  _Aligner | |
| _CachedRMSD | |
 _lDDTDecomposer | |
  _lDDTGreedySearcher | |
| _QWidget | |
| TrajWidget | |
| AAIndex | |
| AAIndexData | |
| additive | |
| Mat2 | |
| Mat4 | |
| Quat | Unit quaternion |
| Vec2 | |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
| CoordFrame | |
| Vec3List | |
| Vec4 | |
| Vec4 | |
| Color | |
| Color | |
| Phase | Manages phases og Complex numbers |
| Point | Class encapsulating 1D to 3D point |
| Peak | |
| ResNum | |
| additive1 | |
| Mat3 | |
| AdjacencyBitmap | |
| AdminRights | |
| AlgorithmBase | Algorithm base class |
| ConstModIPAlgorithm | In-place modification const algorithm |
| ButterworthLowPassFilter | Butterworth Low Pass Filter |
| ButterworthHighPassFilter | Butterworth High Pass Filter |
| CrossCorrelate | |
| FermiHighPassFilter | Fermi High Pass Filter |
| FermiLowPassFilter | Fermi Low Pass Filter |
| FractionalShift | |
| GaussianHighPassFilter | Gaussian High Pass Filter |
| GaussianLowPassFilter | Gaussian Low Pass Filter |
| HighPassFilter | High Pass Filter |
| LowPassFilter | Low Pass Filter |
| Normalizer | |
| ImageStateConstModIPAlgorithm< FNC > | In-place modifying image state const visitor plus ip algorithm |
| ConstModOPAlgorithm | Out-of-place modification const algorithm |
| DFT | |
| ImageStateConstModOPAlgorithm< FNC > | Out-of-place modifying image state const visitor plus op algorithm |
| ModIPAlgorithm | In-place modification algorithm |
| ImageStateModIPAlgorithm< FNC > | In-place modifying image state visitor plus ip algorithm |
| ImageStateMorphAlgorithm< FNC > | Morph visitor plus ip algorithm |
| ModOPAlgorithm | Out-of-place modification algorithm |
| Cartesian | |
| EllipticPolar | |
| Polar | |
| ImageStateModOPAlgorithm< FNC > | Out-of-place modifying image state visitor plus op algorithm |
 NonModAlgorithm | Non-modifying Algorithm, abstract base class |
 ImageStateNonModAlgorithm< FNC > | Non-modifying image state visitor plus non-mod algorithm |
| AlignedColumn | Provides access to a column in a aligned region or a sequence alignment |
| AlignedCuboid | Axis-aligned cuboid |
| AlignedPatch | |
| AlignedRegion | Region in a sequence alignment |
| AlignmentHandle | Representation of a multiple sequence alignemnt consisting of two or more sequences |
| AlignmentOpts | Options for local and global sequence alignment algorithms |
| AminoAcidSet | Amino acid bit set |
| AngleViolationInfo | |
| AssemblyInfo | |
| AtomEntry | |
| AtomGroup | |
| AtomGroupEntry | |
| AtomProp | |
| AtomSpec | |
| AutoCorrelateFnc | |
| BackboneTrace | |
| basic_istream | |
| BinaryIStream< CONVERSIONTYPE > | |
| basic_ostream | |
| BinaryOStream< CONVERSIONTYPE > | |
| Beacon | |
| binary_dispatch_ip< FNC > | In-place binary dispatch |
| binary_dispatch_op< FNC > | Out-of-place binary dispatch |
| BinaryColExpr | |
| BinaryDataSink | |
| BinaryDataSource | |
| Bitmap | |
| BlastHit | |
| BlockModifier | |
| GromacsBlockModifier | |
| HeuristicBlockModifier | |
| BondEntry | |
| BondLengthInfo | |
| BondSpec | |
| BondTable< ATOM > | |
| BondTableEntry< ATOM > | |
| BondViolationInfo | |
| Builder | |
| BuildingBlock | |
| BUInfo | |
| ByChainGetCol | |
| ByElementGetCol | |
| CADResult | |
| ChainData | |
| ChainMapper | |
| CHARMMData | |
| Checker | |
| ChemClass | |
| ChemType | |
| ChiDefinition | |
| Circle2 | |
| CircleMask | |
| Circle2 | |
| ClashEvent | |
| ClashInfo | |
| ClashingDistances | List of reference atom-atom distances to detect clashes between non-bonded atoms |
| ClashingInfo | |
| cluster | |
| ColorOp | |
| BasicGradientColorOp | |
| ByChainColorOp | |
| ByElementColorOp | |
| GradientColorOp | |
| EntityViewColorOp | |
| GradientLevelColorOp | |
| MapHandleColorOp | |
| MapHandleColorOp | |
| UniformColorOp | |
| complex | |
| complexint16 | |
| complexint16 | |
| complexint32 | |
| complexint32 | |
| complexint8 | |
| complexint8 | |
| Compound | Knows about the atoms and bonds of a chemical compounds |
| CompoundLibBase | |
| CompoundLib | |
| MinimalCompoundLib | |
| ConjFnc | |
| Conopology | |
| ConstData | Abstract base class for read-only data |
| ConstImageHandle | Read-only ImageHandle implementation |
| Data | Abstract base class for data |
| ImageHandle | Manage shared instances of images |
| NullData | Null data singleton |
| ConstGenericPropContainer< H > | |
