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

### - a -

- abort() : BALL::DockingAlgorithm, BALL::VIEW::DownloadElectronDensity, BALL::VIEW::DownloadPDBFile
- abortClicked() : BALL::VIEW::DockProgressDialog
- abortScript() : BALL::VIEW::PyWidget
- abortTest() : BALL::VIEW::TestFramework
- aboutToExit() : BALL::VIEW::MainControl
- 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
- acceptCombinedDatapoints() : BALL::MPISupport
- acceptDatapoints() : BALL::MPISupport
- acceptNavigationRequest() : BALL::VIEW::HTMLPage
- 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
- activatedItem_() : BALL::VIEW::MolecularControl
- activatedOrderItem_() : BALL::VIEW::EditMode, BALL::VIEW::Scene
- add() : BALL::ConformationSet, BALL::Result, BALL::SmartsMatcher::RecStruct_, BALL::VIEW::RaytraceableContourSurfaceDialog
- 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
- addEdge() : BALL::SmartsParser
- 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 >
- 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
- 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
- advancedClicked() : BALL::VIEW::DockResultDialog
- AdvancedElectrostatic() : BALL::AdvancedElectrostatic
- advancedOptions() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- after() : BALL::String
- ala_pressed() : BALL::VIEW::PeptideDialog
- algAdvancedPressed() : BALL::VIEW::DockDialog
- algorithmChosen() : BALL::VIEW::DockDialog
- ALLModel() : BALL::QSAR::ALLModel
- allowPaste_() : BALL::VIEW::MolecularControl
- alreadySeenThisAtom() : BALL::GAFFCESParser::CESPredicate
- althausCompute_() : BALL::PoseClustering
- AmberBend() : BALL::AmberBend
- AmberConfigurationDialog() : BALL::VIEW::AmberConfigurationDialog
- AmberEvaluation() : BALL::AmberEvaluation
- AmberFF() : BALL::AmberFF
- AmberNonBonded() : BALL::AmberNonBonded
- AmberStretch() : BALL::AmberStretch
- AmberTorsion() : BALL::AmberTorsion
- ambientFactorChanged() : BALL::VIEW::MaterialSettings
- AminoAcidDescriptor() : BALL::Peptides::AminoAcidDescriptor
- AmiraMeshFile() : BALL::AmiraMeshFile
- AncestorIteratorTraits() : BALL::Composite::AncestorIteratorTraits
- angle_changed() : BALL::VIEW::PeptideDialog
- animate_() : BALL::VIEW::Scene
- animateClicked() : BALL::VIEW::SnapshotVisualisationDialog
- animationSpeedChanged() : BALL::VIEW::SnapshotVisualisationDialog
- AnimationThread() : BALL::VIEW::AnimationThread
- AnisotropyShiftProcessor() : BALL::AnisotropyShiftProcessor
- annotateAliphaticAndAromaticRingAtoms_() : BALL::GAFFTypeProcessor
- annotateBondTypes_() : BALL::GAFFTypeProcessor
- annotatePlanarRingAtoms_() : BALL::GAFFTypeProcessor
- annotateRingSizes_() : BALL::GAFFTypeProcessor
- AntechamberFile() : BALL::AntechamberFile
- append() : BALL::AtomContainer, BALL::Chain, BALL::DCDFile, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, 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::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
- 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
- APSMatcher() : BALL::GAFFCESParser::APSMatcher
- APSTerm() : BALL::GAFFCESParser::APSMatcher::APSTerm
- areInOneAromaticRing() : BALL::MMFF94
- areInOneRing() : BALL::MMFF94
- arg_pressed() : BALL::VIEW::PeptideDialog
- AromaticityProcessor() : BALL::AromaticityProcessor
- AromaticRing() : BALL::CHPI::AromaticRing, BALL::CHPISlick::AromaticRing
- AromaticRingStacking() : BALL::AromaticRingStacking
- aromatize() : BALL::AromaticityProcessor
- aromatizeSimple() : BALL::AromaticityProcessor
- asn_pressed() : BALL::VIEW::PeptideDialog
- asp_pressed() : BALL::VIEW::PeptideDialog
- assembleSD_() : BALL::SDGenerator
- assign() : BALL::String, BALL::Templates
- 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
- 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::Assignment_
- 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::AStarBondOrderStrategy
- at() : BALL::PDBRecords, BALL::String
- Atom() : BALL::Atom
- AtomBijection() : BALL::AtomBijection
- AtomBondModelBaseProcessor() : BALL::VIEW::AtomBondModelBaseProcessor
- AtomChargeColorProcessor() : BALL::VIEW::AtomChargeColorProcessor
- AtomContainer() : BALL::AtomContainer
- AtomContainerIteratorTraits() : BALL::AtomContainerIteratorTraits
- AtomDistanceColorProcessor() : BALL::VIEW::AtomDistanceColorProcessor
- AtomEntry() : BALL::PDB::Structure::AtomEntry
- AtomicPolarizabilities() : BALL::AtomicPolarizabilities
- AtomInformationContent() : BALL::AtomInformationContent
- AtomIteratorTraits() : BALL::AtomIteratorTraits
- AtomOverview() : BALL::VIEW::AtomOverview
- atomProperties_() : BALL::VIEW::PTEDialog
- atomPropertiesTriggered_() : BALL::VIEW::EditMode
- AtomTyper() : BALL::AtomTyper
- AtomTypes() : BALL::AtomTypes
- AtomVector() : BALL::AtomVector
- attachBridged_() : BALL::SDGenerator
- attachCore_() : BALL::SDGenerator
- attachFused_() : BALL::SDGenerator
- attachSpiro_() : BALL::SDGenerator
- attachTemplate_() : BALL::SDGenerator
- autoActivatePlugin() : BALL::PluginManager
- AutoDeletable() : BALL::AutoDeletable
- AutomaticModelCreator() : BALL::QSAR::AutomaticModelCreator
- autoScale() : BALL::VIEW::GridVisualizationDialog, BALL::VIEW::ModifyRepresentationDialog
- autoScaleRequested() : BALL::VIEW::GridColorWidget
- AverageBondAngle_() : BALL::HybridisationProcessor
- averageLinkageClustering() : BALL::BinaryFingerprintMethods