英文:
rdkit.Chem.rdmolfiles.MolToMolFile(NoneType, str)
问题
以下是您提供的代码的翻译部分：
我正在尝试使用rdkit Python库将smi格式转换为sdf格式。我正在运行以下一行Python代码。
def convertir_smi_sdf(file_smi):
leer = [i for i in open(file_smi)]
print(f"Total de smi: {len(leer)}")
cont = 0
cont_tot = []
for i in leer:
nom_mol = i.split()[1]
smi_mol = i.split()[0]
mol_smi = Chem.MolFromSmiles(smi_mol)
Chem.MolToMolFile(mol_smi, f'{nom_mol}.sdf')
cont += 1
cont_tot.append(cont)
print(f"Se ha convertido {cont_tot[-1]} smiles a SDF")
任何帮助都将非常感激。
我需要将这些smiles格式分隔成不同的sdf文件。
错误：
[![Error][1]][1]
输出：
[![Output][2]][2]
[1]: https://i.stack.imgur.com/KBja9.png
[2]: https://i.stack.imgur.com/rQcXd.png
请注意，我已经保留了代码中的格式和引用部分，而只对代码本身进行了翻译。
英文:
I am trying to convert smi to sdf format using rdkit python library. I am running following line of python code.
def convertir_smi_sdf(file_smi):
leer = [i for i in open(file_smi)]
print(f"Total de smi: {len(leer)}")
cont = 0
cont_tot = []
for i in leer:
nom_mol = i.split()[1]
smi_mol = i.split()[0]
mol_smi = Chem.MolFromSmiles(smi_mol)
Chem.MolToMolFile(mol_smi, f'{nom_mol}.sdf')
cont += 1
cont_tot.append(cont)
print(f"Se ha convertido {cont_tot[-1]} smiles a SDF")
Any help is highly appreciated
I need this to separate this smiles format in distints sdf archives.
Error:
Output:
答案1
得分: 1
这些类型的错误总是意味着一件事：你输入的SMILES字符串是无效的。在你的情况下，你之所以会收到错误信息，是因为SMILES字符串Cl[Pt](Cl)([NH4])[NH4]是无效的。请参见下面的图片。两个氮原子都形成了5个键，而没有任何正电荷。
当你在RdKit中解析它时，会得到如下的警告：
要处理这个问题，要么手动修复这个SMILES，要么完全忽略它。要忽略它，只需像下面这样传递参数sanitize=False：
mol_smi = Chem.MolFromSmiles(smi_mol, sanitize=False)
只是一个警告：通过添加sanitize=False，你将忽略所有无效的SMILES。
英文:
These kinds of errors always mean one thing: The SMILES you're inputting is invalid. In your case, you're getting the error because of the SMILES string Cl[Pt](Cl)([NH4])[NH4] which is invalid. See its picture below. Both Nitrogen atoms are forming 5 bonds without any positive charge on them.
When you parse it in RdKit, you'll get a warning like this:
To deal with this, either fix this SMILES manually or ignore it completely. To ignore it, just pass the argument sanitize=False as below:
mol_smi = Chem.MolFromSmiles(smi_mol, sanitize=False)
Just a warning: by adding sanitize=False, you'll be ignoring all the invalid SMILES.
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