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 <rmrmg.c...@gmail.com> wrote:
> On Thu, 8 Dec 2016 23:21:24 -0800
> James Johnson <totalboron...@gmail.com> 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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