DrawRDKBits raised RDKit error when it applied to the compounds that contains imidazole.

[yamasakih]

Description:

• RDKit Version: 2018.09.1
• Platform: MaxOS 10.13.6

When I apply RDKFingerprint to the compounds that contains imidazole as substructure,
RDKit Error raised like below.

from rdkit import rdBase, Chem
from rdkit.Chem import AllChem, Draw
from rdkit.Chem.Draw import DrawRDKitBit, DrawRDKitBits, IPythonConsole

mol = Chem.MolFromSmiles('c1cncn(C)1')
bi = {}
_ = AllChem.RDKFingerprint(mol, minPath=1, maxPath=5, bitInfo=bi)
tuples = [(mol, k, bi) for k in bi.keys()]
DrawRDKitBits(tuples)

result:

RDKit ERROR: [18:31:04] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4
RDKit ERROR: 
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-fa9fb99cd597> in <module>()
----> 1 DrawRDKitBits(tuples, molsPerRow=8)

~/anaconda3/lib/python3.6/site-packages/rdkit/Chem/Draw/IPythonConsole.py in DrawRDKitBits(*args, **kwargs)
    256   else:
    257     fn = Draw.DrawRDKitBits
--> 258   return _DrawBit(fn, *args, **kwargs)
    259 DrawRDKitBits.__doc__ = Draw.DrawRDKitBits.__doc__
    260 

~/anaconda3/lib/python3.6/site-packages/rdkit/Chem/Draw/IPythonConsole.py in _DrawBit(fn, *args, **kwargs)
    200   if 'useSVG' not in kwargs:
    201     kwargs['useSVG'] = ipython_useSVG
--> 202   res = fn(*args, **kwargs)
    203   if kwargs['useSVG']:
    204     return SVG(res)

~/anaconda3/lib/python3.6/site-packages/rdkit/Chem/Draw/__init__.py in DrawRDKitBits(tpls, **kwargs)
    731     bondpath = bitInfo[bitId][whichExample]
    732     envs.append((mol, bondpath))
--> 733   return DrawRDKitEnvs(envs, **kwargs)
    734 
    735 def DrawRDKitBit(mol, bitId, bitInfo, whichExample=0, **kwargs):

~/anaconda3/lib/python3.6/site-packages/rdkit/Chem/Draw/__init__.py in DrawRDKitEnvs(envs, molsPerRow, subImgSize, baseRad, useSVG, aromaticColor, extraColor, nonAromaticColor, legends, **kwargs)
    825   drawer.DrawMolecules(submols, legends=legends, highlightAtoms=highlightAtoms,
    826                        highlightAtomColors=atomColors, highlightBonds=highlightBonds,
--> 827                        highlightBondColors=bondColors, highlightAtomRadii=highlightRadii, **kwargs)
    828   drawer.FinishDrawing()
    829   return drawer.GetDrawingText()

ValueError: Sanitization error: Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4

I think that imidazole is caused by not being able to kekulize if it does not have hydrogen.

mol = Chem.MolFromSmiles('c1cncn1')

result:

RDKit ERROR: [06:51:21] Can't kekulize mol.  Unkekulized atoms: 0 1 2 3 4
RDKit ERROR: 

[greglandrum]

Confirmed.
A bit more specific about what is causing the problem:

mol = Chem.MolFromSmiles('c1cncn(C)1')
bi = {}
_ = AllChem.RDKFingerprint(mol, minPath=1, maxPath=5, bitInfo=bi)
tuples = [(mol, k, bi) for k in bi.keys()]
DrawRDKitBits((tuples[38],))

[greglandrum]

Here's a reproducible of the root cause, which is a kekulization failure caused by the PathToSubmol() call.

mol = Chem.MolFromSmiles('c1cncn(C)1')
bondPath = [0, 1, 2, 3, 5]
submol = Chem.PathToSubmol(mol, bondPath)
submol.UpdatePropertyCache()
submol.Debug()
Chem.Kekulize(submol)