Similarity maps for circular fingerprints. Similarity map of molecule 2 (middle) and molecule 3 (bottom) using Morgan2 (left), CountMorgan2 (middle) and FeatMorgan2 (right). The reference compound is molecule 1 (left panel in Figure 2). Color scheme: removing bits decreases similarity (i.e. positive difference) (green), no change in similarity (gray), removing bits increases similarity (i.e. negative difference) (pink). The bit vectors of the circular fingerprints had the size 1024 bits.