Abstract
We describe an approach for the computational modeling of complex reaction systems, based on a language that allows the description of general types of chemical reactions. These descriptions are compiled and automatically executed to generate the entire reaction network. The language provides a general method for describing reactions–not limited to a specific class of chemical transformations. Reactions are described using a sequence of commands to characterize the reaction site, the transformation of the reactants to products, and, if desired, thermodynamic constraints to determine the dominant steps within each reaction type. These commands allow flexibility in the types of reaction systems that can be analyzed and may also be used to adjust the level of detail within a specific reaction network. The commands were developed to mimic the natural way in which a generic reaction is often described ~nformally.
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