Normalization (or standardization) of compound structure representations is an important step in preparing compounds for further analysis, including reliable substructure searching. Thus, the various effects of parsing the SMILES strings from the steps above to create a molecule object, plus subsequent normalization, were investigated using three different open access chemistry toolkits: RDKit (version 2020.03.2) , the Chemistry Development Kit (CDK, version 2.5) and OpenChemLib (OCL, version 2021.11.3) . The approaches used were: