA_IdealCoord
• path_dist_ : core::scoring::AtomNeighbor
• 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_to_parameter_files_ : core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential
• path_to_torsion_files_ : core::scoring::rna::RNA_TorsionPotential
• pAtoms : core::scoring::sc::_PROBE
• 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_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
• Pcalc : core::scoring::electron_density::ElectronDensity
• pcc_structure : core::scoring::electron_density::PattersonCorrEnergy
• pd_ : core::scoring::packstat::MultiProbePerSphereAccumulator
• pdb2pose_ : core::pose::PDBInfo , core::pose::PDBPoseMap
• pdb_ : core::scoring::motif::ResPairMotif
• pdb_codes_ : core::io::sequence_comparation::DesignContrast
• pdb_file_names_ : core::io::sequence_comparation::DesignContrast
• pdb_info_ : core::pose::Pose
• pdb_lines_ : core::import_pose::PDBSilentStruct
• pdbid_ : core::fragment::AnnotatedFragData
• pdie : core::scoring::APBSConfig::R_PARAM
• pdime : core::scoring::APBSConfig
• penalty_ : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• penalty_at_1M_ : core::scoring::methods::IntermolEnergy
• pep_next_ : core::environment::FoldTreeSketch::Node
• pep_prev_ : core::environment::FoldTreeSketch::Node
• PEPTIDE : core::kinematics::Edge
• peptoid_rotlib_n_bins_per_rot_ : core::chemical::ResidueType
• peptoid_rotlib_n_rots_ : core::chemical::ResidueType
• peptoid_rotlib_path_ : core::chemical::ResidueType
• peptoid_rotlibs_ : core::pack::dunbrack::RotamerLibrary
• period_ : core::chemical::Element , core::scoring::methods::BBIndepCartBondedParameters
• periodicity_ : core::scoring::constraints::OffsetPeriodicBoundFunc , core::scoring::constraints::PeriodicBoundFunc , core::scoring::dna::TorsionFourierComponent
• perturbed_ : core::pack::interaction_graph::FASTERNode
• perturbed_two_body_energies_ : core::pack::interaction_graph::FASTERNode
• pH_ : core::scoring::methods::pHEnergy
• phase_ : core::scoring::dna::TorsionFourierComponent
• phenix_home_ : core::scoring::cryst::PhenixInterface
• phi_ : core::chemical::AddConnect , core::chemical::Adduct , core::chemical::AtomICoor , 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
• PHI_BINRANGE : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• phi_max_ : core::util::ABEGO
• phi_min_ : core::util::ABEGO
• phi_psi_bins_above_thold_ : core::scoring::Ramachandran
• PHIPSI_BINRANGE : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >
• pi_charge_to_en_inflection_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_contribution_ : core::chemical::gasteiger::GasteigerAtomTypeData
• pi_orbitals_binding_ : core::chemical::gasteiger::GasteigerAtomTypeData
• placeholder_info_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue_ : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• pleat_weird : core::scoring::dssp::StrandPairing
• pleating1 : core::scoring::dssp::StrandPairing
• pleating_ : core::scoring::dssp::Pairing
• po_bar : core::scoring::electron_density::ElectronDensity
• point : core::scoring::sc::_PROBE
• point_graph : core::conformation::AddEdgeVisitor< Vertex, Edge >
• point_graph_ : core::scoring::Energies
• points_ : core::scoring::func::FourPointsFunc
• poisson_boltzmann_potential_ : core::scoring::methods::PoissonBoltzmannEnergy
• polar_ : core::pack::task::operation::ResidueTypeFilter
• polar_charge_cutoff_ : core::scoring::sasa::SasaCalc
• polar_expansion_radius_ : core::pack::interaction_graph::RotamerDotsRadiusData
• pos1_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• pos2_ : core::scoring::DenseNeighborConstIterator , core::scoring::DenseNeighborIterator , core::scoring::dssp::Pairing , core::scoring::OneToAllNeighborConstIterator , core::scoring::OneToAllNeighborIterator
• pos_ : core::fragment::NonContinuousFrame , core::pack::task::operation::ResiduePDBIndexIs::ChainPos , core::scoring::PeptideBondedNeighborConstIterator , core::scoring::PeptideBondedNeighborIterator
• 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::graph::Edge , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::EdgeBase
• pos_map_ : core::sequence::AnnotatedSequence
• pose : core::pose::signals::DestructionEvent , core::pose::signals::GeneralEvent
• pose1_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose2_ : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose_ : core::fragment::picking_old::vall::eval::EnergyEval , 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::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
• pose_by_state_ : core::scoring::methods::PBLifetimeCache
• 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::PattersonCorrEnergy , core::scoring::electron_density_atomwise::ElecDensAtomwiseEnergy
• pose_ptr_ : core::pose::metrics::PoseMetricContainer
• pose_to_local_numbers_ : core::environment::SequenceAnnotation
• poses_ : core::pack::rotamer_set::UnboundRotamersOperation
• position : core::conformation::signals::IdentityEvent , core::conformation::signals::LengthEvent
• position_ : core::chemical::sdf::MolFileIOAtom , core::chemical::Selector_UPPER_POSITION , core::environment::LocalPosition , core::kinematics::tree::Atom_ , core::scoring::methods::D2H_SA_Energy , core::scoring::motif::Xfrag , core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity
• position_index_ : core::fragment::picking_old::vall::VallResidue
