Re: [Rdkit-discuss] H atoms at ring junction

2023-06-08 Thread Jean-Marc Nuzillard
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

Re: [Rdkit-discuss] H atoms at ring junction

2023-06-08 Thread Paolo Tosco
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

Re: [Rdkit-discuss] H atoms at ring junction

2023-06-08 Thread Jean-Marc Nuzillard
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

Re: [Rdkit-discuss] H atoms at ring junction

2023-06-07 Thread Jeremy Monat
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

Re: [Rdkit-discuss] H atoms at ring junction

2023-06-05 Thread Jean-Marc Nuzillard
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

[Rdkit-discuss] H atoms at ring junction

2023-06-01 Thread Paolo Tosco
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

[Rdkit-discuss] H atoms at ring junction

2023-06-01 Thread Jean-Marc Nuzillard
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