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

- a -

• A : BALL::LennardJones::Values
• a : BALL::PDB::RecordCRYST1::UnitCell , BALL::PDB::Structure::UnitCellInfo
• A : BALL::Potential1210::Values
• a : 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_B_FORMAT : BALL::LennardJones
• a_i_ : BALL::ConjugateGradientMinimizer
• A_STAR : BALL::AssignBondOrderProcessor::Algorithm
• abbreviation_common : BALL::NMRStarFile::MolecularSystem
• abop : BALL::BondOrderAssignmentStrategy , BALL::PartialBondOrderAssignment
• abort() : BALL::DockingAlgorithm
• ABORT : BALL::Processor
• abort() : BALL::VIEW::DownloadElectronDensity , BALL::VIEW::DownloadPDBFile
• 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
• abortClicked() : BALL::VIEW::DockProgressDialog
• aborted_ : BALL::EnergyMinimizer , BALL::VIEW::DownloadElectronDensity , BALL::VIEW::DownloadPDBFile
• abortScript() : BALL::VIEW::PyWidget
• abortTest() : BALL::VIEW::TestFramework
• about() : BALL::Mainframe
• about_to_quit_ : BALL::VIEW::MainControl , BALL::VIEW::RenderSetup
• aboutToExit() : BALL::VIEW::MainControl
• 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::Element
• ac_ : BALL::AssignBondOrderProcessor , BALL::VIEW::FieldLineCreator
• ac_split_() : BALL::AntechamberFile
• accept() : BALL::VIEW::AmberConfigurationDialog , BALL::VIEW::AssignBondOrderConfigurationDialog , BALL::VIEW::AtomOverview , BALL::VIEW::CharmmConfigurationDialog , BALL::VIEW::ClippingDialog , BALL::VIEW::CompositeProperties , BALL::VIEW::EditSingleShortcut , BALL::VIEW::ExportGeometryDialog , BALL::VIEW::FDPBDialog , BALL::VIEW::FieldLinesDialog , BALL::VIEW::GeometricFitDialog , BALL::VIEW::GridVisualizationDialog , BALL::VIEW::LabelDialog , BALL::VIEW::MinimizationDialog , BALL::VIEW::MMFF94ConfigurationDialog , BALL::VIEW::ModifyRepresentationDialog , BALL::VIEW::MolecularDynamicsDialog , BALL::VIEW::RaytraceableContourSurfaceDialog , BALL::VIEW::RunGAMESSDialog
• acceptCombinedDatapoints() : BALL::MPISupport
• acceptDatapoints() : BALL::MPISupport
• 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
• ACTINIUM : BALL::Element
• 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
• activate() : BALL::BALLPlugin , BALL::TCPServer , BALL::VIEW::EditMode , BALL::VIEW::InteractionMode , BALL::VIEW::MoveMode , BALL::VIEW::PickingMode , BALL::VIEW::RotateMode , BALL::VIEW::ServerWidget
• activate_async() : BALL::TCPServerThread
• activated_item_ : BALL::VIEW::AssignBondOrderResultsDialog
• activatedItem_() : BALL::VIEW::MolecularControl
• activatedOrderItem_() : BALL::VIEW::EditMode , BALL::VIEW::Scene
• active_ : BALL::VIEW::ClippingPlane
• ACTIVE_STEREO : BALL::VIEW::Renderer
• 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() : BALL::ConformationSet , BALL::Result , BALL::SmartsMatcher::RecStruct_
• ADD : BALL::VIEW::DatasetMessage
• add() : BALL::VIEW::RaytraceableContourSurfaceDialog
• ADD : BALL::VIEW::RepresentationMessage
• add_button_ : BALL::VIEW::PubChemDialog
• ADD_CHAIN_RESIDUE_ID : BALL::Atom
• ADD_HBONDS : BALL::HBondProcessor::Default , BALL::HBondProcessor::Option
