  geom | |
  Axis | |
 AlignedCuboid | Axis-aligned cuboid |
| Line2 | Line2 |
| Rectangle2 | |
| Polygon2 | |
| Ellipse2 | |
| Hyperbola2 | |
| Circle2 | |
| Line3 | Line3 |
| Plane | |
| Sphere | |
| CuboidAxis | Cuboid axis defined by a normalized direction vector and a half extent |
| Cuboid | Arbitrary oriented bounding cuboid |
| Rotation3 | |
| GeomException | |
| DivideByZeroException | |
| OutOfRangeException | |
| VectorAdditions | |
| Mat2 | |
| Mat3 | |
| Mat4 | |
| PointCloud | |
| PointCloudManager | |
| Quat | Unit quaternion |
| Transform | Basic and essential transformation class, including translation, rotation and center of rotation |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
 Vec4 | |
| OpenMM | |
| ost | |
 bindings | |
| blast | |
| AlignedPatch | |
| BlastHit | |
| BlastError | |
| cadscore | |
| CADResult | |
| clustalw | |
| dockq | |
| DockQResult | |
| dssp | |
| hbplus | |
| HBond | |
| hhblits | |
| hhblits2 | |
| HHblitsHit | |
| HHblitsHeader | |
| HHblits | |
| hhblits3 | |
| HHblitsHit | |
| HHblitsHeader | |
| HHblits | |
| ialign | |
| iAlignResult | |
| kclust | |
| cluster | |
| lga | |
| GDTResult | |
| mmseqs2 | |
| msms | |
| MsmsProcessError | |
| naccess | |
| tmtools | |
| TMScoreResult | |
| utils | |
| TempDirWithFiles | |
| TMAlignResult | |
| MMAlignResult | |
| conop | |
| cleanup | |
| AminoAcidSetIterator | |
| AminoAcidSet | Amino acid bit set |
| Date | |
| AtomSpec | |
| BondSpec | |
| Compound | Knows about the atoms and bonds of a chemical compounds |
| CompoundLib | |
| CompoundLibBase | |
| Conopology | |
| Diag | |
| DiagError | |
| Diagnostics | |
| HeuristicProcessor | |
| MinimalCompoundLib | |
| Checker | |
| Processor | |
| RingFinder | Class for finding rings in an entity |
| RuleBasedProcessor | |
| db | |
| LinearCharacterContainer | |
| LinearPositionContainer | |
| AssemblyInfo | |
| LinearIndexer | |
| PreparedStatement | |
| DatabaseError | |
| RowSet | Row set iterator |
| Database | SQLite database handle |
| dng_startup | |
| geom | |
| gfx | |
| detail | |
| PrebuildSphereEntry | |
| impl | |
| BackboneTrace | |
| CartoonRenderer | Display entity in cartoon mode |
| ConnectRendererBase | |
| CPKRenderer | |
| CustomRenderer | |
| DebugRenderer | |
| RGBAColor | |
| AtomEntry | |
| BondEntry | |
| GfxView | |
| NodeEntry | |
| TraceProfileEntry | |
| SplineEntry | |
| Spline | |
| EntityRenderer | |
| ByElementGetCol | |
| ByChainGetCol | |
| UniformGetCol | |
| GradientLevelGetCol | |
| EntityViewGetCol | |
| MapHandleGetCol | |
| FastSphereRenderer | |
| VData | |
| LineTraceRenderer | Render backbone trace of entity |
| IsosurfaceGenerator | |
| IsosurfaceGeneratorS | |
| OcRangeVector | |
| OctreeNode | |
| MapOctree | Octree datastructure for 3D images |
| EdgeDesc | |
| OctreeIsocont | Isocontouring of maps using an octree-optimization |
| Beacon | |
| SceneFX | |
| SimpleRenderer | Simple line-based rendererer at full connectivity detail |
| SlineRenderer | |
| TraceRenderer | Render backbone trace of entity |
| TraceRendererBase | |
| map_iso | |
| py_gfx_obj | |
| PyGfxObj | |
| RenderMode | |
| Bitmap | |
| ColladaExporter | |
| Color | |
| BasicGradientColorOp | |
| ByChainColorOp | |
| ByElementColorOp | |
| ColorOp | |
| EntityViewColorOp | |
| GradientColorOp | |
| GradientLevelColorOp | |
| MapHandleColorOp | |
| UniformColorOp | |
| Entity | Graphical rendering of mol::EntityHandle entites |
| Exporter | |
| GfxNode | |
| GfxNodeVisitor | |
| GfxObj | Main class for all graphic objects |
| GfxObjBase | Main interface for all graphic objects, both in C++ and Python |
| SpherePrim | |
| CylinderPrim | |
