Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation

Chemical reactions are described by edge relabeling graph transformation rules, in which a substrate chemical graph is transformed into a product chemical graph by breaking existing bonds and creating new bonds between atoms. These edge relabeling graph transformation rules are themselves chemical graphs, where the order of a bond before the chemical reaction is distinguished from the order of the bond after the chemical reaction. The approach is illustrated by an implementation on top of the PerlMol collection of Perl modules for computational chemistry.