The degree of differentiation between stereoisomers should be proportional to the number of stereochemical changes between any two stereoisomers, and should also be smaller than the difference to a different molecule such as a structural isomer. We tested the ability of our chiral fingerprints for this task for small and large molecules separately. As a test case for small molecules, we computed Jaccard distances between all pairs involving the 203 structural isomers of 1,4-diaminocyclohexane (15), a ring fragment which is enriched in bioactive molecules from ChEMBL, and between all pairs of stereoisomers in the set. We similarly analyzed all pairs involving the 48 structural isomers of 4-aminopiperazine ( ), a similar drug scaffold, and the stereoisomeric pairs within the set. In both cases, all six fingerprints ranked pairs stereoisomers closer to each other than pairs of structural isomers (Figure ).