stereo changes after tautomer canonicalization

Input and output are attached.  I am getting a canonical tautomer. The input molecule has chiral flag. Stereo on some centers are changing .

Here is the code (.NET):

 

TautomerizationPlugin plugin = new TautomerizationPlugin();

plugin.setMaxStructureCount(1000);

 

plugin.setProtectAllTetrahedralStereoCenters(true);

plugin.setProtectAromaticity(true);

plugin.setProtectDoubleBondStereo(true);

plugin.setProtectEsterGroups(true);

plugin.setProtectLabeledTetrahedralStereoCenters(false);

plugin.setExcludeAntiAromaticCompounds(true);

plugin.setRationalTautomerGenerationMode(true);

plugin.setTakeCanonicalForm(true);

            chemaxon.struc.Molecule m = MolImporter.importMol(molfile);

            plugin.setMolecule(m);

            var ret = plugin.run();

            int count = plugin.getStructureCount();

            chemaxon.struc.Molecule mol = plugin.getStructure(0);

            return mol.toFormat("mol");

 

Hi,

 

The problem is that the "H" atoms are not arranged  around the chiral center.

Please insert the bolded code line into your code.

...

plugin.setTakeCanonicalForm(true);

plugin.setCleanResultStructures(true);//arrange the "H" atoms around a chiral center

...

Jozsi

Unfortunately adding that line of code doesn't help. I still get my case.

Hi,

 

I have attached two figures about  the canonical forms which were generated after inserting of the bold line.

Please let me see your result.

Jozsi

static TautomerizationPlugin plugin = new TautomerizationPlugin();
plugin.setProtectAllTetrahedralStereoCenters(true);
plugin.setProtectAromaticity(true);
plugin.setProtectDoubleBondStereo(true);
plugin.setProtectEsterGroups(true);
plugin.setProtectLabeledTetrahedralStereoCenters(true);
plugin.setExcludeAntiAromaticCompounds(true);
plugin.setMaxStructureCount(1000);
plugin.setRationalTautomerGenerationMode(true);
plugin.setTakeCanonicalForm(true);
plugin.setCleanResultStructures(true);

string plugin_errors=String.Empty;
chemaxon.struc.Molecule m = MolImporter.importMol(molfile);
plugin.setMolecule(m);
var ret = plugin.run();
int count = plugin.getStructureCount();
plugin_errors = plugin.getErrorMessage();
chemaxon.struc.Molecule mol = plugin.getStructure(0);
return mol.toFormat("mol");

Hi,

 

Which version of plugin do you use?

 

Jozsi

The one that comes with JChem_NET_API_5_11_628

Hi,

Thank you!

I was able to reproduce the bug. We fix it asap.

Jozsi

Guys,

I am not trying to be difficult here.. but I would appreciate any ETA on this.

Thanks.

Hi,

The fix will be released  in 2 weeks  in  the 5.12 version.  

Jozsi

On more case when stereo gets lost:

 

input:

InChI=1/C13H13NO2S/c1-16-11-5-7-12(8-6-11)17(15)13-4-2-3-10(14)9-13/h2-9H,14H2,1H3/t17-/s2

 

output:

InChI=1/C13H13NO2S/c1-16-11-5-7-12(8-6-11)17(15)13-4-2-3-10(14)9-13/h2-9H,14H2,1H3/t17?

 

PLease see that your patch will cover it as well.

Hi,

 

Thanks.  This sulfoxid bug and a couple of other bug in respect of the "R,S" stero info have been fixed.

I hope that all  fix will be available in the outcoming patch.

Jozsi

Folks,

 

When 5.12 is coming out? I was hoping you release it before the spring ACS meeting.

Ken

Hi,

Version 5.12 was released yesterday

Jozsi

Great!! Is there a way to subscribe to updates announcement?

Hi Kenneth,

Sure there are quite a few ways to subscribe to these kind of notifications. One is to subscribe to our newsletter. You can do it here: http://eepurl.com/hm9yE

If you want to get notification from our support forum, you should track the topics that interests you (there is a track button on the top left corner of the forum topic): Marvin is here, you'll find JChem here, JChem for Excel is here and Instant JChem will be over here.

I hope that answers your question. Have a nice day,

Janos