User 55ffa2f197
03-03-2010 17:08:00
Set absolute stereo suppose to add the mrvStereoGroup tags to the strucutures that are already drawn properly with chiral centers and associated bonds. However when we run throuch such molecules through the standardizer it superficially added the absStereo="true" for the molecule but really did not add the stereo tags to the chiral atoms at all. When we drawn such molecule in Marvin sketch and select the absolute stereo options for the chiral atoms the abs were correctly put next to the atoms correctly, and associated mrvStereoGroup tags.
Following are the atom lables I copied from MRV formatted records concerning these instances
Here is what standardizer produced concerned with the stereo atoms a4, and a8
<molecule title="abc" molID="m1" absStereo="true">
...<atom id="a4" elementType="C"
x2="-2.894266666666667" y2="1.2708266666666668" />
Here is what was gerenated from Marvin sketch, which is the right one, and what we would expect
<molecule title="Oxa_Core_Set01.cdx" molID="m1" absStereo="true">
<atom id="a8" elementType="C" mrvStereoGroup="abs"
x2="-3.410026666666667" y2="-2.1509600000000004" />
We are in urgent need to fix the problem. A code snnipet from the developers is really appreicated. Of course I hope you can reproduce what we saw.