- p -

• p1_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p1_deriv() : core::scoring::constraints::AngleConstraint
• p1_theta_deriv() : core::scoring::constraints::AngleConstraint
• p2_cosine_deriv() : core::scoring::constraints::DihedralConstraint
• p2_deriv() : core::scoring::constraints::AngleConstraint
• P_AA() : core::scoring::P_AA
• P_AA_Energy() : core::scoring::methods::P_AA_Energy
• P_AA_energy() : core::scoring::P_AA
• P_AA_initialize() : core::scoring::P_AA
• P_AA_pp_Energy() : core::scoring::methods::P_AA_pp_Energy
• P_AA_pp_energy() : core::scoring::P_AA
• p_atom_index() : core::chemical::rna::RNA_ResidueType
• pack_missing_sidechains() : core::import_pose::ImportPoseOptions
• pack_phosphate_penalty() : core::scoring::methods::FreeDOF_Options
• pack_residue() : core::pack::task::PackerTask , core::pack::task::PackerTask_
• packed_rotamer_2_regular_rotamer() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• packed_rotno() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packed_rotno_2_rotwell() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• packed_rotno_2_sorted_rotno() : core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N > , core::pack::dunbrack::RotamericSingleResiduePeptoidLibrary< T, N >
• PackedDunbrackRotamer() : core::pack::dunbrack::PackedDunbrackRotamer< S, N, P >
• packer_task() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• PackerEnergyAdd() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergyMultiply() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerEnergySubtract() : core::pack::rotamer_set::symmetry::SymmetricRotamerSet_
• PackerTask_() : core::pack::task::PackerTask_
• packing_interaction_cutoff() : core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy
• PackingScore() : core::scoring::packstat::PackingScore
• PackingScoreResData() : core::scoring::packstat::PackingScoreResData
• PackStatEnergy() : core::scoring::methods::PackStatEnergy
• pages() : core::fragment::picking_old::concepts::Book< Pages >
• pair_dp() : core::scoring::SecondaryStructurePotential
• pair_energy_H() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::etable::TableLookupEvaluator
• pair_energy_H_v() : core::scoring::etable::AnalyticEtableEvaluator , core::scoring::etable::EtableEvaluator , core::scoring::etable::TableLookupEvaluator
• pair_term_energy() : core::scoring::PairEPotential
• pair_term_energy_and_deriv() : core::scoring::PairEPotential
• pair_term_energy_exists() : core::scoring::PairEPotential
• paired() : core::scoring::dssp::Dssp , core::scoring::dssp::StrandPairing , core::scoring::dssp::StrandPairingSet
• PairEnergy() : core::scoring::methods::PairEnergy
• PairEPotential() : core::scoring::PairEPotential
• Pairing() : core::scoring::dssp::Pairing
• pairs() : core::sequence::PairScoringScheme
• PairScoringScheme() : core::sequence::PairScoringScheme
• param() : core::scoring::packing::HolesParamsRes
• Parameters() : core::conformation::parametric::Parameters
• parameters() : core::conformation::parametric::ParametersSet
• parameters_for_restype() : core::scoring::methods::IdealParametersDatabase
• parameters_set() : core::conformation::Conformation
• ParametersSet() : core::conformation::parametric::ParametersSet
• params_database_tag() : core::scoring::hbonds::HBondOptions
• parent() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::optimization::DOF_Node
• parent_id() : core::optimization::DOF_DataPoint
• parse() : core::chemical::sdf::CtabParserBase , core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser , core::chemical::sdf::SDFParser , core::io::pdb::PDB_DReader
• parse_atom_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_atom_pair_constraint() : core::scoring::constraints::ConstraintIO
• parse_body_line() : core::pack::task::ResfileContents
• parse_bond_line() : core::chemical::sdf::CtabV2000Parser , core::chemical::sdf::CtabV3000Parser
• parse_chain_endings() : core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T >
