In this work we address the issue of creating systematic representations of a large range of catalytic structures commonly used in computational research. This methodology is based on graph techniques first employed in cheminformatics but here utilizing graphs which originate from the bulk rather than from the adsorbed molecule, resulting in a unique representation for any adsorption structure. We also provide means for automatically generating 3D initial guesses which are specific to these unique graph representations based on simple geometric rules. Finally, we have packaged these tools into an open-source Python package called CatKit, which is available at to make these techniques freely accessible to the community.