From Chemical Rules to Term Rewriting

In this paper, rule-based programming is explored in the field of automated generation of chemical reaction mechanisms. We explore a class of graphs and a graph rewriting relation where vertices are preserved and only edges are changed. We show how to represent cyclic labeled graphs by decorated labeled trees or forests, then how to transform trees into terms. A graph rewriting relation is defined, then simulated by a tree rewriting relation, which can be in turn simulated by a rewriting relation on equivalence classes of terms. As a consequence, this kind of graph rewriting can be implemented using term rewriting. This study is motivated by the design of the GasEl system for the generation of kinetics reactions mechanisms. In GasEl, chemical reactions correspond to graph rewrite rules and are implemented by conditional rewriting rules in ELAN. The control of their application is done through the ELAN strategy language