Re: [Rdkit-discuss] Create an asymmetric carbon.
Hi Paolo,
the SetChiralTag() function is exactly what I missed.
Many thanks for your help,
Best regards,
Jean-Marc
Le 26/05/2021 à 18:21, Paolo Tosco a écrit :
Hi Jean-Marc,
You can use Chem.Atom.SetChiralTag():
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.drawOptions.addAtomIndices = True
IPythonConsole.ipython_useSVG=True
m = Chem.AddHs(Chem.MolFromSmiles('CCO'))
m
image.png
a = m.GetAtomWithIdx(6)
a.SetIsotope(2)
chiral_c = m.GetAtomWithIdx(1)
Chem.FindMolChiralCenters(m, force=True, includeUnassigned=True,
useLegacyImplementation=False)
[(1, '?')]
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED
chiral_c.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)
Chem.AssignStereochemistry(m, cleanIt=True, force=True)
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW
Chem.FindMolChiralCenters(m, force=True, includeUnassigned=True,
useLegacyImplementation=False)
[(1, 'S')]
m
image.png
chiral_c.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW)
Chem.AssignStereochemistry(m, cleanIt=True, force=True)
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, 'R')]
m
image.png
Cheers,
p.
On Wed, May 26, 2021 at 5:20 PM Jean-Marc Nuzillard
mailto:jm.nuzill...@univ-reims.fr>> wrote:
Dear all,
starting from ethanol with added Hs:
>>> m = Chem.AddHs(Chem.MolFromSmiles('CCO'))
the C atom of the CH2 group is indexed by "1" and is bound to H
atoms
indexed "6" and "7".
Replacing the H atom indexed "6" by a deuterium atom
>>> a = m.GetAtomWithIdx(6)
>>> a.SetIsotope(2)
creates an undefined asymmetric carbon atom:
>>>
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, '?')]
How is it possible to create, starting from this molecule m, two
molecules, m1 and m2, with opposite absolute configurations?
Many thanks in advance,
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
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
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
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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Re: [Rdkit-discuss] Create an asymmetric carbon.
Hi Jean-Marc,
You can use Chem.Atom.SetChiralTag():
from rdkit import Chem
from rdkit.Chem.Draw import IPythonConsole
IPythonConsole.drawOptions.addAtomIndices = True
IPythonConsole.ipython_useSVG=True
m = Chem.AddHs(Chem.MolFromSmiles('CCO'))
m
[image: image.png]
a = m.GetAtomWithIdx(6)
a.SetIsotope(2)
chiral_c = m.GetAtomWithIdx(1)
Chem.FindMolChiralCenters(m, force=True, includeUnassigned=True,
useLegacyImplementation=False)
[(1, '?')]
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_UNSPECIFIED
chiral_c.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CW)
Chem.AssignStereochemistry(m, cleanIt=True, force=True)
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW
Chem.FindMolChiralCenters(m, force=True, includeUnassigned=True,
useLegacyImplementation=False)
[(1, 'S')]
m
[image: image.png]
chiral_c.SetChiralTag(Chem.ChiralType.CHI_TETRAHEDRAL_CCW)
Chem.AssignStereochemistry(m, cleanIt=True, force=True)
chiral_c.GetChiralTag()
rdkit.Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, 'R')]
m
[image: image.png]
Cheers,
p.
On Wed, May 26, 2021 at 5:20 PM Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:
> Dear all,
>
> starting from ethanol with added Hs:
>
> >>> m = Chem.AddHs(Chem.MolFromSmiles('CCO'))
>
> the C atom of the CH2 group is indexed by "1" and is bound to H atoms
> indexed "6" and "7".
>
> Replacing the H atom indexed "6" by a deuterium atom
> >>> a = m.GetAtomWithIdx(6)
> >>> a.SetIsotope(2)
>
> creates an undefined asymmetric carbon atom:
> >>>
>
> Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
> [(1, '?')]
>
> How is it possible to create, starting from this molecule m, two
> molecules, m1 and m2, with opposite absolute configurations?
>
> Many thanks in advance,
>
> 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
>
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/icmr
> http://eos.univ-reims.fr/LSD/CSNteam.html
>
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
>
>
>
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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[Rdkit-discuss] Create an asymmetric carbon.
Dear all,
starting from ethanol with added Hs:
>>> m = Chem.AddHs(Chem.MolFromSmiles('CCO'))
the C atom of the CH2 group is indexed by "1" and is bound to H atoms
indexed "6" and "7".
Replacing the H atom indexed "6" by a deuterium atom
>>> a = m.GetAtomWithIdx(6)
>>> a.SetIsotope(2)
creates an undefined asymmetric carbon atom:
>>>
Chem.FindMolChiralCenters(m,force=True,includeUnassigned=True,useLegacyImplementation=False)
[(1, '?')]
How is it possible to create, starting from this molecule m, two
molecules, m1 and m2, with opposite absolute configurations?
Many thanks in advance,
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
Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/
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