Hybrid of a Reaction and a Reaction pattern. A reaction plus complete atom map, where node expressions may be SMILES or SMARTS.
Can be stored in databases (replace every SMARTS node expression by '*' to get a valid reaction).
Useful as a tool for manipulation of molecule objects.
A transformation is 'applied' to a molecule or set of molecules. The result is a sequence of reactions, each of which has the given molecules as reactants and the molecules which result from the reaction as products. (Note that a transformation can be applied in either direction).
In theory, transformations can be abstracted from sets of specific reaction instances (generalization).