measure = 'tanimoto' morganradius = 2 dmetric = None fpcode = None # old OE codes: #fpcodes={'lingo':OEFPType_Lingo, # 'maccs':OEFPType_MACCS166, # 'path':OEFPType_Path} fpcodes = { 'rdkit': FingerprintMols.GetRDKFingerprint, 'maccs': MACCSkeys.GenMACCSKeys, 'morgan': lambda mol: AllChem.GetMorganFingerprintAsBitVect(mol, morganradius), 'atompairs': lambda mol: Chem.GetAtomPairFingerPrint(mol, 2) } # tversky(F1, F2)= F1@F2 / ( a*sum(F1) + b*sum(F2) - (1-a-b)* F1@F2 ) dmetrics = { 'tanimoto': DataStructs.TanimotoSimilarity, # a, b = 1, 1 'dice': DataStructs.DiceSimilarity, # a, b = 0.5, 0.5 'cosine': DataStructs.CosineSimilarity, 'tversky': lambda m1, m2: DataStructs.TverskySimilarity(m1, m2, 0.5, 0.5), 'sokal': DataStructs.SokalSimilarity } ######################### # Module initialization # #########################