| TextPrim | |
| GfxTestObj | |
| GLWinBase | |
| GostExporter | |
| Gradient | Color gradient |
| Stop | |
| GradientManager | |
| InputEvent | |
| MapIso | Isocontour rendering for 3D image data |
| MapSlab | Render slice of 3d image |
| Material | |
| PovState | |
| PrimList | |
| Primitive | Base class for geometric primitives such as cuboids, and circles |
| Cuboid | Rendered cuboid in 3D space |
| Quad | Simple rendered quad in 3D space |
| CartoonRenderOptions | |
| CPKRenderOptions | |
| CustomRenderOptions | |
| LineRenderOptions | |
| LineTraceRenderOptions | |
| RenderOptions | |
| SimpleRenderOptions | |
| SlineRenderOptions | |
| TraceRenderOptions | |
| Viewport | |
| Scene | Main class for organization and root for the graphical display |
| SceneObserver | Interface for observing graphical objects |
| Selection | |
| Shader | |
| Surface | |
| SymmetryOp | |
| SymmetryNode | Renders all child nodes and the symmetry related copies |
| Texture | |
| IndexedVertexArray | |
| Entry | |
| NormalizerTriEntry | |
| NormalizerVertexEntry | |
| GfxNodeListAttrProxy | |
| GfxNodeListProxy | |
| gui | |
| dng | |
| init | |
| OstOptionParser | |
| menu | |
| FileMenu | |
| ClipWidget | |
| ExportSceneDialog | |
| SceneMenu | |
| WindowMenu | |
| HelpMenu | |
| superpositiondialog | |
| ChainComboBox | |
| SuperpositionDialog | |
 termuse | |
 TerminalUsageDialog | |
| gosty_startup | |
| helpwidget | |
| DocWidget | |
| Help | |
| init_context_menu | |
| SelectRefDialog | |
| ShowResultDialog | |
| CalculateSurfaceSettingsDialog | |
| SurfaceContextMenu | |
| SecStructContextMenu | |
| AlignmentContextMenu | |
| SelectMenuPoints | |
| init_menubar | |
| InitMenuBar | |
| init_spacenav | |
| SpacenavControl | |
| init_splash | |
| SplashDialog | |
| scene | |
| color_options_widget | |
| ColorOptionsWidget | |
| ByElementWidget | |
| ByChainWidget | |
| ByEntityWidget | |
| color_select_widget | |
| ColorSelectWidget | |
| combo_options_widget | |
| ComboOptionsWidget | |
| cpk_widget | |
| CPKWidget | |
| custom_widget | |
| CustomWidget | |
| gradient_editor_widget | |
| GradientEditor | |
| GradientPreview | |
| GradientEdit | |
| MyGradientStop | |
| gradient_info_handler | |
| GradientInfoHandler | |
| gradient_list_model | |
| GradientListModel | |
| gradient_preset_widget | |
| GradientPresetWidget | |
| hsc_widget | |
| HSCWidget | |
| immutable_gradient_info_handler | |
| ImmutableGradientInfoHandler | |
| immutable_preset_info_handler | |
| ImmutablePresetInfoHandler | |
| init_inspector | |
| inspector_widget | |
| InspectorWidget | |
| InspectorDialog | |
| line_trace_widget | |
| LineTraceWidget | |
| map_level_widget | |
| AdditionalSettingsWidget | |
| MapLevelWidget | |
| LevelPreview | |
| preset | |
| Preset | |
| preset_editor_list_model | |
| PresetEditorListModel | |
| preset_editor_widget | |
| PresetEditor | |
| UniformColorOpWidget | |
| GradientLevelColorOpWidget | |
| ByElementColorOpWidget | |
| ByChainColorOpWidget | |
| RenderOpWidget | |
| VisibilityOpWidget | |
| preset_info_handler | |
| PresetInfoHandler | |
| preset_list_model | |
| PresetListModel | |
| preset_widget | |
| PresetWidget | |
| query_editor | |
| QueryEditorWidget | |
| QueryDialog | |
| remote | |
| RemoteLoader | |
| render_mode_widget | |
| RenderModeWidget | |
| render_op | |
| RenderOp | |
| render_options_widget | |
| RenderOptionsWidget | |
| EmptyMode | |
| scene_observer_impl | |
| SceneObserverImpl | |
| scene_selection_helper | |
| SelHelper | |
| simple_widget | |
| SimpleWidget | |
| sline_widget | |
| SlineWidget | |
| toolbar_options_widget | |
| ToolBarOptionsWidget | |
