While BuildAMol was not designed to simulate true chemical reactions, it offers functionalities to achieve similar outcomes for specific reaction types. This is achieved by a user-extensible library of functional groups. When reacting two fragments, functional groups automatically infer the binder and deleter atoms needed to link both fragments. Therefore, substitution reactions can be mimic to a certain extent, by using either the Molecule.react with method or top-level react function or the + operator. It is important to note that due to its core principle of atom substitution, BuildAMol currently cannot handle addition reactions, where a new bond is formed without the removal of existing atoms.