| GenericPropContainer< H > | Base class for the handler classes |
| ConstGenericPropContainer< AtomBase > | |
| GenericPropContainer< AtomBase > | |
| AtomBase | Base class for AtomHandle and AtomView |
| AtomHandle | Handle to atom datatype |
| AtomView | Definition of AtomView |
| ConstGenericPropContainer< BondHandle > | |
| GenericPropContainer< BondHandle > | |
| BondHandle | Chemical bond |
| ConstGenericPropContainer< ChainBase > | |
| GenericPropContainer< ChainBase > | |
| ChainBase | Base class for ChainHandle and ChainView |
| ChainHandle | Linear chain of residues |
| ChainView | Definition of ChainView |
| ConstGenericPropContainer< ConstSequenceHandle > | |
| ConstSequenceHandle | Immutable sequence |
| ConstGenericPropContainer< EntityBase > | |
| GenericPropContainer< EntityBase > | |
| EntityBase | Definition of EntityBase |
| EntityHandle | Protein or molecule |
| EntityView | Definition of EntityView |
| ConstGenericPropContainer< ResidueBase > | |
| GenericPropContainer< ResidueBase > | |
| ResidueBase | Base class for ResidueHandle and ResidueView |
| ResidueHandle | Residue handle |
| ResidueView | Residue view |
| ConstGenericPropContainer< SequenceHandle > | |
| GenericPropContainer< SequenceHandle > | |
| SequenceHandle | Mutable sequence handle |
| ConstSequenceList | List of immutable sequences |
| Contact | |
| ContactEntity | |
| ContactPredictionScoreResult | |
| ContactScorer | |
| ContactScorerResultICS | |
| ContactScorerResultIPS | |
| ContactWeightMatrix | Matrix to weight pairs of amino-acids |
| ContextProfile | |
| ContextProfileDB | |
| Convert< CONVERSIONTYPE, VALUETYPE > | |
| CoordGroupHandle | Coordinate group, for trajectories and such |
| CoordSource | Coordinate source |
| InMemCoordSource | In-memory coordinate source |
| CosFnc | |
| CRDReader | CHARMM coordinate file import |
| Cuboid | Arbitrary oriented bounding cuboid |
| CuboidAxis | Cuboid axis defined by a normalized direction vector and a half extent |
| CustomCompound | |
| CylinderPrim | |
| Database | SQLite database handle |
| DataObserver | Abstract base class of data observer |
| Argand | |
| DataViewerPanelBase | |
| DataViewerPanel | |
| FFTPanel | |
| ParentDataObserver | |
| Date | |
| def_visitor | |
| VectorAdditions< Container > | |
| DefaultPepLib | |
| Diag | |
| Diagnostics | |
| Dihedral | Low level dihedral implementation |
| TorsionImpl | |
| DiscreteShrinkFnc | Shrink image by integral amount |
| Dist2Mean | Container for distances to mean for N structures. Main functionality: Get/Set, ExportXXX |
| DistanceMap | |
| Distances | Container for a pair wise distance for each structure. Each structure is identified by its index in the originally used alignment |
| DockQResult | |
| Domain | |
| Domains | |
| DSSPAccessibilityParam | |
| EdgeDesc | |
| EditorBase | Base class for entity editors |
| ICSEditor | Editor for internal molecule coordinates |
| XCSEditor | External coordinate system editor |
| EleImpl | |
| Ellipse2 | |
| enable_shared_from_this | |
| GfxNode | |
| GfxObjBase | Main interface for all graphic objects, both in C++ and Python |
| GfxObj | Main class for all graphic objects |
| Entity | Graphical rendering of mol::EntityHandle entites |
| GfxTestObj | |
| MapIso | Isocontour rendering for 3D image data |
| MapSlab | Render slice of 3d image |
| PrimList | |
| PyGfxObj | |
| Surface | |
| Primitive | Base class for geometric primitives such as cuboids, and circles |
| Cuboid | Rendered cuboid in 3D space |
| Quad | Simple rendered quad in 3D space |
| SymmetryNode | Renders all child nodes and the symmetry related copies |
| AtomImpl | Atom implementation |
| ChainImpl | |
| ConnectorImpl | |
| EntityImpl | |
| ResidueImpl | |
| TorsionImpl | |
| EntityIOHandler | Pure abstract base class for entity io handlers |
| EntityIOCRDHandler | |
| EntityIOCRDHandler | |
| EntityIOMAEHandler | |
| EntityIOMAEHandler | |
| EntityIOMMCIFHandler | |
| EntityIOMMCIFHandler | |
| EntityIOPDBHandler | |
| EntityIOPDBHandler | |
| EntityIOPQRHandler | |
| EntityIOPQRHandler | |
| EntityIOSDFHandler | |
| EntityIOSDFHandler | |
| EntityIOHandlerFactoryBase | Pure abstract base class for creation of a specfic entity io handle |
| EntityIOHandlerFactory< HANDLER > | |
| EntityIOHandlerFactory< HANDLER > | |
| EntityObserver | |
| EntityPropertyMapper | |