| trace_widget | |
| TraceWidget | |
| tube_widget | |
| TubeWidget | |
| uniform_color_widget | |
| UniformColorWidget | |
| visibility_op | |
| VisibilityOp | |
| wireframe_widget | |
| WireframeWidget | |
| table | |
| TableModel | |
| Table | |
| trajectory_viewer | |
| TrajWidget | |
| AdminRights | |
| DockWidget | |
| FileBrowser | Simplistic file browser |
| FileLoader | |
| FileTypeDialog | Dialog to select a file type |
| FileViewer | Simplistic file viewer |
| GLCanvas | |
| GLWin | |
| GostyApp | |
| GostyMainWindow | |
| MainArea | Main window area It is implemented as a MDI (multi document interface). This allows you to add custom widgets to it |
| MainWindow | |
| LogReader | |
| MessageLevel | |
| MessageBoxWidget | |
| MessageWidget | |
| BottomBar | Bottom Bar |
| ButtonBar | Button box |
| ButtonBox | Button box |
| DropBox | |
| EventButton | Button box |
| WidgetState | |
| 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 |
| PanelBarWidgetHolder | |
| 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 |
| SideBar | Bottom Bar |
| SplitterPanelBar | Bottom Bar |
| DragTabBar | Tabbed drag widget |
| TabbedDragWidget | Tabbed drag widget |
| TabbedPanelBar | Tabbed bar |
| Perspective | |
| OstCompleterBase | |
| OstDirModel | |
| Gutter | |
| MainThreadRunner | |
| OutputRedirector | |
| PathCompleter | |
| PythonCompleter | |
| PythonContext | |
| PythonContextParser | |
| PythonInterpreter | |
| PythonInterpreterWorker | |
| PythonShell | Interactive python shell |
| GutterBlock | |
| PythonShellTextDocumentLayout | |
| PythonShellWidget | |
| PythonSyntaxHighlighter | |
| Range | |
| PythonToken | |
| PythonTokenizer | |
| ShellHistory | |
| State | |
| StateMachine | |
| TextLogger | |
| TransitionBase | |
| AutomaticTransition | |
| SignalTransition | |
| KeyEventTransition | |
| MouseEventTransition | |
| TransitionGuard | |
| HistoryGuard | |
| EditPositionGuard | |
| BlockStatusGuard | |
| SceneMenu | |
| SceneSelection | |
| ContextMenu | |
| CurrentSelectionNode | |
| CustomPartNode | |
| EntityNode | |
| EntityPartNode | |
| GfxSceneNode | |
| LabelNode | |
| RenderModeNode | |
| RenderModesNode | |
| RootNode | |
| SceneNode | |
| SceneWin | |
| SceneWinModel | Data model for scene win |
| AlignPropertiesPainter | |
| AlignmentViewObject | |
| BackgroundPainter | |
| BaseRow | |
| BaseViewObject | |
| ConservationPainter | |
| Painter | |
| SecStrRow | |
| SeqSecStrPainter | |
| SeqSelectionPainter | |
| SeqTextPainter | |
| SequenceDelegate | |
| SequenceModel | |
| SequenceRow | |
| SeqSearchBar | Search bar to search in multiple sequence alignment |
| SequenceTableView | QTableView with first column not moving |
| SequenceViewObject | |
| SequenceViewer | QTableView with first column not moving |
| TickPainter | |
| TitleRow | |
| ThinSplitter | Splitter with 1 pixel wide handles |
| Manipulator | Rigid body manipulator |
| MapTool | |
| Measurement | |
| MeasureTool | |
| MouseEvent | |
| SelectionTool | |
| Tool | Base class for tools |
| ToolBar | |
| ToolManager | |
| ToolOption | |
| ToolOptionNum | |
| ToolOptionEnum | |
| Tuple | |
| ToolOptionButton | |
| ToolOptionGroup | |
| ToolOptions | Tool options |
| EnumOptBinder | |
| IntOptBinder | |
| FloatOptBinder | |
| ToolOptionsWidget | |
| ToolOptionsWin | |
| Widget | Base class for widgets |
| WidgetGeomHandler | |
| PooledWidget | |
| 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 |
| WidgetFactory | |
| WidgetRegistry | Central registry for widgets |
| WidgetStateSaverConfig | |
| WidgetStateSaver | |
| WidgetStateSaver< BASE, T1, T2 > | |
| WidgetStateSaver< BASE, T1 > | |
