CORE DESIGN:

Transformations:

'Real' object in toolkit.

Hybrid of a Reaction and a Reaction pattern. A reaction plus complete atom map, where node expressions may be SMILES or SMARTS.

Additional requirements:

• must have unit stoichiometry,
• the atom map must account for every atom on both sides of reaction unambiguously.

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).

Node rules:

• Can be any SMARTS, if the node expression and its bonding are unchanged in the transformation,
• valid SMILES node expressions,
• or SMARTS with atom property changes (TBD).