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

[Jean-Marc N. <jm....@un...>]

Dear Paolo,

your code works perfectly well.

Running it with the SMILES of trans-decalin, C1CC[C@H]2CCCC[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 trans-decalin I propose, generated by rdkit from a 
molblock
devoid of H atoms, has explicit H atoms inside at the ring junction.
So, starting from an isomeric SMILES, I would like to produce PNG 
drawings that retain
the existing configuration information and do not show H atoms at ring 
junctions.

Best,

Jean-Marc


Le 27/07/2023 à 10:33, Paolo Tosco a écrit :
> 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 simplify your code and get the expected wedging as follows:
>
> 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 = "C=C[C@@](/C=C/c1ccc(cc1)O)(CCC=C(C)C)C"
> filenameOut = "img.png"
> mol = Chem.MolFromSmiles(smi)
> rdDepictor.SetPreferCoordGen(True)
> rdDepictor.Compute2DCoords(mol)
> d2d = rdMolDraw2D.MolDraw2DCairo(350, 300)
> dopts = d2d.drawOptions()
> dopts.baseFontSize = 0.6
> d2d.DrawMolecule(mol, legend='', highlightAtoms=[])
> d2d.FinishDrawing()
> bio = BytesIO(d2d.GetDrawingText())
> draw_code = Image.open(bio)
> draw_code.save(filenameOut)
>
>
> Cheers.
> p.
>
>> On 27 Jul 2023, at 07:31, Jean-Marc Nuzillard 
>> <jm....@un...> wrote:
>>
>> 
>> 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 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:
>>>     <wAS5dAnxRREFAFxp.png>
>>>
>>>
>>>     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
>>>     Rdk...@li...
>>>     https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>> -- 
>>> David Cosgrove
>>> Freelance computational chemistry and chemoinformatics developer
>>> http://cozchemix.co.uk
>>>
>>
>>
>> -- 
>> 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
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


-- 
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