Dear Jean-Marc,
you may retain the original mol block wedging and avoid introducing H atoms
as follows:
from rdkit import Chem
from rdkit.Chem.Draw import rdMolDraw2D
from IPython.display import SVG
mol = Chem.MolFromMolBlock("""trans-decalin
RDKit 2D
10 11 0 0 0 0 0 0 0 0999 V2000
1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
-3.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2.59810. C 0 0 0 0 0 0 0 0 0 0 0 0
-1.50002.59810. C 0 0 0 0 0 0 0 0 0 0 0 0
-0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
4 3 1 1
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 6
9 10 1 0
10 1 1 0
9 4 1 0
M END
""")
drawer = rdMolDraw2D.MolDraw2DSVG(300, 200)
drawer.drawOptions().prepareMolsBeforeDrawing = False
mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol, addChiralHs=False,
wedgeBonds=False)
Chem.ReapplyMolBlockWedging(mol_draw)
drawer.DrawMolecule(mol_draw)
drawer.FinishDrawing()
SVG(drawer.GetDrawingText())
Cheers,
p.
On Thursday, June 1, 2023, Jean-Marc Nuzillard
wrote:
> Dear all,
>
> starting from this mol block:
> trans-decalin
> RDKit 2D
>
> 10 11 0 0 0 0 0 0 0 0999 V2000
> 1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.7500 -1.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.50000.0. C 0 0 0 0 0 0 0 0 0 0 0 0
>-3.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
>-3.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
>-3.2.59810. C 0 0 0 0 0 0 0 0 0 0 0 0
>-1.50002.59810. C 0 0 0 0 0 0 0 0 0 0 0 0
>-0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.75001.29900. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 4 3 1 1
> 4 5 1 0
> 5 6 1 0
> 6 7 1 0
> 7 8 1 0
> 9 8 1 6
> 9 10 1 0
> 10 1 1 0
> 9 4 1 0
> M END
>
> I tried to experiment with the great post recently published
> in the rdkit-blog about drawing options.
> The Mol block hereabove has no explicit hydrogen
> but the function DrawMolecule()
> adds two hydrogen atoms at the ring junction :
>
> Even though this feature can be very helpful,
> is it possible to let wedges along C-C bonds
> carry out the geometry information without
> introducing H atoms at the ring junction?
>
> Best,
>
> Jean-Marc Nuzillard
>
> --
> 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 : -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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