Impact of 'nBits' on GetMorganFingerprintAsBitVect()

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Impact of 'nBits' on GetMorganFingerprintAsBitVect()

This section provides a tutorial example on impact of the 'nBits' option on fingerprint generation with rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect() function.

The 'nBits' option in the rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect() function call allows you to control the number of bits (length) of the fingerprint. The default is nBits=2048, which is capable to represent 2048 identifiers in a perfect scenario.

Generating shorter fingerprints can save data storage. But it also reduces the accuracy the final fingerprints.

1. For example, "CCCCCCCC" and "OOOOOOOO" are 2 completely different molecules with a zero similarity between them. But their fingerprints share 3 common bits, when fpSize=16 is used. And that gives a 0.33 similarity score.

from rdkit.Chem import AllChem
from rdkit import DataStructs
mol = AllChem.MolFromSmiles('CCCCCCCC')
fp1 = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=16)
print(fp1.ToBitString())

mol = AllChem.MolFromSmiles('OOOOOOOO')
fp2 = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=16)
print(fp2.ToBitString())

print(DataStructs.FingerprintSimilarity(fp1, fp2))

# output 
1100101100100001
0110011100000000
 ^    ^^
0.3333333333333333

The main reason for two different identifiers turning on the same bit in the fingerprint is that the fingerprint is not long enough to allow them to use different bits.

2. Now if we use "fpSize=64", "CCCCCCCC" and "OOOOOOOO" will share only 1 bit in their fingerprints. And that lowers the similarity score to 0.08, much more accurate now.

mol = AllChem.MolFromSmiles('CCCCCCCC')
fp1 = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=64)
print(fp1.ToBitString())

mol = AllChem.MolFromSmiles('OOOOOOOO')
fp2 = AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits=64)
print(fp2.ToBitString())

print(DataStructs.FingerprintSimilarity(fp1, fp2))

# output 
0000000000000001100000000010000001001010000000000000000100000000
0000011000000000011000000000000000000001000000000100010100000000
                                                       ^
0.07142857142857142