  BALL | |
  __private | |
| Constants | |
| Exception | |
 GeneralException | |
| IndexUnderflow | |
| SizeUnderflow | |
| IndexOverflow | |
| InvalidArgument | |
| InvalidRange | |
| InvalidSize | |
| OutOfRange | |
| InvalidFormat | |
| IllegalSelfOperation | |
| NullPointer | |
| InvalidIterator | |
| IncompatibleIterators | |
| NotImplemented | |
| IllegalTreeOperation | |
| OutOfMemory | |
| BufferOverflow | |
| DivisionByZero | |
| OutOfGrid | |
| FileNotFound | |
| IllegalPosition | |
| ParseError | |
| Precondition | |
| Postcondition | |
| InvalidOption | Exception to be thrown if an invalid option is given |
| TooManyErrors | Exception to be thrown if too many errors occur, e.g. in ForceField |
| TooManyBonds | Exception to be thrown if too many bonds for one atom |
| CUDAError | |
| NoBufferAvailable | |
| FormatUnsupported | |
| NotInitialized | |
| GlobalExceptionHandler | |
| MatrixHasWrongDimension | |
| VectorHasWrongDimension | |
| MatrixNotRegular | |
| MatrixNotQuadratic | |
| MatrixIsSingular | |
| SingularIterator | |
 Uninitialized | |
| GRAPH | |
| UndoEliminateOperation | |
| IllegalStateException | |
| UnconnectedGraphException | |
| GraphTraits | |
| EditableEdgeCopier | |
| EditableVertexCopier | |
| PostOrderFolding | |
| Maths | |
| MolmecSupport | |
| PDB | |
| RecordTypeFormat | |
| Residue | |
| RecordUNKNOWN | |
| RecordANISOU | |
| RecordATOM | |
| RecordAUTHOR | |
| RecordCAVEAT | |
| RecordCISPEP | |
| RecordCOMPND | |
| RecordCONECT | |
| RecordCON06 | |
| RecordCON061 | |
| RecordCON062 | |
| RecordCON063 | |
| RecordCON064 | |
| RecordCRYST1 | |
| UnitCell | |
| RecordDBREF | |
| EndingDatabaseSegment | |
| EndingSequence | |
| InitialDatabaseSegment | |
| InitialSequence | |
| RecordEND | |
| RecordENDMDL | |
| RecordEXPDTA | |
| RecordFORMUL | |
| RecordFTNOTE | |
| RecordHEADER | |
| RecordHELIX | |
| RecordHET | |
| RecordHETATM | |
| RecordHETNAM | |
| RecordHETSYN | |
| RecordHYDBND | |
| HydrogenAtom | |
| HydrogenPartnerAtom | |
| RecordJRNL | |
| RecordKEYWDS | |
| RecordLINK | |
| LinkPartner | |
| RecordMASTER | |
| RecordMODEL | |
| RecordMODRES | |
| RecordMTRIX1 | |
| RecordMTRIX2 | |
| RecordMTRIX3 | |
| RecordOBSLTE | |
| RecordORIGX1 | |
| RecordORIGX2 | |
| RecordORIGX3 | |
| RecordREMARK | |
| RecordREVDAT | |
| RecordSCALE1 | |
| RecordSCALE2 | |
| RecordSCALE3 | |
| RecordSEQADV | |
| RecordSEQRES | |
| RecordSHEET | |
| RecordSIGATM | |
| RecordSIGUIJ | |
| RecordSITE | |
| RecordSLTBRG | |
| PartnerAtom | |
| RecordSOURCE | |
| RecordSPRSDE | |
| RecordSSBOND | |
| RecordTER | |
| RecordTITLE | |
| RecordTURN | |
| RecordTVECT | |
| BookKeeping | |
| Structure | |
| AtomEntry | |
| ConectAtomList | |
| NCSMatrix | |
| UnitCellInfo | |
| AdditionalAtomInfo | |
| Peptides | |
| AminoAcidDescriptor | |
| PeptideBuilder | |
 NameConverter | This class provides conversion of atom names between naming schemata |
 Default | Default values for options |
| Option | Option names |
| QSAR | |
| Exception | |
| InvalidActivityID | |
| PropertyError | |
| SingularMatrixError | |
| InconsistentUsage | |
| KernelParameterError | |
| WrongDataType | |
| NoPCAVariance | |
| ModelParameterError | |
| TooManyPLSComponents | |
| WrongFileFormat | |
| FeatureSelectionParameterError | |
| ConfigurationReadingError | |
| ALLModel | |
| AutomaticModelCreator | |
| BayesModel | |
| ClassificationModel | |
| ClassificationValidation | |
| InputConfiguration | |
| InputPartitioningConfiguration | |
| ModelConfiguration | |
| FeatureSelectionConfiguration | |
| ValidationConfiguration | |
| PredictionConfiguration | |
| ConfigIO | |
| FeatureSelection | |
| FitModel | |
| GPModel | |
| Kernel | |
| KernelModel | |
| KNNModel | |
| KPCRModel | |
| KPLSModel | |
| LatentVariableModel | |
| LDAModel | |
| LibsvmModel | |
| svm_model | |
| LinearModel | |
| LogitModel | |
| MLRModel | |
| Model | |
| ModelFactory | |
