problems regenerating structure tables for jchem-2006-08-17

When I try to regenerate the tables via

Code:

jcman -u

I get several errors of this form:

Code:

Error at molecule 3267 java.lang.RuntimeException: MultiFaceAtom does not have any visible face         at chemaxon.struc.graphics.MAtomSetPoint$MultiFaceAtom.getVisible(MAtomSetPoint.java:65)         at chemaxon.struc.graphics.MAtomSetPoint.finishCloning(MAtomSetPoint.java:445)         at chemaxon.struc.graphics.MPolyline.finishCloning(MPolyline.java:1237)         at chemaxon.struc.MDocument.<init>(MDocument.java:253)         at chemaxon.struc.MDocument.<init>(MDocument.java:191)         at chemaxon.struc.MDocument.cloneDocument(MDocument.java:399)         at chemaxon.struc.MDocument.cloneMainMoleculeGraph(MDocument.java:419)         at chemaxon.marvin.util.MolExportModule.preconvert(MolExportModule.java:530)         at chemaxon.marvin.modules.CxsmilesExport.preconvert(CxsmilesExport.java:202)         at chemaxon.marvin.modules.SmilesExport.toSMILES(SmilesExport.java:591)         at chemaxon.marvin.modules.CxsmilesExport.convert(CxsmilesExport.java:278)         at chemaxon.struc.Molecule.exportToObject(Molecule.java:1105)         at chemaxon.struc.Molecule.exportToObject(Molecule.java:1070)         at chemaxon.struc.Molecule.exportToFormat(Molecule.java:919)         at chemaxon.struc.Molecule.toFormat(Molecule.java:897)         at chemaxon.util.MolHandler.toFormat(MolHandler.java:402)         at chemaxon.jchem.db.UpdateHandler.getSmiles(UpdateHandler.java:774)         at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:859)         at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1758)         at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1737)         at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:75)

Is it safe to ignore these? Eventually jcman finishes with a "done" message on each table.

Hi,





- During regeneration we do not stop at problematic rows, we only print the stack trace. This ensures that one can finish regeneration even if there are unexpected problems with some structures.





- The calculated columns (e.g. fingerprints, smiles) will not be updated for such problematic structures, which means they may not match correctly during structure search with the new version.





- "Error at molecule 3267" : this means the value of the "cd_id" column for problematic structure is the displayed number. Using this you can easily locate /view /export the structure if needed for analysis (my colleagues will probably ask you for this).





(Actually in future versions I'll make this error message state more explicitly that it refers to the cd_id value.)





We will get back to you soon to further clarify the situation.





Best regards,





Szilard

Hi,





The same problem was also reported in an other thread, please see my answer there:





http://www.chemaxon.com/forum/viewpost7643.html#7643





Best regards,





Szilard