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

### - a -

- A : BALL::LennardJones::Values, BALL::Potential1210::Values
- a : BALL::PDB::RecordCRYST1::UnitCell, BALL::PDB::Structure::UnitCellInfo, BALL::SortedPosition2, BALL::SortedPosition3, BALL::TSimpleBox3< T >
- a0 : BALL::Constant
- a1 : BALL::HybridisationProcessor::AtomNames_
- a2 : BALL::HybridisationProcessor::AtomNames_
- a3 : BALL::HybridisationProcessor::AtomNames_
- A_ : BALL::LennardJones, BALL::Pair6_12RDFIntegrator, BALL::Potential1210, BALL::StructureMapper
- a_i_ : BALL::ConjugateGradientMinimizer
- A_STAR : BALL::AssignBondOrderProcessor::Algorithm
- abbreviation_common : BALL::NMRStarFile::MolecularSystem
- abop : BALL::BondOrderAssignmentStrategy, BALL::PartialBondOrderAssignment
- abort_ : BALL::DockingAlgorithm, BALL::VIEW::DockingFinishedMessage
- abort_by_energy_enabled_ : BALL::EnergyMinimizer, BALL::MolecularDynamics
- abort_energy_ : BALL::EnergyMinimizer, BALL::MolecularDynamics
- abort_test : BALL::VIEW::TestFramework
- aborted_ : BALL::EnergyMinimizer, BALL::VIEW::DownloadElectronDensity, BALL::VIEW::DownloadPDBFile
- about_to_quit_ : BALL::VIEW::MainControl, BALL::VIEW::RenderSetup
- ABSOLUTE_TEMPERATURE : BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option, BALL::PCMCavFreeEnergyProcessor::Default, BALL::PCMCavFreeEnergyProcessor::Option, BALL::PierottiCavFreeEnergyProcessor::Default, BALL::PierottiCavFreeEnergyProcessor::Option, BALL::ReissCavFreeEnergyProcessor::Default, BALL::ReissCavFreeEnergyProcessor::Option
- ac : BALL::BondOrderAssignment
- ac_ : BALL::AssignBondOrderProcessor, BALL::VIEW::FieldLineCreator
- acceptor_ : BALL::HBondProcessor::HBond, BALL::TCPServer
- acceptor_types_ : BALL::HBondShiftProcessor
- acceptors_ : BALL::HBondProcessor, BALL::HBondShiftProcessor
- accession_code : BALL::NMRStarFile::MolecularSystem::RelatedDB, BALL::NMRStarFile::MonomericPolymer::HomologDB
- action : BALL::VIEW::Hotkey
- action1_ : BALL::VIEW::PubChemDialog
- action2_ : BALL::VIEW::PubChemDialog
- action_ : BALL::VIEW::TestFramework, BALL::VIEW::UndoManagerDialog
- actions_ : BALL::VIEW::DatasetController, BALL::VIEW::InteractionModeManager
- actions_for_one_set_ : BALL::VIEW::DatasetController
- activated_item_ : BALL::VIEW::AssignBondOrderResultsDialog
- active_ : BALL::VIEW::ClippingPlane
- active_stereo_action_ : BALL::VIEW::Scene
- activities : BALL::QSAR::InputConfiguration
- activity_names : BALL::QSAR::InputConfiguration
- adapt_char_ : BALL::TRRFile
- adapt_double_ : BALL::TRRFile
- adapt_float_ : BALL::DCDFile, BALL::TRRFile
- adapt_size_ : BALL::DCDFile, BALL::TRRFile
- add_button_ : BALL::VIEW::PubChemDialog
- ADD_HBONDS : BALL::HBondProcessor::Default, BALL::HBondProcessor::Option
- ADD_HYDROGENS : BALL::AssignBondOrderProcessor::Default, BALL::AssignBondOrderProcessor::Option
