Hi Francois,
The important thing here is to pass a DrawingOptions structure that you
pass along. Here's an example:
drawOptions = Draw.DrawingOptions()
drawOptions.elemDict={}
drawOptions.bgColor=None
fig, maxweight = SimilarityMaps.GetSimilarityMapForFingerprint(refmol, mol,
SimilarityMaps.GetMorganFingerprint,
options=drawOptions)
And a gist which, for some reason, isn't rendering properly for me:
https://gist.github.com/greglandrum/99cff91b9f2315cccc7d475b015ffe96
-greg
On Thu, Jul 11, 2019 at 10:25 AM Francois Berenger <[email protected]> wrote:
> Dear rdkiters,
>
> I am playing with rdkit.Chem.Draw:
> ---
> sim_map = Draw.SimilarityMaps.\
> GetSimilarityMapFromWeights(mol, weights)
> ---
>
> I don't like that in the created figure, the map colors overlap
> with atoms and bonds colors.
> It makes the map less readable.
> I would prefer all labels and bonds to be black, only the map
> to bring colors.
>
> Also, since atoms have labels, I feel that coloring them
> (and their bonds) is some unnecessary duplication of information.
>
> Can the atom labels and bonds default coloring scheme be turned off?
>
> From my reading of rdkit code, it seems that the elemDict in
> Draw.DrawingOptions should be emptied.
>
> I don't know how to pass such an option, and if this is even possible,
> to GetSimilarityMapFromWeights.
>
> Thanks a lot,
> F.
>
>
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