While BuildAMol is able at generate a wide variety of molecular structures, its atom-substitution strategy introduces limitations for certain reaction types. Since it requires an atomic "leaving group" for substitution, BuildAMol cannot directly simulate reactions that do not involve atom removal, such as the reduction of double bonds. Additionally, the system is primarily designed for creating linear or branched structures. Although optimization techniques can enable BuildAMol to generate cyclic molecules, it is not the most efficient approach for this specific task.