| EntityRenderer | |
| ConnectRendererBase | |
| CPKRenderer | |
| CustomRenderer | |
| SimpleRenderer | Simple line-based rendererer at full connectivity detail |
| TraceRendererBase | |
| CartoonRenderer | Display entity in cartoon mode |
| DebugRenderer | |
| LineTraceRenderer | Render backbone trace of entity |
| SlineRenderer | |
| TraceRenderer | Render backbone trace of entity |
| EntityViewGetCol | |
| EntityViewVisitor | EntityViewVisitor interface |
| SDFWriter | |
| SDFWriter | |
| EntityVisitor | EntityVisitor interface |
| CRDWriter | CHARMM coordinate file export |
| CRDWriter | CHARMM coordinate file export |
| PQRWriter | CHARMM coordinate file export |
| PQRWriter | CHARMM coordinate file export |
| IndexedVertexArray::Entry | |
| equality_comparable | |
| Mat2 | |
| Mat3 | |
| Mat4 | |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
| Vec4 | |
| Phase | Manages phases og Complex numbers |
| Exception | |
| MsmsProcessError | |
| DisconnectedGraphError | |
| NoSymmetryError | |
| QSscoreError | QS scoring |
| ExpFnc | |
| ExplicitConvoluteFnc | |
| ExplicitCorrelateFnc | |
| Exporter | |
| ColladaExporter | |
| GostExporter | |
| Extent | Defines lower and upper valid indices |
| ExtentMask | |
| ExtentIterator | Extent iterator |
| FastSphereRenderer | |
| FFReader | |
| FFTFnc | |
| FileLoader | |
| FindMemParam | |
| FixedString< LENGTH > | String class that uses an array of static size to hold the characters |
| FNC | |
| ImageStateConstModIPAlgorithm< FNC > | In-place modifying image state const visitor plus ip algorithm |
| ImageStateConstModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateConstModOPAlgorithm< FNC > | Out-of-place modifying image state const visitor plus op algorithm |
| ImageStateConstModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateModIPAlgorithm< FNC > | In-place modifying image state visitor plus ip algorithm |
| ImageStateModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateModOPAlgorithm< FNC > | Out-of-place modifying image state visitor plus op algorithm |
| ImageStateModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateMorphAlgorithm< FNC > | Morph visitor plus ip algorithm |
| ImageStateMorphVisitor< FNC > | Morphing image state visitor |
| ImageStateNonModAlgorithm< FNC > | Non-modifying image state visitor plus non-mod algorithm |
| ImageStateNonModVisitor< FNC > | Non-modifying image state visitor |
| Forcefield | |
| FormattedLine | |
| FragmentImpl | |
| FrequencyDomain | |
| GaussianFilterBase | Gaussian Filter |
| GaussianGradientMagnitudeFilterBase | First Derivative Gaussian Filter |
| GaussianLaplacianFilterBase | Gaussian Filter |
| GDTResult | |
| GenericPropContainerImpl | Base class for the implementation |
| AtomImpl | Atom implementation |
| ChainImpl | |
| ConnectorImpl | |
| EntityImpl | |
| ResidueImpl | |
| SequenceImpl | |
| GenProp | Struct to store info about GenericProperties parsed from the |
| GfxNodeListAttrProxy | |
| GfxNodeVisitor | |
| GfxView | |
| GLWinBase | |
| GLCanvas | |
| Gradient | Color gradient |
| GradientLevelGetCol | |
| GradientManager | |
| GromacsData | |
| GromacsPositionRuleEvaluator | |
| GutterBlock | |
| HalfFrequencyDomain | |
| HBond | |
| HBond | |
| HBondableAtoms | |
| HBondAcceptor | |
| HBondDonor | |
| Help | |
| HHblits | |
| HHblits | |
| HHblitsHeader | |
| HHblitsHeader | |
| HHblitsHit | |
| HHblitsHit | |
| HighestPeakSearch3DBase | |
| HistogramBase | |
| HMMData | |
| HydrogenConstructor | |
| GromacsHydrogenConstructor | |
| HeuristicHydrogenConstructor | |
| Hyperbola2 | |
| iAlignResult | |
| ImageFormatBase | |
| DAT | |
| DAT | |
| DF3 | |
| DF3 | |
| DM3 | |
| DM3 | |
| DX | |
| DX | |
| IPL | |
| IPL | |
| MRC | |
| CCP4 | |
| CCP4 | |
| MRC | |
| Nanoscope | |
| Nanoscope | |
| PNG | |
| PNG | |
| Situs | |
| Situs | |
| Spider | |
| Spider | |
| TIF | |
| JPK | |
| JPK | |
| TIF | |
| UndefinedImageFormat | |
| UndefinedImageFormat | |
| ImageStateBase | |
| ImageStateImpl< T, D > | |
| ImageStateConstModIPVisitorBase | In-place modifying image state const visitor base class |
| ImageStateConstModIPAlgorithm< FNC > | In-place modifying image state const visitor plus ip algorithm |
| ImageStateConstModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateConstModOPVisitorBase | Out-of-place modifying image state const visitor base class |
