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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