A rolling stone

So there's a plugin in bioclipse called "moss" (or, I suppose MoSS).

It has an Atom class. It has a Bond class. It has graphs for chemicals, smiles parsers, ...

Just like the CDK, in fact. Perhaps I should check one of my projects (tailor) which also has Atom, Bond, Chain, PDBReader.

You can't have too many implementations of the same thing :)