Remarkably, our chiral MAP fingerprints are able to distinguish stereoisomers even in cases involving up to thousands of stereoisomers where the chiral versions of ECFP and AP do not perform well. Furthermore, the chiral MAP Jaccard distances between enantiomers or stereoisomers are generally shorter than for structural isomers, allowing to use chiral MAP fingerprints as a refinement of their achiral version. Because MAP4C computes faster than MAP6C due to the small number of atom pairs considered, we recommend MAP4C as the molecular fingerprint of choice for comparing molecules spanning from small drug-like building blocks to large natural products and peptides. The distance distributions are grouped by Levenshtein distance, used to determine the number of mutations from any sequence to polymyxin B2. MAPC fingerprints display a higher performance than the other fingerprints when it comes to distinguishing all possible diastereomers and structural isomers from each other. This is not the case for APC, which has difficulties distinguishing diastereomers, and ECPFC fingerprints, which cannot distinguish diastereomers or structural isomers robustly. MAPC fingerprints also consistently assign lower distances to diastereomers than structural isomers. APC follows the same trend, although the lower diastereomer distances are skewed due to the APC fingerprint not being able to robustly distinguish all diastereomers. ECFPC show a complete overlap of Jaccard distances for diastereomers and structural isomers. Finally, the overall Jaccard distances increase with increasing Levenshtein distance for MAPC fingerprints, indicating that the obtained distances align with intuitive changes such as stereocenter or residue mutations.