That's a bug in the new drawing code with molecules that have no extent in
either the X or Y directions. Here's the github item:
https://github.com/rdkit/rdkit/issues/1271
I'm surprised that the non-SVG version is working for you.
On Wed, Jan 18, 2017 at 11:19 PM, Curt Fischer <cu...@stanford.edu> wrote:
> Hi all,
>
> I'm not sure if this topic has come up before, but SVG rendering in
> Jupyter notebooks seems to make small molecules like methanol and water
> completely invisible. The same molecules render successfully for me using
> non-SVG renderers.
>
> Can others reproduce this behavior? Are there any easy-ish fixes for this?
>
> Curt
>
>
> *# import rdkit components*
> *from rdkit import Chem*
> *from rdkit.Chem import Draw*
> *from rdkit.Chem.Draw import IPythonConsole*
>
> *# two very small molecules*
> *methanol = Chem.MolFromSmiles('CO')*
> *water = Chem.MolFromSmiles('O')*
>
> *# SVG rendering seems to make small molecules like water and methanol
> completely invisible*
> *IPythonConsole.ipython_useSVG=True*
> *Draw.MolsToGridImage([water, methanol])*
>
> *# With SVG off the molecules are visible*
> *IPythonConsole.ipython_useSVG=False*
> *Draw.MolsToGridImage([water, methanol])*
>
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