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 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss