Similarly, although Open Babel's path-based (or Daylight-type) fingerprint FP2 was developed for similarity searching of databases, we realised that users wanted to use the information in the fingerprint for other purposes. From time to time, someone would ask on the mailing list what fragments corresponded to each of the 1024 bits. At first, our response was to point out that we couldn't really say as (a) more than one fragment might correspond to a particular bit and (b) the hashing algorithm that was used to link the fragments and the bits only worked one-way.
Eventually we realised that people wanted something more, and so Chris added an output option to describe the fragments and their corresponding bits. These can be used just like fragments from other fragmentation schemes (looking for privileged fragments, unusual fragments, whatever), and the purpose of this blog post is to show how to get to grips with these fragments by visualising them.
The example molecule is:
obabel -:N1CC1C(=O)Cl -O example.pngAnd here are the corresponding fragments generated by the FP2 fingerprint (scroll to zoom in the image below, click+drag to pan):