plot_descriptors() occasionally throws a KekulizeException

[hgandhi2411]

Occurs for ECFP descriptors

---------------------------------------------------------------------------
KekulizeException                         Traceback (most recent call last)
/scratch/hgandhi/tmp/ipykernel_41403/692804871.py in <module>
      8         exmol.plot_descriptors(space, output_file=f"alprozolam_{d}.svg")
      9     else:
---> 10         svg = exmol.plot_descriptors(space, output_file=f"alprozolam_{d}.svg", return_svg=True)
     11         plt.close()
     12         skunk.display(svg)

/gpfs/fs2/scratch/hgandhi/exmol/exmol/exmol.py in plot_descriptors(examples, output_file, fig, figure_kwargs, title, return_svg)
   1253                     ringColor=None,
   1254                     extraColor=(0.8, 0.8, 0.8),
-> 1255                     useSVG=True,
   1256                 )
   1257                 # TODO: Why?

~/.conda/envs/exmol/lib/python3.7/site-packages/rdkit/Chem/Draw/IPythonConsole.py in DrawMorganBit(mol, bitId, bitInfo, drawOptions, **kwargs)
    302   else:
    303     fn = Draw.DrawMorganBit
--> 304   return _DrawBit(fn, mol, bitId, bitInfo, drawOptions=drawOptions, **kwargs)
    305 
    306 

~/.conda/envs/exmol/lib/python3.7/site-packages/rdkit/Chem/Draw/IPythonConsole.py in _DrawBit(fn, *args, **kwargs)
    275     kwargs['useSVG'] = ipython_useSVG
    276 
--> 277   res = fn(*args, **kwargs)
    278   if kwargs['useSVG']:
    279     return SVG(res)

~/.conda/envs/exmol/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py in DrawMorganBit(mol, bitId, bitInfo, whichExample, **kwargs)
    699 def DrawMorganBit(mol, bitId, bitInfo, whichExample=0, **kwargs):
    700   atomId, radius = bitInfo[bitId][whichExample]
--> 701   return DrawMorganEnv(mol, atomId, radius, **kwargs)
    702 
    703 

~/.conda/envs/exmol/lib/python3.7/site-packages/rdkit/Chem/Draw/__init__.py in DrawMorganEnv(mol, atomId, radius, molSize, baseRad, useSVG, aromaticColor, ringColor, centerColor, extraColor, drawOptions, **kwargs)
    866                       highlightAtomColors=menv.atomColors, highlightBonds=menv.highlightBonds,
    867                       highlightBondColors=menv.bondColors, highlightAtomRadii=menv.highlightRadii,
--> 868                       **kwargs)
    869   drawer.FinishDrawing()
    870   return drawer.GetDrawingText()

KekulizeException: Can't kekulize mol.  Unkekulized atoms: 1 3 4 5 6 8 9

[whitead]

Is this just a drawing problem?

[hgandhi2411]

Yes, this is a drawing problem