Reactant molecules were loaded into MØD using SMILES format . In MØD, graphs provide a framework for representing chemical reactions where molecules can be treated as nodes in a graph, while the edges connecting them represent reactions. Reactions are processed by application of reaction rules which provide templates describing which transformations substructures in reactant molecules can undergo (Figure ). Products of such reactions then become reactants for subsequent iterations of this process, leading to a concatenated chain of reactions (hereafter termed "generations"). The product graphs are then output in an internally canonicalized SMILES format. It should be noted that information allowing reconstruction of the entire network can be exported from MØD to other desired formats and parsed by other software for further analysis. ) applied to cyclopentanone (the graph G) as implemented in MØD. The blue highlighted bonds in L are broken and the green highlighted bonds in R are created in the course of the reaction, bonds in black do not change. The graph H is the product of the reaction (2-(1-hydroxypropyl)cyclopentan-1-one), while D is an intermediary graph in the transformation algorithm. This reaction normally proceeds through the action of a base (e.g., Ca(OH) 2 , KOH or NaOH), the availability of such bases in the medium is assumed. B: The same reaction shown as a fragment of a reaction network, formally a directed multi-hypergraph . Reactions between species store the information about which reaction rule was used to generate the products.