Yes !
Cheers,
Jean-Marc
Le 27/07/2023 à 12:54, Paolo Tosco a écrit :
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 = "C1CC[C@H]2[C@@H]2C1"
filenameOut = "img.png"
mol =
Dear Jean-Marc.Then you only need addChiralHs=False:from rdkit import Chemfrom rdkit.Chem.Draw import rdDepictorfrom rdkit.Chem.Draw import rdMolDraw2Dfrom PIL import Imagefrom io import BytesIO
smi = "C1CC[C@H]2[C@@H]2C1"filenameOut = "img.png"
mol = Chem.MolFromSmiles(smi)
Dear Paolo,
your code works perfectly well.
Running it with the SMILES of trans-decalin, C1CC[C@H]2[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
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
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
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
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
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