RDKit: "TypeError: 'Mol' object is not iterable" when attempting looped enumeration

Question

我正在尝试使用 RDKit 枚举大型化合物库，并将结果输出为 CSV 文件中的单列 SMILES 字符串。我能够成功使用以下代码：

import os
os.chdir('xxx')
from rdkit import Chem
from rdkit.Chem import rdChemReactions
from rdkit.Chem import AllChem
rxn = rdChemReactions.ReactionFromSmarts('xxx')
rct1 = Chem.SDMolSupplier('reactants_1.sdf')
rct2 = Chem.SDMolSupplier('reactants_2.sdf')
prods = AllChem.EnumerateLibraryFromReaction(rxn,[rct1,rct2])
prods2 = [Chem.MolToSmiles(x[0]) for x in list(prods)]
import csv
with open('output.csv', 'w', newline='') as f:
    writer = csv.writer(f)
    for item in prods2:
        writer.writerow([item])

但是，内存使用率非常高。为了减少内存使用，我尝试执行迭代枚举，我将在“reactants_1”的时间取一个分子，与“reactants_2”中的所有分子反应，写生成的化合物到 CSV 文件，然后迭代：

import os
import csv
os.chdir('xxx')
from rdkit import Chem
from rdkit.Chem import rdChemReactions
from rdkit.Chem import AllChem
rxn = rdChemReactions.ReactionFromSmarts('xxx')
rct1 = Chem.SDMolSupplier('reactants_1.sdf')
rct2 = Chem.SDMolSupplier('reactants_2.sdf')
with open('output.csv', 'w', newline='') as f:
    for compound in rct1:
        prods = AllChem.EnumerateLibraryFromReaction(rxn,[compound,rct2])
        prods2 = [Chem.MolToSmiles(x[0]) for x in list(prods)]
        writer = csv.writer(f)
        for item in prods2:
            writer.writerow([item])

但是，在这种情况下，我收到以下错误行“prods2 = [Chem.MolToSmiles(x[0]) for x in list(prods)]”：“TypeError：'Mol' 对象不可迭代”。在第一个实例中，我能够毫无问题地迭代 'Mol' 对象。关于如何解决此问题的任何想法，或者在枚举大型复合集时我可以通过任何其他方式大幅降低 RAM 使用率的任何想法？

Answer 1

EnumerateLibraryFromReaction 期望 list.

所以这应该有效：

import os
import csv
os.chdir('xxx')
from rdkit import Chem
from rdkit.Chem import rdChemReactions
from rdkit.Chem import AllChem
rxn = rdChemReactions.ReactionFromSmarts('xxx')
rct1 = Chem.SDMolSupplier('reactants_1.sdf')
rct2 = Chem.SDMolSupplier('reactants_2.sdf')
with open('output.csv', 'w', newline='') as f:
    for compound in rct1:
        compound = [compound] # put the mol into a list
        prods = AllChem.EnumerateLibraryFromReaction(rxn,[compound,rct2])
        prods2 = [Chem.MolToSmiles(x[0]) for x in list(prods)]
        writer = csv.writer(f)
        for item in prods2:
            writer.writerow([item])

RDKit: "TypeError: 'Mol' object is not iterable" when attempting looped enumeration

RDKit: "TypeError: 'Mol' object is not iterable" when attempting looped enumeration

python

enumeration

chemistry

rdkit

cheminformatics