- a -

• A : BALL::LennardJones::Values , BALL::Potential1210::Values
• a : BALL::PDB::Structure::UnitCellInfo , BALL::SortedPosition3 , BALL::TSimpleBox3< T > , BALL::PDB::RecordCRYST1::UnitCell , BALL::BindingPocketProcessor::Sphere_ , BALL::SortedPosition2
• a0 : BALL::Constant
• a1 : BALL::HybridisationProcessor::AtomNames_
• a2 : BALL::HybridisationProcessor::AtomNames_
• a3 : BALL::HybridisationProcessor::AtomNames_
• A_ : BALL::StructureMapper
• a_ : BALL::FermiBaseFunction , BALL::NucleotideMapping
• A_ : BALL::LennardJones , BALL::Potential1210 , BALL::Pair6_12RDFIntegrator
• a_i_ : BALL::ConjugateGradientMinimizer
• A_STAR : BALL::AssignBondOrderProcessor::Algorithm
• a_to_b_ : BALL::NucleotideMapping
• abbreviation_common : BALL::NMRStarFile::MolecularSystem
• abonds : BALL::Kekuliser::AtomInfo
• abop : BALL::BondOrderAssignmentStrategy , BALL::PartialBondOrderAssignment
• abort_ : BALL::DockingAlgorithm , BALL::VIEW::DockingFinishedMessage
• abort_by_energy_enabled_ : BALL::MolecularDynamics , BALL::EnergyMinimizer
• abort_energy_ : BALL::MolecularDynamics , BALL::EnergyMinimizer
• abort_test : BALL::VIEW::TestFramework
• aborted_ : BALL::EnergyMinimizer , BALL::VIEW::DownloadElectronDensity , BALL::VIEW::DownloadPDBFile
• about_to_quit_ : BALL::VIEW::MainControl
• ABSOLUTE_TEMPERATURE : BALL::NonpolarSolvation::Option , BALL::NonpolarSolvation::Default , BALL::PCMCavFreeEnergyProcessor::Option , BALL::PCMCavFreeEnergyProcessor::Default , BALL::PierottiCavFreeEnergyProcessor::Option , BALL::PierottiCavFreeEnergyProcessor::Default , BALL::ReissCavFreeEnergyProcessor::Option , BALL::ReissCavFreeEnergyProcessor::Default
• absolute_temperature_ : BALL::NonpolarSolvation
• ac : BALL::BondOrderAssignment
• ac_ : BALL::GeneralizedBornModel , BALL::AssignBondOrderProcessor , BALL::VIEW::FieldLineCreator
• acceptor_ : BALL::HBondProcessor::HBond , BALL::TCPServer
• acceptor_occupied_ : BALL::HBondShiftProcessor
• acceptor_types_ : BALL::HBondShiftProcessor
• acceptors_ : BALL::HBondShiftProcessor , BALL::HBondProcessor
• accession_code : BALL::NMRStarFile::MonomericPolymer::HomologDB , BALL::NMRStarFile::MolecularSystem::RelatedDB
• acidic_color_ : BALL::VIEW::ResidueTypeColorProcessor
• action : BALL::VIEW::Hotkey
• action1_ : BALL::VIEW::PubChemDialog
• action2_ : BALL::VIEW::PubChemDialog
• action_ : BALL::VIEW::TestFramework , BALL::VIEW::UndoManagerDialog , BALL::VIEW::DockingController
• actions_ : BALL::VIEW::DatasetController
• actions_for_one_set_ : BALL::VIEW::DatasetController
• activated_item_ : BALL::VIEW::AssignBondOrderResultsDialog
• active_ : BALL::VIEW::ClippingPlane
• active_index_ : BALL::VIEW::PluginDialog
• active_stereo_action_ : BALL::VIEW::Scene
• activities : 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::Option , BALL::HBondProcessor::Default
• ADD_HYDROGENS : BALL::AssignBondOrderProcessor::Option , BALL::AssignBondOrderProcessor::Default
• add_hydrogens : BALL::FragmentDB
• add_hydrogens_action_ : BALL::VIEW::EditableScene
• add_hydrogens_id_ : BALL::VIEW::MolecularStructure
