The modeling of complex reaction systems is necessary in the design, analysis, and control of many processes. The large number of reactants, reactions, and reaction intermediates involved make the modeling and even the description of such systems difficult. We have developed an algorithm that automatically generates complex reaction networks. The algorithm utilizes the known general types of steps to generate the mechanistic reaction network for any given feed. It is based on a specially designed computer language that can describe generic reaction sites and the generic transformation of the reactants to produces. The commands in the language allow flexibility in the types of reaction systems that may be analyzed, and they may be used to adjust the level of detail of a specific reaction network. Auxiliary methods represent molecular structures, identify important substructures (such as rings), and canonicalize structures to avoid duplicates.