| NBModel | |
| NonLinearModel | |
| OPLSModel | |
| PCRModel | |
| PLSModel | |
| QSARData | |
| RegistryEntry | |
| Registry | |
| RegressionModel | |
| RegressionValidation | |
| BackupData | |
| RRModel | |
| SNBModel | |
| Statistics | |
| SVMModel | |
| SVRModel | |
| Validation | |
| RTTI | |
| SimpleDownloaderHelper | |
| HelperThread | |
| DLThread | |
| UPThread | |
| BasicHelper | |
| DLArrayHelper | |
| DLHelper | |
| QFtpHackThread | |
| QFtpHackHelper | |
| SysInfo | |
| VIEW | |
| ColorExtension2 | |
| MultiColorExtension | |
| ColorHSV | |
| ColorMap | |
| ColorRGBA | |
| ColorUnit | |
| NotInHexFormat | |
| ColorUnitHue | |
| Dataset | |
| DatasetController | |
| RaytraceableGrid | |
| RegularData3DController | |
| TrajectoryController | |
| DockResultController | |
| VectorGridController | |
| RaytraceableGridController | |
| Vertex | |
| Vertex2 | |
| AmberConfigurationDialog | |
| AssignBondOrderConfigurationDialog | |
| AssignBondOrderResultsDialog | |
| AtomOverview | |
| ApplyProcessor | |
| OverviewProcessor | |
| BondProperties | |
| CharmmConfigurationDialog | |
| ClippingDialog | |
| ColoringSettingsDialog | |
| CompositeProperties | |
| ContourSurfaceDialog | |
| DisplayProperties | |
| DockDialog | |
| DockProgressDialog | |
| DockResultDialog | |
| Compare_ | |
| DownloadElectronDensity | |
| DownloadPDBFile | |
| EditOperationDialog | |
| EditSettings | |
| EditSingleShortcut | |
| ExportGeometryDialog | |
| FDPBDialog | |
| FieldLinesDialog | |
| GeometricFitDialog | |
| GridVisualizationDialog | |
| LabelDialog | |
| LightSettings | |
| MainControlPreferences | |
| MaterialSettings | |
| MinimizationDialog | |
| MMFF94ConfigurationDialog | |
| ModelSettingsDialog | |
| ModifyRepresentationDialog | |
| MolecularDynamicsDialog | |
| MolecularFileDialog | |
| NetworkPreferences | |
| OpenBruker1DFile | |
| OpenBruker2DFile | |
| OpenSavePreferences | |
| ParsedFunctionDialog | |
| PeptideDialog | |
| PluginModel | |
| PluginDialog | |
| Preferences | |
| PTEDialog | |
| PubChemDialog | |
| ParsedResult_ | |
| PythonSettings | |
| RaytraceableContourSurfaceDialog | |
| RunGAMESSDialog | |
| ServerPreferences | |
| SetCamera | |
| SetClippingPlane | |
| ShortcutDialog | |
| SnapshotVisualisationDialog | |
| StageSettings | |
| StereoSettingsDialog | |
| UndoManagerDialog | |
| ButtonEvent | |
| DeviceEvent | |
| FakeDriver | |
| HeadTrackingEvent | |
| InputDeviceDriver | |
| InputPlugin | |
| MotionTrackingEvent | |
| NotificationEvent | |
| TransformationEvent6D | |
| ClippingPlane | |
| LogEvent | Event class used for thread safe output to logview |
| CompositeManager | |
| ConnectionObject | |
| GeometricObject | |
| IconLoader | |
| MainControl | |
| Message | |
| DatasetMessage | |
| CompositeMessage | |
| SceneMessage | |
| GenericSelectionMessage | |
| ControlSelectionMessage | |
| NewSelectionMessage | |
| GeometricObjectSelectionMessage | |
| RepresentationMessage | Base class for all messages concerning a Representation |
| MolecularTaskMessage | |
| ShowDisplayPropertiesMessage | |
| CreateRepresentationMessage | |
| DeselectControlsMessage | |
| TransformationMessage | |
| FinishedSimulationMessage | |
| SyncClippingPlanesMessage | |
| ShowHelpMessage | |
| RegisterHelpSystemMessage | |
| DockingFinishedMessage | Message to notify docking has finished |
| ModelInformation | |
| ModularWidget | |
| PreferencesEntry | |
| ExtendedPreferencesObject | |
| Representation | |
| RepresentationManager | |
| ServerWidget | |
| BALLViewServer | |
| NotCompositeObject | |
| ShortcutRegistry | |
| SnapshotManagerInterface | |
| LightSource | |
| Camera | |
| Stage | |
| RaytracingMaterial | |
| MessageEvent | |
| BALLThread | |
| CalculateFDPBThread | |
| UpdateRepresentationThread | |
| SimulationThread | |
| EnergyMinimizerThread | Thread for EnergyMinimization |
| MDSimulationThread | Thread for MDSimulation |
