Dear Paolo,
your code works perfectly well.
Running it with the SMILES of trans-decalin, C1CC[C@H]2CCCC[C@@H]2C1,
I obtained
.
The code with ReapplyMolBlockWedging() inside (that you proposed me
in a previous post) was intended to have no H atom displayed at ring
junctions.
Sure, the SMILES of trans-decalin I propose, generated by rdkit from a
molblock
devoid of H atoms, has explicit H atoms inside at the ring junction.
So, starting from an isomeric SMILES, I would like to produce PNG
drawings that retain
the existing configuration information and do not show H atoms at ring
junctions.
Best,
Jean-Marc
Le 27/07/2023 à 10:33, Paolo Tosco a écrit :
Dear Jean-Marc,
You are generating the molecule from SMILES, therefore it does not
have molblock wedging information.
When you call ReapplyMolBlockWedging(), first existing wedging info
will be stripped.
Then, the molblock wedging will be applied, but there is none.
Hence, you get no wedging.
You may simplify your code and get the expected wedging as follows:
from rdkit import Chem
from rdkit.Chem.Draw import rdDepictor
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)
rdDepictor.SetPreferCoordGen(True)
rdDepictor.Compute2DCoords(mol)
d2d = rdMolDraw2D.MolDraw2DCairo(350, 300)
dopts = d2d.drawOptions()
dopts.baseFontSize = 0.6
d2d.DrawMolecule(mol, legend='', highlightAtoms=[])
d2d.FinishDrawing()
bio = BytesIO(d2d.GetDrawingText())
draw_code = Image.open(bio)
draw_code.save(filenameOut)
Cheers.
p.
On 27 Jul 2023, at 07:31, Jean-Marc Nuzillard
<jm.nuzill...@univ-reims.fr> wrote:
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:
<wAS5dAnxRREFAFxp.png>
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
_______________________________________________
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
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
