This paper discusses different fingerprint methods and its applications, it focuses on extended connectivity fingerprints but it also mentions functional connectivity fingerprints, which are used in pharmacophores. It also explains in detail an algorithm to generate extended connectivity fingerprints.
Rogers, David, and Mathew Hahn. “Extended-Connectivity Fingerprints.” Journal of Chemical Information and Modeling 50, no. 5 (2010): 742–54.
This paper discusses different fingerprint methods and its applications, it focuses on extended connectivity fingerprints but it also mentions functional connectivity fingerprints, which are used in pharmacophores. It also explains in detail an algorithm to generate extended connectivity fingerprints.