• parse_coordinate_constraint() : core::scoring::constraints::ConstraintIO
• parse_def() : core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::IncludeCurrent , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::ReadResfile , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::TaskOperation
• parse_disulf_file() : core::io::raw_data::DisulfideFile
• parse_energies() : core::io::silent::SilentStruct
• parse_file() : core::chemical::sdf::MolFileIOReader
• parse_files() : core::scoring::orbitals::OrbitalsLookup
• parse_header_line() : core::pack::task::ResfileContents
• parse_heterogen_name_for_carbohydrate_residues() : core::io::pdb::FileData
• parse_in_progress() : core::io::pdb::HeaderInformation
• parse_mainchain_torsions() : core::scoring::bin_transitions::BinTransitionCalculator
• parse_my_tag() : core::chemical::ResidueLoaderOptions , core::conformation::symmetry::SymmDataOptions , core::import_pose::ImportPoseOptions , core::io::pdb::FileDataOptions , core::io::pdb::PDB_DReaderOptions , core::io::silent::SilentFileOptions , core::pack::task::residue_selector::AndResidueSelector , core::pack::task::residue_selector::ChainSelector , core::pack::task::residue_selector::ClashBasedRepackShellSelector , core::pack::task::residue_selector::InterGroupInterfaceByVectorSelector , core::pack::task::residue_selector::JumpDownstreamSelector , core::pack::task::residue_selector::JumpUpstreamSelector , core::pack::task::residue_selector::NeighborhoodResidueSelector , core::pack::task::residue_selector::NotResidueSelector , core::pack::task::residue_selector::NumNeighborsSelector , core::pack::task::residue_selector::OrResidueSelector , core::pack::task::residue_selector::ResidueIndexSelector , core::pack::task::residue_selector::ResidueSelector , core::pack::task::residue_selector::TrueResidueSelector , core::scoring::electron_density::ElectronDensityOptions , core::scoring::etable::EtableOptions , core::scoring::fiber_diffraction::FiberDiffractionOptions , core::scoring::hbonds::HBondOptions
• parse_optional_data() : core::chemical::sdf::SDFParser
• parse_PDBnum_icode() : core::pack::task::ResfileContents
• parse_property_line() : core::chemical::sdf::CtabV2000Parser
• parse_resid() : core::pack::task::ResfileContents
• parse_residue() : core::scoring::constraints::ConstraintIO
• parse_sub_filters_tag() : core::pack::task::operation::ResFilterComposition
• parse_tag() : core::pack::task::operation::AddBehaviorRLT , core::pack::task::operation::ChainIs , core::pack::task::operation::DisallowIfNonnative , core::pack::task::operation::DisallowIfNonnativeRLT , core::pack::task::operation::ExtraChiCutoff , core::pack::task::operation::ExtraRotamers , core::pack::task::operation::ExtraRotamersGeneric , core::pack::task::operation::InitializeFromCommandline , core::pack::task::operation::OperateOnCertainResidues , core::pack::task::operation::OperateOnResidueSubset , core::pack::task::operation::PreventRepacking , core::pack::task::operation::ReadResfile , core::pack::task::operation::ReadResfileAndObeyLengthEvents , core::pack::task::operation::ReplicateTask , core::pack::task::operation::ResFilter , core::pack::task::operation::ResFilterComposition , core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResidueIndexIs , core::pack::task::operation::ResidueName3Is , core::pack::task::operation::ResiduePDBIndexIs , core::pack::task::operation::ResiduePDBInfoHasLabel , core::pack::task::operation::ResidueTypeFilter , core::pack::task::operation::ResLvlTaskOperation , core::pack::task::operation::RestrictAbsentCanonicalAAS , core::pack::task::operation::RestrictAbsentCanonicalAASRLT , core::pack::task::operation::RestrictResidueToRepacking , core::pack::task::operation::RestrictToRepacking , core::pack::task::operation::RotamerExplosion , core::pack::task::operation::TaskOperation
• partial_assign_relaxed_state() : core::pack::interaction_graph::FASTERNode