• ADD_HYDROGENS : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
• add_hydrogens : BALL::FragmentDB
• ADD_HYDROGENS : BALL::VIEW::MolecularTaskMessage
• add_hydrogens_action_ : BALL::VIEW::Scene
• add_menu_ : BALL::VIEW::EditMode
• add_missing_hydrogens_ : BALL::AssignBondOrderProcessor
• ADD_RESIDUE_ID : BALL::Atom , BALL::Residue
• ADD_TO_GEOMETRIC_CONTROL : BALL::VIEW::RepresentationMessage
• ADD_VARIANT_EXTENSIONS : BALL::Atom , BALL::Residue
• ADD_VARIANT_EXTENSIONS_AND_CHAIN_RESIDUE_ID : BALL::Atom
• ADD_VARIANT_EXTENSIONS_AND_ID : BALL::Atom , BALL::Residue
• addAlgorithm() : BALL::VIEW::DockDialog
• addAllRecords_() : BALL::PDBFile
• addAminoAcid() : BALL::Peptides::PeptideBuilder
• addAtom() : BALL::VIEW::AtomDistanceColorProcessor
• addAtom_() : BALL::MOPACOutputFile
• AddBackboneModel() : BALL::VIEW::AddBackboneModel
• AddBallAndStickModel() : BALL::VIEW::AddBallAndStickModel
• addBasisOption() : BALL::GAMESSLogFile
• AddCartoonModel() : BALL::VIEW::AddCartoonModel
• addCESelementConnectionPredicate() : BALL::GAFFCESParser::CESPredicate
• addCESelementPredicate() : BALL::GAFFCESParser::CESPredicate
• addCESwildcardsConnectionPredicate() : BALL::GAFFCESParser::CESPredicate
• addCESwildcardsPredicate() : BALL::GAFFCESParser::CESPredicate
• addChild() : BALL::ConnectedToPredicate::CTPNode
• addCoefficient() : BALL::GAMESSLogFile
• addComplex() : BALL::ScoringOptimizer
• addComponent() : BALL::ComposedEnergyProcessor
• addComposite() : BALL::VIEW::MolecularControl
• addConformation() : BALL::FlexibleMolecule , BALL::Receptor
• addDataItem() : BALL::CIFFile::SaveFrame
• addDataPath() : BALL::Path
• addDirectory() : BALL::VIEW::PluginDirectoryModel
• AddDV3_() : BALL::MMFF94OutOfPlaneBend , BALL::MMFF94Torsion
• ADDED__ATOM : BALL::VIEW::EditOperation
• ADDED__BOND : BALL::VIEW::EditOperation
• addEdge() : BALL::SmartsParser
• addEditOperation() : BALL::VIEW::EditOperationDialog
• addEmptyRow() : BALL::VIEW::HotkeyTable
• addEntry() : BALL::QSAR::Registry
• addFlexConformation() : BALL::Receptor
• addFullyFlexibleResidue() : BALL::FlexDefinition
• addGlWindow() : BALL::VIEW::Scene
• addHydrogen_() : BALL::AddHydrogenProcessor
• AddHydrogenProcessor() : BALL::AddHydrogenProcessor
• addHydrogens() : BALL::VIEW::MolecularStructure
• addInteraction() : BALL::Atom , BALL::MolecularInteractions
• addItem_() : BALL::VIEW::GeometricControl
• Addition() : BALL::Addition< First, Second, DataType >
• additional_grid_distance_ : BALL::VIEW::ColorProcessor
• AdditionalAtomInfo() : BALL::PDB::AdditionalAtomInfo
• AdditionalBagProperties_() : BALL::FPTBondOrderStrategy::AdditionalBagProperties_
• addLambda() : BALL::QSAR::Model
• addLightPressed() : BALL::VIEW::LightSettings
• addLightSource() : BALL::VIEW::Stage
• AddLineModel() : BALL::VIEW::AddLineModel
• addMenu() : BALL::VIEW::MainControl
• addMissingHydrogens() : BALL::SmilesParser
• addModel_() : BALL::VIEW::RaytraceableContourSurfaceDialog
• addModularWidget() : BALL::VIEW::MainControl
• addMonomericPolymer() : BALL::NMRStarFile
• addMovable_() : BALL::ResidueRotamerSet
• addMutation() : BALL::DNAMutator , BALL::Mutator
• addNeededObjects_() : BALL::PersistenceManager
• addNewAND() : BALL::GAFFCESParser::CESPredicate
• addNewOR() : BALL::GAFFCESParser::CESPredicate
• addNode() : BALL::SmartsParser
• addPair() : BALL::CIFFile::Item
• addParameterDescription() : BALL::Options
• addPlane_() : BALL::VIEW::DemoTutorialDialog
• addPluginDirectory() : BALL::PluginManager , BALL::VIEW::PluginDialog
• addPointerPair_() : BALL::PersistenceManager
• addPropertiesFromSPAtom() : BALL::SmartsParser::SPAtom
• addProperty() : BALL::Conformation
• addProperty_() : BALL::VIEW::PropertyEditor
• addRecursiveEdge() : BALL::SmartsParser
• addRepresentation() : BALL::VIEW::GeometricControl
• addResult() : BALL::DockResultFile
• addRingConnection() : BALL::SmartsParser
• addRotamer() : BALL::ResidueRotamerSet , BALL::RotamerLibrary
• addRotamerFlexibleResidue() : BALL::FlexDefinition
• addRow() : BALL::VIEW::GenericControl
• addScoreContributions() : BALL::Rescoring
• addScoring() : BALL::DockResult
• addScoringFunction() : BALL::VIEW::DockDialog , BALL::VIEW::DockResultDialog
• addSolutionToStructures() : BALL::VIEW::AssignBondOrderResultsDialog
• addSolvent() : BALL::PeriodicBoundary
• addSPEdge() : BALL::SmartsParser::SPNode
• addStructure_() : BALL::VIEW::EditMode
• AddSurfaceModel() : BALL::VIEW::AddSurfaceModel
• addTag() : BALL::CIFFile::Item , BALL::VIEW::LabelDialog
• addToolBarEntries() : BALL::VIEW::EditMode , BALL::VIEW::InteractionMode , BALL::VIEW::InteractionModeManager , BALL::VIEW::ModularWidget , BALL::VIEW::Scene
• addTriangles_() : BALL::TContourSurface< T >
• addTruePredicate() : BALL::GAFFCESParser::CESPredicate
• addValue() : BALL::CIFFile::Item
• AddVanDerWaalsModel() : BALL::VIEW::AddVanDerWaalsModel
• addVariants() : BALL::Enumerator< Container, SiteIterator, Variant >
• addWidget_() : BALL::VIEW::PropEditorWidget
• adjacent_edges_ : BALL::NodeItem< Node, Edge >
• advanced : BALL::ParameterDescription
• advanced_options_modified_ : BALL::VIEW::DisplayProperties
• advancedClicked() : BALL::VIEW::DockResultDialog
• AdvancedElectrostatic() : BALL::AdvancedElectrostatic
• advancedOptions() : BALL::VIEW::MinimizationDialog , BALL::VIEW::MolecularDynamicsDialog
• after() : BALL::String
• Ag : BALL::Element
• ai : BALL::MMFF94VDWParameters::VDWEntry
• Aij_ : BALL::LennardJones
• Al : BALL::Element
• AL : BALL::SmilesParser
• ala_pressed() : BALL::VIEW::PeptideDialog
• algAdvancedPressed() : BALL::VIEW::DockDialog
• ALGORITHM : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
• Algorithm : BALL::VIEW::DockingController
• ALGORITHM_NAME : BALL::RingPerceptionProcessor::Default , BALL::RingPerceptionProcessor::Option
• algorithmChosen() : BALL::VIEW::DockDialog
• Alignment : BALL::NucleotideMapping
• ALIPHATIC : BALL::SmartsParser::SPAtom
• all_amino_acids_ : BALL::VIEW::PeptideDialog
• all_aromatic_atoms_ : BALL::Kekuliser
• ALL_ATOMS : BALL::VIEW::LabelModel
• all_atoms_ : BALL::SmilesParser
• all_fragments_ : BALL::FragmentDistanceCollector
• all_hydrogen_are_targets_ : BALL::HaighMallionShiftProcessor
• ALL_HYDROGENS : BALL::HydrogenBond
• ALL_INTERMEDIATE_POSES : BALL::DockingAlgorithm
