User 104a68add6
06-05-2005 17:11:41
Hi,
We recently upgraded from jchem 2.2.1 to 3.0.5. This was in preparation for a jchem cartridge install. On our test system, we used the jcman interface to convert the structures in our structure table, because they become obsolete whenever we do an upgrade. It automatically prompts us and always seems to work fine. We also ran that conversion on our production system.
During our installation of the jchem cartridge onto the production system, after successful install on a test system, we had some troubles (you have since helped us there, thank you). We thought that the jcman conversion may have been the problem. We not only had logins denied, but the cartridge query would hang in such a way that we needed to use the orakill utility to stop it. So we thought perhaps the structures had become corrupted.
We have an automated script that uses the MolImporter API to put new structures into the jchem structure table, whenever a chemist adds a structure to our corporate database. If we truncate the jchem structure table, this script will determine that all of our structures need to be imported (it reads the other table that contains the structure information and checks the difference between that and the structure table). Through the jchem 2.2.1, this process of truncation and rebuilding has worked as well.
So we truncated the structure table on our production system, and regenerated our entire structure database using the script. Now, for 39 of our compounds, we are getting the following error :
Error in molecule 184
java.lang.IllegalArgumentException:
Some features of [#8]C(=O)CC[C@H](N[#114])C([#114])=O.[#6]C(=O)O[C@@]12CO[C@@H]1C[C@H]([#8])[C@]3([#6])[C@@H]2[C@H](OC(=O)c4ccccc4)[C@]5([#8])C[C@H](OC(=O)[C@H](OC(=O)CC[C@H](N[#114])C([#114])=O)[C@@H](NC(=O)OC([#6])([#6])[#6])c6ccccc6)C([#6])=C([C@@H]([#8])C3=O)C5([#6])[#6] cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.
at chemaxon.struc.Molecule.toObject(Molecule.java:1040)
at chemaxon.struc.Molecule.toFormat(Molecule.java:902)
at chemaxon.util.MolHandler.toFormat(MolHandler.java:427)
at chemaxon.jchem.db.UpdateHandler.getSmiles(UpdateHandler.java:707)
at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:813)
at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:1022)
at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:771)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1356)
at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:263)
at chemaxon.jchem.db.Importer.importMols(Importer.java:423)
at com.ctiseattle.data.tools.impexp.structure.MolImporter.execute(MolImporter.java:213)
at com.ctiseattle.data.tools.impexp.structure.MolImporter.main(MolImporter.java:365)
I'm wondering what changed in the upgrade to make these molecules unacceptable to the MolImporter.
Thanks,
Julie
We recently upgraded from jchem 2.2.1 to 3.0.5. This was in preparation for a jchem cartridge install. On our test system, we used the jcman interface to convert the structures in our structure table, because they become obsolete whenever we do an upgrade. It automatically prompts us and always seems to work fine. We also ran that conversion on our production system.
During our installation of the jchem cartridge onto the production system, after successful install on a test system, we had some troubles (you have since helped us there, thank you). We thought that the jcman conversion may have been the problem. We not only had logins denied, but the cartridge query would hang in such a way that we needed to use the orakill utility to stop it. So we thought perhaps the structures had become corrupted.
We have an automated script that uses the MolImporter API to put new structures into the jchem structure table, whenever a chemist adds a structure to our corporate database. If we truncate the jchem structure table, this script will determine that all of our structures need to be imported (it reads the other table that contains the structure information and checks the difference between that and the structure table). Through the jchem 2.2.1, this process of truncation and rebuilding has worked as well.
So we truncated the structure table on our production system, and regenerated our entire structure database using the script. Now, for 39 of our compounds, we are getting the following error :
Error in molecule 184
java.lang.IllegalArgumentException:
Some features of [#8]C(=O)CC[C@H](N[#114])C([#114])=O.[#6]C(=O)O[C@@]12CO[C@@H]1C[C@H]([#8])[C@]3([#6])[C@@H]2[C@H](OC(=O)c4ccccc4)[C@]5([#8])C[C@H](OC(=O)[C@H](OC(=O)CC[C@H](N[#114])C([#114])=O)[C@@H](NC(=O)OC([#6])([#6])[#6])c6ccccc6)C([#6])=C([C@@H]([#8])C3=O)C5([#6])[#6] cannot be converted to smiles/cxsmiles. Use the smarts or cxsmarts format.
at chemaxon.struc.Molecule.toObject(Molecule.java:1040)
at chemaxon.struc.Molecule.toFormat(Molecule.java:902)
at chemaxon.util.MolHandler.toFormat(MolHandler.java:427)
at chemaxon.jchem.db.UpdateHandler.getSmiles(UpdateHandler.java:707)
at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:813)
at chemaxon.jchem.db.UpdateHandler.setFields(UpdateHandler.java:1022)
at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:771)
at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:1356)
at chemaxon.jchem.db.FileToSQLHandler.importFile(FileToSQLHandler.java:263)
at chemaxon.jchem.db.Importer.importMols(Importer.java:423)
at com.ctiseattle.data.tools.impexp.structure.MolImporter.execute(MolImporter.java:213)
at com.ctiseattle.data.tools.impexp.structure.MolImporter.main(MolImporter.java:365)
I'm wondering what changed in the upgrade to make these molecules unacceptable to the MolImporter.
Thanks,
Julie