| WidgetStateSaver< BASE > | |
| OneOf | |
| TwoOf | |
| ManyOf | |
| img | |
| alg | |
| MirrorFnc | |
| ShiftFnc | |
| TransformFnc | |
| AnisotropicFilter | |
| AutoCorrelateFnc | |
| ConjFnc | |
| ExplicitConvoluteFnc | |
| ExplicitCorrelateFnc | |
| CrossCorrelate | |
| SliceFnc | |
| DFT | |
| DiscreteShrinkFnc | Shrink image by integral amount |
| FFTException | |
| FFTFnc | |
| LowPassFilter | Low Pass Filter |
| HighPassFilter | High Pass Filter |
| GaussianLowPassFilter | Gaussian Low Pass Filter |
| GaussianHighPassFilter | Gaussian High Pass Filter |
| FermiLowPassFilter | Fermi Low Pass Filter |
| FermiHighPassFilter | Fermi High Pass Filter |
| ButterworthLowPassFilter | Butterworth Low Pass Filter |
| ButterworthHighPassFilter | Butterworth High Pass Filter |
| FractionalShift | |
| GaussianFilterBase | Gaussian Filter |
| GaussianGradientMagnitudeFilterBase | First Derivative Gaussian Filter |
| GaussianLaplacianFilterBase | Gaussian Filter |
| HighestPeakSearch3DBase | |
| HistogramError | |
| HistogramBase | |
| LineAverageBase | Computes mean value of columns or lines |
| LineIterator | Line iterator generator |
| LocalSigmaThresholdBase | |
| MaskImageBase | |
| LinearNormalizer | Linear normalization |
| LinearRangeNormalizer | |
| LogNormalizer | Log normalization |
| LogRangeNormalizer | |
| TransmissionToODNormalizer | |
| Normalizer | |
| Polar | |
| EllipticPolar | |
| Cartesian | |
| PowerSpectrumFnc | |
| RandomizeFnc | |
| SmoothMaskImageBase | |
| StatBase | |
| StatAccumulator | |
| StatMinMaxBase | |
| CosFnc | |
| ExpFnc | |
| LogFnc | |
| Log10Fnc | |
| SinFnc | |
| SqrtFnc | |
| TanFnc | |
| PowFnc | |
| Transformation | Transformation base class |
| Rotate2D | Rotate in XY plane |
| Rotate2D90 | Rotate 90 degree CW in XY plane |
| Scale | Apply scale |
| Translate | Apply translation |
| detail | |
| PasteFnc | |
| gui | |
| Argand | |
| DataViewer | Data viewer |
| DataViewerPanel | |
| DataViewerPanelBase | |
| DrawOverlay | |
| ParentDataObserver | |
| FFTPanel | |
| InfoPanelLabel | |
| InfoPanel | |
| MaskOverlay | |
| NullOverlay | |
| Overlay | |
| OverlayManager | |
| OverlayCustomActCheckBox | |
| OverlayCustomVisCheckBox | |
| OverlayCustomLockCheckBox | |
| OverlayManagerGUI | |
| OverlayManagerObserver | Abstract observer base class for the OverlayManager |
| PointlistOverlay | |
| PointlistOverlayBaseSettings | |
| PointlistOverlayBase | |
| SymbolDrawingStrategy | |
| SquareDrawingStrategy | |
| CrosshairBaseDrawingStrategy | |
| CrosshairCircleDrawingStrategy | |
| CrosshairSquareDrawingStrategy | |
| CircleDrawingStrategy | |
| ViewerNormalizer | |
| image_state | |
| dispatch | |
| unary_dispatch_ip | In-place unary dispatch |
| unary_dispatch_op | Out-of-place unary dispatch |
| binary_dispatch_ip | In-place binary dispatch |
| binary_dispatch_op | Out-of-place binary dispatch |
| DispatchException | |
| ImageStateImpl | |
| ImageStateNonModAlgorithm | Non-modifying image state visitor plus non-mod algorithm |
| ImageStateModIPAlgorithm | In-place modifying image state visitor plus ip algorithm |
| ImageStateConstModIPAlgorithm | In-place modifying image state const visitor plus ip algorithm |
| ImageStateModOPAlgorithm | Out-of-place modifying image state visitor plus op algorithm |
| ImageStateConstModOPAlgorithm | Out-of-place modifying image state const visitor plus op algorithm |
| ImageStateMorphAlgorithm | Morph visitor plus ip algorithm |
| ImageStateBase | |
| FrequencyDomain | |
| HalfFrequencyDomain | |
| SpatialDomain | |
| InvalidImageStateVisitor | ImageStateVisitor general exception |
