The results for generating SMIRKS patterns for the polypeptide highlighted the importance of cluster ordering (Section 4.2.2). From these results we do not have an obvious answer about ordering clusters based on size. With further research it may be possible to establish a universal ordering based on already clustered fragments that could be considered. Perhaps we should instead consider the quantitative parameters assigned to the fragment and experiment with ordering parameters based on those instead. Another approach would be to consider hierarchical clustering algorithms , where the order of clusters could be determined before the stage of generating SMIRKS patterns.