Reply – MACCS Fingerprints in pybel
Your Name
or Cancel
In Reply To
MACCS Fingerprints in pybel
— by david.lagorce david.lagorce
Hello all,

According to Noel O'Boyle useful "guiding lights", here is a special procedure to use MACCS fingerprint method in python pybel links.
Indeed, MACCS is only available in OpenBabel 2.2.3 command line method...

import pybel
pybel._fingerprinters = pybel._getplugins(pybel.ob.OBFingerprint.FindFingerprint, pybel.fps)
mol = pybel.readstring("smi", "CCCC(=O)Cl")
print mol.calcfp("MACCS").bits
# [103, 107, 114, 115, 132, 134, 147, 154, 155, 160, 164]

Alternatively, Noel advice to use the included in cinfony, which has this feature already.