Comparison by Clustering
The clustering methods for structure comparison works by first finding small similar substructures in the two structures, and then constructing larger similar substructures by joining smaller ones
Generally they allow for insertions, deletions and topological permutations
The word clustering is a bit misleading, not all ”objects” have to be clustered. It is used here, since it is widely used in papers describing the relevant methods. (Perhaps grouping would be better)