• partial_assign_state() : core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• partial_assign_state_with_lowest_one_body_energy() : core::pack::interaction_graph::FASTERNode
• partial_charge() : core::chemical::sdf::MolFileIOAtom
• Particle() : core::optimization::Particle
• ParticleSwarmMinimizer() : core::optimization::ParticleSwarmMinimizer
• partition_by_jump() : core::kinematics::FoldTree
• partition_by_residue() : core::kinematics::FoldTree
• partition_coloring() : core::kinematics::FoldTree
• pass_metropolis() : core::pack::annealer::SimAnnealerBase
• patch_str() : core::sequence::AnnotatedSequence
• path_dist() : core::scoring::AtomNeighbor
• path_distance() : core::chemical::ResidueType , core::conformation::Residue , core::scoring::etable::count_pair::CountPairGeneric
• path_distance_OK() : core::scoring::carbon_hbonds::CarbonHBondEnergy
• path_distances() : core::chemical::ResidueType , core::conformation::Residue
• PattersonCorrEnergy() : core::scoring::electron_density::PattersonCorrEnergy
• pb_bound_tag() : core::scoring::methods::EnergyMethodOptions
• pb_unbound_tag() : core::scoring::methods::EnergyMethodOptions
• pbest() : core::optimization::Particle
• PBLifetimeCache() : core::scoring::methods::PBLifetimeCache
• pd_edge_table_all_zeros() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• pdb() : core::scoring::motif::ResPairMotif
• pdb2pose() : core::pose::PDBInfo
• PDB_DReaderOptions() : core::io::pdb::PDB_DReaderOptions
• pdb_info() : core::pose::Pose
• pdbid() : core::fragment::AnnotatedFragData , core::fragment::FragData
• PDBInfo() : core::pose::PDBInfo
• pdbpos() : core::fragment::AnnotatedFragData , core::fragment::FragData
• PDBPoseInputStream() : core::import_pose::pose_stream::PDBPoseInputStream
• PDBPoseMap() : core::pose::PDBPoseMap
• PDBSilentStruct() : core::import_pose::PDBSilentStruct
• PDBSilentStructCreator() : core::import_pose::PDBSilentStructCreator
• PDEdge() : core::pack::interaction_graph::PDEdge
• PDInteractionGraph() : core::pack::interaction_graph::PDInteractionGraph
• PDNode() : core::pack::interaction_graph::PDNode
• penalty() : core::fragment::picking_old::vall::eval::ABEGOEval , core::scoring::MembraneEmbed
• PeptideBondedEnergyContainer() : core::scoring::PeptideBondedEnergyContainer
• PeptideBondedNeighborConstIterator() : core::scoring::PeptideBondedNeighborConstIterator
• PeptideBondedNeighborIterator() : core::scoring::PeptideBondedNeighborIterator
• PeptideBondEnergy() : core::scoring::methods::PeptideBondEnergy
• perform_checks() : core::chemical::ResidueType
• period() : core::scoring::methods::BBDepCartBondedParameters , core::scoring::methods::BBIndepCartBondedParameters , core::scoring::methods::CartBondedParameters
• PeriodicBoundFunc() : core::scoring::constraints::PeriodicBoundFunc
• PeriodicFunc() : core::scoring::func::PeriodicFunc
• periodicity() : core::scoring::dna::TorsionFourierComponent
• PerSphereAccumulator() : core::scoring::packstat::PerSphereAccumulator
• perturb_dBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_sBR_and_relax() : core::pack::interaction_graph::FASTERInteractionGraph
• perturb_weights() : core::scoring::ScoreFunction
• phase() : core::scoring::dna::TorsionFourierComponent
• pHEnergy() : core::scoring::methods::pHEnergy
• PhenixInterface() : core::scoring::cryst::PhenixInterface
• phi() : core::chemical::Adduct , core::chemical::AtomICoor , core::chemical::orbitals::ICoorOrbitalData , core::fragment::picking_old::vall::VallResidue , core::io::raw_data::DecoyStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::pose::Pose , core::scoring::motif::Xfres
• phi_max() : core::util::ABEGO
• phi_min() : core::util::ABEGO
• phipsi_in_allowed_rama() : core::scoring::Ramachandran
• phipsi_in_forbidden_rama() : core::scoring::Ramachandran
• pick_a_rotamer() : core::pack::annealer::RotamerAssigningAnnealer
• pick_a_rotamer_for_node() : core::pack::annealer::RotamerAssigningAnnealer
