Substructure-based fingerprints are the most diverse, with only KR not connecting to algorithms belonging to different categories. PubChem and MACCS are linked to Daylight and AP respectively, while ESTATE is related to FCFP. This indicates that the fragment choices of these encodings are mostly orthogonal with each other and that, overall, this category is correlated to path-based and circular approaches. Pharmacophore fingerprints are separated from all other categories, consistently with the correlation matrix and their pairwise similarity distribution. The closest neighbor from a different class is AP, which is connected to PH2, reflecting the fact that that both algorithms rely on distances between atom pairs.