Errors upgrading from 3.1.5 to 3.2.1 - ChemAxon Forum Archive

User 818520b6b8

27-11-2006 14:20:18

Hi,

I'm getting the following errors when regenerating tables with JCMan to upgrade from 3.1.5 to 3.2.1:

java.lang.NumberFormatException: For input string: "2341298123034284"

at java.lang.NumberFormatException.forInputString(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

at chemaxon.jchem.db.DatabaseProperties.getIntProperty(DatabaseProperties.java:282)

at chemaxon.jchem.db.DatabaseOptions.getRegistrationCode(DatabaseOptions.java:461)

at chemaxon.jchem.db.DatabaseOptions.getFromDatabase(DatabaseOptions.java:223)

at chemaxon.jchem.db.UpdateHandler.initFields(UpdateHandler.java:514)

at chemaxon.jchem.db.UpdateHandler.<init>(UpdateHandler.java:448)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:66)

java.io.IOException: Unknown amino acid

at chemaxon.marvin.modules.PeptideReader.findAminoAcids(PeptideReader.java:278)

at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:115)

at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:71)

at chemaxon.formats.MolImporter.readMol(MolImporter.java:763)

at chemaxon.formats.MolImporter.read(MolImporter.java:595)

at chemaxon.formats.MolImporter.read(MolImporter.java:561)

at chemaxon.util.MolHandler.importMol(MolHandler.java:683)

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

at chemaxon.util.MolHandler.<init>(MolHandler.java:122)

at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:993)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:866)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 234379

java.lang.ArrayIndexOutOfBoundsException: 60

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1658)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 270817

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 272741

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 275574

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 277652

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 284148

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 284149

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 284150

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 284280

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 290584

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 296006

java.lang.ArrayIndexOutOfBoundsException: 122

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1658)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 296007

java.lang.ArrayIndexOutOfBoundsException: 166

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1658)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 302285

java.lang.ArrayIndexOutOfBoundsException: -1

at chemaxon.struc.CGraph.getEdge(CGraph.java:343)

at chemaxon.struc.MoleculeGraph.getBond(MoleculeGraph.java:1207)

at chemaxon.marvin.modules.Parity.copyInfoToOriginal(Parity.java:1958)

at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:576)

at chemaxon.marvin.modules.Parity.setParity(Parity.java:454)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:170)

at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1882)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1125)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1664)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 303903

java.lang.ArrayIndexOutOfBoundsException: 24

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1658)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 304791

java.lang.ArrayIndexOutOfBoundsException: 7

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1658)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1745)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

*************************************************************

The first 2 errors do not correspond to any particular structure.

For the folowing 14 errors I'm uploading the corresponding SDFile.

Thanks.

User 818520b6b8

28-11-2006 07:37:34

I'm getting one of the errors listed above when performing a search on the upgraded tables.

This search is performed with a custom application based on JChem 3.2.1:

java.lang.NumberFormatException: For input string: "23462623456346"

at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)

at java.lang.Integer.parseInt(Integer.java)

at java.lang.Integer.parseInt(Integer.java:518)

at chemaxon.jchem.db.DatabaseProperties.getIntProperty(DatabaseProperties.java:282)

at chemaxon.jchem.db.DatabaseOptions.getRegistrationCode(DatabaseOptions.java:461)

at chemaxon.jchem.db.JChemSearch.checkLicense(JChemSearch.java:4463)

at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2334)

at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2233)

at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2105)

at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2125)

at jchem.SearchStructure.getViewerResults(SearchStructure.java:650)

at jchem.SearchStructure.searchButton_actionPerformed(SearchStructure.java:517)

at jchem.SearchStructure.access$6000371(SearchStructure.java:64)

at jchem.SearchStructure$4.actionPerformed(SearchStructure.java:196)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1786)

at javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1839)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)

at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:245)

at java.awt.Component.processMouseEvent(Component.java:5100)

at java.awt.Component.processEvent(Component.java:4897)

at java.awt.Container.processEvent(Container.java:1569)

at java.awt.Component.dispatchEventImpl(Component.java:3615)

at java.awt.Container.dispatchEventImpl(Container.java:1627)

at java.awt.Component.dispatchEvent(Component.java)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3198)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3128)

at java.awt.Container.dispatchEventImpl(Container.java:1613)

at java.awt.Window.dispatchEventImpl(Window.java)

at java.awt.Component.dispatchEvent(Component.java)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:458)

at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)

