 Avogadro | |
  Core | |
   internal | |
    ArrayRefContainer | |
   Array | Base class for array containers |
   AtomTemplate | |
   AtomTyper | The AtomTyper class provides a base interface for generating a list of type identifiers describing the atoms in a molecule |
   AvoSpglib | Interface between Avogadro and Spglib |
   BasisSet | BasisSet contains basis set data |
   BondTemplate | |
   Color3f | Representation of an RGB color using three floats |
   CoordinateBlockGenerator | Creates an aligned, formatted block of atomic coordinates |
   ArraySet | Base class for array type containers |
    Holder | |
    PlaceHolder | |
   CoordinateSet | Templated class for array type containers |
   CrystalTools | Collection of static functions that perform common crystallographic operations on a Core::Molecule |
   Cube | Provide a data structure for regularly spaced 3D grids |
   Elements | Stores basic data about chemical elements |
   GaussianSet | A container for Gaussian type outputs from QM codes |
   GaussianSetTools | Provide tools to calculate molecular orbitals, electron densities and other derived data stored in a GaussianSet result |
   Graph | Graph data structure |
   Mesh | Encapsulation of a triangular mesh that makes up a surface |
   Molecule | Chemical molecule |
   Atom | |
   Bond | |
   Mutex | Simple wrapper for the C++11 or Boost mutex class |
   NameAtomTyper | Simple implementation of AtomTyper that assigns element names to each atom |
   RingPerceiver | |
   SlaterSet | SlaterSet Class |
   SlaterSetTools | Provide tools to calculate molecular orbitals, electron densities and other derived data stored in a GaussianSet result |
   SpaceGroups | The Spacegroups class stores basic data about crystal spacegroups |
   SymbolAtomTyper | Simple implementation of AtomTyper that assigns element symbols to each atom |
   UnitCell | Representation of a crystal's unit cell |
   Variant | Union of data values |
   VariantMap | Map between string keys and variant values |
   MoleculeDeserializer | Implementation of ProtoCall::Serialization::Deserializer |
   MoleculeSerializer | Implementation of ProtoCall::Serialization::Serializer |
  Io | |
   CjsonFormat | Implementation of the Chemical JSON format |
   CmlFormat | Implementation of the Chemical Markup Language format |
   FileFormat | General API for file formats |
   FileFormatManager | Class to manage registration, searching and creation of file formats |
   GromacsFormat | Simple GROMACS .gro file reader |
   Hdf5DataFormat | Access to data stored in HDF5 files |
   MdlFormat | Implementation of the generic MDL format |
   PoscarFormat | Implementation of the generic POSCAR format |
   XyzFormat | Implementation of the generic xyz format |
  MoleQueue | |
   BatchJob | Manages a collection of jobs that are configured using the same InputGenerator and MoleQueue options. For use with InputGeneratorDialog::configureBatchJob(BatchJob&) |
   InputGenerator | Interface to input generator scripts |
   InputGeneratorDialog | Thin wrapper around InputGeneratorWidget for standalone use |
   InputGeneratorWidget | User interface for configuring, saving, editing, and running input files produced by InputGenerator scripts |
   MoleQueueDialog | Thin wrapper around MoleQueueWidget for standalone use |
   MoleQueueManager | Access to a MoleQueue server |
   MoleQueueQueueListModel | Qt item model representing the tree of available queues and programs in a running MoleQueue process |
   MoleQueueWidget | Widget for configuring and submitting a MoleQueue::JobObject |
  QtGui | |
   ContainerWidget | A widget that contains a single view widget, along with standard buttons for splitting, maximizing, closing |
   CustomElementDialog | Dialog window for mapping custom elements into elemental types |
   ElementDetail | |
   ElementItem | |
   ElementTranslator | Internationalization of element names |
   ExtensionPlugin | The base class for extension plugin factories in Avogadro |
   ExtensionPluginFactory | The base class for extension plugin factories in Avogadro |
   FileBrowseWidget | |
   FileFormatDialog | |
   GenericHighlighter | Regexp-based programmable syntax highlighter |
    Rule | Stores a syntax highlighting rule as a set of QRegExp patterns and a text format |
   HydrogenTools | |
   MeshGenerator | Class that can generate Mesh objects from Cube objects |
   Molecule | A QObject derived molecule object with signals/slots |
   MoleculeSystem | |
   MoleculeModel | A model containing molecules |
   MultiViewWidget | A widget that contains other views, taking on responsibility for defining the active view, the layout of the subviews and ownership of the widgets |
   PeriodicTableScene | |