| ImageStateConstModOPAlgorithm< FNC > | Out-of-place modifying image state const visitor plus op algorithm |
| ImageStateConstModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateModIPVisitorBase | In-place modifying image state visitor base class |
| ImageStateModIPAlgorithm< FNC > | In-place modifying image state visitor plus ip algorithm |
| ImageStateModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateModOPVisitorBase | Out-of-place modifying image state visitor base class |
| ImageStateModOPAlgorithm< FNC > | Out-of-place modifying image state visitor plus op algorithm |
| ImageStateModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateMorphVisitorBase | Morphing image state visitor base class |
| ImageStateMorphAlgorithm< FNC > | Morph visitor plus ip algorithm |
| ImageStateMorphVisitor< FNC > | Morphing image state visitor |
| ImageStateNonModVisitorBase | Non-modifying image state visitor base class |
| ImageStateNonModAlgorithm< FNC > | Non-modifying image state visitor plus non-mod algorithm |
| ImageStateNonModVisitor< FNC > | Non-modifying image state visitor |
| ImmutableGradientInfoHandler | |
| ImmutablePresetInfoHandler | |
| Index | |
| Index< D > | |
| IndexBase< D > | |
| IndexBase< 1 > | |
| Index< 1 > | |
| IndexBase< 2 > | |
| Index< 2 > | |
| IndexBase< 3 > | |
| Index< 3 > | |
| IndexBase< 4 > | |
| Index< 4 > | |
| IndexBase< 5 > | |
| Index< 5 > | |
| IndexBase< 6 > | |
| Index< 6 > | |
| IndexBase< 7 > | |
| Index< 7 > | |
| IndexedVertexArray | |
| IndexIterator< D > | |
| IndexIterator | |
| InfoConstVisitor | |
| InfoGroup | |
| InfoHandle | Main info handle |
| InfoImpl | |
| InfoItem | |
| InfoPath | Encapsulates path to info groups and items |
| InfoSet | |
| InfoVisitor | |
| VerboseInfoVisitor | |
| InputEvent | |
| InsDel | Get insertions and deletions of an alignment |
| Interaction | |
| IOManager | Central registry for input/output handlers |
| IOProfile | |
| IOProfileRegistry | |
| IOProfiles | |
| IsosurfaceGenerator | |
| IsosurfaceGeneratorS | |
| iterator | |
| circular_iter< T > | |
| const_circular_iter< T > | |
| AminoAcidSetIterator | |
| pointer_it< T > | |
| AlignedColumnIterator | |
| SequenceListIterator< T, I > | |
| lDDTBSScorer | |
| lDDTLocalScore | |
| lDDTScorer | |
| lDDTScorer | |
| lDDTSettings | |
| LDT | |
| LigandScorer | |
| Line2 | Line2 |
| Line3 | Line3 |
| LinearCharacterContainer | |
| LinearIndexer | |
| LinearPositionContainer | |
| LineAverageBase | Computes mean value of columns or lines |
| LineIterator | Line iterator generator |
| LineSlice | |
| LocalSigmaThresholdBase | |
| Log10Fnc | |
| LogFnc | |
| Logger | |
| LogSink | |
| FileLogSink | |
| LogReader | |
| MultiLogSink | |
| StreamLogSink | |
| StreamLogSink | |
| StringLogSink | |
| LPaddedFloat | |
| LPaddedInt | |
| MAEReader | |
| ManyOf | |
| MapHandleGetCol | |
| MapIOHandler | |
| DF3MapIOHandler | |
| DF3MapIOHandler | |
| MapIODatHandler | |
| MapIODatHandler | |
| MapIODm3Handler | |
| MapIODm3Handler | |
| MapIODxHandler | |
| MapIODxHandler | |
| MapIOIPLHandler | |
| MapIOIPLHandler | |
| MapIOMrcHandler | |
| MapIOMrcHandler | |
| MapIONanoscopeHandler | |
| MapIONanoscopeHandler | |
| MapIOPngHandler | |
| MapIOPngHandler | |
| MapIOSitusHandler | |
| MapIOSitusHandler | |
| MapIOSpiHandler | |
| MapIOSpiHandler | |
| MapIOTiffHandler | |
| MapIOJpkHandler | |
| MapIOJpkHandler | |
| MapIOTiffHandler | |
| MapIOHandlerFactoryBase | |
| MapIOHandlerFactory< HANDLER > | |
| MapIOHandlerFactory< HANDLER > | |
| MapOctree | Octree datastructure for 3D images |
| MappingResult | |
| MaskBase | |
| CircleMask | |
| CompositeMask | |
| ExtentMask | |
| InvertedMask | |
| PolygonMask | |
| SphericalMask | |
| MaskImageBase | |
| MaskVisitor | |
| Material | |
| MeanlDDT | |
| MeanSquareMinimizer | |
| Measurement | |
| MirrorFnc | |
| MMAlignResult | |
| MMCifInfo | Container class for additional information from MMCif files |
| MMCifInfoBioUnit | |
| MMCifInfoCitation | |
| MMCifInfoEntityBranchLink | Store information on branched structures (oligosaccharides) |
| MMCifInfoObsolete | Container class for information on obsolete entries |
| MMCifInfoRevisions | Container class for information on file revisions See Python doc |
| MMCifInfoStructDetails | |
| MMCifInfoStructRef | |
