Hi,
I’m out-of-office this week and don’t have access to a computer, but I
suspect that that is a bug.
The drawing code should not generate errors like that.
Which version of the rdkit are you running?
-greg
On Mon, 29 Apr 2019 at 15:55, Jasmin <zweitm...@posteo.de> wrote:
> Hello!
>
> When running the following Code:
>
> testmol = Chem.MolFromSmiles('c1cccn2cccc12')
> info = {}
> fp = AllChem.GetMorganFingerprintAsBitVect(testmol, 2, nBits=1024,
> bitInfo=info)
> drawing = []
> for key in info:
> drawing.append((testmol, key, {key: info[key]}))
> Draw.DrawMorganBits(drawing)
>
> I get the following error:
>
> ValueError: Sanitization error: Can't kekulize mol. Unkekulized atoms:
> 0 1 2 6 7
>
> I can track the problem down to bit 470: ((3, 2), (5, 2))
> There seems to be a problem with this somewhat unusual aromatic
> structure. The problem also appears with other similar structures like
> 1,2,4-Triazolo[1,5-a]pyrimidine and Pyroxsulam.
> Any ideas how to fix this? Can I somehow sanitize the molecule before
> creating the fingerprint?
>
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
