Very nice! The picture in the thread above didn't come through for me. I
re-ran that code and got the following output, included as both an inline
PNG and an attached SVG so hopefully it shows up for folks in at least one:
[image: h_atoms_at_ring_jn.png]
On Mon, Jun 5, 2023 at 3:15 AM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
> Dear Paolo,
>
> many thanks, your solution worked like a charm!
>
> Best regards,
>
> Jean-Marc
>
>
> Le 01/06/2023 à 23:57, Paolo Tosco a écrit :
>
> 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
> 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -3.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
> 0.7500 1.2990 0.0000 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 <jm.nuzill...@univ-reims.fr>
> wrote:
>
>> Dear all,
>>
>> starting from this mol block:
>> trans-decalin
>> RDKit 2D
>>
>> 10 11 0 0 0 0 0 0 0 0999 V2000
>> 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -3.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> -0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.7500 1.2990 0.0000 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 : 0000-0002-5120-2556
>> Tel : +33 (0)3 26 91 82 10
>> http://www.univ-reims.fr/icmr
>> https://nuzillard.github.io/PyLSD
>>
>>
>
> --
> 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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