Hi Tyler,

That's a perfectly reasonable request and it is something that you should
be able to do with the RDKit reaction handling code, but unfortunately it
is not currently possible.

This type of problem tends to not have a quick fix, but I will take a look
and see.

-greg




On Sat, Aug 12, 2017 at 1:22 AM, Tyler Backman <tback...@lbl.gov> wrote:

> I am trying to write a series of dehydratase reactions with RDKit that
> create specific double bond stereochemistry, but I have found that if
> I install one double bond, it often reverses the stereochemistry on
> other bonds, if they are present.
>
> For example, I create the following molecule which currently has a cis
> double bond:
>
> ### BEGIN EXAMPLE CODE BLOCK ###
> import rdkit
> chain = rdkit.Chem.MolFromSmiles('O=C([S])C[C@@H](O)/C=[C]\C')
> ### END EXAMPLE CODE BLOCK ###
>
> Then I perform the following reaction:
>
> ### BEGIN EXAMPLE CODE BLOCK ###
> rxn = rdkit.Chem.AllChem.ReactionFromSmarts(('[C:1][C:
> 2]([O:3])[C:4][C:6](=[O:7])[S:8]>>'
>                                   '[C:1]/[C:2]=[C:4]\[C:6](=[O:
> 7])[S:8].[O:3]'))
> prod = rxn.RunReactants((chain,))[0][0]
> print(rdkit.Chem.MolToSmiles(prod, isomericSmiles=True))
> ### BEGIN EXAMPLE CODE BLOCK ###
>
> This outputs the following molecule, which has the new cis double
> bond, but the previous one has now reverted to trans:
>
> C/[C]=C/C=C\C(=O)[S]
>
> Any ideas? I would like to create a new cis double bond without
> modifying the stereochemistry of any pre-existing double bonds in the
> structure.
>
> I am using RDKit Release_2017_03_3 on Python 3.4.2 under Debian 8.
>
> Sincerely,
>
> Tyler W. H. Backman
> Postdoctoral Fellow
> Lawrence Berkeley National Laboratory
> Joint BioEnergy Institute
> Agile BioFoundry
>
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