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
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