Reaction Center and Environment:
Reacting center (in red) includes atoms and bonds which are directly
involved in the reaction. They include:
- bonds which change order (or orientation) during the reaction,
- atoms connected to these bonds, and
- atoms whose properties change (include charge, stereo).
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.
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.