ChemAxon 9c0afc9aaf

28-11-2006 09:01:46

Hi,

Quote:

java.lang.NumberFormatException: For input string: "2341298123034284"

at java.lang.NumberFormatException.forInputString(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

at java.lang.Integer.parseInt(Unknown Source)

This is because you have specified a registration code which is too large for an integer (which we use at the moment).

You second post is the same error.

(the actual number in your the post has been altered)

We will print a better error message ("Invalid registration code") in the future.

Until then please enter the correct registration key in the options dialog of JChemManager (jcman).

Quote:

java.io.IOException: Unknown amino acid

This is also related to a specific structure, but the error reporting should be improved for this part.

The error reporting will be fixed in the next JChem version, so it will print the cd_id for this structure too, and then you can send it for analysis.

Thank you for collecting the remaining structures in an SDfile.

We will investigate them soon, and let you know what we have found.

The current effect of these errors is the following on your system:

Calculated values (e.g. fingerprints) for the affected structures are not updated in this case, so they are not guaranteed to be found during structure search.

I hope we can fix the problems very soon.

Best regards,

Szilard

User 818520b6b8

28-11-2006 09:50:46

The problem with the licenses was that, for some reason, when connecting to a 3.1.5 database with JCman this keys are removed. They were null, so just entering them again solved the problem.

I have a question regarding standardization. When upgrading from 3.1.5 to 3.2.1 the standardization configuration is removed from JCHEMPROPERTIES table, so I have to regenerate the table again with the custom configuration file. Is it better to recreate the table fro scratch and the standardize it, or leave it, upgrade it, and then regenerate with the custom configuration file?

Thanks.

ChemAxon 9c0afc9aaf

28-11-2006 10:37:09

Hi,

Quote:

The problem with the licenses was that, for some reason, when connecting to a 3.1.5 database with JCman this keys are removed. They were null, so just entering them again solved the problem.

Actually the registration key did not disappear, but was changed - at least according to the error log you sent.

(But maybe you have already tried to re-type it at the time of the error, but you just did not exactly copy it the first time.)

Quote:

I have a question regarding standardization. When upgrading from 3.1.5 to 3.2.1 the standardization configuration is removed from JCHEMPROPERTIES table,

The disappearance of settings is wierd, nobody reported anything like this so far.

Haven't you made backup copies of the property table or manipulated it in any other way ?

If not, could you send a detailed description of the system, so I can try to reproduce the situation ?

(OS, RDBMS, JDBC driver version, Java version)

Also how did you upgrade ?

Quote:

Is it better to recreate the table fro scratch and the standardize it, or leave it, upgrade it, and then regenerate with the custom configuration file?

You do not need to create the table again.

I recommend changing the standardization in the "Regenerate" menu of jcman (this will also regenerate the table).

Best regards,

Szilard

User 818520b6b8

28-11-2006 11:03:38

The upgrade process was as follows:

- Connect to database with new JChem release 3.2.1.

- Answer 'YES' to the question regarding structures tables versions.

The first error was the one related to license key.

Solaris 9

Oracle RDBMS 9.2.0.5

JDBC 10.2.0.1

Java 1.4.2_05

ChemAxon 9c0afc9aaf

05-12-2006 09:49:04

Hi,

The exception ArrayIndexOutOfBoundsException concerning the reported structures have fixed, and the fix will be present in the next release of Marvin and JChem.

I'll let you know if I find out something about the upgrade problem.

Best regards,

Szilard

User 818520b6b8

12-12-2006 08:06:00

What is this next release number? 3.2.2 or 3.2.3 ?

Thanks.

ChemAxon 9c0afc9aaf

12-12-2006 09:02:55

3.2.2., which was released on December 8.

http://www.chemaxon.com/jchem/changes.html

Best regards,

Szilard

User 818520b6b8

12-12-2006 14:32:26

I got the following errors upgrading our "standardized" table from 3.1.5 to 3.2.2

Error at molecule with cd_id: 219366

java.util.NoSuchElementException

at java.util.StringTokenizer.nextToken(Unknown Source)

at chemaxon.formats.MFileFormatUtil.canBe3LetterPeptide(MFileFormatUtil.java:554)

at chemaxon.formats.MolInputStream.init(MolInputStream.java:374)

at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:102)

at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:44)

at chemaxon.util.MolHandler.importMol(MolHandler.java:680)

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

at chemaxon.util.MolHandler.<init>(MolHandler.java:122)

at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:993)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:866)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 234379

java.lang.ArrayIndexOutOfBoundsException: 60

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1682)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1770)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 296006

java.lang.ArrayIndexOutOfBoundsException: 122

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1682)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1770)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

Error at molecule with cd_id: 296007

java.lang.ArrayIndexOutOfBoundsException: 166

at chemaxon.marvin.modules.Parity.getParity(Parity.java:288)

at chemaxon.marvin.modules.Parity.modfunc(Parity.java:137)

at chemaxon.struc.MoleculeGraph.getParity(MoleculeGraph.java:1738)

at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:281)

at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:63)

at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:694)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:668)

at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:648)

at chemaxon.reaction.Standardizer.performImplH(Standardizer.java:1087)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1682)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1770)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:886)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)

ChemAxon 9c0afc9aaf

13-12-2006 11:33:04

Hi,

We could already reproduce the ArrayIndexOutOfBoundsException, and my colleagues are investigating the problem.

However the attached SDF only contains 3 structures.

I see some ID numbers belonging to the structures, but I'm not sure they exactly correspond to the stack trace.

Could you export the 4 structures in MRV format with the cd_id included ?

(jcman is the best suited tool for this)

I'm particularly interested in the first structure (that comes with a different exception).

If it's not a problem for you could you check and send us the source stored in the cd_structure field please ?

It's easiest to view it in DB a GUI (e.g. Toad), but in the worst case you can also use sqlplus (if using Oracle):

Code:

select UTL_RAW.CAST_TO_VARCHAR2(cd_structure) from <table_name> where cd_id=219366;

