Impact of 'useCounts' on GetMorganFingerprint()

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

The 'useCounts' option in the rdkit.Chem.rdMolDescriptors.GetMorganFingerprint() function call allows you to control whether or not counts of identifier duplications are included in the fingerprint. The default value is useCounts=True.

1. For example, molecule "CC" will produce 2 duplicate identifiers with useCounts=True in the fingerprint.

from rdkit.Chem import AllChem
from rdkit.DataStructs.cDataStructs import UIntSparseIntVect
radius = 0
bitInfo = {}
mol = AllChem.MolFromSmiles('CC')
fp = AllChem.GetMorganFingerprint(mol, radius, useCounts=True, 
  bitInfo=bitInfo)
display(UIntSparseIntVect.GetLength(fp))
display(UIntSparseIntVect.GetNonzeroElements(fp))
display(UIntSparseIntVect.GetTotalVal(fp))
print(bitInfo)

# output: 
4294967295
{2246728737: 2}
2
{2246728737: ((0, 0), (1, 0))}

Output "GetNonzeroElements(fp)={2246728737: 2}" shows the count of duplications of identifier "2246728737" is 2 in the fingerprint.

2. If useCounts=False is used, "CC" will produce only a single identifier in the fingerprint.

radius = 0
bitInfo = {}
mol = AllChem.MolFromSmiles('CC')
fp = AllChem.GetMorganFingerprint(mol, radius, useCounts=False, 
  bitInfo=bitInfo)
display(UIntSparseIntVect.GetLength(fp))
display(UIntSparseIntVect.GetNonzeroElements(fp))
display(UIntSparseIntVect.GetTotalVal(fp))
print(bitInfo)

# output: 
4294967295
{2246728737: 1}
1
{2246728737: ((0, 0), (1, 0))}

But you can still use bitInfo to see which identifier is duplicated and how many times.

Conclusion: We should keep the default of useCounts=True to include the counts of identifier duplications in the fingerprint. This allows use to differentiate molecules with the same local substructure repeating with different times.

Table of Contents

 About This Book

 SMILES (Simplified Molecular-Input Line-Entry System)

 Open Babel: The Open Source Chemistry Toolbox

 Using Open Babel Command: "obabel"

 Generating SVG Pictures with Open Babel

 Substructure Search with Open Babel

 Similarity Search with Open Babel

 Fingerprint Index for Fastsearch with Open Babel

 Stereochemistry with Open Babel

 Command Line Tools Provided by Open Babel

 RDKit: Open-Source Cheminformatics Software

 rdkit.Chem.rdchem - The Core Module

 rdkit.Chem.rdmolfiles - Molecular File Module

 rdkit.Chem.rdDepictor - Compute 2D Coordinates

 rdkit.Chem.Draw - Handle Molecule Images

 Molecule Substructure Search with RDKit

 rdkit.Chem.rdmolops - Molecule Operations

 Daylight Fingerprint Generator in RDKit

Morgan Fingerprint Generator in RDKit

 What Is Morgan Fingerprint Generator in RDKit

 GetMorganFingerprint() Method in RDKit

 Impact of 'radius' on GetMorganFingerprint()

Impact of 'useCounts' on GetMorganFingerprint()

 Impact of 'invariants' on GetMorganFingerprint()

 Impact of 'useBondTypes' on GetMorganFingerprint()

 Impact of 'fromAtoms' on GetMorganFingerprint()

 GetMorganFingerprintAsBitVect() Method in RDKit

 Impact of 'nBits' on GetMorganFingerprintAsBitVect()

 GetHashedMorganFingerprint() Method in RDKit

 Impact of 'nBits' on GetHashedMorganFingerprint()

 GetMorganGenerator() Method in RDKit

 Morgan Fingerprint Generator in RDKit for FCFP

 RDKit Performance on Substructure Search

 Introduction to Molecular Fingerprints

 OCSR (Optical Chemical Structure Recognition)

 AlphaFold - Protein Structure Prediction

 Resources and Tools

 Cheminformatics Related Terminologies

 References

 Full Version in PDF/EPUB