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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)
Ajay Managaon
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1 Answers1

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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.

Tarquinius
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