Modeling chemical reactions and mechanisms can be of great benefit to the chemical process industry. A typical chemical mechanism is a database composed of thousands of reactions involving a hundred or more species. A fundamental prerequisite of mechanism analysis and classification is the ability to map atomic reactions. Reaction mapping is also fundamental in the analysis of biological pathways, enzymatic reaction data, tracer experiments, and the consistency checking of pathway databases. Biological molecules often have complex structures that can be nearly impossible to validate manually. Until now, reaction mapping approaches have relied on solutions based on attempts to partially solve NP-Complete problems or limiting the type of reaction processed. This book presents algorithms that are uniquely capable of mapping any reaction that can be represented as a set of chemical graphs, efficiently and optimally. MechA, a system built for mechanism analysis using an expert system as well as these algorithms is also described. This book should be of interest to those with a background in cheminformatics, bioinformatics, algorithms, expert systems, or chemical engineering.