JChemManager import error 5.12.1

Looks like all importing fails when using jcman if you have IUPAC name generation ("name") configured for a chemical terms table.  See error below.

Error while evaluating expression:
name
    chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: Name generation interrupted: java.lang.InterruptedExcep
tion, expression: name
Caused by:
Error while evaluating expression:
name
    chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: Name generation interrupted: java.lang.InterruptedExcep
tion
        at chemaxon.jchem.base.search.StructureRecordMakerImpl.calcChemTermColValues(StructureRecordMakerImpl.java:827)
        at chemaxon.jchem.base.search.StructureRecordMakerImpl.init(StructureRecordMakerImpl.java:594)
        at chemaxon.jchem.base.search.StructureRecordMakerImpl.initRecord(StructureRecordMakerImpl.java:433)
        ... 20 more
Caused by: chemaxon.nfunk.jep.ParseException: Error while evaluating expression:
name
    chemaxon.marvin.io.formats.name.nameexport.IUPACNamer$Error: Name generation interrupted: java.lang.InterruptedExcep
tion
        at chemaxon.nfunk.jep.JEP.getValueAsObject(JEP.java:502)
        at chemaxon.jep.ChemJEP.evaluate(ChemJEP.java:149)
        at chemaxon.jchem.base.search.StructureRecordMakerImpl.calcChemTermColValues(StructureRecordMakerImpl.java:804)
        ... 22 more

Hi Matthew,

Thank you for the observation, we start to investigate this issue. Have you copied the whole stacktrace or only a part of it? Could you send us example structure(s) taking part in failing import?

Best regards,

Krisztina

 

 

Upon further investigation we found that any error in chemical terms halts the importing process.  We reverted back to 5.11.3, we see the same errors (failures in chemical terms) but the importing continues, which is the desired effect. 

It would be helpful if you send us a few molecules concerned to track down the cause of the failing import. If you feel the structures confidential to paste in a public forum you can contact me or jcb-support at chemaxon.com in email.

Thanks,

Krisztina

You can use any structure that fails any chemical terms calculation which halts importing:

Name failure structures:

c1ccc2c(c1)c3c([nH]2)nc4nnc(n4n3)SCC(=O)Nc5nc6ccccc6s5

CCn1c(n[nH]c1=O)C2CCN(CC2)C(=O)C3=C([C@@H](C(=N3)C)C(=O)OCC)C

C/(=N/C(=O)Nc1ccc(cc1)Cl)/c2ccc(cc2)OC(=O)c3ccc(cc3)Cl

logd("7.4") failure structures:

CCn1c(n[nH]c1=O)C2CCN(CC2)C(=O)C3=C([C@H](C(=N3)C)C(=O)OCC)C

CCn1c(n[nH]c1=O)C2CCN(CC2)C(=O)C3=C([C@@H](C(=N3)C)C(=O)OCC)C

Hi Matthew,

Thank you for the examples. We found that both versions (5.11.3 and 5.12.1) operate the same way.

If 'Halt if an error occurs' is checked on the Import dialog of JChem Manager, then the import process is halts at the first molecule with non-calculable chemical term data and the same error message is displayed as what you have posted.

If 'Halt if an error occurs' is unchecked,  then the import process imports all the molecules and the chemical term field of molecules with non-calculable chemical term data remains empty.

Please let us know if the problem persists.

Krisztina