Reactor also supports the Daylight mapping style where all matching atoms should be mapped instead of mapping changing atoms. A reaction atom is called matching if it is not an orphan atom: it exists on both sides of the reaction.

If the reaction is partially mapped or not mapped at all, Reactor can use automatical mapping to match the reactant and product sides. Predefined maps are never changed, only unmapped atoms will be mapped by the automapping procedure. Stereo centers and query features are not considered in the current version of automapping, therefore it is suggested to pre-map these atoms manually.