   PeriodicTableView | This class implements the view of the periodic table showing all elements |
   PersistentAtom | The PersistentAtom object provides a container for a persistent atom reference that can be held onto. The atom() method gets the underlying atom using the unique ID mechanism of the molecule |
   PersistentBond | The PersistentBond object provides a container for a persistent bond reference that can be held onto. The bond() method gets the underlying bond using the unique ID mechanism of the molecule |
   PythonScript | Implements a interface for calling short-lived python utility scripts |
   RWMolecule | Editable molecule class that automatically populates an undo stack |
   RWAtom | |
   RWBond | |
   ScenePlugin | |
   ScenePluginFactory | The base class for scene plugin factories in Avogadro |
   ScenePluginModel | A model containing scene plugins that will build up the scene |
   ToolPlugin | The base class for plugins that interact with QtOpenGL::GLWidget |
   ToolPluginFactory | The base class for tool plugin factories in Avogadro |
   ViewFactory | Pure virtual that provides a method of dynamically adding views to the MultiViewWidget class |
  Rendering | |
   AmbientOcclusionSphereGeometry | One or more spheres |
   BufferObject | Buffer object to store geometry/attribute data on the GPU |
   Camera | Utility functionality useful in camera's used with 3D scenes |
   CylinderColor | |
   CylinderGeometry | The CylinderGeometry contains one or more cylinders |
   Drawable | The base class for all drawable geometry and types |
   GeometryNode | Common base of all geometry nodes |
   GeometryVisitor | Visitor that determines the geometry of the scene |
   GLRenderer | Render the scene using OpenGL calls |
   GLRenderVisitor | Visitor that takes care of rendering the scene |
   GroupNode | Common API for grouping child nodes |
   LineStripGeometry | Used to store sets of line strips |
    PackedVertex | |
   MeshGeometry | The MeshGeometry is used for triangle mesh geometry |
    PackedVertex | |
   Node | Base class for all items in the scene |
   POVRayVisitor | Visitor that visits scene elements and creates a POV-Ray input file |
   Identifier | |
   Primitive | |
    Identifier | |
   Sphere | |
   Cylinder | |
   ColorTextureVertex | Pack the vertex data into a contiguous array |
   ColorNormalVertex | Pack the vertex data into a contiguous array |
   Scene | The Scene contains data ready to be rendered |
   Shader | Vertex or Fragment shader, combined into a ShaderProgram |
   ShaderProgram | The ShaderProgram uses one or more Shader objects |
   SphereColor | |
   SphereGeometry | One or more spheres |
   TextLabel2D | Renders text in an overlay plane, anchored to a point in window coordinates |
   TextLabel3D | Renders billboarded text that is anchored to a point in world coordinates |
   TextLabelBase | Generic implementation of a text drawable |
   TextProperties | Controls formatting options for text |
   TextRenderStrategy | Defines an interface for generating text images |
   Texture2D | Manages texture resources in graphics libraries |
   TransformNode | Applies a transform to all child nodes |
   Visitor | Base class for all Node visitors |
   VolumeGeometry | Regularly spaced volumetric data set |
  QtOpenGL | |
   GLWidget | QGLWidget derived object for displaying 3D molecular geometry |
   QtTextRenderStrategy | Uses the Qt toolkit to render text |
  QtPlugins | |
   ThreeDMol | Extension to launch a ThreeDMolDialog |
   ThreeDMolDialog | Dialog which displays basic molecular properties |
   Apbs | Integration with the APBS package, primarily reading the OpenDX output files produced by it at this point |
   ApbsDialog | Dialog for running APBS |
   ApbsOutputDialog | Dialog indicating a successful run of APBS |
   OpenDxReader | Provide a reader for OpenDX files |
   BallAndStick | Render a molecule in the ball and stick style |
   BondCentricTool | BondCentricTool manipulates molecular geometry by adjusting bond angles/lengths |
   Bonding | Performs bonding operations on demand |
   ClientServer | Plugin used to connect to and perform remote operations on an Avodadro server |
   ConnectionSettingsDialog | Dialog to set the connection settings for connecting to a remote server |
   CoordinateEditor | CoordinateEditor implements the plugin interface for the coordinate editor extension |
   CoordinateEditorDialog | Implements a free-text coordinate editor |
   CoordinateTextEdit | Extends QTextEdit to provide context tooltips and highlighting for syntax errors |
   CopyPaste | Allows interaction with the system clipboard |
   Crystal | Tools for crystal-specific editing/analysis |
   CrystalScene | Render the unit cell boundaries |
   ImportCrystalDialog | Dialog for importing a crystal from the clipboard |
