from frowns import Smiles listOfSmiles = ["CCN", "NCC", "CCC"] duplicates = {} for smile in listOfSmiles: mol = Smiles.smilin(smile) canonicalString = mol.cansmiles() if duplicates.has_key(canonicalString): print "found duplicate molecule", smile else: duplicates[canonicalString] = 1 print len(duplicates), "unique molecules found"