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
example_rdkit_custom_highlight.ipynb
Description: application/ipynb
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