Can't kekulize mol. Unkekulized atoms: 11 12 14 15 16

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1

Hi
I tried to execute the following workflow :
03_Clustering – KNIME Community Hub

But have one error on the 2nd script Python script “attach the sidechains
using code in a Jupyter notebook”

nb = knime_jupyter.load_notebook(notebook_directory=“knime://knime.workflow/”,
notebook_name=“Enumerate.ipynb”,
only_include_tag=“export”)
from rdkit import Chem
import pandas as pd

new_mols =

try:
for core,chains in zip(input_table[‘Explicit Core’],input_table[‘sidechains’]):
chains = Chem.MolFromSmiles(chains)

  new_mols.append(nb.attach_sidechains_to_core(core,chains))

output_table = input_table.copy()
output_table['mol'] = new_mols

Issue :
WARNING: not removing hydrogen atom with dummy atom neighbors
Can’t kekulize mol. Unkekulized atoms: 11 12 14 15 16

Thanks , if anyone have some solution to resolve this issue

2

Hi @mdahmani and welcome to the forum.

This workflow is attributed to @greglandrum, so let me tag him here and see if he (or someone on his team) can provide some insight.

3

Hi @ScottF
Thanks for your reply !
Mohamed