- add_hydrogens : BALL::FragmentDB
- add_hydrogens_action_ : BALL::VIEW::Scene
- add_menu_ : BALL::VIEW::EditMode
- add_missing_hydrogens_ : BALL::AssignBondOrderProcessor
- additional_grid_distance_ : BALL::VIEW::ColorProcessor
- adjacent_edges_ : BALL::NodeItem< Node, Edge >
- advanced : BALL::ParamFile::ParameterDescription
- advanced_options_modified_ : BALL::VIEW::DisplayProperties
- ai : BALL::MMFF94VDWParameters::VDWEntry
- Aij_ : BALL::LennardJones
- ALGORITHM : BALL::AssignBondOrderProcessor::Default, BALL::AssignBondOrderProcessor::Option
- all_amino_acids_ : BALL::VIEW::PeptideDialog
- all_aromatic_atoms_ : BALL::Kekuliser
- all_atoms_ : BALL::SmilesParser
- all_fragments_ : BALL::FragmentDistanceCollector
- all_hydrogen_are_targets_ : BALL::HaighMallionShiftProcessor
- ALL_LIG_NONB_PAIRS : BALL::ScoringFunction::Default, BALL::ScoringFunction::Option
- all_ligand_nonbonded_ : BALL::ScoringFunction
- all_names_ : BALL::VIEW::GLRenderer
- all_residues_hashgrid_ : BALL::ScoringFunction
- all_small_beers_ : BALL::RingPerceptionProcessor
- all_small_rings_ : BALL::RingPerceptionProcessor
- all_torsions_ : BALL::ResidueTorsions
- ALLOWED_INTERMOL_OVERLAP : BALL::ScoringFunction::Default, BALL::ScoringFunction::Option
- allowed_intermolecular_overlap_ : BALL::ScoringFunction
- ALLOWED_INTRAMOL_OVERLAP : BALL::ScoringFunction::Default, BALL::ScoringFunction::Option
- allowed_intramolecular_overlap_ : BALL::ScoringFunction
- allowed_values : BALL::ParamFile::ParameterDescription
- ALPHA : BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option, BALL::RegularExpression
- alpha : BALL::PDB::RecordCRYST1::UnitCell, BALL::PDB::Structure::UnitCellInfo
- alpha_ : BALL::AssignBondOrderProcessor, BALL::CCP4File, BALL::CrystalInfo, BALL::DSN6File, BALL::LineSearch, BALL::PairExpInteractionEnergyProcessor, BALL::PairExpRDFIntegrator
- alpha_blending_ : BALL::VIEW::ColorMap
- alpha_i : BALL::MMFF94VDWParameters::VDWEntry
- alpha_proton_oxygen_hydrogen_separation_distance_ : BALL::HBondShiftProcessor
- ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE : BALL::HBondProcessor
- ALPHANUMERIC : BALL::RegularExpression
- alternate_location_indicator : BALL::PDB::RecordANISOU, BALL::PDB::RecordATOM, BALL::PDB::RecordHETATM, BALL::PDB::RecordHYDBND::HydrogenAtom, BALL::PDB::RecordHYDBND::HydrogenPartnerAtom, BALL::PDB::RecordLINK::LinkPartner, BALL::PDB::RecordSIGATM, BALL::PDB::RecordSIGUIJ, BALL::PDB::RecordSLTBRG::PartnerAtom
- alternate_location_indicator_ : BALL::PDBFile
- amber_nb_ : BALL::Electrostatic
- ambient_color : BALL::VIEW::Stage::Material
- ambient_intensity : BALL::VIEW::Stage::Material
- ambiguity_code : BALL::NMRStarFile::NMRAtomData
- amide_proton_factor_ : BALL::HBondShiftProcessor
- amide_proton_oxygen_hydrogen_separation_distance_ : BALL::HBondShiftProcessor