| MMCifInfoStructRefSeq | |
| MMCifInfoStructRefSeqDif | |
| MMCifInfoTransOp | |
| MMPreprocessor | |
| Modeller | |
| ModelRepository | |
| MolckSettings | |
| MouseEvent | |
| multiplicative | |
| Mat4 | |
| Quat | Unit quaternion |
| Quat | Unit quaternion |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
| Vec4 | |
| Color | |
| Phase | Manages phases og Complex numbers |
| multiplicative2 | |
| Mat2 | |
| Mat3 | |
| NACCESSAccessibilityParam | |
| Node | |
| LogicOPNode | |
| SelNode | |
| NodeEntry | |
| NormalizeFnc | Abstract normalizer base class |
| IndexedVertexArray::NormalizerTriEntry | |
| IndexedVertexArray::NormalizerVertexEntry | |
| object | |
| GfxNodeListProxy | |
| MappedLDDTScorer | |
| OligoLDDTScorer | Oligo-lDDT scores |
| QSscoreEntity | |
| Table | |
| _fake_std_streams | |
| _TestInfo | |
| XMLTestRunner | |
| XMLTestRunnerTest.NullStream | |
| Observable | Templated observable class |
| Observer | |
| TrajObserver | |
| TrajWriter | |
| OcRangeVector | |
| OctreeIsocont | Isocontouring of maps using an octree-optimization |
| OctreeNode | |
| OMF | |
| OneOf | |
| OpBase | |
| AndOp | |
| OrOp | |
| XorOp | |
| OptionParser | |
| OstOptionParser | |
| OstOptionParser | |
| OverlapResult | |
| OverlayManager | |
| OverlayManagerObserver | Abstract observer base class for the OverlayManager |
| OverlayManagerGUI | |
| PagedArray< T, P > | Vector style container that splits content in pages, suited for large amounts of data. Comes with serialization functionality |
| PagedArray< char, 1048576 > | |
| PagedArray< uint64_t, 1048576 > | |
| PairSubstWeightMatrix | Position-independet pair substitution weight matrix |
| PairToTupleConverter< T1, T2 > | Helper to convert between python tuple and std::pair |
| PasteFnc | |
| PDBize | |
| PDBReader | |
| PDBWriter | |
| RasterImage::Pixel | Single pixel spec |
| PixelSampling | Helper class to handle pixel sampling |
| Plane | |
| PodVector< T > | Vector container that treats its data as POD - even if it isn't in the strict sense |
| PointCloud | |
| PointCloudManager | |
| Polygon2 | |
| PolygonMask | |
| PooledWidget | |
| PovState | |
| PowerSpectrumFnc | |
| PowFnc | |
| PQRReader | CHARMM coordinate file import |
| PrebuildSphereEntry | |
| PreparedStatement | |
| Preset | |
| Processor | |
| HeuristicProcessor | |
| RuleBasedProcessor | |
| Profile | |
| ProfileColumn | Defines profile of 20 frequencies for one residue |
| ProfileDB | Contains a DB of profiles (identified by a unique name (String)) |
| ProfileHandle | Provides a profile for a sequence |
| ProfileIOHandler | Pure abstract base class for profile io handlers |
| HhmIOHandler | |
| HhmIOHandler | |
| PssmIOHandler | |
| PssmIOHandler | |
| ProfileIOHandlerFactoryBase | Pure abstract base class for creation of a specfic io handler |
| ProfileIOHandlerFactory< HANDLER > | |
| ProfileIOHandlerFactory< HANDLER > | |
| Progress | |
| Prop | |
| PtrObserver< T > | |
| PythonContext | |
| PythonContextParser | |
| PythonToken | |
| PythonTokenizer | |
| QAbstractItemModel | |
| SceneWinModel | Data model for scene win |
| QAbstractListModel | |
| GradientListModel | |
| PresetEditorListModel | |
| PresetListModel | |
| QAbstractTableModel | |
| SequenceModel | |
| TableModel | |
| QCheckBox | |
| OverlayCustomLockCheckBox | |
| OverlayCustomVisCheckBox | |
| QComboBox | |
| ChainComboBox | |
| QCompleter | |
| OstCompleterBase | |
| PathCompleter | |
| PythonCompleter | |
| QDialog | |
| ExportSceneDialog | |
| SuperpositionDialog | |
| TerminalUsageDialog | |
| FileTypeDialog | Dialog to select a file type |
| CalculateSurfaceSettingsDialog | |
| SelectRefDialog | |
| ShowResultDialog | |
| SplashDialog | |
| InspectorDialog | |
| ByChainColorOpWidget | |
| ByElementColorOpWidget | |
| GradientLevelColorOpWidget | |
| PresetEditor | |
| RenderOpWidget | |
| UniformColorOpWidget | |
| VisibilityOpWidget | |
| QueryDialog | |
| PointlistOverlayBaseSettings | |
| QDirModel | |
| OstDirModel | |
| QDockWidget | |
| DockWidget | |
| QItemDelegate | |
| SequenceDelegate | |
| QMainWindow | |
| MainWindow | |
| DataViewer | Data viewer |
| WidgetStateSaver< QMainWindow > | |
| GostyMainWindow | |
| QMdiArea | |
| MainArea | Main window area It is implemented as a MDI (multi document interface). This allows you to add custom widgets to it |
