英文:
How to catch the error message from Chem.MolFromSmiles('Formula')
问题
from rdkit import Chem
m = Chem.MolFromSmiles('OCC1OC(C(C(C1O)O)O)[C]1(C)(CO)CC(=O)C=C(C1CCC(=O)C)C')
m
try:
if m is None:
raise ValueError("Invalid chemical structure")
except Exception as e:
print(str(e))
英文:
I'm new to this rdkit, below is the code that I'm using to get the chemical image from the formula,
from rdkit import Chem
m = Chem.MolFromSmiles('OCC1OC(C(C(C1O)O)O)[C]1(C)(CO)CC(=O)C=C(C1CCC(=O)C)C')
m
if the code is correct, it displays the structre. The above code displays the error saying
"[15:23:55] Explicit valence for atom # 11 C, 5, is greater than permitted"
I tried adding try catch but, it does not help.
I need to catch this exception/Message and display it to the user.
How can we do this?Issue Image Here
try:
from rdkit import Chem
m = Chem.MolFromSmiles('OCC1OC(C(C(C1O)O)O)[C]1(C)(CO)CC(=O)C=C(C1CCC(=O)C)C')
m
except Exception as e:
print(e)
答案1
得分: 1
不是错误，而是警告。您的代码在执行该赋值时不会出错。因此，没有错误可捕获。
但是您的解决方案位于Chem.MolFromSmiles的返回值中。如果它无法构建出SMILES的mol对象，它会返回None，而当它成功地“处理SMILES”时，它会返回mol对象。
当然，您可以自己引发错误！
from rdkit import Chem
m = Chem.MolFromSmiles('OCC1OC(C(C(C1O)O)O)[C]1(C)(CO)CC(=O)C=C(C1CCC(=O)C)C')
if m is None:
print("嘿，用户，出现了错误！")
# 或者甚至引发一个错误：
if m is None:
raise ValueError("无法解释SMILES为mol对象")
我知道我的答案不够完整。我的解决方案没有向用户传达警告。我觉得这可能相当困难。如果有解决方案，可能可以利用logging或warnings包找到。我也对此很感兴趣，但迄今为止还没有成功。
英文:
It is not an Error, it is a Warning. Your code does not break doing that assignment. So there is no Error to catch.
But your solution lays within the return of Chem.MolFromSmiles. If it fails to build a mol object of your SMILES it returns None, whereas it returns the mol object when it manages to "deal with the SMILES properly".
For sure you can raise an error yourself!
from rdkit import Chem
m = Chem.MolFromSmiles('OCC1OC(C(C(C1O)O)O)[C]1(C)(CO)CC(=O)C=C(C1CCC(=O)C)C')
if m is None:
print("hey user, there was an error!")
# or even raise an error:
if m is None:
raise ValueError("Could not interpret SMILES to mol object")
I know my answer is lacking. My solution is not forwarding the warning to the user. I feel like it is quite hard to do. If there is a solution it might be found utilizing logging or warnings package. I would also be interested in that but couldn't manage so far myself.
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