| ImageStateNonModVisitorBase | Non-modifying image state visitor base class |
| ImageStateNonModVisitor | Non-modifying image state visitor |
| ImageStateModIPVisitorBase | In-place modifying image state visitor base class |
| ImageStateModIPVisitor | In-place modifying image state visitor |
| ImageStateConstModIPVisitorBase | In-place modifying image state const visitor base class |
| ImageStateConstModIPVisitor | In-place modifying image state visitor |
| ImageStateModOPVisitorBase | Out-of-place modifying image state visitor base class |
| ImageStateModOPVisitor | Out-of-place modifying image state visitor |
| ImageStateConstModOPVisitorBase | Out-of-place modifying image state const visitor base class |
| ImageStateConstModOPVisitor | Out-of-place modifying image state visitor |
| ImageStateMorphVisitorBase | Morphing image state visitor base class |
| ImageStateMorphVisitor | Morphing image state visitor |
| Index | |
| IndexIterator | |
| ValueHolder | |
| physics | |
| detail | |
| quantity | |
| multiply_dimensions | |
| divide_dimensions | |
| Scalar | |
| util | |
| CircleMask | |
| OpBase | |
| AndOp | |
| OrOp | |
| XorOp | |
| CompositeMask | |
| ConstData | Abstract base class for read-only data |
| Data | Abstract base class for data |
| AlgorithmBase | Algorithm base class |
| NonModAlgorithm | Non-modifying Algorithm, abstract base class |
| ModIPAlgorithm | In-place modification algorithm |
| ConstModIPAlgorithm | In-place modification const algorithm |
| ModOPAlgorithm | Out-of-place modification algorithm |
| ConstModOPAlgorithm | Out-of-place modification const algorithm |
| InvalidObserver | |
| DataObserver | Abstract base class of data observer |
| InvalidExtentException | |
| Extent | Defines lower and upper valid indices |
| ExtentIterator | Extent iterator |
| ExtentMask | |
| InvalidImageHandle | Exception thrown upon invalid image handle usage |
| ImageHandle | Manage shared instances of images |
| ConstImageHandle | Read-only ImageHandle implementation |
| ImageList | Manages a collection of images |
| InvertedMask | |
| MaskBase | |
| MaskVisitor | |
| NormalizeFnc | Abstract normalizer base class |
| NormalizerImpl | |
| NoOpNormalizer | |
| RangeHandler | |
| NullData | Null data singleton |
| Observable | Templated observable class |
| Peak | |
| Phase | Manages phases og Complex numbers |
| InvalidSampling | |
| PixelSampling | Helper class to handle pixel sampling |
| Point | Class encapsulating 1D to 3D point |
| PointList | List of points |
| PolygonMask | |
| Progress | |
| RasterImage | Generic raster image |
| Pixel | Single pixel spec |
| Size | Class encapsulating 1D to 3D size |
| SphericalMask | |
| info | |
| detail | |
| EleImpl | |
| InfoImpl | |
| InfoError | |
| InfoGroup | |
| InfoHandle | Main info handle |
| InfoItem | |
| InfoPath | Encapsulates path to info groups and items |
| InfoSet | |
| VerboseInfoVisitor | |
| InfoVisitor | |
| InfoConstVisitor | |
| io | |
| detail | |
| SerializeWriteHelper | |
| SerializeWriteHelper< false, T > | |
| SerializeWriteHelper< true, T > | |
| SerializeHelper | |
| SerializeHelper< false, T > | |
| SerializeHelper< true, T > | |
| tiff_warning_handler_wrapper | |
| complexint32 | |
| complexint16 | |
| complexint8 | |
| fmt | |
| LPadded | |
| RPadded | |
| LPaddedInt | |
| LPaddedFloat | |
| jpk_tags | |
| remote | |
| RemoteRepository | |
| repository | |
| ModelRepository | |
| BinaryDataSink | |
| BinaryDataSource | |
| ChemdictParser | |
| ClustalIOHandler | |
| Convert | |
| BinaryOStream | |
| BinaryIStream | |
| CRDReader | CHARMM coordinate file import |
| CRDWriter | CHARMM coordinate file export |
| EntityIOCRDHandler | |