• potential_ : core::scoring::disulfides::CentroidDisulfideEnergy , core::scoring::disulfides::DisulfideMatchingEnergy , core::scoring::disulfides::FullatomDisulfideEnergy , core::scoring::dna::DNAChiEnergy , 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::EnvEnergy , core::scoring::methods::Fa_MbenvEnergy , core::scoring::methods::Fa_MbsolvEnergy , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , 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::OmegaTetherEnergy , core::scoring::methods::PairEnergy , core::scoring::methods::ProQ_Energy , core::scoring::methods::Rama2BOffsetEnergy , core::scoring::methods::RamachandranEnergy2B , core::scoring::methods::RamachandranEnergy , core::scoring::methods::SecondaryStructureEnergy , core::scoring::methods::SmoothCenPairEnergy , core::scoring::methods::SmoothEnvEnergy , core::scoring::methods::WaterAdductHBondEnergy , core::scoring::PoissonBoltzmannPotential
• 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
• pqr : core::scoring::APBSWrapper
• pqr_filename_ : core::scoring::PoissonBoltzmannPotential
• pr_idx_ : core::scoring::packstat::MultiProbePerSphereAccumulator , core::scoring::packstat::MultiProbePoseAccumulator
• pre_talaris2013_geometries : core::init::pre_talaris_2013_behavior_settings
• preallocate_ : core::fragment::picking_old::vall::VallLibrarian
• precalculated_bb_bb_energy_ : core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy , core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy
• precision_ : core::io::silent::SilentStruct
• pred_ : core::scoring::ExcludedResPredicate , core::scoring::ResRangePredicate , core::scoring::SelectedResPredicate
• pred_burial_ : core::scoring::methods::BurialEnergy
• prefactor_ : core::scoring::rna::RNA_FullAtomStackingEnergy
• prefix_len : core::kinematics::Node
• prepared_for_simA_ : core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >
• prepared_for_simulated_annealing_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• preped_for_sim_annealing_ : core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• prepro_restype_data_ : core::scoring::methods::IdealParametersDatabase
• preserve_c_beta_ : core::pack::task::ResidueLevelTask_
• preserve_crystinfo_ : core::io::pdb::FileDataOptions
• preserve_header_ : core::io::pdb::FileDataOptions
• prevburied : core::scoring::sc::MolecularSurfaceCalculator
• previous_ : core::graph::EdgeListElement
• previous_hash_value_ : core::scoring::methods::LinearChainbreakEnergy
• prevp : core::scoring::sc::MolecularSurfaceCalculator
• primary_atom_id_ : core::scoring::constraints::BackboneStubConstraint
• primary_backbone_target_ : core::scoring::constraints::BackboneStubConstraint
• primary_sidechain_target_ : core::scoring::constraints::BackboneStubConstraint
• prior_probs_ : core::sequence::ProfSimScoringScheme
• pro_cd_cprev_n_ca_interres_torsion_params_ : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index_ : core::scoring::methods::ResidueCartBondedParameters
• pro_nv_ : core::scoring::methods::CartesianBondedEnergy
• prob_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::BBIndNRChiSample< P > , core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• PROB_DELTA : core::pack::dunbrack::SingleResidueDunbrackLibrary
• prob_profile_ : core::scoring::methods::ProQ_Energy
• prob_to_accumulate_buried_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• prob_to_accumulate_nonburied_ : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• probA_ : core::scoring::packstat::PackingScore
• probability : core::pack::dunbrack::ChiSet
• probability_ : core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::ProbSortClass
• probability_matrix_ : core::scoring::bin_transitions::BinTransitionData
• probB_ : core::scoring::packstat::PackingScore
• 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
• probe_scorefxn_ : core::scoring::rna::data::RNA_DMS_Potential
• probes : core::scoring::sc::MolecularSurfaceCalculator
• procrastinated_ : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::LazyNode
• profile_ : core::fragment::picking_old::vall::VallResidue , core::sequence::SequenceProfile
• progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
• 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
• proline_corrections_ : core::pack::interaction_graph::OnTheFlyEdge , core::pack::interaction_graph::SymmOnTheFlyEdge
• properties_ : core::chemical::Element , core::chemical::gasteiger::GasteigerAtomTypeData , core::chemical::ResidueType , core::chemical::Selector_PROPERTY
• 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
• proposed_energy_ : core::pack::interaction_graph::SimpleEdge
• ProQ_potential_ : core::scoring::ScoringManager
• protein_gaussian_variance_per_residue_ : core::scoring::loop_graph::LoopGraph
• proton_chi_extra_samples_ : core::chemical::ResidueType
• proton_chi_samples_ : core::chemical::ResidueType
• proton_chis_ : core::chemical::ResidueType
• prune_cavity_burial_probe_radii : core::scoring::packstat::SasaOptions
• prune_max_delta : core::scoring::packstat::SasaOptions
• prune_max_iters : core::scoring::packstat::SasaOptions
• pseudo_bonds_ : core::conformation::PseudoBondCollection
• pseudobonds_ : core::conformation::Residue
• psi_ : core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::scoring::motif::Xfres
• PSI_BINRANGE : core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• psi_max_ : core::util::ABEGO
• psi_min_ : core::util::ABEGO
• pts_ : core::scoring::SecondaryStructurePotential
• put_intra_into_total_ : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions