Here either bonds that were present in input molfile are gone and output bond stereo dosn't have either flag. Input is attached.
My plugin settings:
plugin = new TautomerizationPlugin();
The problem is with the input. The file that you sent to us has the bond type information: 2 4, which means that it is a double bond, with 4 as stereo chemistry informations. The problem is that in the specification of this format, double bonds can not has 4 as stereochemistry (only single bonds), the same settings (cis or trans, or it is also called either) is 3 for double bonds. You can try the attached molecule to see it.
Please let me know: was this file generated entirely (from the drowing to an empty canvas) with our product, or it was originaly imported from some other chemical drawing tool? If it was made only by our product, than do you remember the workflow, that generated it?
Sorry, my bad. The input is not correct.