Thanks a lot!
It's working for my project!
But, in the later way, STEREOTRANS (STEREOCIS) can be replaced by STEREOE
(STEREOZ), can't it?
I mean it might cause a problem that we consider one of N atom becomes C
atom or both.
Thanks, greg
On Thu, Feb 7, 2019 at 2:31 PM Greg Landrum <greg.land...@gmail.com> wrote:
> 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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