Impact of 'useBondOrder' on RDKFingerprint()

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Daylight Fingerprint Generator in RDKit

∟Impact of 'useBondOrder' on RDKFingerprint()

This section provides a tutorial example on impact of the 'useBondOrder' option on fingerprint generation with rdkit.Chem.rdmolops.RDKFingerprint() function.

The 'useBondOrder' option in the rdkit.Chem.rdmolops.RDKFingerprint() function call allows you to control whether bond order (bond type) should be considered in unique subgraphs determination. If useBondOrder=True is used, different bond orders are considered as different subgraphs. If useBondOrder=False is used, different bond orders are considered as the same bond.

1. For example, "CC" and "C=C" are considered as 2 different subgraphs when "useBondOrder=True" is used. Their hash values set bit 28 and bit 52 in the fingerprint of molecule "CC=C".

from rdkit import Chem
atomBits = []
bitInfo = {}
mol = Chem.MolFromSmiles('CC=C')
fp = Chem.RDKFingerprint(mol, 
  fpSize=64, nBitsPerHash=1, useBondOrder=True, 
  atomBits=atomBits, bitInfo=bitInfo)
print(fp.ToBitString())
print(fp.GetNumOnBits())
print(atomBits)
print(bitInfo)

# output: 
0000000000000000010000000000100000000000000000000000100000000000
3
[[28, 17], [28, 52, 17], [52, 17]]
{17: [[0, 1]], 28: [[0]], 52: [[1]]}

2. For the same molecule, "CC" and "C=C" are considered as identical subgraphs when "useBondOrder=False" is used. Their shared hash value sets bit 28 in the fingerprint.

atomBits = []
bitInfo = {}
mol = Chem.MolFromSmiles('CC=C')
fp = Chem.RDKFingerprint(mol, 
  fpSize=64, nBitsPerHash=1, useBondOrder=False, 
  atomBits=atomBits, bitInfo=bitInfo)
print(fp.ToBitString())
print(fp.GetNumOnBits())
print(atomBits)
print(bitInfo)

# output:
0000000000000000000001000000100000000000000000000000000000000000
2
[[28, 21], [28, 21], [28, 21]]
{21: [[0, 1]], 28: [[0], [1]]}