| EntityIOHandler | Pure abstract base class for entity io handlers |
| EntityIOHandlerFactoryBase | Pure abstract base class for creation of a specfic entity io handle |
| EntityIOHandlerFactory | |
| MAEReader | |
| EntityIOMAEHandler | |
| EntityIOMMCIFHandler | |
| EntityIOPDBHandler | |
| PQRReader | CHARMM coordinate file import |
| PQRWriter | CHARMM coordinate file export |
| EntityIOPQRHandler | |
| EntityIOSDFHandler | |
| FastaIOHandler | |
| LineSlice | |
| FormattedLine | |
| HhmIOHandler | |
| ImageFormatBase | |
| UndefinedImageFormat | |
| DAT | |
| MapIODatHandler | |
| DF3 | |
| DF3MapIOHandler | |
| DM3 | |
| MapIODm3Handler | |
| DX | |
| MapIODxHandler | |
| MapIOHandler | |
| MapIOHandlerFactoryBase | |
| MapIOHandlerFactory | |
| IPL | |
| MapIOIPLHandler | |
| JPK | |
| MapIOJpkHandler | |
| MRC | |
| CCP4 | |
| MapIOMrcHandler | |
| Nanoscope | |
| MapIONanoscopeHandler | |
| PNG | |
| MapIOPngHandler | |
| Situs | |
| MapIOSitusHandler | |
| Spider | |
| MapIOSpiHandler | |
| TIF | |
| MapIOTiffHandler | |
| IOException | |
| IOUnknownFormatException | |
| IOFileAlreadyLoadedException | |
| IOManager | Central registry for input/output handlers |
| IOProfile | |
| IOProfileRegistry | |
| MMCifInfoStructDetails | |
| MMCifInfoTransOp | |
| MMCifInfoBioUnit | |
| MMCifInfoCitation | |
| MMCifInfoObsolete | Container class for information on obsolete entries |
| MMCifInfoRevisions | Container class for information on file revisions See Python doc |
| MMCifInfoStructRef | |
| MMCifInfoStructRefSeq | |
| MMCifInfoStructRefSeqDif | |
| MMCifInfoEntityBranchLink | Store information on branched structures (oligosaccharides) |
| MMCifInfo | Container class for additional information from MMCif files |
| MMCifReader | Reader for the mmcif file format |
| SidechainAtomRule | |
| ChiDefinition | |
| ResidueDefinition | |
| ChainData | |
| DefaultPepLib | |
| OMF | |
| PDBReader | |
| PDBWriter | |
| SDFReader | |
| SDFWriter | |
| StarDataItem | |
| StarLoopDesc | |
| StarParser | Parser for the STAR file format |
| SurfaceIOHandler | |
| SurfaceIOHandlerFactoryBase | |
| SurfaceIOHandlerFactory | |
| SurfaceIOMSMSHandler | |
| PirIOHandler | |
| ProfileIOHandler | Pure abstract base class for profile io handlers |
| ProfileIOHandlerFactoryBase | Pure abstract base class for creation of a specfic io handler |
| ProfileIOHandlerFactory | |
| PromodIOHandler | |
| PssmIOHandler | |
| SequenceIOHandler | Pure abstract base class for entity io handlers |
| SequenceIOHandlerFactoryBase | Pure abstract base class for creation of a specfic alignment io handler |
| SequenceIOHandlerFactory | |
| IOProfiles | |
| mol | |
| alg | |
| chain_mapping | |
| MappingResult | |
| ReprResult | |
| ChainMapper | |
| _Aligner | |
| _lDDTDecomposer | |
| _lDDTGreedySearcher | |
| _QSScoreGreedySearcher | |
| contact_score | |
| ContactEntity | |
| ContactScorerResultICS | |
| ContactScorerResultIPS | |
| ContactScorer | |
| dockq | |
| hbond | |
| HBondableAtoms | |
| HBondDonor | |
| HBondAcceptor | |
| HBond | |
| helix_kinks | |
| lddt | |
| CustomCompound | |
| SymmetrySettings | |
| lDDTScorer | |
| ligand_scoring | |
| LigandScorer | |
| NoSymmetryError | |
| DisconnectedGraphError | |
| qsscore | |
| QSEntity | |
| QSScorerResult | |
| QSScorer | |
| qsscoring | |
| QSscoreError | QS scoring |
| QSscorer | |
| QSscoreEntity | |
| OligoLDDTScorer | Oligo-lDDT scores |
| MappedLDDTScorer | |
| _CachedRMSD | |
| scoring | |
| lDDTBSScorer | |
| Scorer | |
| stereochemistry | |
| ClashInfo | |
| BondViolationInfo | |
| AngleViolationInfo | |
| structure_analysis | |
| superpose | |
| trajectory_analysis | |
