Modeling chemical reactions and mechanisms can be ofgreat benefit to the chemical process industry. Atypical chemical mechanism is a database composed ofthousands of reactions involving a hundred or morespecies. A fundamental prerequisite of mechanismanalysis and classification is the ability to mapatomic reactions. Reaction mapping is alsofundamental in the analysis of biologicalpathways, enzymatic reaction data, tracerexperiments, and the consistencychecking of pathway databases. Biological moleculesoften have complex structures that can be nearlyimpossible to validate manually. Until now, reactionmapping approaches have relied on solutions based onattempts to partially solve NP-Complete problems orlimiting the type of reaction processed. This bookpresents algorithms that are uniquely capable ofmapping any reaction that can be represented as a setof chemical graphs, efficiently and optimally.MechA, a system built for mechanism analysis using anexpert system as well as these algorithms is alsodescribed. This book should be of interest to thosewith a background in cheminformatics, bioinformatics,algorithms, expert systems, or chemical engineering.