- p -

p_ : core::optimization::Particle
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_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
paapp1_ : core::scoring::Rama2BOffset
paapp2_ : core::scoring::Rama2BOffset
pack_missing_sidechains_ : core::import_pose::ImportPoseOptions
pack_phosphate_penalty_ : core::scoring::methods::FreeMoietyEnergy
pack_residue_ : core::pack::task::PackerTask_
packed_rotno_ : core::pack::dunbrack::BBDepNRChiSample< P > , core::pack::dunbrack::PackedDunbrackRotamer< S, 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_neighbor_graph_ : core::optimization::SingleResidueMultifunc
packer_task_ : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
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
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
Param_TE : core::scoring::GenBornPotential
Param_TF : core::scoring::GenBornPotential
Param_TG : core::scoring::GenBornPotential
Param_TH : core::scoring::GenBornPotential
Param_THH : core::scoring::GenBornPotential
ParamB : core::scoring::GenBornPotential
ParamD : core::scoring::GenBornPotential
parameter_values_as_res_lists_ : core::pose::full_model_info::FullModelParameters
parameter_values_at_res_ : core::pose::full_model_info::FullModelParameters
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
parents_ : core::chemical::ResidueType
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
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
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_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
PDB_Records_ : core::io::pdb::Field
pdbid_ : core::fragment::AnnotatedFragData
pdie : core::scoring::APBSConfig::R_PARAM
pdime : core::scoring::APBSConfig
penalties : core::conformation::membrane::EmbedSearchParams
penalties_ : core::membrane::io::EmbedSearchParamsOptions
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
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
phi_max_ : core::util::ABEGO
phi_mean_ : core::pack::dunbrack::CoarseRotamer
phi_min_ : core::util::ABEGO
phi_sdev_ : core::pack::dunbrack::CoarseRotamer
PHIPSI_BINRANGE : core::pack::dunbrack::cenrot::SingleResidueCenrotLibrary , core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T >
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::RotamerDots
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
pose_ : core::fragment::picking_old::vall::eval::EnergyEval , core::membrane::geometry::EmbeddingFactory , 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_chemical_checksum_ : core::scoring::constraints::NamedAtomPairConstraint
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_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::Selector_UPPER_POSITION , core::environment::LocalPosition , core::kinematics::tree::Atom_ , core::scoring::methods::D2H_SA_Energy , core::scoring::rna::RNA_Datum
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::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_file_ : core::membrane::MembraneProteinFactory
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
prime_and_switch_ : core::scoring::cryst::PhenixInterface
PrincipalQuantumNumber_strings : core::chemical::ElectronConfiguration
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_profile_ : core::scoring::methods::ProQ_Energy
prob_to_accumulate_buried_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
prob_to_accumulate_nonburied_ : core::pack::dunbrack::SingleResidueDunbrackLibrary
probA_ : core::scoring::packstat::PackingScore
probability : core::pack::dunbrack::ChiSet
probability_ : core::pack::dunbrack::CoarseRotamer , core::pack::dunbrack::DunbrackRotamerSampleData , core::pack::dunbrack::ProbSortClass
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
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::CacheableSequenceProfile , core::sequence::SequenceProfile
progress_through_sBR_ : core::pack::annealer::FASTERAnnealer
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
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 >
psi_max_ : core::util::ABEGO
psi_min_ : core::util::ABEGO
pts_ : core::scoring::SecondaryStructurePotential