Transforms:

• Transforms represent generic reactions.

• Expressed using the SMIRKS language. As a subset of SMARTS, all valid SMIRKS are valid reaction queries.

• Additional requirements:
  • must have unit stoichiometry,
  • atom maps must be pairwise and unambiguous. Any atoms which are not mapped in the transform are considered external and come from outside of the reaction.
  • explicit hydrogens are used,
  • atom expressions may be SMARTS for nodes whose bonding doesn't change, otherwise limited SMARTS.

• A transform is 'applied' to a molecule or set of molecules. The result is a set of reactions, each of which has the given molecules as reactants and the molecules which result from the reaction as products. (Note that a transform can be applied in either direction).

• Transforms can be abstracted from specific reactions (generalization).