Thanks again!
Jean-Marc
Le 08/06/2023 à 10:31, Paolo Tosco a écrit :
Dear Jean-Marc,
I wrote my email in an iPad, and probably attaching the image failed
somehow.
You may save the SVG image to a file as follows; it is a plain text
XML string:
svg_image = drawer.GetDrawingText()
with
Dear Jean-Marc,I wrote my email in an iPad, and probably attaching the image failed somehow.You may save the SVG image to a file as follows; it is a plain text XML string:svg_image = drawer.GetDrawingText()with open(“ h_atoms_at_ring_jn.svg”, “w”) as hnd: hnd.write(svg_image)Cheers,p.On 8 Jun
I guessed that for some reason the drawing did not show up in Paolo's reply
to my question but I did not try to investigate further to find an
explanation,
since I run his code without any problem and was then able to adapt it
for the
creation of PNG images.
How did you create file
Very nice! The picture in the thread above didn't come through for me. I
re-ran that code and got the following output, included as both an inline
PNG and an attached SVG so hopefully it shows up for folks in at least one:
[image: h_atoms_at_ring_jn.png]
On Mon, Jun 5, 2023 at 3:15 AM Jean-Marc
Dear Paolo,
many thanks, your solution worked like a charm!
Best regards,
Jean-Marc
Le 01/06/2023 à 23:57, Paolo Tosco a écrit :
Dear Jean-Marc,
you may retain the original mol block wedging and avoid introducing H
atoms as follows:
from rdkit import Chem
from rdkit.Chem.Draw import
Dear Jean-Marc,
you may retain the original mol block wedging and avoid introducing H atoms
as follows:
from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
mol = Chem.MolFromMolBlock("""trans-decalin
RDKit 2D
10 11 0 0 0 0 0 0 0
Dear all,
starting from this mol block:
trans-decalin
RDKit 2D
10 11 0 0 0 0 0 0 0 0999 V2000
1.5000 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0. C 0 0
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