| QMenu | |
| FileMenu | |
| HelpMenu | |
| SceneMenu | |
| WindowMenu | |
| QObject | |
| AlignmentContextMenu | |
| SecStructContextMenu | |
| SelectMenuPoints | |
| SurfaceContextMenu | |
| InitMenuBar | |
| SpacenavControl | |
| QObject | |
| BaseRow | |
| SequenceRow | |
| SecStrRow | |
| TitleRow | |
| BaseViewObject | |
| SequenceViewObject | |
| AlignmentViewObject | |
| ContextMenu | |
| EnumOptBinder | |
| FloatOptBinder | |
| GostyApp | |
| IntOptBinder | |
| LogReader | |
| MainThreadRunner | |
| OutputRedirector | |
| Painter | |
| AlignPropertiesPainter | |
| BackgroundPainter | |
| ConservationPainter | |
| SeqSecStrPainter | |
| SeqSelectionPainter | |
| SeqTextPainter | |
| TickPainter | |
| Perspective | |
| PythonInterpreter | |
| PythonInterpreterWorker | |
| SceneMenu | |
| SceneNode | |
| EntityPartNode | |
| CurrentSelectionNode | |
| CustomPartNode | |
| RenderModeNode | |
| GfxSceneNode | |
| EntityNode | |
| LabelNode | |
| RenderModesNode | |
| RootNode | |
| SceneSelection | |
| State | |
| StateMachine | |
| TextLogger | |
| Tool | Base class for tools |
| Manipulator | Rigid body manipulator |
| MapTool | |
| MeasureTool | |
| SelectionTool | |
| ToolManager | |
| ToolOption | |
| ToolOptionButton | |
| ToolOptionEnum | |
| ToolOptionNum< T, C > | |
| ToolOptionGroup | |
| ToolOptions | Tool options |
| TransitionBase | |
| AutomaticTransition | |
| KeyEventTransition | |
| MouseEventTransition | |
| SignalTransition | |
| TransitionGuard | |
| BlockStatusGuard | |
| EditPositionGuard | |
| HistoryGuard | |
| WidgetFactory | |
| WidgetGeomHandler | |
| WidgetPool | This Widget pool manages instances of widgets Widgets can be added to this pool by simply passing the classname and the amount of available instances. This class is coupled to the WidgetRegistry |
| WidgetRegistry | Central registry for widgets |
| Overlay | |
| DrawOverlay | |
| MaskOverlay | |
| NullOverlay | |
| PointlistOverlayBase | |
| PointlistOverlay | |
| QOpenGLWindow | |
| GLCanvas | |
| QPlainTextDocumentLayout | |
| PythonShellTextDocumentLayout | |
| QPlainTextEdit | |
| PythonShellWidget | |
| QRadioButton | |
| OverlayCustomActCheckBox | |
| QSEntity | |
| QSplitter | |
| ThinSplitter | Splitter with 1 pixel wide handles |
| QSScorer | |
| _QSScoreGreedySearcher | |
| QSscorer | |
| QSScorerResult | |
| QStackedWidget | |
| AdditionalSettingsWidget | |
| QSyntaxHighlighter | |
| PythonSyntaxHighlighter | |
| QTabBar | |
| DragTabBar | Tabbed drag widget |
| QTableView | |
| SequenceTableView | QTableView with first column not moving |
| Table | |
| QTabWidget | |
| TabbedDragWidget | Tabbed drag widget |
| QTextStream | |
| TextLogger | |
| QToolBar | |
| ToolBar | |
| QToolButton | |
| EventButton | Button box |
| quantity< Dimensions > | |
| quantity< detail::scalar_dimension > | |
| Scalar | |
| Query | Selection Query |
| QueryErrorDesc | |
| QueryFlag | Query flags |
| QueryImpl | Query statement implementation |
| QueryLexer | |
| QueryState | Holds state used during query evaluation |
| QueryToken | |
| QueryViewWrapper | |
| QWidget | |
| DocWidget | |
| ByChainWidget | |
| ByElementWidget | |
| ByEntityWidget | |
| ColorSelectWidget | |
| ComboOptionsWidget | |
| GradientEdit | |
| GradientEditor | |
| GradientPreview | |
| GradientPresetWidget | |
| LevelPreview | |
| MapLevelWidget | |
| PresetWidget | |
| QueryEditorWidget | |
| RemoteLoader | |
| RenderModeWidget | |
| EmptyMode | |
| ToolBarOptionsWidget | |
| UniformColorWidget | |
| WireframeWidget | |
| RandomizeFnc | |
| Range | |
| Range | |
| RangeHandler | |
| LinearRangeNormalizer | |
| LogRangeNormalizer | |
| ViewerNormalizer | |
| RasterImage | Generic raster image |
| Rectangle2 | |
| RefMode | |
| RemoteRepository | |
| RenderOp | |
| RenderOptions | |
| CartoonRenderOptions | |
| CPKRenderOptions | |
| CustomRenderOptions | |
| LineRenderOptions | |
| LineTraceRenderOptions | |
| SimpleRenderOptions | |
| SlineRenderOptions | |
| TraceRenderOptions | |
| ReprResult | |
| ResidueDefinition | |
| ResidueNames | |
| RGBAColor | |
| RingFinder | Class for finding rings in an entity |
| Rotation3 | |
| RowSet< R > | Row set iterator |
| runtime_error | |
| GeomException | |
| DivideByZeroException | |
| OutOfRangeException | |
| Error | |
| InvalidatedPointer | |
| DiagError | |
| DatabaseError | |