• add_missing_hydrogens_ : BALL::AssignBondOrderProcessor
• additional_grid_distance_ : BALL::VIEW::ColorProcessor
• adjacent_edges_ : BALL::NodeItem< Node, Edge >
• advanced_options_modified_ : BALL::VIEW::DisplayProperties
• ai : BALL::MMFF94VDWParameters::VDWEntry
• Aij_ : BALL::LennardJones
• alg_ : BALL::VIEW::DockProgressDialog
• ALGORITHM : BALL::AssignBondOrderProcessor::Option , BALL::AssignBondOrderProcessor::Default
• algorithm_dialogs_ : BALL::VIEW::DockDialog
• ALGORITHM_NAME : BALL::RingPerceptionProcessor::Option , BALL::RingPerceptionProcessor::Default
• algorithm_opt_ : BALL::VIEW::DockDialog
• algorithm_type_ : BALL::AmberNonBonded , BALL::CharmmNonBonded , BALL::MMFF94NonBonded , BALL::RotationalEntropyLoss
• all_amino_acids_ : BALL::VIEW::PeptideDialog
• all_aromatic_atoms_ : BALL::Kekuliser
• all_aromatic_rings_ : BALL::CHPI
• all_atoms_ : BALL::SmilesParser
• all_CH_groups_ : BALL::CHPI
• all_fragments_ : BALL::FragmentDistanceCollector
• all_hydrogen_are_targets_ : BALL::HaighMallionShiftProcessor
• all_names_ : BALL::VIEW::GLRenderer
• all_small_beers_ : BALL::RingPerceptionProcessor
• all_small_rings_ : BALL::RingPerceptionProcessor
• all_torsions_ : BALL::ResidueTorsions
• allDiffEquations_ : BALL::QSAR::FitModel
• allEquations_ : BALL::QSAR::FitModel
• allowed_sf_ : BALL::VIEW::DockDialog
• ALPHA : BALL::RegularExpression , BALL::PairExpInteractionEnergyProcessor::Option , BALL::PairExpInteractionEnergyProcessor::Default
• alpha : BALL::PDB::RecordCRYST1::UnitCell , BALL::PDB::Structure::UnitCellInfo
• alpha_ : BALL::VIEW::ColorRGBA , BALL::CrystalInfo , BALL::CCP4File , BALL::DSN6File , BALL::LineSearch , BALL::PairExpInteractionEnergyProcessor , BALL::PairExpRDFIntegrator , BALL::AssignBondOrderProcessor
• 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
• already_used_ : BALL::HydrogenBond
• alternate_location_indicator : BALL::PDB::RecordANISOU , BALL::PDB::RecordATOM , BALL::PDB::RecordHETATM , BALL::PDB::RecordHYDBND::HydrogenPartnerAtom , BALL::PDB::RecordHYDBND::HydrogenAtom , BALL::PDB::RecordLINK::LinkPartner , BALL::PDB::RecordSIGATM , BALL::PDB::RecordSIGUIJ , BALL::PDB::RecordSLTBRG::PartnerAtom
• alternate_location_indicator_ : BALL::PDBFile , BALL::PDBAtom
• amber_ : BALL::VIEW::AmberConfigurationDialog , BALL::VIEW::MolecularStructure
• amber_dialog_ : BALL::VIEW::MinimizationDialog , BALL::VIEW::MolecularDynamicsDialog , BALL::VIEW::MolecularStructure
• amber_ff_id_ : BALL::VIEW::MolecularStructure
• ambient_ : BALL::VIEW::Stage
• ambient_color : BALL::VIEW::Stage::RaytracingMaterial
• ambient_intensity : BALL::VIEW::Stage::RaytracingMaterial
• 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
• ancestor_ : BALL::Composite::AncestorIteratorTraits
• ang_num_ : BALL::GeometricFit::RotationAngles_
• 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::Option , BALL::CHPI::Default
• angle_tolerance_ : BALL::AromaticRingStacking , BALL::CHPI
• 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::Option , BALL::AssignBondOrderProcessor::Default
