RDKit：尝试循环枚举时"TypeError: 'Mol' object is not iterable"

Question

我正试图使用RDKit枚举大型化合物库，并将结果输出为CSV文件中的一列SMILES字符串。我能够成功地使用以下代码：

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])

然而，内存使用率非常高。为了减少内存使用，我尝试进行迭代枚举，每次取一个分子为"1"；reatants_1"；，使其与"分子"中的所有分子反应；reatants_2"；，将生成的化合物写入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])

然而，在这种情况下，对于行"；prods2＝[列表中x的化学摩尔ToSmiles(x[0]((prods(]"："TypeError:"Mol"对象不可迭代；。我能够在第一个实例中对"Mol"对象进行迭代而没有问题。关于如何解决这个问题，或者在枚举大型复合集时，我可以用任何其他方法大幅降低RAM使用率，有什么想法吗？

Answer 1

EnumerateLibraryFromReaction需要一个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])