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Here is a list of all variables with links to the classes they belong to:

### - p -

- P : BALL::Rotamer
- p : BALL::TCircle3< T >, BALL::TLine3< T >, BALL::TPlane3< T >, BALL::TriangulatedSphere::Face, BALL::TSphere3< T >, boost::hash< RTpieCpp::InstanceHandle >::conv, boost::hash< RTpieCpp::MeshHandle >::conv
- p_i_ : BALL::ConjugateGradientMinimizer
- p_t_ : BALL::ConjugateGradientMinimizer
- pair_items : BALL::CIFFile::SaveFrame
- pairwise_scores_ : BALL::PoseClustering
- par1 : BALL::QSAR::Kernel
- par2 : BALL::QSAR::Kernel
- parameter_filename_ : BALL::DockingAlgorithm
- parameterDefaults : BALL::QSAR::RegistryEntry
- parameterNames : BALL::QSAR::RegistryEntry
- parameters_ : BALL::ClaverieParameter, BALL::ForceField, BALL::GeneticAlgorithm, BALL::MMFF94BendParameters, BALL::MMFF94ESParameters, BALL::MMFF94PlaneParameters, BALL::MMFF94StretchBendParameters, BALL::MMFF94StretchParameters, BALL::MMFF94Torsion, BALL::MMFF94TorsionParameters, BALL::MMFF94VDWParameters, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::ShiftModel, BALL::ShiftModule
- parameters_by_row_ : BALL::MMFF94StretchBendParameters
- parameters_initialized_ : BALL::AmberFF, BALL::CharmmFF, BALL::MMFF94
- parent : BALL::GAFFCESParser::CESPredicate, BALL::HashGridBox3< Item >
- parent_ : BALL::ConformationSet, BALL::FPTBondOrderStrategy::FPTBondOrderAssignment_, BALL::NMRStarFile::NMRAtomDataSet, BALL::SimpleDownloaderHelper::HelperThread, BALL::VIEW::AtomOverview
- PARENT_DIRECTORY : BALL::FileSystem
- parent_widget_ : BALL::VIEW::ServerWidget::BALLViewServer
- parity : BALL::MOLFile::AtomStruct
- pars_ : BALL::Bruker1DFile
- PARSE_INI_FILE : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- PARSE_PARTIAL_CHARGES : BALL::PDBFile::Default, BALL::PDBFile::Option
- parse_partial_charges_ : BALL::PDBFile
- parser_ : BALL::GAFFCESParser::CESPredicate
- parsf1_ : BALL::Bruker2DFile
- parsf2_ : BALL::Bruker2DFile
- partial_charge : BALL::PDB::RecordATOM
- partner_atom : BALL::PDB::RecordSLTBRG
- partner_residue : BALL::PDB::RecordSSBOND
- partner_type_to_htype_ : BALL::MMFF94AtomTyper
- past_the_end_ : BALL::Enumerator< Container, SiteIterator, Variant >::IteratorTraits_
- paste_action_ : BALL::VIEW::MolecularControl
- paste_id_ : BALL::VIEW::MolecularControl
- path_ : BALL::Path, BALL::SimpleDownloaderHelper::HelperThread
- path_array_ : BALL::Path
- path_array_valid_ : BALL::Path
- PATH_SEPARATOR : BALL::FileSystem
- pause_ : BALL::DockingAlgorithm
- pb_solver_ : BALL::PB
- pbcis_ : BALL::MMFF94ESParameters
- pbuf_ : BALL::LogStreamBuf
- pcount : BALL::TriangulatedSphere::Face
- PDB_atom_map_ : BALL::PDBFile
- pdb_id : BALL::PDB::AdditionalAtomInfo
- peak_list_ : BALL::Experiment< PeakListType >
- peak_set_ : BALL::GeometricFit
- peaklist_ : BALL::CreateSpectrumProcessor
- peaks_ : BALL::ShiftModel1D, BALL::ShiftModel2D
- peeling_order_ : BALL::RingAnalyser
- penalties_ : BALL::AssignBondOrderProcessor, BALL::FPTBondOrderStrategy
- penalty : BALL::FPTBondOrderStrategy::Assignment_
- penalty_ : BALL::Constraint
- PENALTY_MOBILE : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- PENALTY_STATIC : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- periodic_boundary : BALL::ForceField
- PERIODIC_BOX_ADD_SOLVENT : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_DISTANCE : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_ENABLED : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_LOWER : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_SOLVENT_FILE : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_BOX_UPPER : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- PERIODIC_WATER_FILE : BALL::PeriodicBoundary::Default, BALL::PeriodicBoundary::Option
- permutation : BALL::TreeWidthImplementation< UndirectedGraph >::QuickBB< Lowerbound, Upperbound >::QuickBBState
- phase : BALL::AmberTorsion::SingleAmberTorsion, BALL::CharmmTorsion::SingleCharmmTorsion, BALL::CosineTorsion::SingleValues, BALL::QuadraticImproperTorsion::Values
- phi_ : BALL::GeometricFit::RotationAngles_, BALL::Peptides::AminoAcidDescriptor, BALL::ResidueRotamerSet
- phi_grid : BALL::FDPB
- PHI_MAX : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- PHI_MIN : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- phis_ : BALL::MMFF94ESParameters
- PI : BALL::Constant
- pi_ : BALL::PoseClustering
- pick_select_ : BALL::VIEW::PickingMode
- picking_mode_ : BALL::VIEW::GLRenderer
- pilp : BALL::MMFF94AtomType
- pixel_buffer_ : BALL::VIEW::GLOffscreenTarget
- planBackward_ : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- planCalculated_ : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- PLANCK : BALL::Constant
- plane_ : BALL::VIEW::SetClippingPlane
- plane_to_item_ : BALL::VIEW::GeometricControl
- planForward_ : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- plus_ : BALL::DSN6File
- point : BALL::RSComputer::ProbePosition, BALL::SESSingularityCleaner::ProbeIntersection
- point_ : BALL::SASVertex, BALL::SESTriangulator, BALL::SESVertex, BALL::TBox3< T >, BALL::TrianglePoint, BALL::VIEW::ClippingPlane, BALL::VIEW::GridVisualisation
- point_ptr_ : BALL::VIEW::Sphere
- pointer_list_ : BALL::PersistenceManager
- pointer_map_ : BALL::PersistenceManager
- points : BALL::VIEW::GridVisualisation
- points_ : BALL::TriangulatedSurface
- POL_ES_THRESHOLD : BALL::Polarity
- POLAR : BALL::SLICKEnergy::Default, BALL::SLICKEnergy::Option, BALL::SLICKScore::Default, BALL::SLICKScore::Option
- POLAR_AVG : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_CHARGE_RULES : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_FOCUS_GRID_AROUND_LIGAND : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_GB : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_METHOD : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_OVERWRITE_CHARGES : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_OVERWRITE_RADII : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- POLAR_RADIUS_RULES : BALL::PolarSolvation::Default, BALL::PolarSolvation::Option
- polymer_class : BALL::NMRStarFile::MonomericPolymer
- pool_ : BALL::SmartsMatcher
- pools_ : BALL::GeneticAlgorithm
- POPULATION : BALL::EvolutionaryDocking::Default, BALL::EvolutionaryDocking::Option
- POPULATION_NUMBER : BALL::EvolutionaryDocking::Default, BALL::EvolutionaryDocking::Option
- population_size_ : BALL::GeneticAlgorithm
- port_ : BALL::TCPServer, BALL::VIEW::ServerWidget::BALLViewServer
- pos_C : BALL::HBondProcessor::ResidueData
- pos_H : BALL::HBondProcessor::ResidueData
- pos_N : BALL::HBondProcessor::ResidueData
- pos_O : BALL::HBondProcessor::ResidueData
- posbridges_ : BALL::SecondaryStructureProcessor
- poses : BALL::PoseClustering::ClusterProperties
- poses_ : BALL::PoseClustering
- position : BALL::HMOFile::HMOCharge, BALL::MOL2File::AtomStruct, BALL::MOLFile::AtomStruct
- position_ : BALL::Atom, BALL::Composite::CompositeIteratorTraits, BALL::Enumerator< Container, SiteIterator, Variant >::IteratorTraits_, BALL::Enumerator< Container, SiteIterator, Variant >, BALL::HashSet< Key >::IteratorTraits, BALL::Peak< PositionType >, BALL::VIEW::LightSource
- position_data_size : BALL::TRRFile::TRRHeader
- POSITION_VALUE_NA : BALL::NMRStarFile
- post_dock_optimization_ : BALL::DockProblem
- POST_OPTIMIZATION_STEP_WIDTH : BALL::IMGDock::Default, BALL::IMGDock::Option
- POST_OPTIMIZATION_STEPS : BALL::IMGDock::Default, BALL::IMGDock::Option
- potential_energy_ : BALL::SnapShot
- potential_grid_ : BALL::VIEW::FieldLineCreator
- pov_nr_ : BALL::VIEW::Scene
- pre_translation_a_ : BALL::GeometricFit
- pre_translation_b_ : BALL::GeometricFit
- PRECISION : BALL::BinaryFingerprintMethods::Default, BALL::BinaryFingerprintMethods::Option
- precision_ : BALL::TRRFile
- predicate : BALL::ExpressionParser::SyntaxTree
- predicate_ : BALL::CompositeIteratorTraits, BALL::ExpressionTree
- predicted_affinities_ : BALL::Rescoring
- PREDICTION_METHOD : BALL::HBondProcessor::Default, BALL::HBondProcessor::Option
- predictions : BALL::ScoringOptimizer::Result
- preferences_ : BALL::VIEW::DisplayProperties, BALL::VIEW::PyWidget