• pick_a_rotamer_for_sBR() : core::pack::annealer::FASTERAnnealer
• pick_baserotamer_from_rotblock() : core::pack::rotamer_set::ContinuousRotamerSet
• pick_rotamer_for_node() : core::pack::annealer::FASTERAnnealer
• place() : core::conformation::Residue
• place_adducts() : core::chemical::ResidueTypeSet
• place_sidechain_in_pose() : core::scoring::motif::Xfres
• placeholder_info() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• placeholder_residue() : core::scoring::FACTSPoseInfo , core::scoring::GenBornPoseInfo
• Pleating() : core::scoring::dssp::Pairing
• Point() : core::scoring::packstat::Point
• point_graph() : core::scoring::Energies
• PointGraphEdgeData() : core::conformation::PointGraphEdgeData
• PointGraphVertexData() : core::conformation::PointGraphVertexData
• PointPair() : core::scoring::packstat::PointPair
• PoissonBoltzmannEnergy() : core::scoring::methods::PoissonBoltzmannEnergy
• PoissonBoltzmannPotential() : core::scoring::PoissonBoltzmannPotential
• polar_energy_pack_corrector() : core::scoring::FACTSPotential
• polar_hydrogens() : core::chemical::ResidueType
• PolarHydrogenFilter() : core::chemical::PolarHydrogenFilter
• polymer_direction() : core::kinematics::Edge
• polymeric_oriented_sequence_distance() : core::conformation::Residue
• polymeric_sequence_distance() : core::conformation::Residue
• Polynomial_1d() : core::scoring::hbonds::Polynomial_1d
• pop() : core::graph::NegSpaceElement< T >
• pop_passport() : core::conformation::Conformation
• populate_matrix() : core::scoring::bin_transitions::BinTransitionCalculator
• pos() : core::fragment::NonContinuousFrame
• Pos1() : core::scoring::dssp::Pairing
• Pos2() : core::scoring::dssp::Pairing
• pose() : core::fragment::picking_old::vall::eval::EnergyEval , core::optimization::AtomTreeMultifunc , core::optimization::CartesianMultifunc , 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::pose::datacache::CacheablePoseRawPtr
• Pose() : core::pose::Pose
• pose1() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose1ptr() : core::scoring::motif::MotifHit
• pose2() : core::scoring::motif::MotifHit , core::scoring::motif::ResPairMotifQuery
• pose2pdb() : core::pose::PDBInfo
• pose2ptr() : core::scoring::motif::MotifHit
• pose_is_setup_for_density_scoring() : core::scoring::electron_density::FastDensEnergy
• pose_raw_unfolded_state_energymap() : core::scoring::UnfoldedStatePotential
• pose_res_no() : core::scoring::constraints::FabConstraint
• PoseBalls() : core::scoring::packing::PoseBalls
• PoseBallsLite() : core::scoring::packing::PoseBallsLite
• PoseFromPDBLoader() : core::import_pose::PoseFromPDBLoader
• PoseInputStream() : core::import_pose::pose_stream::PoseInputStream
• PoseMetricCalculator() : core::pose::metrics::PoseMetricCalculator
• PoseMetricContainer() : core::pose::metrics::PoseMetricContainer
• position() : core::chemical::sdf::MolFileIOAtom , core::environment::LocalPosition , core::kinematics::tree::Atom , core::kinematics::tree::Atom_ , core::scoring::motif::Xfrag , core::scoring::rna::data::RNA_Datum , core::scoring::rna::data::RNA_Reactivity
• position_index() : core::fragment::picking_old::vall::VallResidue
• PositionConservedResiduesStore() : core::pose::datacache::PositionConservedResiduesStore
• PositionDdGInfo() : core::io::PositionDdGInfo::PositionDdGInfo
• possible_root() : core::kinematics::FoldTree
• PossibleAtomTypesForAtom() : core::chemical::gasteiger::PossibleAtomTypesForAtom
• post_catalog_op() : core::fragment::picking_old::vall::eval::VallFragmentEval
• post_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• potential_twobody_memory_use() : core::pack::interaction_graph::DoubleLazyEdge
• PQR() : core::scoring::PQR
• pre_catalog_op() : core::fragment::picking_old::vall::eval::ABEGOEval , core::fragment::picking_old::vall::eval::EnergyEval , core::fragment::picking_old::vall::eval::IdentityEval , core::fragment::picking_old::vall::eval::VallFragmentEval
• pre_catalog_ops() : core::fragment::picking_old::vall::VallLibrarian
• pre_nresidue_change() : core::conformation::Conformation
• pre_talaris_2013_behavior_settings() : core::init::pre_talaris_2013_behavior_settings
• preallocate() : core::fragment::picking_old::vall::VallLibrarian
• precalc_context() : core::scoring::elec::FA_GrpElecEnergy
• precalc_etable_coefficients() : core::scoring::etable::Etable , core::scoring::etable::MembEtable
• precalculate_bb_bb_energy_for_design() : core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy , core::scoring::geometric_solvation::GeometricSolEnergyEvaluator
• precision() : core::io::silent::SilentStruct
• precompute_two_body_energies() : core::pack::rotamer_set::RotamerSets , core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• precompute_unweighted_score() : core::scoring::electron_density_atomwise::ElectronDensityAtomwise
• PrecomputedPairEnergiesEdge() : core::pack::interaction_graph::PrecomputedPairEnergiesEdge
• PrecomputedPairEnergiesInteractionGraph() : core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph
• PrecomputedPairEnergiesNode() : core::pack::interaction_graph::PrecomputedPairEnergiesNode
• Predicate() : core::scoring::Predicate
• preferred_root_res() : core::pose::full_model_info::FullModelInfo
• prep_aa_submatrix() : core::pack::interaction_graph::DoubleLazyEdge
• prep_for_neighbors_perturbation() : core::pack::interaction_graph::FASTERNode
• prepare_constraints_energy_container() : core::scoring::constraints::ConstraintsEnergy
• prepare_for_FASTER() : core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::FASTERNode
• prepare_for_new_residue_type() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• prepare_for_perturbation() : core::pack::interaction_graph::FASTERNode
• prepare_for_residue_pair() : core::scoring::etable::BaseEtableEnergy< Derived >
• prepare_for_scoring() : core::scoring::NeighborList
• prepare_for_simulated_annealing() : core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G > , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::BackgroundToFirstClassEdge< V, E, G > , core::pack::interaction_graph::DensePDEdge , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDEdge , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::EdgeBase , core::pack::interaction_graph::FASTEREdge , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundEdge< V, E, G > , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchEdge< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDEdge , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SurfaceBackgroundEdge< V, E, G > , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceEdge< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistEdge , core::pack::interaction_graph::SymmMinimalistInteractionGraph , core::pack::interaction_graph::SymmMinimalistNode
• prepare_for_simulated_annealing_no_deletion() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::PDEdge
• prepare_neighbor_graphs() : core::scoring::Energies
• prepare_otf_graph() : core::pack::rotamer_set::RotamerSets
• prepare_rotamers_for_packing() : core::scoring::elec::FA_ElecEnergy , core::scoring::elec::FA_ElecEnergyAroAll , core::scoring::elec::FA_ElecEnergyAroAro , core::scoring::elec::FA_GrpElecEnergy , core::scoring::elec::RNA_FA_ElecEnergy , core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondEnergy , core::scoring::methods::CustomAtomPairEnergy , core::scoring::methods::EnergyMethod , core::scoring::methods::FACTSEnergy , core::scoring::methods::GenBornEnergy , core::scoring::methods::LK_BallEnergy , core::scoring::methods::MMLJEnergyInter , core::scoring::methods::PairEnergy , core::scoring::orbitals::OrbitalsScore , core::scoring::ScoreFunction , core::scoring::vdwaals::VDW_Energy
• prepare_sets_for_packing() : core::pack::rotamer_set::RotamerSets
• prepare_symm_otf_interaction_graph() : core::pack::rotamer_set::symmetry::SymmetricRotamerSets
• prepend_edge() : core::kinematics::FoldTree
