How to find Tanimoto Similarity between two compounds using RDkit?

Question

I want to calculate the Tanimoto Similarity between two compounds. How can I use the RDkit package for it?

Answer 1

Here are steps to calculate the Tanimoto Similarity between two compounds using the RDkit python module:

• Create molecules using the given smiles for the compounds.
• Generate fingerprints for compounds using their molecules.
• Use the fingerprints to calculate the Tanimoto Similarity between the compounds.

Here is an example to show which functions from the RDkit package you need to use to calculate the Tanimoto Similarity.

from rdkit import Chem

from rdkit import DataStructs

from rdkit.Chem import AllChem

smi1 = 'COC1=CC=C(C=C1)N2C(=O)C3=C(N=C2[C@H]4CCCN4)C(=CC(=C3)[N+](=O)[O-])C'

smi2 = 'CN1CCN(/C(=N/C=2C=CC(=CC2C(=O)NC=3C=CC=CC3)[N+](=O)[O-])/C1)C'

# create molecule using given smiles

mol1 = Chem.MolFromSmiles(smi1)

mol2 = Chem.MolFromSmiles(smi2)

# generate fingerprints

fpgen = AllChem.GetRDKitFPGenerator()

fp1 = fpgen.GetFingerprint(mol1)

fp2 = fpgen.GetFingerprint(mol2)

# compute Tanimoto Similarity using fingerprints

simi = DataStructs.TanimotoSimilarity(fp1, fp2)

print(simi)