| views | |
| NACCESSAccessibilityParam | |
| DSSPAccessibilityParam | |
| OverlapResult | |
| AdjacencyBitmap | |
| BUInfo | |
| Contact | |
| LDT | |
| DistanceMatrix | |
| UniqueAtomIdentifier | Contains the infomation needed to uniquely identify an atom in a structure |
| Domain | |
| Domains | |
| BondLengthInfo | |
| ClashEvent | |
| ClashingInfo | |
| StereoChemicalBondViolation | |
| StereoChemicalAngleViolation | |
| StereoChemistryInfo | |
| ClashingDistances | List of reference atom-atom distances to detect clashes between non-bonded atoms |
| StereoChemicalParams | List of stereo chemical parameters (Bonds and angles) |
| FindMemParam | |
| StereoChemicalProps | |
| lDDTSettings | |
| lDDTLocalScore | |
| lDDTScorer | |
| MolckSettings | |
| PDBize | |
| SecStructureSegment | Consecutive secondary structure element |
| SimilarityMatrix | |
| 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 |
| MeanSquareMinimizer | |
| impl | |
| tok | |
| AtomGroupEntry | |
| AtomGroup | |
| AtomImpl | Atom implementation |
| AtomProp | |
| ChainImpl | |
| ConnectorImpl | |
| Dihedral | Low level dihedral implementation |
| EntityImpl | |
| FragmentImpl | |
| pointer_it | |
| WithinParam | |
| StringOrRegexParam | |
| Node | |
| LogicOPNode | |
| SelNode | |
| QueryToken | |
| QueryLexer | |
| SelStmt | |
| SelItem | |
| GenProp | Struct to store info about GenericProperties parsed from the |
| QueryImpl | Query statement implementation |
| ResidueImpl | |
| SurfaceImpl | |
| TorsionImpl | |
| mm | |
| antechamber | |
| impl | |
| IndexBase | |
| HydrogenConstructor | |
| TerminiConstructor | |
| BlockModifier | |
| BuildingBlock | |
| GromacsData | |
| CHARMMData | |
| MMPreprocessor | |
| FFReader | |
| ResidueNames | |
| Forcefield | |
| GromacsPositionRuleEvaluator | |
| GromacsHydrogenConstructor | |
| GromacsBlockModifier | |
| HeuristicHydrogenConstructor | |
| HeuristicBlockModifier | |
| Index | |
| Index< 1 > | |
| Index< 2 > | |
| Index< 3 > | |
| Index< 4 > | |
| Index< 5 > | |
| Index< 6 > | |
| Index< 7 > | |
| IndexIterator | |
| Interaction | |
| Modeller | |
| Observer | |
| TrajObserver | |
| TrajWriter | |
| TerminiExceptions | |
| Settings | |
| Simulation | |
| StateExtractor | |
| Steep | |
| SystemCreator | |
| Topology | |
| TopologyCreator | |
| AtomBase | Base class for AtomHandle and AtomView |
| AtomHandle | Handle to atom datatype |
| AtomView | Definition of AtomView |
| BondHandle | Chemical bond |
| BondTableEntry | |
| BondTable | |
| Builder | |
| ChainBase | Base class for ChainHandle and ChainView |
| ChainHandle | Linear chain of residues |
| ChainView | Definition of ChainView |
| ChemClass | |
| ChemType | |
| CoordFrame | |
| CoordGroupHandle | Coordinate group, for trajectories and such |
| CoordSource | Coordinate source |
| EditorBase | Base class for entity editors |
| EntityBase | Definition of EntityBase |
| EntityHandle | Protein or molecule |
| EntityObserver | |
| EntityPropertyMapper | |
| EntityView | Definition of EntityView |
| EntityVisitor | EntityVisitor interface |
| EntityViewVisitor | EntityViewVisitor interface |
| ICSEditor | Editor for internal molecule coordinates |
| InMemCoordSource | In-memory coordinate source |
| NotConnectedError | Error to indicate that two atoms that are supposed to be connected are not |
| Prop | |
| PropertyError | |
| QueryFlag | Query flags |
| Query | Selection Query |
| QueryErrorDesc | |
| QueryError | |
| QueryState | Holds state used during query evaluation |
| QueryViewWrapper | |
| ResidueBase | Base class for ResidueHandle and ResidueView |
| ResidueHandle | Residue handle |
| ResNum | |
