E.3. Fingerprints

This section presents fingerprint types used by the Mychem software. Further details about fingerprints are given in an article written by Andrew Dalke. In short, fingerprints are a bit string representation of a molecule. Most of them can be classified in two categories:

E.3.1. FP2

FP2 fingerprints index small molecule fragments based on linear segments of up to 7 atoms in length. They are hash fingerprints. The specification of the FP2 fingerprints is available on the Open Babel Website.

E.3.2. FP3

FP3 fingerprints index small molecule fragments based on a list of SMART patterns. They are hash fingerprints. The SMART patterns are listed in the file named patterns.txt, that is distributed with the Open Babel software. The specification of the FP3 fingerprints is available on the Open Babel Website.

E.3.3. FP4

FP4 fingerprints index small molecule fragments based on a list of SMART patterns. They are hash fingerprints. The SMART patterns are listed in the file named SMARTS_InteLigand.txt, that is distributed with the Open Babel software. The specification of the FP4 fingerprints is available on the Open Babel Website.