| DockingThread | Thread for Docking |
| AtomBondModelBaseProcessor | |
| AddBackboneModel | |
| ModelPart | |
| AddBallAndStickModel | |
| AddCartoonModel | |
| ColorByGridProcessor | |
| ColorProcessor | |
| InterpolateColorProcessor | |
| FieldLineCreator | |
| ForceModel | |
| HBondModelProcessor | |
| LabelModel | |
| AddLineModel | |
| ModelProcessor | |
| ElementColorProcessor | |
| ResidueNumberColorProcessor | |
| PositionColorProcessor | |
| ChainColorProcessor | |
| MoleculeColorProcessor | |
| ResidueNameColorProcessor | |
| AtomChargeColorProcessor | |
| AtomDistanceColorProcessor | |
| CustomColorProcessor | |
| TemperatureFactorColorProcessor | |
| OccupancyColorProcessor | |
| ForceColorProcessor | |
| SecondaryStructureColorProcessor | |
| ResidueTypeColorProcessor | |
| AddSurfaceModel | |
| AddVanDerWaalsModel | |
| InputDevPluginHandler | |
| VIEWPlugin | |
| Box | |
| Disc | |
| GridVisualisation | |
| Label | |
| Line | |
| Mesh | |
| MultiLine | |
| Point | |
| QuadMesh | |
| Quadruple | |
| SimpleBox | |
| Sphere | |
| Tube | |
| TwoColoredLine | |
| TwoColoredTube | |
| BufferedRenderer | |
| GLDisplayList | |
| DisplayListRedeclaration | |
| NestedDisplayList | |
| NoDisplayListAvailable | |
| GLOffscreenTarget | |
| GLRenderer | |
| WrongModes | |
| GLRenderWindow | |
| ChannelFormat | |
| PixelFormat | |
| POVRenderer | |
| POVRendererClippingPlane | |
| Renderer | |
| RenderSetup | |
| Resolution | |
| FrameBufferFormat | |
| FrameBuffer | |
| RenderTarget | |
| RenderWindow | |
| STLRenderer | |
| TilingRenderer | |
| MeshBuffer | |
| VRMLRenderer | |
| CanvasWidget | |
| PixmapItem | |
| ColorButton | |
| ColorTable | |
| DatasetControl | |
| DockingController | |
| DockWidget | |
| EditableScene | |
| EditOperation | |
| EditFunctions | |
| FileObserver | |
| TreeWidget | |
| GenericControl | |
| GeometricControl | |
| GridColorWidget | |
| MyTextBrowser | |
| HelpViewer | |
| ComboBoxDelegate | |
| HotkeyTable | |
| DragLogView | |
| LogView | |
| MolecularControl | |
| MyTreeWidgetItem | |
| MolecularStructure | |
| PropEditorWidget | |
| BoolEditorWidget | |
| IntEditorWidget | |
| UIntEditorWidget | |
| FloatEditorWidget | |
| DoubleEditorWidget | |
| StringEditorWidget | |
| PropDeleteWidget | |
| PDBInfoEditorWidget | |
| EditorPDBInfoDialog | |
| PropertyEditor | |
| PythonHighlighter | |
| PythonValidator | |
| RunPythonThread | |
| Hotkey | |
| PyWidget | |
| MyLineEdit | |
| MyTextEdit | |
| RegularData1DWidget | |
| DockableRegularData1DWidget | |
| RegularData2DWidget | |
| DockableRegularData2DWidget | |
| Scene | |
| AnimationThread | |
| SDWidget | |
| Default | Default values for options |
| Option | Option names |
| ShortcutTableView | |
| ShortcutTableModel | |
| TestFramework | |
| MyEventThread | |
| MyMouseEvent | |
| TextEditorWidget | |
| LineNumbers | |
| DemoTutorialDialog | |
| GlobalInitializer | |
| Limits | |
| Limits< float > | |
| Limits< double > | |
| Limits< bool > | |
| Limits< char > | |
| Limits< signed char > | |
| Limits< unsigned char > | |
| Limits< short > | |
| Limits< unsigned short > | |
| Limits< int > | |
| Limits< unsigned int > | |
| Limits< long > | |
| Limits< unsigned long > | |
| LogStreamBuf | |
| LoglineStruct | |
| StreamStruct | |
| LogStreamNotifier | |
| LogStream | |
| AutoDeletable | |
| UnaryFunctor | |
| BinaryFunctor | |
| BaseIterator | |
| ConstBidirectionalIterator | |
| BidirectionalIterator | Mutable bidirectional iterator |
| Client | |
| InvalidClient | |
| NoPersistentObject | |
| Comparator | |
| Composite | |
| AncestorIteratorTraits | |
| ChildCompositeIteratorTraits | |
| CompositeIteratorTraits | |
| Embeddable | |
| EnumeratorIndex | |
| IncompatibleIndex | |
| Enumerator | |
| IteratorTraits_ | |
| Factory | |
| ConstForwardIterator | |
| ForwardIterator | |
| MolecularInformation | |
| MoleculeObjectCreator | |
| Object | |