• ALL_ITEMS : BALL::VIEW::LabelModel
• ALL_LIG_NONB_PAIRS : BALL::ScoringFunction::Default , BALL::ScoringFunction::Option
• all_ligand_nonbonded_ : BALL::ScoringFunction
• all_names_ : BALL::VIEW::GLRenderer
• ALL_RESIDUES : BALL::VIEW::LabelModel
• all_residues_hashgrid_ : BALL::ScoringFunction
• all_small_beers_ : BALL::RingPerceptionProcessor
• all_small_rings_ : BALL::RingPerceptionProcessor
• all_torsions_ : BALL::ResidueTorsions
• ALLModel() : BALL::QSAR::ALLModel
• allocator_type : BALL::String
• 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::ParameterDescription
• allowPaste_() : BALL::VIEW::MolecularControl
• ALMOST_SIMPLICIAL : BALL::TreeWidthImplementation< EditableGraph >::QuickBB< Lowerbound, Upperbound >
• ALPHA : BALL::PairExpInteractionEnergyProcessor::Default , BALL::PairExpInteractionEnergyProcessor::Option
• alpha : BALL::PDB::RecordCRYST1::UnitCell , BALL::PDB::Structure::UnitCellInfo
• ALPHA : BALL::RegularExpression
• alpha_ : BALL::AssignBondOrderProcessor , BALL::CCP4File , BALL::CrystalInfo , BALL::DSN6File , BALL::LineSearch , BALL::PairExpInteractionEnergyProcessor , BALL::PairExpRDFIntegrator
• alpha_blending_ : BALL::VIEW::ColorMap
• ALPHA_CHANNEL : BALL::VIEW::ChannelFormat
• alpha_i : BALL::MMFF94VDWParameters::VDWEntry
• alpha_proton_oxygen_hydrogen_separation_distance_ : BALL::HBondShiftProcessor
• ALPHA_PROTON_OXYGEN_SEPARATION_DISTANCE : BALL::HBondProcessor
• ALPHANUMERIC : BALL::RegularExpression
• alreadySeenThisAtom() : BALL::GAFFCESParser::CESPredicate
• 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
• althausCompute_() : BALL::PoseClustering
• ALUMINUM : BALL::Element
• Am : BALL::Element
• AMBER_FF : BALL::VIEW::DockingController , BALL::VIEW::MolecularStructure
• amber_nb_ : BALL::Electrostatic
• AmberBend() : BALL::AmberBend
• AmberConfigurationDialog() : BALL::VIEW::AmberConfigurationDialog
• AmberEvaluation() : BALL::AmberEvaluation
• AmberFF() : BALL::AmberFF
• AmberNonBonded() : BALL::AmberNonBonded
• AmberStretch() : BALL::AmberStretch
• AmberTorsion() : BALL::AmberTorsion
• AMBIENT : BALL::VIEW::LightSource
• ambient_ : BALL::VIEW::Stage
• ambient_color : BALL::VIEW::Stage::Material
• ambient_intensity : BALL::VIEW::Stage::Material
• ambientFactorChanged() : BALL::VIEW::MaterialSettings
• ambiguity_code : BALL::NMRStarFile::NMRAtomData
• AMERICIUM : BALL::Element
• 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
• AminoAcidDescriptor() : BALL::Peptides::AminoAcidDescriptor
• AmiraMeshFile() : BALL::AmiraMeshFile
• AncestorConstIterator : BALL::Composite
• AncestorIterator : BALL::Composite
• AncestorIteratorTraits : BALL::Composite , BALL::Composite::AncestorIteratorTraits
• AND : BALL::ExpressionTree , BALL::SmartsParser
• AND_LOW : BALL::SmartsParser
• angle : BALL::MMFF94Torsion::Torsion
• angle_ : BALL::RSEdge , BALL::SASEdge , BALL::VIEW::LightSource
• angle_action_ : BALL::VIEW::MolecularControl
• angle_changed() : BALL::VIEW::PeptideDialog
• angle_measure : BALL::PDB::RecordCISPEP
• ANGLE_TOLERANCE : BALL::CHPI::Default , BALL::CHPI::Option , BALL::CHPISlick::Default , BALL::CHPISlick::Option
• animate_() : BALL::VIEW::Scene
• animateClicked() : BALL::VIEW::SnapshotVisualisationDialog
• 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
• animationSpeedChanged() : BALL::VIEW::SnapshotVisualisationDialog
• AnimationThread() : BALL::VIEW::AnimationThread , BALL::VIEW::Scene
• anion : BALL::MMFF94AtomTyper::AromaticType
• AnisotropyShiftProcessor() : BALL::AnisotropyShiftProcessor
• annotateAliphaticAndAromaticRingAtoms_() : BALL::GAFFTypeProcessor
• annotateBondTypes_() : BALL::GAFFTypeProcessor
• annotatePlanarRingAtoms_() : BALL::GAFFTypeProcessor
• annotateRingSizes_() : BALL::GAFFTypeProcessor
• AntechamberFile() : BALL::AntechamberFile
• ANTIMONY : BALL::Element
• ANY : BALL::SmartsParser::SPBond
• ANY_TYPE : BALL::Atom
• ANY_ZE : BALL::SmartsParser
• append() : BALL::AtomContainer , BALL::Chain , BALL::DCDFile , BALL::Molecule , BALL::Nucleotide , BALL::Residue , BALL::SecondaryStructure , BALL::String , BALL::System , BALL::TrajectoryFile , BALL::TRRFile
• appendChild() : BALL::Composite , BALL::ExpressionTree
• appendHotkey() : BALL::VIEW::HotkeyTable
• appendIconPath() : BALL::VIEW::IconLoader
• appendLine() : BALL::INIFile
• appendSection() : BALL::INIFile
• appendText() : BALL::VIEW::PyWidget
• appendText_() : BALL::VIEW::PyWidget
• appendToHistory_() : BALL::VIEW::PyWidget
• applied : BALL::GRAPH::UndoEliminateOperation< UndirectedGraph > , BALL::VIEW::Preferences
• apply() : BALL::AssignBondOrderProcessor , BALL::BondOrderAssignment , BALL::Composite , BALL::ElectrostaticPotentialCalculator , BALL::HashGrid3< Item > , BALL::HashGridBox3< Item > , BALL::HashSet< Key > , BALL::INIFile , BALL::List< Value > , BALL::PTE_ , BALL::ResourceEntry , BALL::ResourceFile , BALL::TContour< T > , BALL::VIEW::DisplayProperties , BALL::VIEW::LightSettings , BALL::VIEW::MaterialSettings , BALL::VIEW::PropEditorWidget , BALL::VIEW::PropertyEditor , BALL::VIEW::StageSettings , BALL::VIEW::StereoSettingsDialog
• apply_() : BALL::AssignBondOrderProcessor , BALL::VIEW::BoolEditorWidget , BALL::VIEW::DoubleEditorWidget , BALL::VIEW::FloatEditorWidget , BALL::VIEW::IntEditorWidget , BALL::VIEW::PDBInfoEditorWidget , BALL::VIEW::PropDeleteWidget , BALL::VIEW::PropEditorWidget , BALL::VIEW::StringEditorWidget , BALL::VIEW::UIntEditorWidget
• APPLY_FIRST_SOLUTION : BALL::AssignBondOrderProcessor::Default , BALL::AssignBondOrderProcessor::Option
• apply_processor_ : BALL::VIEW::AtomOverview
• applyAncestor() : BALL::Composite
• applyAssignment_() : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
• applyBestConformation() : BALL::EvolutionaryDocking
• applyBonds() : BALL::Atom
• applyChild() : BALL::Composite
• applyChildren() : BALL::ResourceEntry , BALL::ResourceFile
• applyColoringSettings_() : BALL::VIEW::DisplayProperties
• applyConformation() : BALL::Conformation
• applyDescendant() : BALL::Composite
• applyDescendantPostorder() : BALL::Composite
• applyDescendantPreorder() : BALL::Composite
• applyFirstSnapShot() : BALL::SnapShotManager
• applyInterBond() : BALL::AtomContainer
• applyIntraBond() : BALL::AtomContainer
• applyLastSnapShot() : BALL::SnapShotManager
