Reaction Center and Environment:

  1. Reacting center (in red) includes atoms and bonds which are directly involved in the reaction. They include:

  2. One atom shell out from the reacting center (in blue) includes any atoms one away from the reacting atoms, and the bonds connecting them to the reacting center. Similarly, two-atom, three-atom, etc. shells can be included.

  3. The extended environment (green) includes additional conjugation connected to any of the atoms or bonds already included. This includes full inclusion of all aromatic rings, which is necessary to guarantee valid SMILES output.