| GenericPropError | |
| FFTException | |
| HistogramError | |
| DispatchException | |
| InvalidImageStateVisitor | ImageStateVisitor general exception |
| InvalidExtentException | |
| InvalidImageHandle | Exception thrown upon invalid image handle usage |
| InvalidObserver | |
| InvalidSampling | |
| InfoError | |
| IntegrityError | |
| InvalidHandle | Signals access of member functions of invalid handles |
| IOException | |
| IOFileAlreadyLoadedException | |
| IOUnknownFormatException | |
| NotConnectedError | Error to indicate that two atoms that are supposed to be connected are not |
| PropertyError | |
| QueryError | |
| InvalidAlignment | |
| InvalidSequence | |
| RuntimeError | |
| BlastError | |
| FileNotFound | |
| Scene | Main class for organization and root for the graphical display |
| SceneFX | |
| SceneObserver | Interface for observing graphical objects |
| GLWin | |
| SceneObserverImpl | |
| SceneWinModel | Data model for scene win |
| SequenceViewer | QTableView with first column not moving |
| Scorer | |
| SDFReader | |
| SecStructure | Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format |
| SecStructureSegment | Consecutive secondary structure element |
| Selection | |
| SelHelper | |
| SelItem | |
| SelStmt | |
| SequenceIOHandler | Pure abstract base class for entity io handlers |
| ClustalIOHandler | |
| ClustalIOHandler | |
| FastaIOHandler | |
| FastaIOHandler | |
| PirIOHandler | |
| PirIOHandler | |
| PromodIOHandler | |
| PromodIOHandler | |
| SequenceIOHandlerFactoryBase | Pure abstract base class for creation of a specfic alignment io handler |
| SequenceIOHandlerFactory< HANDLER > | |
| SequenceIOHandlerFactory< HANDLER > | |
| SequenceList | List of sequences |
| SequenceListImpl | |
| SerializeHelper< B, T > | |
| SerializeHelper< false, T > | |
| SerializeHelper< true, T > | |
| SerializeWriteHelper< B, T > | |
| SerializeWriteHelper< false, T > | |
| SerializeWriteHelper< true, T > | |
| Settings | |
| Shader | |
| ShellHistory | |
| ShiftFnc | |
| SidechainAtomRule | |
| Simulation | |
| SinFnc | |
| Size | Class encapsulating 1D to 3D size |
| SliceFnc | |
| SmoothMaskImageBase | |
| SpatialDomain | |
| SpatialOrganizer< ITEM, VEC > | Spatial organizer |
| SpatialOrganizer< AtomImplPtr > | |
| SpatialOrganizer< SurfaceVertexID > | |
| Sphere | |
| SphericalMask | |
| Sphere | |
| SpherePrim | |
| Spline | |
| SplineEntry | |
| SqrtFnc | |
| StarDataItem | |
| StarLoopDesc | |
| StarParser | Parser for the STAR file format |
| ChemdictParser | |
| ChemdictParser | |
| MMCifReader | Reader for the mmcif file format |
| MMCifReader | Reader for the mmcif file format |
| StatAccumulator< MAX_MOMENT, DATATYPE > | |
| StatBase | |
| StateExtractor | |
| StatMinMaxBase | |
| Steep | |
| StereoChemicalAngleViolation | |
| StereoChemicalBondViolation | |
| StereoChemicalParams | List of stereo chemical parameters (Bonds and angles) |
| StereoChemicalProps | |
| StereoChemistryInfo | |
| Gradient::Stop | |
| str | |
| AnnoType | |
| StringOrRegexParam | |
| StringRef | Convenient datatype for referencing character data |
| LPadded | |
| RPadded | |
| SubstWeightMatrix | Position-independet substitution weight matrix |
| SuperpositionResult | Stores the number of cycles and the two final EntityViews (in case IterativeSuperposition was applied), the root mean square deviation of the two superposed objects and the transformation matrix (geom::Mat4) to superpose input1 onto input2 |
| SurfaceHandle | |
| SurfaceImpl | |
| SurfaceIOHandler | |
| SurfaceIOMSMSHandler | |
| SurfaceIOMSMSHandler | |
| SurfaceIOHandlerFactoryBase | |
| SurfaceIOHandlerFactory< HANDLER > | |
| SurfaceIOHandlerFactory< HANDLER > | |
| SurfaceTri | |
| SurfaceVertex | |
| SymbolDrawingStrategy | |
| CircleDrawingStrategy | |
| CrosshairBaseDrawingStrategy | |
| CrosshairCircleDrawingStrategy | |
| CrosshairSquareDrawingStrategy | |
| SquareDrawingStrategy | |
| SymmetryOp | |
| SymmetrySettings | |
| SystemCreator | |
| TableCol | |
| TableRow | |
| TableSelector | |
| TanFnc | |
| TempDirWithFiles | |
| TerminiConstructor | |
| TerminiExceptions | |
| TestCase | |
| XMLTestRunnerTest | |
| TestResult | |
| _XMLTestResult | |
| TextPrim | |
| Texture | |
| tiff_warning_handler_wrapper | |
| TMAlignResult | |
| TMScoreResult | |
| Topology | |
| TopologyCreator | |
