Stereoisomer Plugin and Enhanced Stereochemistry

Hi -





I may be misunderstanding exactly how the Enhanced Stereochemistry should function but I believe there is a bug in the Stereoisomer calculator when handling molecules with Enhnaced Stereochemistry defined.





When I define any Enhanced Stereochemistry on a molecule, the Stereoisomer Calculator does not function.  The calculator opens but clicking on the OK button has no effect.





I tried to search for this problem but didn't come across anything.





Examples:





1.  Image:  abs.png





If the plugin recognizes Enhanced Stereochemistry, then I can understand that the Stereoisomer Plugin does not generate anything because the ONLY possible comformation is absolutely defined.





If the plugin does not recognize Enhanced Stereochemistry, then I would expect it to function normally and output all possible isomers.





2.  Image:  or.png





In this example, if the plugin recognizes Enhanced Stereochemistry, I would expect the ABSOLUTE center to stay fixed and the two possible configurations of the OR bond to be generated.





If the plugin does not recognize Enhanced Stereochemistry, then I would


expect it to function normally and output all possible isomers.





3.  Image:  mix.png





I believe this should be exactly like the OR example.





Note:  When setting the ABSOLUTE CHIRALITY flag on a structure (which defines the structure as the absolute stereoisomer) with no enhanced stereochemistry then the plugin works fine.  It is only the Enhanced Stereochemistry that seems to cause a problem.








Thanks for any help or clarification.





David

Hi,





Stereoisomer plugin in Marvin 5.1.4 (or lower) does not handle enhanced stereo information at all. Please remove enhanced stereo flags from your molecules before the calculation (for batch removing you can use Standardizer). 





From Marvin 5.1.5 enhanced stereo information will be cleared by the Stereoiomer plugin before generating the stereoisomers.





In a future version Stereoisomer plugin will handle enhanced stereo data, and will enumerate all possible stereoisomers.





Zsolt

Thanks.  The functionality from 5.1.5 on will be fine for my needs.














David