Superatom groups in Reactor 3.2

I'm having problems with superatom groups in Reactor 3.2:





- compressTest.mrv (groups without mapping) returns a product (CC), but I'm not sure if that's what it should return


- compressTest3.mrv (groups with mapping) returns a Java exception in ReactionPerformer.





We have some reactions in the second form that used to work in Reactor 3.1.7.


Am I creating the reactions incorrectly?

Yes, mapping is the key issue in this case. The superatom of a cotracted abbreviated group can be mapped now in Reactor. Look at the attached remapped reaction.





SDF output provides a contracted abbreviated group on the product side:

Code:

react -r compressTest_remapped.mrv "CC" -f sdf

SMILES does not support abbreviated groups, so the resulting output is ungrouped:

Code:

$ react -r compressTest_remapped.mrv "CC" CC[CH2:3][OH:4]

I think, that your second reaction file should work, the exception seems a bug. We will investigate it.

The problem has been corrected and the corrected tool will be released within a week in version 5.0.2.