Incorrect parsing of CML files

Hi, I have a CML file containing 4 stereocenters. It seems that JChem (5.2.1_1, OS X, JDK 1.6) is parsing the CML incorrectly such that it gets the stereochemistry wrong. The CML file is attached. When I paste the CML into MarvinSketch the stereo centers get labeled R,R,S,S. However the actual order should be R,R, S, R. I have check the CML file using Openbabel, by converting it to a SMILES and then pasting that into MarvinSketch and the result has the correct stereochemistry.

Is this a bug? Or is there some specific settings that must be used to take into account absolute stereocenters?

 

Thanks

Hi,

first of all, sorry for the very late answer.

After testing the file and confirm the stereo configuration data in the attached cml, i can say that this seems to be a bug in our import unfortunatelly. We will fix this in one of the next patch releases of Marvin. In the mean time, i can suggest to use the iupac name of the molecule, that is in the cml file also, and Marvin imports it correctly as i discovered.

We will notify you in this topic when the fix is ready.

Regards
Istvan