| ObjectCreator | |
| PersistenceManager | |
| PersistentObject | |
| UnaryPredicate | |
| BinaryPredicate | |
| PreferencesObject | |
| Processor | |
| UnaryProcessor | |
| BinaryProcessor | |
| NamedProperty | |
| PropertyManager | |
| ConstRandomAccessIterator | |
| RandomAccessIterator | |
| Selectable | |
| TextPersistenceManager | |
| PreciseTime | |
| TimeStamp | |
| Visitor | |
| XDRPersistenceManager | |
| Bit | |
| IllegalOperation | |
| BitVector | |
| TContour | |
| TContourLine | |
| TContourSurface | |
| Cube | |
| MolecularGraph | |
| TreeWidthImplementation | |
| FillInHeuristic | |
| GeneralLowerBoundAlgorithm | Generic lower bound algorithm on graphs |
| GreedyX | |
| MinorMinWidthCriterion | |
| MinorMinWidthReducer | |
| QuickBB | |
| QuickBBState | |
| TreeDecompositionBuilder | |
| TreeWidth | |
| BagContentWriter | |
| ComponentFilter_ | |
| HashGrid3 | |
| BoxIteratorTraits | |
| HashGridBox3 | |
| BoxIteratorTraits | |
| DataIteratorTraits | |
| HashMap | HashMap class based on the STL map (containing serveral convenience functions) |
| IllegalKey | HashMap illegal key exception |
| HashSet | |
| IllegalKey | |
| IteratorTraits | |
| Node | |
| List | |
| Options | |
| Quadruple | |
| TRegularData1D | |
| BlockValueType | The block data type for reading and writing binary data |
| TRegularData2D | |
| BlockValueType | The block data type for reading and writing binary data |
| IndexType | The index type used to refer to a specific element in the grid (x-, and y-index) |
| TRegularData3D | |
| BlockValueType | The block data type for reading and writing binary data |
| IndexType | The index type used to refer to a specific element in the grid (x-, y-, and z-index) |
| RegularExpression | |
| String | |
| Substring | |
| InvalidSubstring | |
| UnboundSubstring | |
| StringHashMap | |
| Triple | |
| ComposedEnergyProcessor | |
| EnergyProcessor | |
| AmiraMeshFile | |
| AntechamberFile | |
| Bruker1DFile | |
| Bruker2DFile | |
| CCP4File | |
| CIFFile | |
| Datablock | |
| Datacontent | |
| Item | |
| SaveFrame | |
| State | |
| DCDFile | |
| DSN6File | |
| GAMESSDatFile | |
| block | |
| State | |
| GAMESSLogFile | |
| State | |
| GenericMolFile | |
| HINFile | |
| INIFile | |
| IteratorTraits_ | Interface for the LineIterator |
| Section | |
| JCAMPFile | |
| JCAMPValue | |
| KCFFile | |
| LineBasedFile | |
| MOL2File | |
| AtomStruct | |
| BondStruct | |
| CommentStruct | |
| MoleculeStruct | |
| SetStruct | A class used for storing TRIPOS sets |
| SubstructureStruct | |
| MOLFile | |
| AtomStruct | |
| BondStruct | |
| CountsStruct | |
| Property | |
| MolFileFactory | |
| NMRStarFile | This class provides methods for reading and assigning chemical shifts |
| BALLToBMRBMapper | |
| EntryInformation | |
| MolecularSystem | |
| ChemicalUnit | |
| RelatedDB | |
| MonomericPolymer | |
| HomologDB | Database with homolog entries |
| NMRAtomData | |
| NMRAtomDataSet | |
| NMRSpectrometer | |
| Sample | |
| Component | |
| SampleCondition | |
| ShiftReferenceElement | |
| ShiftReferenceSet | |
| Parameters | |
| ParameterSection | |
| PDBFile | |
| Default | |
| Option | |
| PDBInfo | |
| PDBRecords | |
| PubChemDownloader | Downloads PubChem entries |
| ResourceEntry | |
| IteratorTraits_ | |
| ResourceFile | |
| SCWRLRotamerFile | Reads Dunbrack/SCWRL rotamer library files |
| SDFile | |
| TrajectoryFile | |
| TrajectoryFileFactory | |
| TRRFile | |
| TRRHeader | |
| XYZFile | |
| Atom | |
| BondIteratorTraits | |
| AtomContainer | |
| AtomContainerIteratorTraits | |
| AtomIteratorTraits | |
| Bond | |
| NotBound | |
| Chain | |
| ChainIteratorTraits | |
| Expression | |
| ExpressionParser | |
| State | |
| SyntaxTree | |
| ExpressionPredicate | |
| ExpressionTree | |
| Fragment | |
| FragmentIteratorTraits | |
| CompositeIteratorTraits | |
| Molecule | |
| MoleculeIteratorTraits | |
| NucleicAcid | |