| TorsionHandle | Named torsion (dihedral) angle |
| TraceProfileEntry | |
| transform | |
| divide_dimensions< D1, D2 > | |
| multiply_dimensions< D1, D2 > | |
| Transform | Basic and essential transformation class, including translation, rotation and center of rotation |
| Transformation | Transformation base class |
| Rotate2D | Rotate in XY plane |
| Rotate2D90 | Rotate 90 degree CW in XY plane |
| Scale | Apply scale |
| Translate | Apply translation |
| TransformFnc | |
| TriMatrix< T > | Triangular matrix template |
| TriMatrix< ost::seq::alg::Distances > | |
| TriMatrix< Real > | |
| DistanceMatrix | |
| SimilarityMatrix | |
| VarianceMap | Container for variances for each entry in a distance map. Main functionality: Get/Set, Min, Max, ExportXXX Get/Set and GetSize taken from TriMatrix |
| ToolOptionEnum::Tuple | |
| TwoOf | |
| types | Structure |
| types | Structure |
| unary_dispatch_ip< FNC > | In-place unary dispatch |
| unary_dispatch_op< FNC > | Out-of-place unary dispatch |
| UniformGetCol | |
| UniqueAtomIdentifier | Contains the infomation needed to uniquely identify an atom in a structure |
| Units | |
| ValueHolder< V > | |
| ValueHolder< T > | |
| FastSphereRenderer::VData | |
| vector | |
| Polygon2 | |
| Vec3List | |
| ImageList | Manages a collection of images |
| PointList | List of points |
| VectorToListConverter< T > | Helper to convert between python list tuple and std::vecot |
| ViewAddFlag | Flags to control the behaviour when adding handles to views |
| Viewport | |
| VisibilityOp | |
| WidgetState | |
| WidgetStateSaverConfig | |
| WithinParam | |
| BASE | |
| WidgetStateSaver< BASE, T1, T2, T3 > | |
| WidgetStateSaver< BASE > | |
| WidgetStateSaver< BASE, T1 > | |
| WidgetStateSaver< BASE, T1, T2 > | |
| ColorSelectWidget | |
| MyGradientStop | |
| ComboOptionsWidget | |
| ColorOptionsWidget | |
| RenderOptionsWidget | |
| Enum | |
| AnnoType | |
| ImageStateConstModIPAlgorithm | |
| NormalizerImpl | |
| LinearNormalizer | Linear normalization |
| LinearRangeNormalizer | |
| LogNormalizer | Log normalization |
| LogRangeNormalizer | |
| TransmissionToODNormalizer | |
| ViewerNormalizer | |
| NoOpNormalizer | |
| ImageStateModIPAlgorithm | |
| AnisotropicFilter | |
| ImmutableGradientInfoHandler | |
| GradientInfoHandler | |
| ImmutablePresetInfoHandler | |
| PresetInfoHandler | |
| QLabel | |
| InfoPanelLabel | |
| QWidget | |
| ClipWidget | |
| FileViewer | Simplistic file viewer |
| Gutter | |
| MessageBoxWidget | |
| MessageLevel | |
| PanelBarWidgetHolder | |
| SeqSearchBar | Search bar to search in multiple sequence alignment |
| ToolOptionsWidget | |
| Widget | Base class for widgets |
| ButtonBar | Button box |
| ButtonBox | Button box |
| DropBox | |
| FileBrowser | Simplistic file browser |
| GLWin | |
| MessageWidget | |
| PanelBar | Panel Bar which may contain other Widgets A PanelBar might have different ViewModes which are PanelWidgetContainer classes. Per default a PanelWidgetContainer has no ViewMode therefore first of all a view mode must be added. Otherwise nothing will be displayed. The ViewMode is responsible for how the widget is displayed. This class keeps only track about the order of the added widgets and the ViewModes |
| BottomBar | Bottom Bar |
| SideBar | Bottom Bar |
| PanelManager | Class which organizes all widgets which are in the side panels This class handles all side bar widgets. It can be used to display, hide or move a widget to a PaneBar. There are three Bars (left, bottom, right) which are organized by this class. Whenever a widget is being removed or added it checks first if the widget type is known and if there are available instances |
| PanelWidgetContainer | A PanelWidgetContainer can display various widgets A PanelWidgetContainer is a abstract class which is used by the PanelBar class as view mode |
| SplitterPanelBar | Bottom Bar |
| TabbedPanelBar | Tabbed bar |
| PythonShell | Interactive python shell |
| SceneWin | |
| SequenceViewer | QTableView with first column not moving |
| ToolOptionsWin | |
| Argand | |
| DataViewerPanelBase | |
| InfoPanel | |
| OverlayManagerGUI | |
| RenderModeWidget | |
| CPKWidget | |
| CustomWidget | |
| HSCWidget | |
| LineTraceWidget | |
| SimpleWidget | |
| SlineWidget | |
| TraceWidget | |
| TubeWidget | |
| ToolBarOptionsWidget | |
| InspectorWidget | |
1.8.5