• prepend_polymer_residue_before_seqpos() : core::conformation::Conformation , core::pose::Pose
• prepend_res() : core::pose::PDBInfo
• PrependMainchainAtom() : core::chemical::PrependMainchainAtom
• preprocess_data() : core::scoring::ResidualDipolarCoupling
• preprocess_pose() : core::import_pose::pose_stream::PoseInputStream
• preserve_c_beta() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• preserve_crystinfo() : core::io::pdb::FileDataOptions
• preserve_header() : core::io::pdb::FileDataOptions
• pretty_print() : core::scoring::mm::MMBondAngleLibrary , core::scoring::mm::MMBondLengthLibrary
• prevent_repacking() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• previous() : core::graph::EdgeListElement
• previous_child() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• previous_sibling() : core::kinematics::tree::Atom , core::kinematics::tree::Atom_
• PrincipalQuantumNumber_strings() : core::chemical::ElectronConfiguration
• print() : core::chemical::AtomType , core::chemical::Bond , core::chemical::Orbital , core::graph::Node , core::pack::interaction_graph::BackgroundNode< V, E, G > , core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DotSphere , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::HPatchBackgroundNode< V, E, G > , core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::HPatchNode< V, E, G > , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::NodeBase , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::RotamerDots , core::pack::interaction_graph::RotamerDotsCache , core::pack::interaction_graph::SimpleNode , core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceNode< V, E, G > , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode , core::pose::metrics::EnergyDependentCalculator , core::pose::metrics::PoseMetricCalculator , core::pose::metrics::PoseMetricContainer , core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceDeltaEnergeticsCalculator , core::pose::metrics::simple_calculators::InterfaceNeighborDefinitionCalculator , core::pose::metrics::simple_calculators::InterfaceSasaDefinitionCalculator , core::pose::metrics::simple_calculators::SasaCalculator2 , core::pose::metrics::simple_calculators::SasaCalculatorLegacy , core::pose::metrics::StructureDependentCalculator , core::scoring::elec::ElecAtom , core::scoring::EMapVector , core::scoring::EnergyNode , core::scoring::etable::etrie::CountPairData_1_1 , core::scoring::etable::etrie::CountPairData_1_2 , core::scoring::etable::etrie::CountPairData_1_3 , core::scoring::etable::etrie::CountPairDataGeneric , core::scoring::etable::etrie::EtableAtom , core::scoring::etable::etrie::TrieCountPair1BC3 , core::scoring::etable::etrie::TrieCountPairAll , core::scoring::etable::etrie::TrieCountPairGeneric , core::scoring::etable::etrie::TrieCountPairNone , core::scoring::hbonds::hbtrie::HBAtom , core::scoring::hbonds::hbtrie::HBCountPairFunction , core::scoring::hbonds::hbtrie::HBCPData , core::scoring::MembraneTopology , core::scoring::MinimizationNode , core::scoring::mm::mmtrie::MMEnergyTableAtom , core::scoring::trie::RotamerTrie< AT, CPDATA > , core::scoring::trie::RotamerTrieBase , core::scoring::trie::TrieNode< AT, CPDATA > , core::scoring::vdwaals::VDWAtom
• print_all_bond_lengths() : core::chemical::IdealBondLengthSet
• print_all_types() : core::chemical::MMAtomTypeSet
• print_allowed_types() : core::pack::task::ResidueLevelTask , core::pack::task::ResidueLevelTask_
• print_bit_string() : core::pack::interaction_graph::RotamerDotsCache
• print_bondangles() : core::chemical::ResidueType
• print_comments() : core::io::silent::SilentStruct
• print_conformation() : core::import_pose::PDBSilentStruct , core::io::raw_data::DecoyStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::raw_data::ScoreStructText , core::io::silent::BinarySilentStruct , core::io::silent::ProteinSilentStruct_Template< T > , core::io::silent::RigidBodySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct
• print_current_energy() : core::pack::interaction_graph::DoubleLazyEdge , core::pack::interaction_graph::LazyEdge , core::pack::interaction_graph::LinearMemEdge , core::pack::interaction_graph::SymmLinearMemEdge , core::pack::interaction_graph::SymmMinimalistEdge
• print_current_state_assignment() : core::pack::interaction_graph::DensePDInteractionGraph , core::pack::interaction_graph::DoubleDensePDInteractionGraph , core::pack::interaction_graph::DoubleLazyInteractionGraph , core::pack::interaction_graph::FASTERInteractionGraph , core::pack::interaction_graph::InteractionGraphBase , core::pack::interaction_graph::LazyInteractionGraph , core::pack::interaction_graph::LinearMemoryInteractionGraph , core::pack::interaction_graph::PDInteractionGraph , core::pack::interaction_graph::SymmLinearMemoryInteractionGraph , core::pack::interaction_graph::SymmMinimalistInteractionGraph
• print_dihedrals() : core::chemical::ResidueType
• print_dot_bit_string() : core::pack::interaction_graph::InvRotamerDots , core::scoring::sasa::LeGrandSasa
• print_header() : core::import_pose::PDBSilentStruct , core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::BinarySilentStruct , core::io::silent::RNA_SilentStruct , core::io::silent::ScoreFileSilentStruct , core::io::silent::ScoreJumpFileSilentStruct , core::io::silent::SilentStruct , core::scoring::motif::ResPairMotif
• print_hpatch_avoidance_stats() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >
• print_info() : core::pose::rna::BasePair
• print_internal_energies() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• print_internal_energies_for_current_state_assignment() : core::pack::interaction_graph::HPatchInteractionGraph< V, E, G > , core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >
• print_metric() : core::pose::Pose
• print_parent_remarks() : core::io::silent::SilentStruct
• print_particles() : core::optimization::ParticleSwarmMinimizer
• print_pretty_path_distances() : core::chemical::ResidueType
• print_quantiles() : core::scoring::motif::XformScore
• print_residue_numbers() : core::io::silent::SilentStruct
• print_score_functions() : core::scoring::disulfides::FullatomDisulfidePotential
• print_score_header() : core::io::silent::SilentStruct
• print_scores() : core::io::raw_data::RawStruct , core::io::raw_data::ScoreStructJSON , core::io::silent::SilentStruct , core::scoring::motif::XformScore
• print_scores_norm() : core::scoring::motif::XformScore
• print_surface_avoidance_stats() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• print_vertex_groups() : core::pack::interaction_graph::InteractionGraphBase
• print_vertices() : core::graph::Graph , core::pack::interaction_graph::InteractionGraphBase
• printGrishinFormat() : core::sequence::SequenceAlignment
• private_data_to_public_array() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• pro_cd_cprev_n_ca_interres_torsion_params() : core::scoring::methods::ResidueCartBondedParameters
• pro_CD_index() : core::scoring::methods::ResidueCartBondedParameters
• prob() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• prob_sum_of_gaussians() : core::scoring::func::SOGFunc_Impl
• prob_to_accumulate() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• 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
• probabilistically_commit_relaxation() : core::pack::interaction_graph::FASTERInteractionGraph
• probability() : core::pack::dunbrack::DunbrackRotamerSampleData
• probability_matrix() : core::scoring::bin_transitions::BinTransitionData
• probability_row() : core::sequence::SequenceProfile
• probability_to_accumulate_while_building_rotamers() : core::pack::dunbrack::SingleResidueDunbrackLibrary , core::pack::dunbrack::SingleResiduePeptoidLibrary
• probabilty_row() : core::sequence::SequenceProfile
• probB() : core::scoring::packstat::PackingScore
• process_energy_change() : core::pose::metrics::PoseMetricContainer
• process_structure_change() : core::pose::metrics::PoseMetricContainer
