Can somebody confirm if cis/trans isomer specification even works?
Example of cis/trans isomerism: https://files.mtstatic.com/site_4334/109916/0?Expires=1526354368&Signature=ZJcI4FAY1k30bf0ZO03ourORoCefbMAfw48Mbzf1NNBU-6pFRs0BvaSYBKL6N5NfGVxgXp9Rb9re6Lz88hnhoPEmE6IOQ7RFuXChEqJ3kq1A02PQOwDkTqHCKZLVns8y7K0j~-yiCYUTCOqyNCCb9vOdO6v7YOqnqdtR8rNNvK0_&Key-Pair-Id=APKAJ5Y6AV4GI7A555NA
I'm getting an "Access Denied" error for your link (so I can't speak to details there), but you should be able to control cis/trans status around double bonds.
If you convert a single bond to a double bond, the substituents of the two atoms making the the double bond should stay more-or-less in the same 3D place as where they started. (Except for the rearrangements necessary to go to the planar conformation around the double bond.) If you already have the double bond, you should be able to build groups on either the cis or trans positions, and expect them to stay on the side you specified. Also, when shaking and wiggling, it should keep the cis/trans status. (Though if you have really bad scores for one, there is a chance that wiggle might flip to the better scoring one.)
If there's a particular situation where the cis/trans status of a double bond isn't being maintained, or if you attempt to build in one conformation but you end up with the other, please let me know under what conditions it's happening, and I can take a closer look.
Disregarud this whole thread - I had made a mistake and thought it was a bug
Sorry