• 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_color_ : BALL::VIEW::ResidueTypeColorProcessor
• aromatic_rings_ : BALL::MMFF94 , BALL::MMFF94ChargeProcessor , BALL::AtomTyper , BALL::Kekuliser
• aromatic_systems_ : BALL::Kekuliser
• aromatic_types_5_map_ : BALL::MMFF94AtomTyper
• arrow_width_ : BALL::VIEW::AddCartoonModel
• ASP_SEPERATION : BALL::BindingPocketProcessor::Option , BALL::BindingPocketProcessor::Default
• aspec : BALL::MMFF94AtomType
• asps_ : BALL::BindingPocketProcessor
• assign_bond_orders_id_ : BALL::VIEW::MolecularStructure
• ASSIGN_CHARGES : BALL::AmberFF::Option , BALL::AmberFF::Default , BALL::CharmmFF::Option , BALL::CharmmFF::Default , BALL::MMFF94::Option , BALL::MMFF94::Default
• assign_charges_id_ : BALL::VIEW::MolecularStructure
• ASSIGN_TYPENAMES : BALL::CharmmFF::Default , BALL::AmberFF::Option , BALL::AmberFF::Default , BALL::CharmmFF::Option , BALL::MMFF94::Option , BALL::MMFF94::Default
• ASSIGN_TYPES : BALL::AmberFF::Default , BALL::AmberFF::Option , BALL::CharmmFF::Option , BALL::CharmmFF::Default , BALL::MMFF94::Option , BALL::MMFF94::Default
• assignment : BALL::FPTBondOrderStrategy::BackTrackingState_
• assignment_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
• asu_ : BALL::CrystalGenerator
• ATIJK : BALL::MMFF94StretchBend::Bend
• atom : BALL::Kekuliser::AtomInfo , BALL::PDB::Structure::AtomEntry , BALL::CharmmEEF1::Data , BALL::FragmentDB::BuildBondsProcessor::Connection , BALL::VIEW::EditableScene::EditOperation
• atom1 : BALL::QuadraticAngleBend::Data , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::MOL2File::BondStruct , BALL::AmberTorsion::SingleAmberTorsion , BALL::MMFF94StretchBend::Bend , BALL::MMFF94StretchBend::Stretch , BALL::MMFF94Torsion::Torsion , BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::LennardJones::Data , BALL::Potential1210::Data , BALL::QuadraticBondStretch::Data , BALL::QuadraticImproperTorsion::Data
• atom2 : BALL::CosineTorsion::Data , BALL::CosineTorsion::SingleData , BALL::LennardJones::Data , BALL::Potential1210::Data , BALL::QuadraticAngleBend::Data , BALL::QuadraticBondStretch::Data , BALL::QuadraticImproperTorsion::Data , BALL::AmberTorsion::SingleAmberTorsion , BALL::MMFF94Torsion::Torsion , BALL::MOL2File::BondStruct , BALL::CharmmTorsion::SingleCharmmTorsion , BALL::MMFF94StretchBend::Bend , BALL::MMFF94StretchBend::Stretch
• atom3 : BALL::CharmmTorsion::SingleCharmmTorsion , BALL::MMFF94StretchBend::Bend , BALL::MMFF94Torsion::Torsion , BALL::QuadraticAngleBend::Data , BALL::CosineTorsion::SingleData , BALL::QuadraticImproperTorsion::Data , BALL::CosineTorsion::Data , BALL::AmberTorsion::SingleAmberTorsion
• atom4 : BALL::CharmmTorsion::SingleCharmmTorsion , BALL::MMFF94Torsion::Torsion , BALL::QuadraticImproperTorsion::Data , BALL::CosineTorsion::SingleData , BALL::CosineTorsion::Data , BALL::AmberTorsion::SingleAmberTorsion
• atom_ : BALL::Peak< PositionType > , BALL::SmartsParser::SPAtom , BALL::SESVertex , BALL::NodeItem< Node, Edge > , BALL::VIEW::BondProperties , BALL::RSVertex , BALL::ReducedSurface
