We provide five main clustering options: "all nodes", "single nodes", "standard", "PE" and "PEM". Except for the "standard" representation which is uniquely defined by its implementation in ToposPro , the other clustering options are only described but not uniquely determined by an explicit algorithm . We also chose not to follow the original implementation of the "standard" representation , primarily because of the required computational cost of determining the minimal ring around each bond. Instead we use a custom algorithm whose main steps are as follows: