bond.GetStereo
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles("F/C=C/F")
>>> for bond in m.GetBonds():
... print bond.GetStereo()
...
STEREONONE
STEREOE
STEREONONE
However, setting bond stereo doesn't appear to be exposed.
I suppose you could permute the smiles strings \ => / but that seems to not
be the right solution.
Cheers,
Brian
On Fri, Dec 9, 2016 at 3:20 PM, James Johnson <[email protected]>
wrote:
> Thank you all for your responses. I got R/S combos to work (awesome!), but
> now I am working on E/Z. I am considering a similar approach (0 would be
> interpreted as E, 1 as Z).
>
> However to do this I would need two functions which I couldn't find
> 1.) Find double bonds that could be E/Z.
> 2.) Set the double bonds to have property E or Z
>
> I actually only need #2 (just make any double bond E/Z as see what
> happens), but #1 would make it more efficient.
>
> How does RDKit handle E/Z stereochem in mol?
>
> Thanks again for the help!
>
> - James
>
> On Fri, Dec 9, 2016 at 8:23 AM, Rafal Roszak <[email protected]> wrote:
>
>> On Thu, 8 Dec 2016 23:21:24 -0800
>> James Johnson <[email protected]> wrote:
>>
>> > Hello all, I am trying to generate R and S from: CCC(C)(Cl)Br
>> >
>> > Below is the code for making the smi to mol file. Can someone give me
>> some
>> > guidance to generate all sterochem possibilities?
>>
>> There are two ways to address this problem:
>> 1. generate all possible SMILESs and for each of them generate 3D
>> structure using molecular modeling (or just embedMolecule) which is in
>> my opinion better
>>
>> 2. generate many 3D structures and extract interesting stereoisomers
>>
>> Links below describe the 1st option:
>> https://github.com/rdkit/rdkit/issues/626
>> https://sourceforge.net/p/rdkit/mailman/message/34488969/
>>
>>
>> Regards,
>> RR
>>
>
>
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