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