Three 'views' of the generic
(1) 3D view
(2) Graph view
(3) Internal representation of lists of vertices and bonds
Cherwell Scientific Publishing 1998
The Generic Chemical Model was designed with the well-behaved organic structures in mind. It uses an abstract representation of a list of vertices to hold information on atoms and groups of atoms. A list of bonds is used to link the atoms (groups of atoms). The internal data model is used 'as needed' by all ChemSymphony's components. It is also used by the system of filters and adapters by which ChemSymphony applets or applications will be linked to external resources. It is not yet clear 'how much' ChemSymphony's data model will need to be enhanced to cope with Daylight's resources. But of course this is in principle an 'open question' since both systems are extensible.
There is one point to make here about ChemSymphony: ChemSymphony has an internal data-model, there is in effect an internal database of file formats, but it is quite 'agnostic' about the file formats it supports. If you do not like the default options, as a developer (or even as a user at runtime) you can over-ride them.
Could the ChemSymphony data-model be improved? Undoubtedly, it can be improved and is being improved. There is no question that a complete interface to the Daylight toolkits will be a significant enhancement.