   SupercellDialog | Dialog for building a supercell from a crystal |
   UnitCellDialog | Dialog for editing a molecule's unit cell |
   VolumeScalingDialog | Dialog with options for adjusting the volume of a Molecule's UnitCell |
   CustomElements | Manipulate custom element types in the current molecule |
   Editor | The Editor tool extends and modifies molecules |
   EditorToolWidget | |
   GamessHighlighter | |
   GamessInput | |
   GamessInputDialog | |
   Hydrogens | Extension to modify hydrogens |
   Licorice | Render a molecule in the licorice style |
   LineFormatInput | Load single-line molecule descriptors through an input dialog |
   LineFormatInputDialog | Dialog to prompt a format and descriptor string |
   Manipulator | Manipulates a molecule's geometry |
   MeasureTool | MeasureTool displays distances and angles between selected atoms |
   Meshes | Render one or more triangular meshes |
   MolecularProperties | Extension to launch a MolecularPropertiesDialog |
   MolecularPropertiesDialog | Dialog which displays basic molecular properties |
   MongoChem | Extension to interact with MongoChem |
   Navigator | The Navigator tool updates the camera in response to user input |
   NetworkDatabases | Queries online databases (currently the NIH structure resolver) and loads the returned structure if one is found |
   OBFileFormat | Implements the FileFormat API for using an OBProcess for file IO |
   OBForceFieldDialog | Used to prompt the user for parameters to be used in an OpenBabel force field optimization |
   OBProcess | Interface to the obabel executable, which is run in a separate process |
   OpenBabel | Implements the ExtensionPlugin interface to expose some OpenBabel functionality |
   OverlayAxes | Render reference axes in the corner of the display |
   PlayerTool | PlayerTool enables playback of trajectories |
   PluginFactory | The base class for plugin factories in Avogadro |
   PluginManager | This class takes care of finding and loading Avogadro plugins |
   POVRay | Performs POVRay operations on demand |
   QTAIMCriticalPointLocator | |
   QTAIMCubature | |
   QTAIMEngine | |
   QTAIMExtension | |
   QTAIMLSODAIntegrator | |
   QTAIMODEIntegrator | |
   QTAIMWavefunction | |
   QTAIMWavefunctionEvaluator | |
   QuantumInput | Implements the extension interface for simulation input generators |
   GaussianSetConcurrent | Uses GaussianSetTools to calculate values of electronic structure properties from quantum output read in |
   QuantumOutput | |
   SlaterSetConcurrent | Uses SlaterSetTools to calculate values of electronic structure properties from quantum output read in |
   SurfaceDialog | The SurfaceDialog presents various properties that have been read in from a quantum output file and provides interface to initiate calculations |
   FileFormatScript | Interfaces with external scripts that implement chemical file reader/writers |
   ScriptFileFormats | This extension registers FileFormat reader/writers that are implemented as external scripts |
   SelectionTool | SelectionTool selects atoms and bonds from the screen |
   SpaceGroup | Space group features for crystals |
   Spectra | The Spectra plugin handles vibrations and spectra |
   VibrationDialog | The VibrationDialog presents vibrational modes |
   VibrationModel | |
   VanDerWaals | Render the molecule as Van der Waals spheres |
   VanDerWaalsAO | Render the molecule as Van der Waals spheres with ambient occlusion |
   Wireframe | Render a molecule in the wireframe style |
  QuantumIO | |
   GUKBasisSet | |
   GamessukOut | |
   GAMESSUSOutput | |
   GaussianCube | |
   GaussianFchk | |
   MoldenFile | |
   MopacAux | |
   NWChemJson | Implementation of the NWChem JSON format |
   NWChemLog | |
  VTK | |
   vtkGLWidget | |
  TypeTraits | |
  TypeTraits< char > | |
  TypeTraits< unsigned char > | |
  TypeTraits< short > | |
  TypeTraits< unsigned short > | |
  TypeTraits< int > | |
  TypeTraits< unsigned int > | |
  TypeTraits< float > | |
  TypeTraits< double > | |
 AvogadroServer | Simple server implementation based on vtkServerSocket, accepting connections and processing ProtoCall requests |
 AvoRemoteFileSystemService | Server side implementation of RemoteFileSystemService. Provides methods for browsing a remote filesystem |
 AvoRemoteMoleculeService | The server side implementation of the RemoteMoleculeService, provides functionality to open a molecule on a remote system |
 FileDialog | Remote file dialog |
 FileDialogFilter | Filter used to filter data in file dialog model |
 FileDialogModel | Remote file dialog model |
 FileDialogModelIconProvider | |
 vtkAvogadroActor | Wrap an Avogadro::Rendering::Scene in a vtkActor derived container so that it can be rendered in a standard VTK widget |