This is the class used generally throughout VMD to represent and access a molecule. It is derived from several base classes which provide the storage and control over the molecule's structure (BaseMolecule), animation list (Animation), and graphical display (DrawMolecule). It still does not contain the abilities to read in new molecular data from different sources, instead these are in classes derived from Molecule. This class is used as the basic class that all other parts of VMD\ are aware of, since once a molecule is read in from some source, it acts just like any other molecule.
The one level of extra functionality which is provided directly by the Molecule class is the ability to read in new coordinate frames from an external coordinate file, either a PDB or a DCD file.