| NucleicAcidIteratorTraits | |
| Nucleotide | |
| NucleotideIteratorTraits | |
| PDBAtom | |
| PDBAtomIteratorTraits | |
| KernelPredicate | Kernel predicate class |
| Protein | |
| ProteinIteratorTraits | |
| Element | |
| PTE_ | |
| SymbolToElement | |
| Residue | |
| ResidueIteratorTraits | |
| SecondaryStructure | |
| SecondaryStructureIteratorTraits | |
| Selector | |
| TruePredicate | |
| FalsePredicate | |
| SelectedPredicate | |
| AtomNamePredicate | |
| AtomTypePredicate | |
| ElementPredicate | |
| ResiduePredicate | |
| ResidueIDPredicate | |
| ProteinPredicate | |
| ChainPredicate | |
| SecondaryStructurePredicate | |
| SolventPredicate | |
| MoleculePredicate | |
| BackBonePredicate | |
| NucleicAcidPredicate | |
| NucleotidePredicate | |
| InRingPredicate | |
| NumberOfBondsPredicate | |
| SingleBondsPredicate | |
| DoubleBondsPredicate | |
| TripleBondsPredicate | |
| AromaticBondsPredicate | |
| ConnectedToPredicate | |
| CTPNode | |
| greater_ | |
| SpHybridizedPredicate | |
| Sp2HybridizedPredicate | |
| Sp3HybridizedPredicate | |
| ChargePredicate | |
| AxialPredicate | |
| Conformation4C1Predicate | |
| RingFinder | |
| SMARTSPredicate | |
| System | |
| TAngle | |
| TBox3 | |
| TCircle3 | |
| CubicSpline1D | |
| CubicSpline2D | |
| TFFT1D | |
| TFFT2D | |
| TFFT3D | |
| DoubleTraits | |
| FloatTraits | |
| LongDoubleTraits | |
| ConstantFunction | |
| MutableConstant | |
| Addition | |
| Subtraction | |
| Product | |
| Division | |
| Reciprocal | |
| SquareFunction | |
| CubicFunction | |
| MutablePower | |
| BaseFilterIterator | |
| ConstBidirectionalFilterIterator | |
| BidirectionalFilterIterator | Mutable bidirectional iterator |
| Matrix | |
| ColumnIteratorTraits | |
| DiagonalIteratorTraits | |
| EigenSolver | |
| ElementColumnIteratorTraits | |
| ElementRowIteratorTraits | |
| ConstForwardFilterIterator | |
| ForwardFilterIterator | |
| Vector | |
| MatrixInverter | |
| StandardTraits | |
| UpperTriangularTraits | |
| LowerTriangularTraits | |
| SymmetricTraits | |
| ConstRandomAccessFilterIterator | |
| RandomAccessFilterIterator | |
| ConstReverseIterator | |
| ReverseIterator | |
| RowIteratorTraits | |
| SVDSolver | |
| VectorIteratorTraits | |
| TLine3 | |
| TMatrix4x4 | Default Type |
| NumericalIntegrator | |
| ParsedFunction | |
| PiecewiseFunction | |
| PiecewisePolynomial | |
| TPlane3 | |
| TQuaternion | |
| RandomNumberGenerator | |
| RombergIntegrator | |
| TSimpleBox3 | |
| TSphere3 | |
| TSurface | |
| Triangle | |
| TVector2 | |
| TVector3 | |
| TVector4 | |
| AmberFF | |
| Default | |
| Option | |
| AmberBend | |
| AmberNonBonded | |
| AmberStretch | |
| AmberTorsion | |
| SingleAmberTorsion | |
| GAFFCESParser | |
| APSMatcher | |
| APSTerm | |
| CESelementConnectionPredicate | |
| CESelementPredicate | |
| CESPredicate | |
| CESwildcardsConnectionPredicate | |
| CESwildcardsPredicate | |
| State | |
| TruePredicate | |
| GAFFTypeProcessor | |
| Default | |
| Option | |
| TypeDefinition | Nested class definitions |
| CharmmFF | |
| Default | |
| Option | |
| CharmmBend | |
| CharmmImproperTorsion | |
| CharmmNonBonded | |
| CharmmStretch | |
| CharmmTorsion | |
| SingleCharmmTorsion | |
| AssignBaseProcessor | Only used for deriving interface |
| AssignTypeProcessor | |
| AssignTypeNameProcessor | |
| AtomVector | |
| BendComponent | |
| ChargeRuleProcessor | |
| ForceField | |
| ForceFieldComponent | |
| Gradient | |
| PeriodicBoundary | |
| Default | Default values |
| Option | |
| RadiusRuleProcessor | |
| RuleEvaluator | |
| RuleProcessor | |
| SnapShot | |
| SnapShotManager | |
| Default | Local class for handling default values for the options |
| Option | Local class for handling options |
| StretchComponent | |
| TypenameRuleProcessor | |
| TypeRuleProcessor | |
| CanonicalMD | |
| AuxFactors | Helper class containing auxiliary factors |
| MicroCanonicalMD | |
| AuxFactors | |
| MolecularDynamics | |
| Default | |
| Option | |
| ConjugateGradientMinimizer | |
| Default | |
| Option | |
| EnergyMinimizer | |
| Default | |
| Option | |
| LineSearch | |
| ShiftedLVMMMinimizer | |
| Default | |
| Option | |
| SteepestDescentMinimizer | |
| StrangLBFGSMinimizer | |
| Default | |
| Option | |
| MMFF94 | |
| Default | |
| Option | |
| MMFF94NonBonded | |
| NonBondedPairData | |
| MMFF94OutOfPlaneBend | |
| OutOfPlaneBend | |
| MMFF94ParametersBase | |
| MMFF94AtomTypeEquivalences | |
| MMFF94AtomType | Class to store the values of an atom type from MMFFPROP.PAR |
| MMFF94AtomTypes | |
| MMFF94StretchParameters | |
| BondData | |
| EmpiricalBondData | |
| MMFF94BendParameters | |
| MMFF94StretchBendParameters | |
| MMFF94TorsionParameters | |
| MMFF94PlaneParameters | |
| MMFF94VDWParameters | |
| VDWEntry | |
| MMFF94ESParameters | |
| MMFF94AtomTyper | |
| AromaticType | |
| MMFF94ChargeProcessor | |
| MMFF94StretchBend | |
| Bend | See MMFFANG.PAR |
| Stretch | |
| StretchBend | |
| MMFF94Torsion | |
| Torsion | See MMFFTOR.PAR |
| AtomTypes | |
| CharmmEEF1 | |
| Data | |
| Values | |
| CosineTorsion | |
| Data | |
| SingleData | |
| SingleValues | |
| Values | |
| ForceFieldParameters | |
| LennardJones | |
| Data | |
| Values | |
| Potential1210 | |
| Data | |
| Values | |
| QuadraticAngleBend | |
| Data | |
| Values | |
| QuadraticBondStretch | |
| Data | |
| Values | |
| QuadraticImproperTorsion | |
| Data | |
| Values | |
| ResidueTorsions | |
| Data | |
| Templates | |
| AnisotropyShiftProcessor | |
| ClearShiftProcessor | |
| CreateSpectrumProcessor | |
| EFShiftProcessor | |
| EmpiricalHSShiftProcessor | |
| Default | Default values for options |
| Option | Option names |
| PropertiesForShift_ | |
| ShiftHyperSurface_ | |
| Experiment | |
| SimpleExperiment1D | |
| HaighMallionShiftProcessor | |
| HBondShiftProcessor | |
| JohnsonBoveyShiftProcessor | |
| Ring | |
| Peak | |
| PeakList | |
| RandomCoilShiftProcessor | |
| ShiftModel | |
| ShiftModel1D | |
| ShiftModel2D | |
| ShiftModule | |
| Spectrum | |
| BALLPlugin | |
| PluginHandler | |
| PluginManager | |
| PyColorRGBAVector | |
| PyCompositeList | |
| Constant | |
| PyDatasetVector | |
| PyIndexList | |
| PyInterpreter | |
| AromaticityProcessor | This processor provides methods for detection and assignment of aromaticity |
| Default | Default values for options |
| Option | Option names |
| ConnectivityBase | |
| ZagrebIndex | |
| BalabanIndexJ | |
| Descriptor | |
| PartialChargeBase | |
| TotalPositivePartialCharge | |
| TotalNegativePartialCharge | |
| RelPositivePartialCharge | |
| RelNegativePartialCharge | |
| PartialChargeProcessor | |
| RingPerceptionProcessor | |
| Default | Default options for the ring perception |
| Option | Option names |
| PathMessage_ | |
| TNode_ | |
| SimpleBase | |
| MolecularWeight | |
| NumberOfBonds | |
| NumberOfSingleBonds | |
| NumberOfDoubleBonds | |
| NumberOfTripleBonds | |
| NumberOfAromaticBonds | |
| NumberOfAtoms | |
| NumberOfBoron | |
| NumberOfCarbon | |
| NumberOfNitrogen | |
| NumberOfOxygen | |
| NumberOfFlourine | |
| NumberOfPhosphorus | |
| NumberOfSulfur | |
| NumberOfChlorine | |
| NumberOfBromine | |
| NumberOfIodine | |
| NumberOfHydrogen | |
| FormalCharge | |
| NumberOfHeavyAtoms | |
| MeanAtomInformationContent | |
| AtomInformationContent | |
| NumberOfRotatableSingleBonds | |
| RelNumberOfRotatableSingleBonds | |
| NumberOfAromaticAtoms | |
| NumberOfHeavyBonds | |
| NumberOfRotatableBonds | |
| RelNumberOfRotatableBonds | |
| VertexAdjacency | |
| VertexAdjacencyEquality | |
| NumberOfHydrogenBondAcceptors | |
| NumberOfHydrogenBondDonors | |
| NumberOfHydrophobicAtoms | |
| BondPolarizabilities | |
| AtomicPolarizabilities | |
| SizeOfSSSR | |
| PrincipalMomentOfInertia | |
| PrincipalMomentOfInertiaX | |
| PrincipalMomentOfInertiaY | |
| PrincipalMomentOfInertiaZ | |
| SurfaceBase | |
| PositiveVdWSurface | |