- preferences_action_ : BALL::VIEW::MainControl
- preferences_dialog_ : BALL::VIEW::MainControl
- preferences_file_ : BALL::VIEW::MainControl
- prefix : BALL::LogStreamBuf::StreamStruct
- prefix_ : BALL::RuleEvaluator, BALL::VIEW::DownloadPDBFile
- pres_size : BALL::TRRFile::TRRHeader
- PRESSURE : BALL::PierottiCavFreeEnergyProcessor::Default, BALL::PierottiCavFreeEnergyProcessor::Option, BALL::ReissCavFreeEnergyProcessor::Default, BALL::ReissCavFreeEnergyProcessor::Option
- prev_shift_val_ : BALL::ShiftedLVMMMinimizer
- primitive_manager_ : BALL::VIEW::MainControl
- print_expected : BALL::QSAR::PredictionConfiguration
- PRINT_TIMING : BALL::FDPB::Default, BALL::FDPB::Option
- priority_queue_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
- probabilities_ : BALL::GeneticAlgorithm
- probe_group_ : BALL::GridAnalysis
- probe_intersections_ : BALL::SESSingularityCleaner
- PROBE_LAYER_RADIUS : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- probe_positions_ : BALL::RSComputer
- PROBE_RADIUS : BALL::FDPB::Default, BALL::FDPB::Option, BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option, BALL::NumericalSAS::Default, BALL::NumericalSAS::Option, BALL::PCMCavFreeEnergyProcessor::Default, BALL::PCMCavFreeEnergyProcessor::Option, BALL::PierottiCavFreeEnergyProcessor::Default, BALL::PierottiCavFreeEnergyProcessor::Option, BALL::ReissCavFreeEnergyProcessor::Default, BALL::ReissCavFreeEnergyProcessor::Option, BALL::UhligCavFreeEnergyProcessor::Default, BALL::UhligCavFreeEnergyProcessor::Option
- probe_radius_ : BALL::ReducedSurface, BALL::SurfaceProcessor
- PROBE_SPHERE_RADIUS : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- PROBE_SPHERE_RADIUS_HYDROGEN_FREE : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- processor_ : BALL::VIEW::AtomOverview
- prod_ : BALL::DSN6File
- progress_bar_ : BALL::VIEW::DownloadElectronDensity, BALL::VIEW::DownloadPDBFile
- project_ : BALL::VIEW::HelpViewer, BALL::VIEW::ShowHelpMessage
- project_target_to_ring_plane_ : BALL::HaighMallionShiftProcessor
- projection_mode_ : BALL::VIEW::Camera
- properties_ : BALL::FPTBondOrderStrategy::FPTBondOrderAssignment_, BALL::SmartsParser::SPAtom
- properties_real_ : BALL::EmpiricalHSShiftProcessor::PropertiesForShift_
- properties_string_ : BALL::EmpiricalHSShiftProcessor::PropertiesForShift_
- PROPERTY__ANISOTROPY_SHIFT : BALL::AnisotropyShiftProcessor
- PROPERTY__EF_SHIFT : BALL::EFShiftProcessor
- PROPERTY__EHS_SHIFT : BALL::EmpiricalHSShiftProcessor
- PROPERTY__EXPERIMENTAL__SHIFT : BALL::ShiftModule
- PROPERTY__HBOND_SHIFT : BALL::HBondShiftProcessor
- PROPERTY__RANDOM_COIL_SHIFT : BALL::RandomCoilShiftProcessor
- PROPERTY__RING_CURRENT_SHIFT : BALL::HaighMallionShiftProcessor, BALL::JohnsonBoveyShiftProcessor
- PROPERTY__SHIFT : BALL::ShiftModule
- property_files_ : BALL::EmpiricalHSShiftProcessor
- property_pairs_ : BALL::EmpiricalHSShiftProcessor
- protein_ : BALL::Rescoring1D, BALL::VIEW::PeptideDialog
- proteinname_ : BALL::Peptides::PeptideBuilder
- proton_list_ : BALL::AnisotropyShiftProcessor, BALL::JohnsonBoveyShiftProcessor
- PROTON_MASS : BALL::Constant
- PSEUDO_ATOMS_INIFile : BALL::Peptides::NameConverter::Default, BALL::Peptides::NameConverter::Option
- pseudo_conventions_ : BALL::Peptides::NameConverter
- pseudo_conversion_table_ : BALL::Peptides::NameConverter
- psi_ : BALL::GeometricFit::RotationAngles_, BALL::Peptides::AminoAcidDescriptor, BALL::ResidueRotamerSet
- PSI_MAX : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- PSI_MIN : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- ptr_ : BALL::TContourSurface< T >::Cube
- PW_GAUSSIAN_WIDTH : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- PW_MAX_DISTANCE : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- PW_SQUARE_WELL : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- python_format : BALL::VIEW::PythonHighlighter
- python_keywords : BALL::VIEW::PythonHighlighter
- python_line_ : BALL::VIEW::TestFramework
- python_patterns : BALL::VIEW::PythonHighlighter
- python_settings_ : BALL::VIEW::PyWidget