Errors regenerating table with custom standardization

Hi,





I'm getting the following errors when regenerating a structure table:





Error at molecule 273826


java.lang.IllegalArgumentException: cannot contract invisible group


at chemaxon.struc.sgroup.SuperatomSgroup.contract(SuperatomSgroup.java:4


25)


at chemaxon.marvin.modules.MolImport.readMol(MolImport.java:252)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:653)


at chemaxon.formats.MolImporter.read(MolImporter.java:557)


at chemaxon.formats.MolImporter.read(MolImporter.java:526)


at chemaxon.util.MolHandler.importMol(MolHandler.java:681)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:188)


at chemaxon.jchem.db.UpdateHandler.setMolecule(UpdateHandler.java:790)


at chemaxon.jchem.db.UpdateHandler.setValuesForFixColumns(UpdateHandler.


java:960)


at chemaxon.jchem.db.UpdateHandler.regenerateTable(UpdateHandler.java:22


15)


at chemaxon.jchem.gui.Regenerator.regenerateTables(Regenerator.java:128)





at chemaxon.jchem.gui.Regenerator.run(Regenerator.java:83)


at java.lang.Thread.run(Unknown Source)

It seems that your SDF file contains two sgroups, both consisting of the same atoms: 1 and 23. This may cause the problem but we investigate this further and will write again soon.

We have solved the molecule import problem in Marvin. However, the drawing of such nested sgroups is still not supported in MarvinSketch.





The correction will be available in the next major JChem / Marvin releases (JChem 3.2 / Marvin 4.1).

Nora wrote:

The correction will be available in the next major JChem / Marvin releases (JChem 3.2 / Marvin 4.1).

Actually we have added the correction to the bug fix branch as well, therefore it will be available in the next minor JChem / Marvin release. I will let you know when it is ready.