Abstract
An important task in cheminformatics is to test whether two molecules are equivalent with respect to their 2D structure. Mathematically, this amounts to solving the graph isomorphism problem for labelled graphs. In this paper, we present an approach which exploits chemical properties and the local neighbourhood of atoms to define highly distinctive node labels. These characteristic labels are the key for clever partitioning molecules into molecule equivalence classes and an effective equivalence test. Based on extensive computational experiments, we show that our algorithm is significantly faster than existing implementations within SMSD, CDK and RDKit. We provide our Java implementation as an easy-to-use, open-source package (via GitHub) which is compatible with CDK. It fully supports the distinction of different isotopes and molecules with radicals.