Dear Samo,
On Mon, Aug 19, 2013 at 4:04 PM, Samo Turk <[email protected]> wrote:
>
> I was playing with ipython notebook and I get interesting error:
>
> from rdkit import Chem
> from rdkit.Chem import Draw
> from rdkit.Chem.Draw import IPythonConsole
>
> mol = Chem.MolFromSmarts('c1ccccc1')
> mol
>
> <draws benzene>
>
> Draw.MolsToGridImage([mol])
>
> ---------------------------------------------------------------------------ValueError
> Traceback (most recent call
> last)<ipython-input-71-4f0b315d518e> in <module>()----> 1
> Draw.MolsToGridImage([mol])
> /usr/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.py in
> MolsToGridImage(mols, molsPerRow, subImgSize, legends, **kwargs) 263
> row = i//molsPerRow 264 col = i%molsPerRow--> 265
> res.paste(MolToImage(mol,subImgSize,legend=legends[i],**kwargs),(col*subImgSize[0],row*subImgSize[1]))
> 266 return res 267
> /usr/lib/python2.7/site-packages/rdkit/Chem/Draw/__init__.py in
> MolToImage(mol, size, kekulize, wedgeBonds, **kwargs) 70 from rdkit
> import Chem 71 mol = Chem.Mol(mol.ToBinary())---> 72
> Chem.Kekulize(mol) 73 74 if not mol.GetNumConformers():
> ValueError: Sanitization error: Can't kekulize mol
>
>
> It works normally on aliphatic structures or if I use MolFromSmiles instead
> of MolFromSmarts. Is kekulization of mols obtained from SMARTS wanted
> behaviour? Is it possible to turn it off?
>
> Very short answer: use Draw.MolsToGridImage([mol],kekulize=False)
A bit of explanation:
The drawing code, by default, tries to kekulize the molecule so that
drawings of aromatic systems look better. This fails for molecules
constructed from SMARTS unless you do partial sanitization of those
molecules (I can explain this if you're interested, but it would be a
distraction here).
The ipython notebook integration code tries to kekulize the molecule; if
that fails, it renders the non-kekulized structure.
I hope this helps,
-greg
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