• ProClosureEnergy() : core::scoring::methods::ProClosureEnergy
• prof_row() : core::sequence::SequenceProfile
• profile() : core::fragment::picking_old::vall::VallResidue , core::sequence::SequenceProfile
• profile_feature() : core::scoring::methods::ProQ_Energy
• profile_index_to_aa() : core::scoring::methods::ProQ_Energy
• profile_mapping() : core::scoring::constraints::SequenceProfileConstraint
• ProfSimScoringScheme() : core::sequence::ProfSimScoringScheme
• prohibit_property_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_property_iplus1() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_i() : core::scoring::bin_transitions::BinTransitionData
• prohibit_res_identity_iplus1() : core::scoring::bin_transitions::BinTransitionData
• project_deltaE_for_substitution() : core::pack::interaction_graph::DensePDNode , core::pack::interaction_graph::DoubleDensePDNode , core::pack::interaction_graph::DoubleLazyNode , core::pack::interaction_graph::FASTERNode , core::pack::interaction_graph::LazyNode , core::pack::interaction_graph::LinearMemNode , core::pack::interaction_graph::PDNode , core::pack::interaction_graph::SymmLinearMemNode , core::pack::interaction_graph::SymmMinimalistNode
• project_deltaE_for_substitution_surface() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE() : core::pack::interaction_graph::SurfaceNode< V, E, G >
• project_surface_deltaE_for_substitution() : core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >
• promote_sameresidue_nonjump_child() : core::kinematics::AtomTree
• properties() : core::chemical::ResidueType
• property() : core::pack::task::operation::ResidueHasProperty , core::pack::task::operation::ResiduePDBInfoHasLabel
• proposed_one_body_energy() : core::pack::interaction_graph::SimpleNode
• ProQ_Energy() : core::scoring::methods::ProQ_Energy
• ProQPotential() : core::scoring::ProQPotential
• protein_position_equal_within() : core::scoring::methods::PoissonBoltzmannEnergy
• ProteinSilentStruct_SinglePrecCreator() : core::io::silent::ProteinSilentStruct_SinglePrecCreator
• ProteinSilentStruct_Template() : core::io::silent::ProteinSilentStruct_Template< T >
• ProteinSilentStructCreator() : core::io::silent::ProteinSilentStructCreator
• proton_chi_2_chi() : core::chemical::ResidueType
• proton_chi_extra_samples() : core::chemical::ResidueType
• proton_chi_samples() : core::chemical::ResidueType
• provide_stored_derivatives() : core::optimization::ArmijoLineMinimization , core::optimization::LineMinimizationAlgorithm , core::optimization::StrongWolfeLineMinimization
• prsa_feature() : core::scoring::methods::ProQ_Energy
• prune_small_bins() : core::scoring::motif::XformScore
• PseudoBond() : core::conformation::PseudoBond
• PseudoBondCollection() : 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::pose::Pose , core::scoring::motif::Xfres
• psi_max() : core::util::ABEGO
• psi_min() : core::util::ABEGO
• pssm_energy_at_frame_seqpos() : core::scoring::methods::NMerPSSMEnergy
• public_array_to_private_data() : core::pack::dunbrack::cenrot::CentroidRotamerSampleData
• push_back() : core::conformation::PseudoBondCollection , core::graph::EdgeList , core::id::SequenceMapping , core::io::silent::SilentFileData , core::pack::task::TaskFactory , core::scoring::dssp::StrandPairingSet , core::scoring::motif::MotifHits
• push_back_raw() : core::scoring::motif::MotifHits
• push_back_rotamer() : core::pack::rotamer_set::RotamerSet_ , core::pack::rotamer_set::RotamerSubset
• push_front() : core::graph::EdgeList
• push_passport() : core::conformation::Conformation
• put_intra_into_total() : core::scoring::etable::BaseEtableEnergy< Derived > , core::scoring::hbonds::HBondOptions , core::scoring::methods::EnergyMethodOptions
• put_jump_stubs_intra_residue() : core::kinematics::FoldTree
• PyEnergyMethodRegistrator() : core::scoring::methods::PyEnergyMethodRegistrator
• pythag() : core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl