[Rdkit-discuss] How do rdFingerprintGenerator.GetMorganGenerator and AllChem.GetMorganFingerprintAsBitVect differ?

[Lewis M. <lew...@gm...>]

Hi all,
Quick question on truncated fingerprints, any help is really appreciated.


I think I've missed a trick on how the new fingerprint generator works. I
thought the below should produce equivalent fingerprints but they are
totally different. Has the implementation changed, or maybe I'm getting the
kwargs incorrect? See below code or this link for a quick visual:
https://github.com/ljmartin/snippets/blob/master/truncated_fingerprints.ipynb
Thanks !

import rdkit
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
from rdkit.Chem import rdFingerprintGenerator
from rdkit.Chem.Draw import IPythonConsole
import numpy as np
from scipy.spatial import distance

mol = Chem.MolFromSmiles('CN1C(=O)CN=C(C2=C1C=CC(=C2)Cl)C3=CC=CC=C3')
#diazepam

gen_mo = rdFingerprintGenerator.GetMorganGenerator(fpSize=256, radius=2)
a = gen_mo.GetFingerprint(mol)
b = AllChem.GetMorganFingerprintAsBitVect(mol,2,256,useFeatures=False)
a_f = [int(i) for i in a.ToBitString()]
b_f = [int(i) for i in b.ToBitString()]
print('NumBits a: %s, NumBits b: %s' % (np.sum(a_f), np.sum(b_f)))
print('Dice Distance %s' % distance.dice(a_f,b_f))


NumBits a: 47, NumBits b: 38
Dice Distance 0.9058823529411765