TypeError：“NoneType”对象不是迭代器 Rdkit VS 代码

Question

我正在尝试通过 Lipinski、Ghose 和 RUle of 3 过滤器从数据库“part1”中过滤分子，但我不断出错。 所以，在我运行这个脚本之后，我在两次提到“progressbar”的那一行得到一个错误“object is not an iterator”。我是新手，希望得到帮助。

下面是我过滤分子数据库的脚本。

from rdkit import Chem
from rdkit.Chem import Descriptors


import progressbar

if __name__ == '__main__':


    molecules = Chem.SDMolSupplier('chemspidersdf/part1.sdf')

    results = {
        "Lipinski Rule of 5": 0,
        "Ghose Filter": 0,
        "Rule of 3 Filter": 0,
    }

    print ("Molecule Database Length: " + str(len(molecules)))

    for i in progressbar.ProgressBar(range(len(molecules))):

        molecule = molecules[i]
        if molecule:

            lipinski = False
            rule_of_3 = False
            ghose_filter = False

            molecular_weight = Descriptors.ExactMolWt(molecule)
            logp = Descriptors.MolLogP(molecule)
            h_bond_donor = Descriptors.NumHDonors(molecule)
            h_bond_acceptors = Descriptors.NumHAcceptors(molecule)
            rotatable_bonds = Descriptors.NumRotatableBonds(molecule)
            number_of_atoms = Chem.rdchem.Mol.GetNumAtoms(molecule)
            molar_refractivity = Chem.Crippen.MolMR(molecule)

            # Lipinski
            if molecular_weight <= 500 and logp <= 5 and h_bond_donor <= 5 and h_bond_acceptors <= 5 and rotatable_bonds <= 5:
                lipinski = True
                results["Lipinski Rule of 5"] += 1

            # Ghose Filter
            if molecular_weight >= 160 and molecular_weight <= 480 and logp >= 0.4 and logp <= 5.6 and number_of_atoms >= 20 and number_of_atoms <= 70 and molar_refractivity >= 40 and molar_refractivity <= 130:
                ghose_filter = True
                results["Ghose Filter"] += 1
     
            # Rule of 3
            if molecular_weight <= 300 and logp <= 3 and h_bond_donor <= 3 and h_bond_acceptors <= 3 and rotatable_bonds <= 3:
                rule_of_3 = True
                results["Rule of 3 Filter"] += 1

      

    print (results)

Answer 1

我假设您使用的是progressbar2。看起来progressbar 应该是小写的：

mols = Chem.SDMolSupplier('path/to/my/mols.sdf')
n_mols = len(mols)
for x in progressbar.progressbar(range(n_mols)):
    # do stuff...

它也可以这样工作：

mols = Chem.SDMolSupplier('path/to/my/mols.sdf')
for mol in progressbar.progressbar(mols):
    if mol is None:
        continue
    # do stuff...