- AMIDE_PROTON_OXYGEN_SEPARATION_DISTANCE : BALL::HBondProcessor
- amide_proton_subtrahend_ : BALL::HBondShiftProcessor
- amide_protons_are_targets_ : BALL::HBondShiftProcessor
- angle : BALL::MMFF94Torsion::Torsion
- angle_ : BALL::RSEdge, BALL::SASEdge, BALL::VIEW::LightSource
- angle_action_ : BALL::VIEW::MolecularControl
- angle_measure : BALL::PDB::RecordCISPEP
- ANGLE_TOLERANCE : BALL::CHPI::Default, BALL::CHPI::Option, BALL::CHPISlick::Default, BALL::CHPISlick::Option
- animation_export_PNG_action_ : BALL::VIEW::Scene
- animation_export_POV_action_ : BALL::VIEW::Scene
- animation_export_VRML_action_ : BALL::VIEW::Scene
- animation_points_ : BALL::VIEW::Scene
- animation_repeat_action_ : BALL::VIEW::Scene
- animation_running_ : BALL::VIEW::SnapshotVisualisationDialog
- animation_smoothness_ : BALL::VIEW::Scene
- animation_thread_ : BALL::VIEW::Scene
- anion : BALL::MMFF94AtomTyper::AromaticType
- applied : BALL::GRAPH::UndoEliminateOperation< UndirectedGraph >
- APPLY_FIRST_SOLUTION : BALL::AssignBondOrderProcessor::Default, BALL::AssignBondOrderProcessor::Option
- apply_processor_ : BALL::VIEW::AtomOverview
- aps_matcher : BALL::GAFFCESParser::CESPredicate
- aps_terms : BALL::GAFFCESParser::APSMatcher
- argument : BALL::ExpressionParser::SyntaxTree
- argument_ : BALL::ExpressionPredicate
- arom : BALL::MMFF94AtomType
- arom_proc_ : BALL::SMARTSPredicate
- aromat_list_ : BALL::JohnsonBoveyShiftProcessor
- aromatic_atoms_ : BALL::Kekuliser
- aromatic_bonds_ : BALL::MMFF94
- aromatic_rings_ : BALL::AtomTyper, BALL::Kekuliser, BALL::MMFF94, BALL::MMFF94ChargeProcessor
- aromatic_systems_ : BALL::Kekuliser
- aromatic_types_5_map_ : BALL::MMFF94AtomTyper
- arrow_width_ : BALL::VIEW::AddCartoonModel
- ASP_SEPERATION : BALL::BindingPocketProcessor::Default, BALL::BindingPocketProcessor::Option
- aspec : BALL::MMFF94AtomType
- ASSIGN_CHARGES : BALL::AmberFF::Default, BALL::AmberFF::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::MMFF94::Default, BALL::MMFF94::Option
- ASSIGN_TYPENAMES : BALL::AmberFF::Default, BALL::AmberFF::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::MMFF94::Default, BALL::MMFF94::Option
- ASSIGN_TYPES : BALL::AmberFF::Default, BALL::AmberFF::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::MMFF94::Default, BALL::MMFF94::Option
- assignment : BALL::FPTBondOrderStrategy::BackTrackingState_
- assignment_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
- asu_ : BALL::CrystalGenerator
- ATIJK : BALL::MMFF94StretchBend::Bend
- atom : BALL::CharmmEEF1::Data, BALL::FragmentDB::BuildBondsProcessor::Connection, BALL::PDB::Structure::AtomEntry, BALL::StaticLigandFragment::Connection, BALL::VIEW::EditOperation
