RdKit idioms
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here we collect together bits of code that you can use in rdkit to get the work done.
from rdkit.Chem import MolFromSmiles, RDKFingerprint from rdkit.DataStructs import TanimotoSimilarity m1 = MolFromSmiles('c1ccccc1') m2 = MolFromSmiles('c1ccccc1CCCC') fp1 = RDKFingerprint(m1) fp2 = RDKFingerprint(m2) print TanimotoSimilarity(fp1, fp2)