Hi I did a quick test on doublebond enumeration using dichoroethylene input as 'ClC=CCl'. What is odd is the command line interface gives the Eand z isomers just fine:
Contents of MolContainers
MolContainer #0 (untitled_line_1)
Mol #0: Cl/C=C/Cl
Mol #1: Cl/C=C\Cl
Saving molecules associated with…
ClC=CCl
but the output gypsum_dl_success.sdf file upon converting to a smiles file containing two cis isomers only:
EMPTY MOLECULE DESCRIBING GYPSUM-DL PARAMETERS
C(=C\Cl)\Cl untitled_line_1
C(=C\Cl)\Cl untitled_line_1