Hi Anthony,
It has something to do with the bounding boxes (they get scaled during the
map generation process).
Using bbox_inches='tight', however, worked for me, i.e.
image.savefig("out.png", bbox_inches='tight')
I hope this helps.
Best,
Sereina
2013/11/4 Anthony Bradley <[email protected]>
> Hi all,
>
>
>
> I’m having some difficulty trying to save the new similarity map images.
> (They’re super cool by the way!)
>
>
>
> If I do the following in a python shell:
>
>
>
> from rdkit import Chem
>
> from rdkit.Chem.Draw import SimilarityMaps
>
> image =
> SimilarityMaps.GetSimilarityMapFromWeights(Chem.MolFromSmiles("CCC"),[1,2,3])
>
> # Just a dummy image
>
> image.savefig("out.png")
>
> # The outputted image is just the bottom left hand corner
>
>
>
> The image saved is cropped to the left hand corner (saved.png). It will
> render perfectly in an IPython notebook however. (ipython.png)
>
>
>
> Am I missing something here about saving Matplotlib images?
>
>
>
> Cheers,
>
>
>
> Anthony
>
>
>
>
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