Getting Exception in Structure Checker command line

Dear Chemaxon Team,

We are getting the below exception when we try the below Jchem Structure Checker command line to check and fix the error in the sd file, where the check and fix options are defined in the xml config file.

Command line:

structurechecker -c checker_configuration.xml -m fix -f sdf -t separated -o out.sdf -l outlog.sdf -rf outreport.sdf input.sdf

Exception:

 

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.core.calculations.Parity.getParity(Parity.java:629)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:3505)

at chemaxon.fixers.WedgeCleanFixer.fix(WedgeCleanFixer.java:38)

at chemaxon.checkers.runner.AdvancedCheckerRunner.fix(AdvancedCheckerRunner.java:71)

at chemaxon.checkers.runner.AdvancedCheckerRunner.fix(AdvancedCheckerRunner.java:110)

at chemaxon.checkers.StructureCheck.processInput(StructureCheck.java:480)

at chemaxon.checkers.StructureCheck.run(StructureCheck.java:375)

at chemaxon.checkers.StructureCheck.main(StructureCheck.java:291)

 

Details:

Version: structure checker 5.10.0

 

Please look into this issue, and reply us the solution ASAP.

 

Thanks & Regards,

D. Senthil kumar vijai.

 

Dear Senthil,

We cannot reproduce the error without your input molecule.

Could you send us an example input file or an example molecule (or an altered one if it is confidental) that caused the exception?

Best regards,

Viktoria