| NegativeVdWSurface | |
| PositivePolarVdWSurface | |
| NegativePolarVdWSurface | |
| HydrophobicVdWSurface | |
| PolarVdWSurface | |
| RelPositiveVdWSurface | |
| RelNegativeVdWSurface | |
| RelPositivePolarVdWSurface | |
| RelNegativePolarVdWSurface | |
| RelHydrophobicVdWSurface | |
| RelPolarVdWSurface | |
| VdWVolume | |
| Density | |
| VdWSurface | |
| ScoringBaseFunction | |
| FermiBaseFunction | |
| LinearBaseFunction | |
| ScoringComponent | |
| ScoringFunction | |
| Default | |
| Option | |
| ScoringTypes | |
| AromaticRingStacking | |
| Default | |
| Option | |
| BuriedPolar | |
| Default | |
| Option | |
| CHPI | |
| AromaticRing | |
| CHGroup | |
| Default | |
| Option | |
| HydrogenBond | |
| Default | |
| Option | |
| Lipophilic | |
| Default | |
| Option | |
| ChemScoreMetal | |
| NonpolarSolvation | |
| Default | |
| Option | |
| PolarSolvation | |
| Default | |
| Option | |
| RotationalEntropyLoss | |
| Default | |
| Option | |
| VanDerWaals | |
| Default | |
| Option | |
| SLICKEnergy | |
| Default | |
| Option | |
| SLICKScore | |
| Default | |
| Option | |
| FresnoTypes | |
| ClaverieParameter | |
| ElectrostaticPotentialCalculator | |
| Default | |
| Option | |
| GeneralizedBornModel | |
| Default | |
| GBParameters | |
| Option | |
| Pair6_12InteractionEnergyProcessor | |
| Default | |
| Option | |
| Pair6_12RDFIntegrator | |
| Default | |
| Option | |
| PairExpInteractionEnergyProcessor | |
| Default | |
| Option | |
| PairExpRDFIntegrator | |
| Default | |
| Option | |
| PCMCavFreeEnergyProcessor | |
| Default | |
| Option | |
| PierottiCavFreeEnergyProcessor | |
| Default | |
| Option | |
| FDPB | |
| Boundary | |
| ChargeDistribution | |
| Default | |
| DielectricSmoothing | |
| FastAtomStruct | |
| Option | |
| ReissCavFreeEnergyProcessor | |
| Default | |
| Option | |
| SolventAtomDescriptor | |
| SolventDescriptor | |
| SolventParameter | |
| UhligCavFreeEnergyProcessor | |
| Default | |
| Option | |
| AddHydrogenProcessor | |
| AssignBondOrderProcessor | Assignment of bond orders from topology information |
| Algorithm | |
| Default | Default values for options |
| Option | Option names |
| AtomBijection | |
| AtomTyper | |
| BindingPocketProcessor | |
| Default | |
| Option | |
| Sphere_ | |
| SphereComparator_ | |
| AStarBondOrderStrategy | |
| Default | |
| Heuristic | |
| Option | Option names |
| BondOrderAssignment | A solution to the bond order assignment problem |
| BondOrderAssignmentStrategy | Base class for bond order assignment algorithms |
| BranchAndBoundBondOrderStrategy | |
| Default | |
| Option | Option names |
| FPTBondOrderStrategy | |
| AdditionalBagProperties_ | |
| Assignment_ | |
| BackTrackingState_ | |
| ComputingData_ | |
| Default | Default option values |
| DPBackTracking_ | |
| StateComparator_ | |
| DPBackTrackingCombiner_ | |
| DPConfig_ | |
| DPJoinMapComparator_ | |
| DPTable_ | |
| EdgeComparator_ | |
| FPTBondOrderAssignment_ | |
| Option | Option names |
| ILPBondOrderStrategy | |
| KGreedyBondOrderStrategy | |
| Default | |
| Option | Option names |
| PartialBondOrderAssignment | A full or partial solution to the AStar-based bond order assignment problem |
| BuildBondsProcessor | |
| Default | Default values for options |
| Option | Option names |
| ConnectedComponentsProcessor | |
| ClearChargeProcessor | |
| ClearRadiusProcessor | |
| AssignRadiusProcessor | |
| AssignChargeProcessor | |
| DNAMutator | |
| AmberEvaluation | |
| ConformationSet | |
| DockingAlgorithm | |
| DockResult | |
| Compare_ | |
| Scoring_ | |
| EnergeticEvaluation | |
| ForceFieldEvaluation | |
| GeometricFit | |
| Default | |
| Option | |
| Peak_ | |
| RotationAngles_ | |
| RandomEvaluation | |
| FragmentDB | |
| BuildBondsProcessor | |
| Connection | |
| NoFragmentNode | |
| NormalizeNamesProcessor | |
| BoundingBoxProcessor | |
| GeometricCenterProcessor | |
| FragmentDistanceCollector | |
