Stereoisomers comparison giving false negative

[franciscohanna92]

Hi there!

I'm trying to do some stereoisomers comparison, but I think Kekule is giving me a false negative. The two stereoisomers that I'm comparing are:

The options for compare are:

{
  "method": 10,
  "doStandardize": false,
  "extraComparisonProperties": [
    "canonicalizationIndex"
  ],
  "lonePair": true,
  "hydrogen_display_type": "IMPLICIT",
  "stereo": true,
  "skeletalMode": true,
  "strictStereoBondGeometry": true,
  "atom": true,
  "compareAtom": true,
  "mass": true,
  "compareMass": true,
  "linkedConnectorCount": true,
  "compareLinkedConnectorCount": true,
  "charge": true,
  "compareCharge": true,
  "radical": true,
  "compareRadical": true,
  "compareStereo": true,
  "hydrogenCount": true,
  "compareHydrogenCount": true,
  "connectedObjCount": true,
  "compareConnectedObjCount": true,
  "bondType": true,
  "compareBondType": true,
  "bondOrder": true,
  "compareBondOrder": true
}

What am I doing wrong here? Is this something that Kekule supports out of the box?

[franciscohanna92]

I see that the comparison for the following works fine:

[partridgejiang]

Hi @franciscohanna92, the test with the latest dist of Kekule.js gives a positive result: Please try again with the latest files on GitHub, since in some old releases, there did exist a bug that causes wrong comparison result on molecules with explicit hydrogen atoms. By the way, when doing molecule comparison, it is recommended to set doStandardize option to true. Otherwise the molecules may not be canonicalized before comparison, thus a wrong result may be invoked too.

[franciscohanna92]

Hi @partridgejiang , thanks for your answer. Indeed, the latest version of Kekule works fine. Sadly, we have a heavily modified version of it, for which its maintainers no longer work on the project.

I see that the point of failure (for the example above) in our Kekule version is this line https://github.com/partridgejiang/Kekule.js/blob/fa64625d6486c0aa752dadd10fedaa15310ce275/src/core/kekule.structures.js#L1208

Any clues on why this may be failing? I'm setting doStandardize: true

[partridgejiang]

Hi @franciscohanna92, please check if /algorithm/kekule.structures.stereos.js has been modified in your version. If not, perhaps you could overwrite it with the file in this repository directly?