• applyLevel() : BALL::Composite
• applyModelSettings_() : BALL::VIEW::DisplayProperties
• applyNextSnapShot() : BALL::SnapShotManager
• applyNostart_() : BALL::ResourceEntry
• applyPostorder() : BALL::Composite
• applyPreferences() : BALL::VIEW::DisplayProperties , BALL::VIEW::MainControl , BALL::VIEW::ModularWidget , BALL::VIEW::Preferences , BALL::VIEW::PyWidget , BALL::VIEW::Scene , BALL::VIEW::ServerWidget
• applyPreferencesClicked_() : BALL::VIEW::MainControl
• applyPreorder() : BALL::Composite
• ApplyProcessor() : BALL::VIEW::AtomOverview::ApplyProcessor
• applyProcessors_() : BALL::VIEW::DockDialog , BALL::VIEW::FDPBDialog
• applySelector() : BALL::VIEW::MolecularControl
• applySettings() : BALL::VIEW::NetworkPreferences
• applySettingsTo() : BALL::VIEW::ColoringSettingsDialog , BALL::VIEW::ModelSettingsDialog
• applySnapShot() : BALL::SnapShot , BALL::SnapShotManager
• applySnapshot() : BALL::VIEW::SnapshotManagerInterface
• applySolution_() : BALL::Kekuliser
• applySplit() : BALL::VIEW::ModifyRepresentationDialog
• applyStereoDefaults() : BALL::VIEW::Scene
• applyTo() : BALL::VIEW::AmberConfigurationDialog , BALL::VIEW::CharmmConfigurationDialog , BALL::VIEW::MMFF94ConfigurationDialog
• applyTo_() : BALL::VIEW::DisplayProperties
• applyTransformation2System() : BALL::PoseClustering
• applyValues_() : BALL::VIEW::DockDialog , BALL::VIEW::FDPBDialog
• aps_matcher : BALL::GAFFCESParser::CESPredicate
• aps_terms : BALL::GAFFCESParser::APSMatcher
• APS_TRUE : BALL::GAFFCESParser::APSMatcher
• APSMatcher() : BALL::GAFFCESParser::APSMatcher
• APSTerm() : BALL::GAFFCESParser::APSMatcher::APSTerm
• APSType : BALL::GAFFCESParser::APSMatcher
• Ar : BALL::Element
• areInOneAromaticRing() : BALL::MMFF94
• areInOneRing() : BALL::MMFF94
• arg_pressed() : BALL::VIEW::PeptideDialog
• ARGENTUM : BALL::Element
• ARGON : BALL::Element
• argument : BALL::ExpressionParser::SyntaxTree
• argument_ : BALL::ExpressionPredicate
• argument_pointer : BALL::UnaryFunctor< ArgumentType, ResultType >
• argument_reference : BALL::UnaryFunctor< ArgumentType, ResultType >
• argument_type : BALL::UnaryFunctor< ArgumentType, ResultType >
• ArgumentIterator : BALL::GRAPH::PostOrderFolding< Tree, From, To, Functor >
• arom : BALL::MMFF94AtomType
• arom_proc_ : BALL::SMARTSPredicate
• aromat_list_ : BALL::JohnsonBoveyShiftProcessor
• AROMATIC : BALL::SmartsParser::SPAtom , BALL::SmartsParser::SPBond
• aromatic_atoms_ : BALL::Kekuliser
• AROMATIC_BOND : BALL::GAFFCESParser::APSMatcher
• AROMATIC_BOND_TO_PARENT : BALL::GAFFCESParser::APSMatcher
• aromatic_bonds_ : BALL::MMFF94
• aromatic_rings_ : BALL::AtomTyper , BALL::Kekuliser , BALL::MMFF94 , BALL::MMFF94ChargeProcessor
• aromatic_systems_ : BALL::Kekuliser
• aromatic_types_5_map_ : BALL::MMFF94AtomTyper
• AromaticityProcessor() : BALL::AromaticityProcessor
• AromaticRing() : BALL::CHPI::AromaticRing , BALL::CHPISlick::AromaticRing
• AromaticRingStacking() : BALL::AromaticRingStacking
• aromatize() : BALL::AromaticityProcessor
• aromatizeSimple() : BALL::AromaticityProcessor
• ARRAY : BALL::JCAMPFile
• arrow_width_ : BALL::VIEW::AddCartoonModel
