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

2023-06-08 Thread Jean-Marc Nuzillard 

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 
 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:




On Mon, Jun 5, 2023 at 3:15 AM Jean-Marc Nuzillard 
 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
 1.50000.0. 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
    1.5000    0.    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
    0.7500   -1.2990    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
   -0.7500   -1.2990    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
   -1.5000    0.    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
   -3.7500    1.2990    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
   -3.    2.5981    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
   -1.5000    2.5981    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
   -0.7500    1.2990    0. C   0  0 0  0  0  0  0  0 
0  0  0  0
    0.7500    1.2990    0. 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

--

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

2023-06-08 Thread Paolo Tosco 
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  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:

  
  
  
On Mon, Jun 5, 2023 at 3:15 AM
  Jean-Marc Nuzillard 
  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
1.50000.0. 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
    1.5000    0.    0. C   0  0  0  0 
0  0  0  0  0  0  0  0
    0.7500   -1.2990    0. C   0  0  0  0 
0  0  0  0  0  0  0  0
   -0.7500   -1.2990    0. C   0  0  0  0 
0  0  0  0  0  0  0  0
   -1.5000    0.    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
   -3.7500    1.2990    0. C   0  0  0  0 
0  0  0  0  0  0  0  0
   -3.    2.5981    0. C   0  0  0  0 
0  0  0  0  0  0  0  0
   -1.5000    2.5981    0. C   0  0  0  0 
0  0  0  0  0 

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

2023-06-08 Thread Jean-Marc Nuzillard 

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 
 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
 1.50000.0. 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
    1.5000    0.    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
    0.7500   -1.2990    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
   -0.7500   -1.2990    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
   -1.5000    0.    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
   -3.7500    1.2990    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
   -3.    2.5981    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
   -1.5000    2.5981    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
   -0.7500    1.2990    0. C   0  0  0  0 0  0  0  0  0 
0  0  0
    0.7500    1.2990    0. 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




--

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

2023-06-07 Thread Jeremy Monat 
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
> 1.50000.0. 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
>>
>>
>
> --
> 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
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
___
Rdkit-discuss mailing list
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Re: [Rdkit-discuss] H atoms at ring junction

2023-06-05 Thread Jean-Marc Nuzillard 

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
 1.50000.0. 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
    1.5000    0.    0. C   0  0  0  0  0  0  0 0  0  0  0  0
    0.7500   -1.2990    0. C   0  0  0  0  0  0  0 0  0  0  0  0
   -0.7500   -1.2990    0. C   0  0  0  0  0  0  0 0  0  0  0  0
   -1.5000    0.    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
   -3.7500    1.2990    0. C   0  0  0  0  0  0  0 0  0  0  0  0
   -3.    2.5981    0. C   0  0  0  0  0  0  0 0  0  0  0  0
   -1.5000    2.5981    0. C   0  0  0  0  0  0  0 0  0  0  0  0
   -0.7500    1.2990    0. C   0  0  0  0  0  0  0 0  0  0  0  0
    0.7500    1.2990    0. 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  




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

2023-06-01 Thread Paolo Tosco 
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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[Rdkit-discuss] H atoms at ring junction

2023-06-01 Thread Jean-Marc Nuzillard 

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.    0. C   0  0  0  0  0  0  0  0  0  0 0  0
    0.7500   -1.2990    0. C   0  0  0  0  0  0  0  0  0  0 0  0
   -0.7500   -1.2990    0. C   0  0  0  0  0  0  0  0  0  0 0  0
   -1.5000    0.    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
   -3.7500    1.2990    0. C   0  0  0  0  0  0  0  0  0  0 0  0
   -3.    2.5981    0. C   0  0  0  0  0  0  0  0  0  0 0  0
   -1.5000    2.5981    0. C   0  0  0  0  0  0  0  0  0  0 0  0
   -0.7500    1.2990    0. C   0  0  0  0  0  0  0  0  0  0 0  0
    0.7500    1.2990    0. 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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