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• abort() : BALL::DockingAlgorithm , BALL::VIEW::DownloadElectronDensity , BALL::VIEW::DownloadPDBFile
• abortClicked() : BALL::VIEW::DockProgressDialog
• abortScript() : BALL::VIEW::PyWidget
• abortTest() : BALL::VIEW::TestFramework
• about() : BALL::Mainframe
• 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 , BALL::VIEW::RunGAMESSDialog
• acceptCombinedDatapoints() : BALL::MPISupport
• acceptDatapoints() : BALL::MPISupport
• 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
• 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 >
• 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
• 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::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::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