RunTimeException

Hi,





Can you help me clarify what the trace below means, what could be causing it, and what I might do to cure it?





-- Bob

Code:

java.lang.RuntimeException: Molecule@e00180[3a,2b] is not a parent of child S-group: SuperatomSgroup@82a1ee[Ph,C].parentMolecule=Molecule@551398[7a,5b]         at chemaxon.struc.Molecule.clonecopySgroups(Molecule.java:975)         at chemaxon.struc.Molecule.clonecopy(Molecule.java:871)         at chemaxon.struc.Molecule.cloneMolecule(Molecule.java:1034)         at chemaxon.struc.Molecule.clone(Molecule.java:1043)         at chemaxon.marvin.modules.CmlExport.appendMolecule0(CmlExport.java:203)         at chemaxon.marvin.modules.CmlExport.appendMolecule(CmlExport.java:138)         at chemaxon.marvin.modules.MrvExport.appendChemicalStruct(MrvExport.java:240)         at chemaxon.marvin.modules.MrvExport.convert(MrvExport.java:60)         at chemaxon.struc.Molecule.exportToObject(Molecule.java:1302)         at chemaxon.struc.Molecule.exportToObject(Molecule.java:1267)         at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1116)         at chemaxon.struc.Molecule.toFormat(Molecule.java:1094)         at com.prenhall.epoch.mechanisms.MechSet.fragInList(MechSet.java:111)         at com.prenhall.epoch.mechanisms.MechSet.subsetIndex(MechSet.java:267)         at com.prenhall.epoch.mechanisms.MechSet.subsetIndex(MechSet.java:234)         at com.prenhall.epoch.mechanisms.MechSet.subset(MechSet.java:288)         at com.prenhall.epoch.mechanisms.Mechanism.validFlowContents(Mechanism.java:180)         at com.prenhall.epoch.answer.impl.MechArrow.isResponseMatching(MechArrow.java:80)         at com.prenhall.epoch.answer.Evaluator.matchResponse(Evaluator.java:394)         at com.prenhall.epoch.problem.Problem.evaluateResponse(Problem.java:922)

Probably, you have got a corrupted molecule. S-groups could not be copied into the new molecule. How did you create this molecule?

It was very odd. The error occurred when I tried to process a molecule *twice* in the same way at two different times. I think the processing involved the command setGUIcontracted() or some other Sgroup-related function. I solved the problem by doing the ungrouping just once when the molecules were created, and not doing it thereafter.





I'm not sure where the corruption set in, but everything behaved fine the first time I did the processing; it was only the second time that the molecule was processed in the same way that the error occurred.

Dear Bob,





Which version are you using?





First of all I need to reproduce the bug, so please send us more details: the molecule and the process you applied on the molecule.





Erika

I wish I could send you more details, but I can't. As I said, I managed to avoid the bug by ensuring that shortcut groups were ungrouped only once. The bug was reproducible, but I could not isolate it, except that it had to do with ungrouping shortcut groups (which I got from the error message). The processing we do on the molecules is too complex for me to send you a simple example.





I guess you'll just have to leave this bug unresolved until someone else encounters it.