- atom1 : BALL::AmberTorsion::SingleAmberTorsion, BALL::CharmmTorsion::SingleCharmmTorsion, BALL::CosineTorsion::Data, BALL::CosineTorsion::SingleData, BALL::LennardJones::Data, BALL::MMFF94StretchBend::Bend, BALL::MMFF94StretchBend::Stretch, BALL::MMFF94Torsion::Torsion, BALL::MOL2File::BondStruct, BALL::Potential1210::Data, BALL::QuadraticAngleBend::Data, BALL::QuadraticBondStretch::Data, BALL::QuadraticImproperTorsion::Data
- atom2 : BALL::AmberTorsion::SingleAmberTorsion, BALL::CharmmTorsion::SingleCharmmTorsion, BALL::CosineTorsion::Data, BALL::CosineTorsion::SingleData, BALL::LennardJones::Data, BALL::MMFF94StretchBend::Bend, BALL::MMFF94StretchBend::Stretch, BALL::MMFF94Torsion::Torsion, BALL::MOL2File::BondStruct, BALL::Potential1210::Data, BALL::QuadraticAngleBend::Data, BALL::QuadraticBondStretch::Data, BALL::QuadraticImproperTorsion::Data
- atom3 : BALL::AmberTorsion::SingleAmberTorsion, BALL::CharmmTorsion::SingleCharmmTorsion, BALL::CosineTorsion::Data, BALL::CosineTorsion::SingleData, BALL::MMFF94StretchBend::Bend, BALL::MMFF94Torsion::Torsion, BALL::QuadraticAngleBend::Data, BALL::QuadraticImproperTorsion::Data
- atom4 : BALL::AmberTorsion::SingleAmberTorsion, BALL::CharmmTorsion::SingleCharmmTorsion, BALL::CosineTorsion::Data, BALL::CosineTorsion::SingleData, BALL::MMFF94Torsion::Torsion, BALL::QuadraticImproperTorsion::Data
- atom_ : BALL::NodeItem< Node, Edge >, BALL::Peak< PositionType >, BALL::ReducedSurface, BALL::RSVertex, BALL::SESVertex, BALL::SmartsParser::SPAtom
- atom_areas_ : BALL::NumericalSAS
- atom_array : BALL::FDPB
- atom_bijection_ : BALL::PoseClustering
- atom_data : BALL::NMRStarFile::NMRAtomDataSet
- atom_distance_ : BALL::VIEW::FieldLineCreator
- ATOM_EXACT_CHANGE : BALL::MOLFile::Property
- atom_forces_ : BALL::SnapShot
- atom_format_ : BALL::MOLFile
- atom_grid_ : BALL::VIEW::ColorProcessor
- atom_group : BALL::NMRStarFile::ShiftReferenceElement
- ATOM_H0_DESIGNATOR : BALL::MOLFile::Property
- ATOM_HYDROGEN_COUNT : BALL::MOLFile::Property
- atom_ID : BALL::NMRStarFile::NMRAtomData
- atom_infos_ : BALL::Kekuliser
- ATOM_INVERSION_RETENTION : BALL::MOLFile::Property
- atom_list_ : BALL::JohnsonBoveyShiftProcessor
- atom_map_ : BALL::PDBFile
- ATOM_MASS_DIFFERENCE : BALL::MOLFile::Property
- atom_name : BALL::NMRStarFile::NMRAtomData, BALL::PDB::RecordANISOU, BALL::PDB::RecordATOM, BALL::PDB::RecordHETATM, BALL::PDB::RecordHYDBND::HydrogenAtom, BALL::PDB::RecordHYDBND::HydrogenPartnerAtom, BALL::PDB::RecordLINK::LinkPartner, BALL::PDB::RecordSIGATM, BALL::PDB::RecordSIGUIJ, BALL::PDB::RecordSLTBRG::PartnerAtom
- atom_name_A : BALL::ResidueTorsions::Data
- atom_name_B : BALL::ResidueTorsions::Data
- atom_name_C : BALL::ResidueTorsions::Data
- atom_name_D : BALL::ResidueTorsions::Data
- atom_name_in_current_strand : BALL::PDB::RecordSHEET
- atom_name_in_previous_strand : BALL::PDB::RecordSHEET
- atom_names : BALL::JohnsonBoveyShiftProcessor::Ring
- atom_number_ : BALL::VIEW::EditMode
