calculating tautomers for one of the attached molecules, the stereo information of the atoms is lost although I choose the option "protect tetrahedral stereo centers". But if I perform a 2D clean before the tautomerization, the stereo information is kept.
Is this behavior intended?
This is not the intended behaviour. The "R/S" labels sholud be shown on the generated tautomer(s).
I tried your 3D structures and I was able to create a correct tautomer structure with the 5.3.0 alpha1 version, see on the attachment , however, I was also able to reproduce the problem you complained. The "R/S" labels were not shown on the stereospecific atoms in certain cases.
We investigate this problem and fix it asap.
Explicit hydrogens are not shown on the the generated structures on your figures. Were they deleted intentionally by you?
I did not delete the explicit hydrogens by intention. They seem to be lost during the tautomer generation.
It seems to us, that some molecule information is lost during the tautomer calculation. If we chain multiple calculations (tautomers --> stereoisomers --> most stable tautomer) this sometimes leads to inconsistent results.
Our current workaround is to start each calculation with an molecule import using the SMILES of the result of the last calculation (and not handing over the molecule object).