Re: [Rdkit-discuss] H atoms at ring junction

Thu, 08 Jun 2023 01:49:18 -0700 

Thanks again!

Jean-Marc


Le 08/06/2023 à 10:31, Paolo Tosco a écrit :

Dear Jean-Marc,
I wrote my email in an iPad, and probably attaching the image failed somehow.
You may save the SVG image to a file as follows; it is a plain text XML string: 

svg_image = drawer.GetDrawingText()
with open(“ h_atoms_at_ring_jn.svg”, “w”) as hnd:
    hnd.write(svg_image)

Cheers,
p.
On 8 Jun 2023, at 10:22, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> wrote: 


I guessed that for some reason the drawing did not show up in Paolo's reply to my question but I did not try to investigate further to find an explanation, since I run his code without any problem and was then able to adapt it for the 
creation of PNG images.

How did you create file h_atoms_at_ring_jn.svg?

The execution of SVG(drawer.GetDrawingText())
returns an object of type IPython.core.display.SVG
that is nicely displayed as a chemical structure by spyder
but from which I do not know how to produce a .svg file.

Best,

Jean-Marc

Le 07/06/2023 à 23:53, Jeremy Monat a écrit :
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: 
<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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--
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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