• ARSENIC : BALL::Element
• As : BALL::Element
• asn_pressed() : BALL::VIEW::PeptideDialog
• asp_pressed() : BALL::VIEW::PeptideDialog
• ASP_SEPERATION : BALL::BindingPocketProcessor::Default , BALL::BindingPocketProcessor::Option
• aspec : BALL::MMFF94AtomType
• ASSEMBLED : BALL::SDGenerator
• assembleSD_() : BALL::SDGenerator
• assign() : BALL::String , BALL::Templates
• 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
• assignAromaticType_5_() : BALL::MMFF94AtomTyper
• assignAtomsByProperty() : BALL::AtomBijection
• assignAtomtype_() : BALL::GAFFTypeProcessor
• assignAtomTypes() : BALL::StructurePreparer
• assignBackboneAtoms() : BALL::AtomBijection
• AssignBaseProcessor() : BALL::AssignBaseProcessor
• AssignBondOrderConfigurationDialog() : BALL::VIEW::AssignBondOrderConfigurationDialog
• AssignBondOrderProcessor() : BALL::AssignBondOrderProcessor , BALL::BondOrderAssignment
• AssignBondOrderResultsDialog() : BALL::VIEW::AssignBondOrderResultsDialog
• assignBondTypes_() : BALL::MMFF94
• assignByName() : BALL::AtomBijection
• assignCAlphaAtoms() : BALL::AtomBijection
• AssignChargeProcessor() : BALL::AssignChargeProcessor
• assignCharges() : BALL::StructurePreparer , BALL::Templates
• assignFormalCharge() : BALL::MMFF94ChargeProcessor
• assignFromAlignment() : BALL::NucleotideMapping
• assignFromDistances() : BALL::NucleotideMapping
• assignment : BALL::FPTBondOrderStrategy::BackTrackingState_
• Assignment_() : BALL::FPTBondOrderStrategy::Assignment_
• assignment_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
• ASSIGNMENT__ELDRIDGE : BALL::FresnoTypes
• ASSIGNMENT__FRESNO : BALL::FresnoTypes
• assignMMFF94AtomTypes() : BALL::StructurePreparer
• assignMMFF94BondType() : BALL::MMFF94
• assignModelType() : BALL::VIEW::AddBackboneModel , BALL::VIEW::AddCartoonModel
• assignNaively() : BALL::NucleotideMapping
• assignNucleotideAtoms_() : BALL::VIEW::AddCartoonModel
• assignParameters() : BALL::CharmmEEF1 , BALL::CosineTorsion , BALL::LennardJones , BALL::MMFF94BendParameters , BALL::MMFF94PlaneParameters , BALL::MMFF94StretchBendParameters , BALL::MMFF94StretchParameters , BALL::MMFF94TorsionParameters , BALL::MMFF94VDWParameters , BALL::Potential1210 , BALL::QuadraticAngleBend , BALL::QuadraticBondStretch , BALL::QuadraticImproperTorsion
• assignPartialCharges_() : BALL::MMFF94ChargeProcessor
• assignPLPAtomTypes() : BALL::StructurePreparer
• assignProteinCharges() : BALL::StructurePreparer
• AssignRadiusProcessor() : BALL::AssignRadiusProcessor
• assignRotamer() : BALL::ScoringFunction
• assignRTD_() : BALL::RingAnalyser
• assignShifts() : BALL::NMRStarFile
• assignSimpleAtomTypes() : BALL::StructurePreparer
• assignSpecificValues_() : BALL::AtomTyper
• assignTo() : BALL::AtomTyper , BALL::MMFF94AtomTyper
• assignTorsion() : BALL::ResidueTorsions
• assignTrivial() : BALL::AtomBijection
• AssignTypeNameProcessor() : BALL::AssignTypeNameProcessor
• assignTypeNames() : BALL::Templates
• AssignTypeProcessor() : BALL::AssignTypeProcessor
• AStarBondOrderStrategy : BALL::AssignBondOrderProcessor , BALL::AStarBondOrderStrategy
• ASTATINE : BALL::Element
