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 2023, at 10:22, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> wrote:
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 h_atoms_at_ring_jn.svg?
The execution of SVG(drawer.GetDrawingText())
returns an object of type IPython.core.display.SVG
that is nicely displayed as a chemical structure by spyder
but from which I do not know how to produce a .svg file.
Best,
Jean-Marc
Le 07/06/2023 à 23:53, Jeremy Monat a écrit :
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:
<h_atoms_at_ring_jn.png>
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 rdMolDraw2D
from IPython.display import SVG
mol = Chem.MolFromMolBlock("""trans-decalin
RDKit 2D
10 11 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
4 3 1 1
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 6
9 10 1 0
10 1 1 0
9 4 1 0
M END
""")
drawer = rdMolDraw2D.MolDraw2DSVG(300, 200)
drawer.drawOptions().prepareMolsBeforeDrawing = False
mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol, addChiralHs=False, wedgeBonds=False)
Chem.ReapplyMolBlockWedging(mol_draw)
drawer.DrawMolecule(mol_draw)
drawer.FinishDrawing()
SVG(drawer.GetDrawingText())
![]()
On Thursday, June 1, 2023, Jean-Marc Nuzillard < jm.nuzill...@univ-reims.fr>
wrote:
Dear all,
starting from this mol block:
trans-decalin
RDKit 2D
10 11 0 0 0 0 0 0 0
0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-3.0000 0.0000 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-3.7500 1.2990 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-3.0000 2.5981 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-1.5000 2.5981 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0
0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
4 3 1 1
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 6
9 10 1 0
10 1 1 0
9 4 1 0
M END
I tried to experiment with the great post
recently published
in the rdkit-blog about drawing options.
The Mol block hereabove has no explicit hydrogen
but the function DrawMolecule()
adds two hydrogen atoms at the ring junction :
![]()
Even though this feature can be very helpful,
is it possible to let wedges along C-C bonds
carry out the geometry information without
introducing H atoms at the ring junction?
Best,
Jean-Marc Nuzillard
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10
http://www.univ-reims.fr/icmr
https://nuzillard.github.io/PyLSD
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10
http://www.univ-reims.fr/icmr
https://nuzillard.github.io/PyLSD
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10
http://www.univ-reims.fr/icmr
https://nuzillard.github.io/PyLSD
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