ArgumentError: rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(Mol, int)

Question

我在使用 RDKit 时遇到了以下问题。我正在尝试创建一个函数，将 SMILES 字符串中的分子编码为指纹。但是出现了 ArgumentError，我想不通。

这是我的代码：

 def get_fp(dfx, method="maccs", n_bits=2048):

    ligands = [Chem.MolFromSmiles(mol) for mol in dfx.canonical_smiles]
    
    if method == "morgan2":
        data1 = []
        for mol in ligands:
            ecfp4 = [int(x) for x in AllChem.GetMorganFingerprintAsBitVect(mol, 2, n_Bits=n_bits)]
            data1.append(ecfp4)
        
        ecfp4_df = pd.DataFrame(data1, index=dfx.index)    
        return ecfp4_df
    
    if method == "morgan3":
        data2 = []
        for mol in ligands:
            ecfp6 = [int(x) for x in AllChem.GetMorganFingerprintAsBitVect(mol, 3, n_Bits=n_bits)]
            data2.append(ecfp6)
        ecfp6_df = pd.DataFrame(data2, index=dfx.index)
        return ecfp6_df
    
    if method == "maccs":
        data3 = []
        for mol in ligands:
            maccs = [int(x) for x in MACCSkeys.GenMACCSKeys(mol)]
            data3.append(maccs)
        maccs_df = pd.DataFrame(data3, index=dfx.index)
        return maccs_df

“maccs”方法有效，但摩根无效。我认为这是一个功能问题但我无法调试它...这是错误：

ArgumentError: Python argument types in rdkit.Chem.rdMolDescriptors.GetMorganFingerprintAsBitVect(Mol, int) did not match C++ signature: GetMorganFingerprintAsBitVect(class RDKit::ROMol mol, unsigned int radius, unsigned int nBits=2048, class boost::python::api::object invariants=[], class boost::python::api::object fromAtoms=[], bool useChirality=False, bool useBondTypes=True, bool useFeatures=False, class boost::python::api::object bitInfo=None, bool includeRedundantEnvironments=False)

谢谢

Answer 1

这只是一个错字。

改变

AllChem.GetMorganFingerprintAsBitVect(mol, 2, n_Bits = n_bits)

至

AllChem.GetMorganFingerprintAsBitVect(mol, 2, nBits = n_bits)