Hi Stephanie,
On Mon, Oct 17, 2016 at 7:58 PM, Stéphanie Valleau <svall...@stanford.edu>
wrote:
> For some reason I do not get a plot of H2 with the following code:
>
> mole = Chem.MolFromSmiles('[H][H]')
> AllChem.Compute2DCoords(mole)
> Draw.MolToFile(mole,name,size=(300,300))
>
> I only get a white square in output, whereas other molecules such as
>
> mole = Chem.MolFromSmiles('[N][CH][OH]')
>
> plot with no trouble.
>
> I am running on MacOsX
>
> Any reason for this?
>
It looks like a bug in AllChem.Compute2DCoords:
In [3]: m = Chem.MolFromSmiles('[H][H]')
...: AllChem.Compute2DCoords(m)
...:
Out[3]: 0
In [4]: print(Chem.MolToMolBlock(m))
RDKit 2D
2 1 0 0 0 0 0 0 0 0999 V2000
nan nan 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
nan nan 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
M END
I'll file that and we'll fix it.
Thanks for finding and reporting the problem.
Best,
-greg
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