Hi Max,
thanks for your reply.
The result you provided is exactly what I was looking for.
However, I think it has more to do with the color of the highlight than
any different setting of the transparency parameter in the underlying
methods. (which is a good thing!)
I was just focusing so much on the transparency effect that I obviously
forgot to try to use lighter tones for the color...
For instance, the snippet below also works for my purpose.
Cheers,
Jose Manuel
snippet:
import matplotlib
from rdkit import rdBase
from rdkit import Chem
# display molecules
from rdkit.Chem import Draw
from rdkit.Chem.Draw import IPythonConsole
from IPython.display import SVG
m = Chem.MolFromSmiles("O1CCCC1") # tetrahydrofuran
highlight=[0] # oxygen
color = matplotlib.colors.ColorConverter().to_rgb('pink')
Draw.MolsToGridImage( [m],highlightAtomLists=[highlight],
highlightAtomColors=[{0:color}])
On 12/20/18 7:33 PM, Max Pinheiro Jr wrote:
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 <mailto: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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