• ASU : BALL::CrystalGenerator
• asu_ : BALL::CrystalGenerator
• At : BALL::Element
• at() : BALL::PDBRecords , BALL::String
• ATIJK : BALL::MMFF94StretchBend::Bend
• Atom() : BALL::Atom , BALL::Bond
• 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
• AtomBijection() : BALL::AtomBijection
• AtomBondModelBaseProcessor() : BALL::VIEW::AtomBondModelBaseProcessor
• AtomBox : BALL::VIEW::ColorProcessor , BALL::VIEW::ModifyRepresentationDialog
• AtomChargeColorProcessor() : BALL::VIEW::AtomChargeColorProcessor
• AtomContainer() : BALL::AtomContainer
• AtomContainerIteratorTraits() : BALL::AtomContainerIteratorTraits
• AtomDistanceColorProcessor() : BALL::VIEW::AtomDistanceColorProcessor
• AtomEntry() : BALL::PDB::Structure::AtomEntry
• AtomGrid : BALL::VIEW::ColorProcessor , BALL::VIEW::ModifyRepresentationDialog
• atomic_coordinate_records : BALL::PDB::BookKeeping
• atomic_number : BALL::GAFFTypeProcessor::TypeDefinition , BALL::MMFF94AtomTyper::AromaticType
• atomic_number_ : BALL::VIEW::Scene
• atomic_property : BALL::GAFFTypeProcessor::TypeDefinition
• AtomicNumber : BALL::Element
• AtomicPolarizabilities() : BALL::AtomicPolarizabilities
• AtomIndexArray : BALL::PeriodicBoundary
• AtomIndexList : BALL::Atom
• AtomIndexMap : BALL::KCFFile
• AtomIndexPair : BALL::PeriodicBoundary
• AtomInformationContent() : BALL::AtomInformationContent
• AtomIteratorTraits() : BALL::AtomIteratorTraits
• AtomOverview() : BALL::VIEW::AtomOverview
• AtomPair : BALL::AtomBijection
• atomProperties_() : BALL::VIEW::PTEDialog
• atomPropertiesTriggered_() : BALL::VIEW::EditMode
• AtomPtrList : BALL::Atom
• AtomPtrMap : BALL::MolecularGraph
• 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
• AtomStatus : BALL::RSComputer
• ATOMTYPE_FILENAME : BALL::GAFFTypeProcessor::Default , BALL::GAFFTypeProcessor::Option
• AtomTyper() : BALL::AtomTyper
• AtomTypes() : BALL::AtomTypes
• AtomVector() : BALL::AtomVector
• attachBridged_() : BALL::SDGenerator
• attachCore_() : BALL::SDGenerator
• attached_hydrogens : BALL::GAFFTypeProcessor::TypeDefinition
• attachFused_() : BALL::SDGenerator
• attachSpiro_() : BALL::SDGenerator
• attachTemplate_() : BALL::SDGenerator
• attenuation_ : BALL::VIEW::LightSource
• Au : BALL::Element
• AURUM : BALL::Element
• authors : BALL::PDB::RecordAUTHOR
• autoactivate_plugins_ : BALL::PluginManager
• autoActivatePlugin() : BALL::PluginManager
• AutoDeletable() : BALL::AutoDeletable
• AutomaticModelCreator() : BALL::QSAR::AutomaticModelCreator
• autoScale() : BALL::VIEW::GridVisualizationDialog , BALL::VIEW::ModifyRepresentationDialog
• autoScaleRequested() : BALL::VIEW::GridColorWidget
• AVERAGE_SECTION_NAME : BALL::CreateSpectrumProcessor
• AverageBondAngle_() : BALL::HybridisationProcessor
• averageLinkageClustering() : BALL::BinaryFingerprintMethods
• AVERAGING__NONE : BALL::PolarSolvation
• AVERAGING__RANDOM : BALL::PolarSolvation
• AVERAGING__RANDOM_FACTOR : BALL::PolarSolvation
• AVERAGING__STATIC : BALL::PolarSolvation
• AveragingMethod : BALL::PolarSolvation
• AVOGADRO : BALL::Constant
• axis_color_ : BALL::VIEW::RegularData1DWidget , BALL::VIEW::RegularData2DWidget