Re: [Rdkit-discuss] Chirality wedge disappears in PNG depiction

[David C. <dav...@gm...>]

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....@un...> 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
>
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>
-- 
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk