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Here is a list of all class members 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_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::Processor
- abort() : BALL::DockingAlgorithm, 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_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::Element
- ac : BALL::BondOrderAssignment
- 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
- acceptCombinedDatapoints() : BALL::MPISupport
- acceptDatapoints() : BALL::MPISupport
- acceptNavigationRequest() : BALL::VIEW::HTMLPage
- 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::VIEW::DatasetMessage, BALL::VIEW::RepresentationMessage
- add() : BALL::ConformationSet, BALL::Result, BALL::SmartsMatcher::RecStruct_, BALL::VIEW::RaytraceableContourSurfaceDialog
- 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, BALL::VIEW::MolecularTaskMessage
- add_hydrogens : BALL::FragmentDB
- 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
- 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
- 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::ParamFile::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::SmilesParser
- Al : BALL::Element
- ala_pressed() : BALL::VIEW::PeptideDialog
- algAdvancedPressed() : BALL::VIEW::DockDialog
- ALGORITHM : BALL::AssignBondOrderProcessor::Default, BALL::AssignBondOrderProcessor::Option
- Algorithm : BALL::VIEW::DockingController
- 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::ParamFile::ParameterDescription
- allowPaste_() : BALL::VIEW::MolecularControl
- ALMOST_SIMPLICIAL : BALL::TreeWidthImplementation< UndirectedGraph >::QuickBB< Lowerbound, Upperbound >
- ALPHA : BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option, BALL::RegularExpression, BALL::VersionInfo
- 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_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_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::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::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