KekulizeException of molecule from Smarts pattern with new RDKit release

[schallerdavid]

Describe the bug
With the new release of RDKit (2022.03.1) we observed a KekulizeException that was not thrown by the previous RDKit release (2021.09.5), which prevents the rendering of a certain Smarts pattern with the Draw.MolsToGridImage functionality.

To Reproduce

from rdkit import Chem
mol = Chem.MolFromSmarts("[#6](:,-[#6]-,:[#7]-,:[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1):,-[#6]:,-[#7]:,-[#6]")
Chem.Kekulize(m1)

Expected behavior
Both version behave consistent.

Configuration (please complete the following information):

• RDKit versions: 2022.03.1 and 2021.09.5
• OS: Ubuntu 20.04, MacOS, Windows
• Python 3.7 - 3.9
• Are you using conda? yes
• If you are using conda, which channel did you install the rdkit from? conda-forge

Additional context
If the KekulizeException is correctly thrown for this Smarts pattern in the new RDKit version, it would be great to still be able to visualize it with Draw.MolsToGridImage. However, I cannot find a possibility to prevent the kekulization of the given molecules in this function, so the KekulizeError always gets thrown.

Thanks in a advance,
David

[greglandrum]

Hi @schallerdavid thanks for the bug report. I'll take a look and see if I can figure out what's going on and how to fix it

[ptosco]

@schallerdavid to visualize all molecules including those failing to kekulize, you can try the following:

from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D, MolsToGridImage

mol_fails = Chem.MolFromSmarts("[#6](:,-[#6]-,:[#7]-,:[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1):,-[#6]:,-[#7]:,-[#6]")
mol_succeeds = Chem.MolFromSmiles("c1ccccn1")

drawOptions = rdMolDraw2D.MolDrawOptions()
drawOptions.prepareMolsBeforeDrawing = False

def prepare_mol(mol):
    try:
        mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol)
    except Chem.KekulizeException:
        mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol, kekulize=False)
        Chem.SanitizeMol(mol_draw, Chem.SANITIZE_ALL ^ Chem.SANITIZE_KEKULIZE)
    return mol_draw

drawOptions = rdMolDraw2D.MolDrawOptions()
drawOptions.prepareMolsBeforeDrawing = False

mols = [mol_succeeds, mol_fails]

MolsToGridImage([prepare_mol(mol) for mol in mols], drawOptions=drawOptions)
[16:56:10] Can't kekulize mol.  Unkekulized atoms: 3