| Avogadro::Animation | Simple frame-based animation for Molecule primitives |
| Avogadro::Atom | Representation of an atom |
| Avogadro::Bond | Representation of a chemical bond |
| Avogadro::Camera | Representation of the camera looking at the molecule |
| Avogadro::Color | Map a primitive (atom, bond, etc.) to a OpenGL red, green, blue, alpha color |
| Avogadro::Color3f | Representation of an RGB color using three floats |
| Avogadro::ColorButton | A button to show the current color and bring up the QColorDialog |
| Avogadro::PrimitiveList::const_iterator | |
| Avogadro::Cube | Data type holding regularly spaced data in a cube |
| Avogadro::Cylinder | |
| Avogadro::DockExtension | |
| Avogadro::DockWidget | |
| Avogadro::ElementDetail | An item box displaying more detailed information on the element |
| Avogadro::ElementItem | An element item, intended to display a single element |
| Avogadro::ElementTranslator | Internationalization of element names |
| Avogadro::Engine | Engine plugin interface |
| Avogadro::Extension | Interface for adding extensions |
| Avogadro::Fragment | A fragment containing atoms and bonds |
| Avogadro::GLHit | Hits from OpenGL selections/picking |
| Avogadro::GLPainter | Implementation of the Painter class using OpenGL |
| Avogadro::GLWidget | GL widget class for rendering molecules |
| Avogadro::IDList | List mapping primitives and unique ids |
| Avogadro::Library | Interface for static calls for versions, installation prefix, and other compiler macros |
| Avogadro::Mesh | Encapsulation of a triangular mesh that makes up a surface |
| Avogadro::MeshGenerator | Class that can generate Mesh objects from Cube objects |
| Avogadro::Molecule | The molecule contains all of the molecular primitives |
| Avogadro::MoleculeFile | |
| Avogadro::Navigate | Navigation functions to simplify common tasks |
| Avogadro::NeighborList | A list container for finding spatial neighbors of atoms |
| Avogadro::Painter | Pure virtual Painter base class to be implemented by painters |
| Avogadro::PainterDevice | |
| Avogadro::PeriodicTableScene | This class encapsulates the scene, all items are contained in it |
| Avogadro::PeriodicTableView | This class implements the view of the PeriodicTableScene |
| Avogadro::PlotAxis | Axis for PlotWidget |
| Avogadro::PlotObject | Encapsulates a data set to be plotted in a PlotWidget |
| Avogadro::PlotPoint | Encapsulates a point in the plot |
| Avogadro::PlotWidget | Generic data plotting widget |
| Avogadro::Plugin | Interface for plugins |
| Avogadro::PluginFactory | |
| Avogadro::PluginItem | |
| Avogadro::PluginManager | |
| Avogadro::Primitive | Base class for all primitives (Molecule, Atom, Bond, Residue, ...) |
| Avogadro::PrimitiveList | Class which set of Primitives |
| Avogadro::Protein | Representation of a protein, including secondary structure |
| Avogadro::PythonEngine | |
| Avogadro::PythonEngineFactory | Generates instances of our PythonEngine class |
| Avogadro::PythonError | Singleton object to store all python errors |
| Avogadro::PythonExtension | |
| Avogadro::PythonExtensionFactory | |
| Avogadro::PythonInterpreter | Class to embed the Python interpreter in Avogadro |
| Avogadro::PythonScript | |
| Avogadro::PythonThread | |
| Avogadro::PythonTool | |
| Avogadro::PythonToolFactory | |
| Avogadro::ReadFileThread | |
| Avogadro::Residue | A biological residue that contains atoms and bonds |
| Avogadro::Sphere | |
| Avogadro::TextMatrixEditor | Widget to edit 3x3 matrices in plain text |
| Avogadro::TextRenderer | |
| Avogadro::Tool | Interface for tool plugins |
| Avogadro::ToolGroup | Manager for GLWidget Tools |
| Avogadro::UndoSequence | Provides a sequence of Undo/Redo commands in a single command |
| Avogadro::ZMatrix::zItem | |
| Avogadro::ZMatrix | Z-matrix internal coordinates for a molecule |