| TranslationProcessor | |
| TransformationProcessor | |
| GraphVertex | |
| GraphFace | |
| GraphTriangle | |
| GraphEdge | |
| HBondProcessor | Computation of hydrogen bonds from topology information |
| Default | Default values for options |
| HBond | |
| Option | Option names |
| PredictionMethod | Default values for options |
| ResidueData | |
| HybridisationProcessor | |
| AtomNames_ | |
| Default | Default values for options |
| Elements_ | |
| Method | |
| Option | Option names |
| Kekuliser | |
| AtomInfo | |
| Mutator | |
| NucleotideMapping | |
| NumericalSAS | |
| Default | |
| Option | |
| PeptideCapProcessor | This processor adds ACE-N and NME-C caps to proteins |
| RadialDistributionFunction | |
| RDFIntegrator | |
| RDFParameter | |
| RDFSection | |
| ReconstructFragmentProcessor | |
| SortedPosition2 | |
| SortedPosition3 | |
| ReducedSurface | |
| RSComputer | |
| ProbePosition | |
| ResidueChecker | |
| Rotamer | |
| ResidueRotamerSet | |
| RotamerProbabilityGreaterThan_ | |
| RingAnalyser | Methods for the analysis of the structure of ringsystems |
| Ring | |
| RMSDMinimizer | |
| IncompatibleCoordinateSets | |
| TooFewCoordinates | |
| RotamerLibrary | Rotamer Library Class |
| RSEdge | |
| RSFace | |
| RSVertex | |
| SASEdge | |
| SASFace | |
| SASVertex | |
| SDGenerator | |
| AtomComparator | |
| Default | Default values for options |
| Option | Option names |
| SecondaryStructureProcessor | Secondary structure extraction from 3D structure |
| SESEdge | |
| SESFace | |
| SESVertex | |
| SideChainPlacementProcessor | |
| Default | Default values for options |
| Method | |
| Option | Option names |
| EdgeItem | |
| TSimpleMolecularGraph | |
| NodeItem | |
| SmartsMatcher | |
| RecStruct_ | Wrapper class which is used as an interface in the matching code to the pool |
| RecStructCore_ | Core structure of the recursive matching algorithm for the object pool |
| RecStructPool_ | Class which does the pool operations of the RecStructCore_ pool |
| SmartsParser | |
| SPAtom | Smarts Parser Atom class |
| Property | Property struct of smarts parser atom |
| PropertyValue | Possible types of the properties |
| SPBond | Bond representation of the smarts parser |
| SPEdge | Edge representation of the smarts parser graph |
| SPNode | Representation of a node in the smarts parser graph |
| State | Parser state (used by the parser itself) |
| SmilesParser | |
| SPAtom | |
| SPBond | |
| State | |
| SolventAccessibleSurface | |
| SolventExcludedSurface | |
| SESComputer | |
| SESSingularityCleaner | |
| ProbeIntersection | |
| StructureMapper | |
| SurfaceProcessor | |
| Triangle | |
| TriangleEdge | |
| TrianglePoint | |
| TriangulatedSAS | |
| SASTriangulator | |
| TriangulatedSES | |
| SESTriangulator | |
| TriangulatedSurface | |
| TriangulatedSphere | |
| Face | |
| UCK | |
| BinaryFileAdaptor | |
| Directory | |
| TransformationManager | |
| File | |
| CannotWrite | |
| FileSystem | |
| MPISupport | |
| TMutex | |
| TMutex< QMutex > | |
| TMutexLocker | |
| TReadWriteLock | |
| TReadWriteLock< QReadWriteLock > | |
| TReadLocker | |
| TWriteLocker | |
| TCPIOStream | |
| TCPServer | |
| TCPServerThread | |
| Path | |
| SimpleDownloader | |
| Timer | |
| CrystalGenerator | |
| CrystalInfo | |
| Default | |
| Option | |
| Mainframe | |
| boost | |
| Ui | |
| MolecularGraphBase | |
| MutexLockerType | |
| QAbstractListModel | |
| QAbstractTableModel | |
| QCanvasRectangle | |
| QCanvasView | |
| QDialog | |
| QDockWidget | |
| QEvent | |
| QGLWidget | |
| QItemDelegate | |
| QLineEdit | |
| QMainWindow | |
| QMouseEvent | |
| QObject | |
| QPaintDevice | |
| QPlainTextEdit | |
| QPushButton | |
| QSyntaxHighlighter | |
| QTableView | |
| QTableWidget | |
| QTextBrowser | |
| QThread | |
| QTreeWidget | |
| QTreeWidgetItem | |
| QValidator | |
| QWidget | |
| ReadLockerType | |
| ReadWriteLockType | |
| WriteLockerType | |
1.8.3.1
