How to use it for small Smiles like Aspirin Smile: CC(=O)Oc1ccccc1C(=O)O

Question

How to use it for small Smiles like Aspirin Smile: CC(=O)Oc1ccccc1C(=O)O

Fatima-Aslam opened this issue 2 years ago · comments

Whenever, I write any small Smiles string
Then I get
[22:10:14] Can't kekulize mol. Unkekulized atoms: 2 3 4 5 6
Traceback (most recent call last):
File "SmilesEnumerator.py", line 272, in
from SmilesEnumerator import SmilesEnumerator
File "D:\MSCS (fatima)\medicinal plants\Research task (August)\Synopsis\SmilesEnumerationCode - Copy\SMILES-enumeration-master (1)\SMILES-enumeration-master\SmilesEnumerator.py", line 276, in
print(sme.randomize_smiles("COc1cnc(nC1N(C)C)c2ccccc2"))
File "D:\MSCS (fatima)\medicinal plants\Research task (August)\Synopsis\SmilesEnumerationCode - Copy\SMILES-enumeration-master (1)\SMILES-enumeration-master\SmilesEnumerator.py", line 170, in randomize_smiles
ans = list(range(m.GetNumAtoms()))
AttributeError: 'NoneType' object has no attribute 'GetNumAtoms'

Please help me to resolve this issue

Esben Jannik Bjerrum · Answer 1 · Mon Oct 03 2022 21:55:17 GMT+0800 (China Standard Time)

I don't think your SMILES are getting parsed by RDKit. All smiles must be parsable by RDKit

Chem.MolFromSmiles("COc1cnc(nC1N(C)C)c2ccccc2")
RDKit ERROR: [13:54:15] Can't kekulize mol. Unkekulized atoms: 2 3 4 5 6
RDKit ERROR:

In this particular instance I think you need to tell RDKit on which aromatic nitrogen the hydrogen is situated.

Fatima · Answer 2 · Tue Oct 11 2022 16:09:17 GMT+0800 (China Standard Time)

Thank you for your reply I have an another question, Everytime I run the code it generates 10 different SMILES against a single a same input SMILE. Can you please explain it? Regards Fatima

…

On Mon, Oct 3, 2022, 6:55 PM Esben Jannik Bjerrum ***@***.***> wrote: I don't think your SMILES are getting parsed by RDKit. All smiles must be parsable by RDKit Chem.MolFromSmiles("COc1cnc(nC1N(C)C)c2ccccc2") RDKit ERROR: [13:54:15] Can't kekulize mol. Unkekulized atoms: 2 3 4 5 6 RDKit ERROR: In this particular instance I think you need to tell RDKit on which aromatic nitrogen the hydrogen is situated. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUW4H5UMWYXTG26WU7263VDWBLQVBANCNFSM6AAAAAAQ2RGTYA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

Esben Jannik Bjerrum · Answer 3 · Tue Oct 11 2022 18:24:40 GMT+0800 (China Standard Time)

Data augmentation with SMILES enumeration is all about generating alternative SMILES for the same molecule.