Szilard

User 818520b6b8

13-12-2006 11:45:45

-ISIS- 04010500282D

253257 0 0 0 0 0 0 0 0999 V2000

XIvVc7pV60

r4xVc6qV60

2gtVc6qV60

XIvVx6nV60

r4xVM8sV60

UdyVzApV60

2gtVM8sV60

NyrVc7pV60

KatVD6mV60

XIvV+4tV60

K7+Vc6qV60

OurVbBnV60

K7+VYsrV80

xaLWr6pV70

KHNWk5qV62

KHNWOhsV60

AvOWr6pV60

AvOWidtV60

jKOWYpmV80

KVQWGhsV60

qtOWVUvV60

67SWUdtV60

bUQW0RwV60

67SWpUvV60

RoTW6TwVH0

HwyV8BjV70

qPxVp0kV66

kyvV8BjV60

qPxVRolV60

kyvVAQhV80

HwyVIjmV60

4a5WmCjV70

S54WE8iV64

2Z2WhBjV60

z44WIGgV66

2Z2WJ3lV80

yT2WpKfV60

Ai5W-JfV60

YLLWfgaV70

GtJWgbZV64

YKIWdeaV60

OtJWkjXV60

xJIWEWcV80

fGIWOoWV80

fLTWBhaV70

ztRWObZV64

1KQWVdaV60

7vRWTjXV64

PIQW6VcV80

TWTWCpWV60

FIQWEnWV60

EZTWkxUV60

ghwViAfV70

2AyVwEgV64

hizVTCfV60

5AyVr6iV60

7jzVsKdV80

wmzVi2jV80

RCHWm6pV70

znIWrGqV64

QSKWB9pV60

0oIWuHsV60

sSKWS8nV80

P2HWgfaV70

TdFWWcZV62

jdFWUoXV60

v7EWPdaV60

J4EWzuWV60

yTCWTkZV70

A7EW6RcV80

a4EWk5VV60

9XCWUFUV70

6zAWPHTV60

MzAWAURV70

oO9W7BUV70

TQPWT5pV70

ruQWh9qV64

URSWE7pV60

uuQWc1sV62

wRSWdFnV80

qGPWYzsV60

jVSWTzsV80

Bc2Wq8pV70

jB4Wl+nV64

Wr5WP6pV60

mB4WizlV60

yr5W87rV80

lv5WxzkV60

ov5WL+iV60

Qe7Wq1iV70

iN9WWzgV60

lN9WvzeV70

w6BW0+hV70

ELCWq8pV70

7wDWl+nV64

ZaFWP6pV60

AwDW2zlV60

-aFW87rV80

8eFWxzkV60

1OHW8zlV80

BeFWhziV80

kS7Wm6pV70

G29WrGqV64

jiAWB9pV60

J29WuHsV60

9jAWS8nV80

421WvBjV70

3a-V6HkV64

K2+VMEjV60

+a-V29mV60

a0+VlMhV80

CzzVc4nV66

7+zVlxoV60

SMyVh9mV60

ll3WiAfV70

7E5WwEgV64

mm6WTCfV60

AE5Wr6iV60

Cn6WsKdV80

-q6Wi2jV60

2r6WrvkV60

sR8W8nlV70

K3AWvmmV60

N3AW2eoV70

4gBWzqlV70

J9sV6CfV70

hdtVb6eV64

zAvVKAfV60

kdtVfEcV60

PBvVy1hV80

YEvVSJbV66

bEvVJSZV60

zrwVkEcV60

08sVCBjV70

OctV4GkV64

g9vV+CjV60

RctV08mV60

6AvVMLhV80

vDvVD3nV60

yDvVMwoV60

XctVIspV70

mqwVCspV80

Bi+Vm6pV70

c80WKAqV62

f80WJ0sV60

xf1WY8pV60

hk1W7xsV60

Ng1WtInV80

mT3WmLsV60

tl1WImuV70

cZ4WtptV70

iV3WNJvV60

w9JWm7jV70

RiHWzCkV62

qiHWv4mV60

w8GWDAjV60

25GWu0nV60

38GWcIhV80

76GW1uoV60

2UEW06mV60

uUEWIqpV60

TtCWd1nV60

utCWmuoV60

gGBW1rpV80

OD-V6CfV70

mh0Wb6eV64

PE2WKAfV60

ph0WfEcV60

rE2Wy1hV80

adEW3AjV70

y8DWW5iV64

ZcBWz8jV60

U8DWbDgV60

ZcBWb0lV80

SXBW6IfV60

+WBWzQdV60

User 818520b6b8

13-12-2006 11:50:47

I'm attaching the sdf and mrv corresponding to 8 structures causing the error, including the first one.

ChemAxon 9c0afc9aaf

13-12-2006 13:48:22

Hi,

I could not reproduce exactly the same exception with the quoted source, as it has multiple errors.

1. One empty line is missing from the front, and this makes the file format unrecognizable. If that was truncated during your posting, maybe it has something that produces the original error.

2. The counts line (which is not compressed) reads like this:

253257 0 0 0 0 0 0 0 0999 V2000

This indicates 253 atoms and 257 bonds.

If this correct at least 510 lines should follow describing these entities, while there are only 176 such lines in your post.

It seems the source got truncated.

Can you rather export the field as a text file and attach it ?

(for cd_structure with cd_id 219366)

Szilard

User 818520b6b8

13-12-2006 14:04:16

Structure for 219366

User 818520b6b8

21-12-2006 07:29:36

Any news on this topic?

The problem seems bigger. I cannot upgrade to 3.2.2 because I cannot perform searches on the standardized table.

I'm getting the following error when searching:

java.lang.ArrayIndexOutOfBoundsException: 1

at chemaxon.struc.CGraph.getSmallestRingSizeForIdx(CGraph.java:1902)

at chemaxon.marvin.util.CleanUtil.setCTWigglyBond(CleanUtil.java:568)

at chemaxon.marvin.util.CleanUtil.setCTWigglyBond(CleanUtil.java:545)

at chemaxon.reaction.Standardizer.clearDoubleBondStereo(Standardizer.java:1164)

at chemaxon.reaction.Standardizer.performClearStereo(Standardizer.java:1128)

at chemaxon.reaction.Standardizer.standardizeComponent(Standardizer.java:1688)

at chemaxon.reaction.Standardizer.standardize(Standardizer.java:1770)

at chemaxon.jchem.db.TableInfo.standardize(TableInfo.java:1171)

at chemaxon.jchem.db.JChemSearch.initQuery(JChemSearch.java:3006)

at chemaxon.jchem.db.JChemSearch.searchCore(JChemSearch.java:2537)

at chemaxon.jchem.db.JChemSearch.search1(JChemSearch.java:2421)

at chemaxon.jchem.db.JChemSearch.search(JChemSearch.java:2239)

at chemaxon.jchem.db.JChemSearch.setRunning(JChemSearch.java:2111)

at chemaxon.jchem.db.JChemSearch.run(JChemSearch.java:2131)

at jchem.SearchStructure.getViewerResults(SearchStructure.java:651)

at jchem.SearchStructure.searchButton_actionPerformed(SearchStructure.java:517)

at jchem.SearchStructure.access$6000371(SearchStructure.java:64)

at jchem.SearchStructure$4.actionPerformed(SearchStructure.java:196)

at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1786)

at javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButton.java:1839)

at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:420)

at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258)

at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:245)

at java.awt.Component.processMouseEvent(Component.java:5100)

at java.awt.Component.processEvent(Component.java:4897)

at java.awt.Container.processEvent(Container.java:1569)

at java.awt.Component.dispatchEventImpl(Component.java:3615)

at java.awt.Container.dispatchEventImpl(Container.java:1627)

at java.awt.Component.dispatchEvent(Component.java)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3198)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3128)

at java.awt.Container.dispatchEventImpl(Container.java:1613)

at java.awt.Window.dispatchEventImpl(Window.java)

at java.awt.Component.dispatchEvent(Component.java)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:458)

at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:201)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:137)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:100)

ChemAxon 9c0afc9aaf

21-12-2006 13:46:33

Hi,

Quote:

Any news on this topic?

Yes, actually I was just about to inform you that the multiple ArrayIndexOutOfBoundsException has been fixed, it will be OK in the next Marvin and JChem release, which we plan to release soon.

(the holidays may cause some delay though)

We could not reproduce the exception so far that is different for others (structure 219366).

Regarding the latest (search) problem:

The exception is related to the particular query structure.

Could you attach the source of this query please ?

Best regards,

Szilard

User 818520b6b8

22-12-2006 08:54:45

Attaching the structure used for searching.

ChemAxon 9c0afc9aaf

22-12-2006 10:19:50

Hi,

We could not reproduce the exception with the attached query structure and JChem 3.2.2.

I could search with this structure, and it also finds itself in the database.

I have used the standardizer configuration you provided in this topic (config.xml).

Best regards,

Szilard

User 818520b6b8

11-01-2007 08:42:50

Error at molecule with cd_id: 219366

java.util.NoSuchElementException

at java.util.StringTokenizer.nextToken(Unknown Source)

at chemaxon.formats.MFileFormatUtil.canBe3LetterPeptide(MFileFormatUtil.java:554)

at chemaxon.formats.MolInputStream.init(MolInputStream.java:373)

at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:102)

at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:44)

at chemaxon.util.MolHandler.importMol(MolHandler.java:680)

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

at chemaxon.util.MolHandler.<init>(MolHandler.java:122)

at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:993)

at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:866)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1888)

at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1866)

at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:76)