Error upgrading from JChem 3.2.3 to JChem 3.2.8

User 818520b6b8

26-07-2007 13:12:43

Hi,





I'm getting lots of errors like this when upgrading from JChem 3.2.3 to JChem 3.2.8:





Error at molecule with cd_id: 276397


java.sql.SQLException: ORA-01461: can bind a LONG value only for insert into a LONG column





at oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:111)


at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:330)


at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:287)


at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:742)


at oracle.jdbc.driver.T4CPreparedStatement.doOall8(T4CPreparedStatement.java:212)


at oracle.jdbc.driver.T4CPreparedStatement.executeForRows(T4CPreparedStatement.java:951)


at oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:1159)


at oracle.jdbc.driver.OraclePreparedStatement.executeInternal(OraclePreparedStatement.java:3284)


at oracle.jdbc.driver.OraclePreparedStatement.executeUpdate(OraclePreparedStatement.java:3367)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2066)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)





The error is only reproducing with some of the structures, not all.





It's an Oracle Database 10.2.0.3





Thank you.

ChemAxon aa7c50abf8

26-07-2007 13:42:46

Hi,





After some googling, I've found several suggestions that this problem might occur when the Oracle client’s character set is not the same or a subset of the Oracle server’s character set. The issue is copiously discussed here:





http://www.theserverside.com/discussions/thread.tss?thread_id=14634





or on metalink under DocId 241358.1.





I also suggest to make sure that your application uses the latest JDBC driver version from Oracle.





Let us know if this helps.





Thanks


Peter

User 818520b6b8

26-07-2007 13:45:54

thanks a lot.





I'll check with latest JDBC version and the same characterset.

User 818520b6b8

27-07-2007 10:11:31

Hi,





the problem was the JDBC version rather than NLS_LANG.





I used latest JDBC version 10.2.0.3 and it works. BUT, now I have real upgrade problems, mainly (not all) related with Peptides:





chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 145301


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 150615


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 151525


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 151687


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 151747


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 171007


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 171085


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 165011


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 170537


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 171005


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 171007


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 171085


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 214165


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 228261


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 228263


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 228265


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H- -OH


at chemaxon.marvin.modules.PeptideReader.convert(PeptideReader.java:124)


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:94)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


chemaxon.formats.MolFormatException: : error in molecule file


at chemaxon.marvin.modules.PeptideImport.readMol(PeptideImport.java:99)


at chemaxon.formats.MolImporter.readMol(MolImporter.java:776)


at chemaxon.formats.MolImporter.read(MolImporter.java:608)


at chemaxon.formats.MolImporter.read(MolImporter.java:574)


at chemaxon.util.MolHandler.importMol(MolHandler.java:704)


at chemaxon.util.MolHandler.setMolecule(MolHandler.java:189)


at chemaxon.util.MolHandler.<init>(MolHandler.java:123)


at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1072)


at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:945)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2003)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)


Error at molecule with cd_id: 252523


java.sql.SQLException: : error in molecule file


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2009)


at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1981)


at chemaxon.jchem.db.Regenerator$RegenThread.run(Regenerator.java:77)

User 818520b6b8

01-08-2007 06:51:38

The same happens when upgrading to 3.2.9

ChemAxon aa7c50abf8

01-08-2007 14:07:44

Please, could you post (or, if confidential, upload to our ftp site) some of the molecules which triggered errors during import?





Thanks


Peter