Hi,
This has gotten a little bit easier in the most recent RDKit version.
Here's a simple example:
In [3]: print(rdkit.__version__)
2018.09.1
In [4]: from rdkit import Chem
In [5]: m = Chem.MolFromSmiles('CN=NC')
In [6]: m.GetBondWithIdx(1).SetStereoAtoms(0,3)
In [7]: m.GetBondWithIdx(1).SetStereo(Chem.BondStereo.STEREOCIS)
In [8]: Chem.AssignStereochemistry(m,force=True)
In [9]: Chem.MolToSmiles(m)
Out[9]: 'C/N=N\\C'
Or a more complicated one that's closer to what it looks like you want to
do:
In [10]: m = Chem.MolFromSmiles('c1ccccc1N=Nc1ccccc1')
In [11]: match = m.GetSubstructMatch(Chem.MolFromSmarts('cN=Nc'))
In [12]: b = m.GetBondBetweenAtoms(match[1],match[2])
In [13]: b.SetStereoAtoms(match[0],match[3])
In [14]: b.SetStereo(Chem.BondStereo.STEREOTRANS)
In [15]: Chem.AssignStereochemistry(m,force=True)
In [16]: Chem.MolToSmiles(m)
Out[16]: 'c1ccc(/N=N/c2ccccc2)cc1'
I hope that helps,
-greg
On Wed, Feb 6, 2019 at 12:31 PM Noki Lee <noki.le...@gmail.com> wrote:
> Hi, RDkit.
>
> I'm looking for a way to change cis-trans for a molecule at the diimide
> part.
> There was a case for the Alkene E-Z change.
>
> https://sourceforge.net/p/rdkit/mailman/message/35011276/
>
> But when I apply above method, it doesn't work for the diimide case.
>
> For examples, let say Mymol be made from azobenzene: c1ccc(N=Nc2ccccc2)cc1
> I wrote down the procedure:
> 1. Detect substructure of N=N part by GetSubstructMatch
> 2. And then apply ENDDOWNRIGHT and ENDUPRIGHT for each atomIdx
> but the result is same for the original one.
>
> Thanks all!
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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