• atom_2_distance_ : BALL::VIEW::AtomDistanceColorProcessor
• atom_areas_ : BALL::NumericalSAS
• atom_array : BALL::FDPB
• atom_data : BALL::NMRStarFile::NMRAtomDataSet
• atom_data_sets_ : BALL::NMRStarFile
• 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::PDB::RecordANISOU , BALL::PDB::RecordATOM , BALL::PDB::RecordHYDBND::HydrogenAtom , BALL::PDB::RecordSLTBRG::PartnerAtom , BALL::PDB::RecordSIGUIJ , BALL::PDB::RecordHYDBND::HydrogenPartnerAtom , BALL::PDB::RecordSIGATM , BALL::PDB::RecordLINK::LinkPartner , BALL::NMRStarFile::NMRAtomData , BALL::PDB::RecordHETATM
• 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_nr_ : BALL::AddHydrogenProcessor
• atom_number_ : BALL::VIEW::EditableScene
• atom_overview_ : BALL::VIEW::MolecularControl
• atom_overview_selection_ : BALL::VIEW::MolecularControl
• atom_pair_vector_ : BALL::MMFF94NonBonded
• atom_pos_ : BALL::VIEW::EditableScene
• atom_positions_ : BALL::SnapShot
• ATOM_REACTION_COMPONENT_NUMBER : BALL::MOLFile::Property
• ATOM_REACTION_COMPONENT_TYPE : BALL::MOLFile::Property
• atom_serial_number : BALL::PDB::RecordCON063 , BALL::PDB::RecordCON061 , BALL::PDB::RecordCON06 , BALL::PDB::RecordCON062 , BALL::PDB::RecordCONECT , BALL::PDB::RecordCON064
• atom_set_ : BALL::VIEW::AtomBondModelBaseProcessor
• 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_vertex_ : BALL::MolecularGraph
• atom_to_virtual_bond_index_ : BALL::AssignBondOrderProcessor
• atom_type : BALL::GAFFTypeProcessor::TypeDefinition , BALL::NMRStarFile::NMRAtomData , BALL::NMRStarFile::ShiftReferenceElement
• ATOM_TYPE_FF_FILENAME : BALL::HybridisationProcessor::Option , BALL::HybridisationProcessor::Default
• 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::Option , BALL::HybridisationProcessor::Default
• atom_typer_ : BALL::MMFF94
• atom_types_ : BALL::MMFF94AtomTyper , BALL::GAFFTypeProcessor , BALL::ForceFieldParameters , BALL::AssignTypeProcessor , BALL::SolventParameter , BALL::MMFF94
• 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::MMFF94AtomTyper::AromaticType , BALL::GAFFTypeProcessor::TypeDefinition
• atomic_number_ : BALL::VIEW::EditableScene , BALL::Element
• atomic_number_to_element_ : BALL::PTE_
• atomic_property : BALL::GAFFTypeProcessor::TypeDefinition
• atomic_radius_ : BALL::Element
• atomic_weight_ : BALL::Element
• atoms : BALL::RingAnalyser::Ring , BALL::PDB::Structure
• atoms_ : BALL::ForceField , BALL::MOL2File , BALL::MMFF94ChargeProcessor , BALL::GeneralizedBornModel , BALL::AtomTyper , BALL::VIEW::AddSurfaceModel
• atoms_to_delete : BALL::BondOrderAssignment
• ATOMTYPE_FILENAME : BALL::GAFFTypeProcessor::Option , BALL::GAFFTypeProcessor::Default
• attached_hydrogens : BALL::GAFFTypeProcessor::TypeDefinition
• attenuation_ : BALL::VIEW::LightSource
• authors : BALL::PDB::RecordAUTHOR
• average_ : BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
• AVERAGE_SECTION_NAME : BALL::CreateSpectrumProcessor
• averaging_ : BALL::PolarSolvation
• AVOGADRO : BALL::Constant
• axis_color_ : BALL::VIEW::RegularData1DWidget , BALL::VIEW::RegularData2DWidget