- atom_overview_ : BALL::VIEW::MolecularControl
- atom_overview_selection_ : BALL::VIEW::MolecularControl
- atom_pairwise_ : BALL::ScoringComponent
- atom_positions_ : BALL::SnapShot
- atom_properties_ : BALL::VIEW::EditMode
- ATOM_REACTION_COMPONENT_NUMBER : BALL::MOLFile::Property
- ATOM_REACTION_COMPONENT_TYPE : BALL::MOLFile::Property
- atom_serial_number : BALL::PDB::RecordCON061, BALL::PDB::RecordCON062, BALL::PDB::RecordCON063, BALL::PDB::RecordCON064, BALL::PDB::RecordCON06, BALL::PDB::RecordCONECT
- atom_status_ : BALL::RSComputer
- ATOM_STEREO_CARE_BOX : BALL::MOLFile::Property
- atom_surface_map_ : BALL::NumericalSAS
- atom_surfaces_ : BALL::NumericalSAS
- atom_to_block_ : BALL::AssignBondOrderProcessor, BALL::FPTBondOrderStrategy
- atom_to_node_ : BALL::TSimpleMolecularGraph< Node, Edge >
- atom_to_test : BALL::GAFFCESParser::CESPredicate
- atom_to_tnode_ : BALL::RingPerceptionProcessor
- atom_to_virtual_bond_index_ : BALL::AssignBondOrderProcessor
- atom_type : BALL::GAFFTypeProcessor::TypeDefinition, BALL::NMRStarFile::NMRAtomData, BALL::NMRStarFile::ShiftReferenceElement
- ATOM_TYPE_FF_FILENAME : BALL::HybridisationProcessor::Default, BALL::HybridisationProcessor::Option
- ATOM_TYPE_FILE : BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option
- atom_type_normalization_factor_ : BALL::AssignBondOrderProcessor
- atom_type_smarts_ : BALL::HybridisationProcessor
- ATOM_TYPE_SMARTS_FILENAME : BALL::HybridisationProcessor::Default, BALL::HybridisationProcessor::Option
- atom_typer_ : BALL::MMFF94
- atom_types_ : BALL::AssignTypeProcessor, BALL::ForceFieldParameters, BALL::GAFFTypeProcessor, BALL::GridedPLP, BALL::MMFF94, BALL::MMFF94AtomTyper, BALL::PLPScoring, BALL::SolventParameter
- atom_types_map_ : BALL::GridBasedScoring
- ATOM_VALENCE : BALL::MOLFile::Property
- atom_vector_ : BALL::MolecularDynamics
- atom_velocities_ : BALL::SnapShot
- atom_volumes_ : BALL::NumericalSAS
- atomic_coordinate_records : BALL::PDB::BookKeeping
- atomic_number : BALL::GAFFTypeProcessor::TypeDefinition, BALL::MMFF94AtomTyper::AromaticType
- atomic_number_ : BALL::VIEW::Scene
- atomic_property : BALL::GAFFTypeProcessor::TypeDefinition
- atoms : BALL::PDB::Structure, BALL::RingAnalyser::Ring, BALL::StaticLigandFragment
- atoms_ : BALL::AtomTyper, BALL::ForceField, BALL::MMFF94ChargeProcessor, BALL::MOL2File, BALL::MOPACOutputFile
- atoms_to_delete : BALL::BondOrderAssignment
- atoms_to_fragments_ : BALL::ScoringFunction
- ATOMTYPE_FILENAME : BALL::GAFFTypeProcessor::Default, BALL::GAFFTypeProcessor::Option
- attached_hydrogens : BALL::GAFFTypeProcessor::TypeDefinition
- attenuation_ : BALL::VIEW::LightSource
- authors : BALL::PDB::RecordAUTHOR
- autoactivate_plugins_ : BALL::PluginManager
- AVERAGE_SECTION_NAME : BALL::CreateSpectrumProcessor
- AVOGADRO : BALL::Constant