Hi Jose,
Have you tried to use the "DrawMolecules" from the
"rdMolDraw2D.MolDraw2DSVG" class? I think this class has some other options
that allow one to change the highlight colors while still keeping the alpha
transparency. I did a test here with your code and it seems to provide the
result you are looking for:
m = Chem.MolFromSmiles("O1CCCC1") # tetrahydrofuran
highlight=[0] # oxygen
matches = m.GetSubstructMatches(Chem.MolFromSmiles('CO'))
print matches
color_1 = {}
color_2 = {}
color_3 = {}
radius = {}
for i,j in zip(matches[0], matches[1]):
color_1[i] = ColorConverter().to_rgb('lightgray')
color_2[j] = ColorConverter().to_rgb('skyblue')
tm = rdMolDraw2D.PrepareMolForDrawing(m)
view = rdMolDraw2D.MolDraw2DSVG(660,350)
option = view.drawOptions()
option.padding=0.13
option.legendFontSize=18
view.DrawMolecules([tm], highlightAtoms=[highlight],
highlightAtomColors=[color_2])
view.FinishDrawing()
svg = view.GetDrawingText()
with open('./example.svg', 'w') as f:
f.write(svg)
SVG(svg.replace('svg:', ''))
I hope it works for you.
All the best,
Max
Em qui, 20 de dez de 2018 às 14:33, Jose Manuel Gally <
jose.manuel.ga...@gmail.com> escreveu:
> Hi all,
>
> I am trying to highlight substructures found in a set of molecules.
>
> However, if I use a specific color in Draw.MolsToGridImage by defining the
> highlightAtomColors parameter, I lose the transparency effect, so some
> atoms can be hidden by the highlight.
>
> Is there a way to set the transparency level (alpha) with defined
> highlightAtomColors?
>
> I could not find any relevant parameter in the documentation (alpha is
> mentioned only once in the calcAtomGaussians docstring) or in this
> mailing list.
>
> I also tried to set a value an additional value in the RGB code (i.e.
> RGBa=(1, 0, 0, 0.5)), but it seems to be simply ignored.
>
> Please find attached a notebook with a very simple example.
>
> Am I missing something obvious?
>
> By default there seems to be some transparency applied when highlighting.
>
> Thank you for your help!
>
> Best regards,
> Jose Manuel
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> Rdkit-discuss@lists.sourceforge.net
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