indol tautomer canonicalization

The 3 attached mol files are 3 flavors of indol derivatives that I want to callapse into same canonical tautomer.

While 1 and 3 return same canonical tautomer with "either" bond on imine, the 2nd one doesn't get altered by canonicalizaiton at all.

How do I achive that all 3 inputs return same canonical tautomer? I would think that using false for double bond stereo should do the job.

Here are my settings:

 

plugin = new TautomerizationPlugin();

            plugin.setProtectAllTetrahedralStereoCenters(true);

            plugin.setProtectAromaticity(true);

            plugin.setProtectDoubleBondStereo(false);

            plugin.setProtectEsterGroups(true);

            plugin.setProtectLabeledTetrahedralStereoCenters(true);

            plugin.setExcludeAntiAromaticCompounds(false);

            plugin.setRationalTautomerGenerationMode(false);

            plugin.setTakeCanonicalForm(true);

            plugin.setMaxStructureCount(1000);

            plugin.setTakeCanonicalForm(true);

            plugin.setCleanResultStructures(true);

 

Thanks,

Ken.

Hi,

The 2nd molecule can not be  tautomerized because the "protect aromatic ring" option is on. This is why the external double bond stereo info also will be unchanged.  The tautomerization regions  are not aromatics in the 1st and the 3rd molecules ,therefore, they can tautomerize.

So it is enough to reset the "plugin.setProtectAromaticity(false)"; I attached  an example code.

I don't have experimental test , but may be better if you accept the rational canonical tautomers,  which provides two output forms for the 3 input structures.

Jozsi