Hi David,
thank you for your suggestion.
Setting wedgeBonds=True does not change anything,
probably because wedging is performed later by
the call to Chem.ReapplyMolBlockWedging()
Best,
Jean-Marc
Le 26/07/2023 à 22:28, David Cosgrove a écrit :
Hi,
I’m away from my computer at the moment, so can’t try anything, but I
wonder if it’s anything to do with the ‘wedgeBonds=False’ option you
gave when preparing the drawing.
Dave
On Wed, 26 Jul 2023 at 20:45, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr> wrote:
Dear all,
I use the following code to produce PNG drawings. I use RDKit
version 2023.03.1 .
The SMILES chain describes a molecule with a single chiral center
of defined configuration.
from rdkit import Chem
from rdkit.Chem import rdCoordGen
from rdkit.Chem.Draw import rdMolDraw2D
from PIL import Image
from io import BytesIO
smi = "C=C[C@@](/C=C/c1ccc(cc1)O)(CCC=C(C)C)C"
filenameOut = "img.png"
mol = Chem.MolFromSmiles(smi)
rdCoordGen.AddCoords(mol)
print(Chem.MolToMolBlock(mol))
d2d = rdMolDraw2D.MolDraw2DCairo(350, 300)
dopts = d2d.drawOptions()
dopts.baseFontSize = 0.6
dopts.prepareMolsBeforeDrawing = False
mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol,
addChiralHs=False, wedgeBonds=False)
Chem.ReapplyMolBlockWedging(mol_draw)
d2d.DrawMolecule(mol_draw, legend='', highlightAtoms=[])
d2d.FinishDrawing()
bio = BytesIO(d2d.GetDrawingText())
draw_code = Image.open(bio)
draw_code.save(filenameOut)
The resulting image does not show the chirality wedge:
The script prints the MolBlock that comes from the SMILES and the
calculation of the 2D atomic coordinates:
_________________
RDKit 2D
19 19 0 0 0 0 0 0 0 0999 V2000
2.0515 1.2242 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0515 1.2214 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5539 0.3540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4459 0.3512 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9435 -0.5162 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9435 -0.5190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4411 -1.3866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4411 -1.3892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9435 -0.5246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4459 0.3428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4459 0.3456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.9435 -0.5274 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.4215 -0.1436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2861 0.3588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1535 -0.1388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0181 0.3636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0153 1.3636 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8855 -0.1338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5567 -0.6460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 9 2 0
9 10 1 0
10 11 2 0
9 12 1 0
3 13 1 0
13 14 1 0
14 15 1 0
15 16 2 0
16 17 1 0
16 18 1 0
3 19 1 1
11 6 1 0
M END
_____________________
The wedge bond (3-19) is apparently here but is not drawn as such.
Is there a remedy for that?
Best regards,
Jean-Marc
--
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
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
--
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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Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
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