| ResidueView | Residue view |
| SecStructure | Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format |
| SpatialOrganizer | Spatial organizer |
| SurfaceHandle | |
| SurfaceVertex | |
| SurfaceTri | |
| TorsionHandle | Named torsion (dihedral) angle |
| ViewAddFlag | Flags to control the behaviour when adding handles to views |
| XCSEditor | External coordinate system editor |
| ost_startup | |
| OstOptionParser | |
| seq | |
| alg | |
| aaindex | |
| AnnoType | |
| AAIndexData | |
| AAIndex | |
| mat | |
| renumber | |
| AlignmentOpts | Options for local and global sequence alignment algorithms |
| ContactPredictionScoreResult | |
| ContactWeightMatrix | Matrix to weight pairs of amino-acids |
| Distances | Container for a pair wise distance for each structure. Each structure is identified by its index in the originally used alignment |
| DistanceMap | |
| ContextProfile | |
| ContextProfileDB | |
| InsDel | Get insertions and deletions of an alignment |
| PairSubstWeightMatrix | Position-independet pair substitution weight matrix |
| RefMode | |
| SubstWeightMatrix | Position-independet substitution weight matrix |
| 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 |
| Dist2Mean | Container for distances to mean for N structures. Main functionality: Get/Set, ExportXXX |
| MeanlDDT | |
| impl | |
| SequenceImpl | |
| SequenceListImpl | |
| SequenceListIterator | |
| AlignedColumn | Provides access to a column in a aligned region or a sequence alignment |
| AlignedColumnIterator | |
| AlignedRegion | Region in a sequence alignment |
| AlignmentHandle | Representation of a multiple sequence alignemnt consisting of two or more sequences |
| InvalidSequence | |
| InvalidAlignment | |
| HMMData | |
| ProfileColumn | Defines profile of 20 frequencies for one residue |
| ProfileHandle | Provides a profile for a sequence |
| ProfileDB | Contains a DB of profiles (identified by a unique name (String)) |
| ConstSequenceHandle | Immutable sequence |
| SequenceHandle | Mutable sequence handle |
| ConstSequenceList | List of immutable sequences |
| SequenceList | List of sequences |
| settings | |
| FileNotFound | |
| stutil | |
| table | |
| BinaryColExpr | |
| TableCol | |
| TableRow | |
| Table | |
| table_selector | |
| TableSelector | |
| testutils | |
| xmlrunner | |
| _TestInfo | |
| _XMLTestResult | |
| XMLTestRunner | |
| _fake_std_streams | |
| XMLTestRunnerTest | |
| NullStream | |
| PairToTupleConverter | Helper to convert between python tuple and std::pair |
| VectorToListConverter | Helper to convert between python list tuple and std::vecot |
| FixedString | String class that uses an array of static size to hold the characters |
| GenericPropError | |
| GenericPropContainerImpl | Base class for the implementation |
| ConstGenericPropContainer | |
| GenericPropContainer | Base class for the handler classes |
| IntegrityError | |
| InvalidHandle | Signals access of member functions of invalid handles |
| Logger | |
| LogSink | |
| StreamLogSink | |
| StringLogSink | |
| FileLogSink | |
| MultiLogSink | |
| Error | |
| PagedArray | Vector style container that splits content in pages, suited for large amounts of data. Comes with serialization functionality |
| PodVector | Vector container that treats its data as POD - even if it isn't in the strict sense |
| Profile | |
| Range | |
| StringRef | Convenient datatype for referencing character data |
| TriMatrix | Triangular matrix template |
| Units | |
| test_image | |
| value_holder_test | |
| circular_iter | |
| const_circular_iter | |
| InvalidatedPointer | |
| PtrObserver | |
| types | Structure |
| types | Structure |
1.8.5
