tautomer canonicalization: either SP3 stereo flag is removed

Hi,

I am reporting a case where chial flag is set in molfile to "chiral" and additionally one atom has stereo parity value of "3" (either or unmarked" ). After canonicalization chiral flag remains but the parity is gone. Input and output molfiles are attached.

It is importnat to retaint parity flag as non standard InChI with "SUU SLUUD" parameters pays attentioin to it and alters InChI depending on that flag.

 

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);

 

Ken

Hi,

Chiral flag has no meaning if the absolute stereo configuration (R or S) is not known for all chiral centers in the molecule. So in this case your input molecule should not have chiral flag. You can use Structure Checker to check chiral flag errors in your input molecule. Structure Checker is integrated into MarvinSketch.

Zsolt