The structures having "single/double bonds with undefined/unknown stereo" gave us some headaches because the generated INCHIKEYs using cdk 1.4.16 (Relative stereo) were different from the INCHIKEYs generated with inchi-1(same Relative Stereo). The undefined/unknown bonds were considered as plain single/double bonds, practically the stereo was ignored.
So we dug into cdk and we found that in InChIGenerator.generateInchiFromCDKAtomContainer the stereo was ignored for next cases:
- single bond and stereo = 4
- double bond and stereo = 3.
We're not chemists, just software developer, so we hope this change is the good one and that it might help others to skip the headache part. Let us know your opinion.