chemaxon.formats.MolFormatException: Cannot recognize format

Hi, All

Today my customer to edit a compound and to save it, but it throws a exception as following:

chemaxon.formats.MolFormatException: Cannot recognize format (base64 or chime?)
Unrecognized file contents:
null
 at chemaxon.formats.recognizer.RecognitionSubsystem.getFormat(RecognitionSubsystem.java:203)
 at chemaxon.formats.MolInputStream.initTextFormat(MolInputStream.java:235)
 at chemaxon.formats.MolInputStream.init(MolInputStream.java:134)
 at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:116)
 at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:58)
 at chemaxon.util.MolHandler.importMol(MolHandler.java:652)
 at chemaxon.util.MolHandler.setMolecule(MolHandler.java:176)
 at chemaxon.util.MolHandler.<init>(MolHandler.java:125)
 at chemaxon.jchem.db.UpdateHandler.readMolecule(UpdateHandler.java:1318)
 at chemaxon.jchem.db.UpdateHandler.init(UpdateHandler.java:1107)
 at chemaxon.jchem.db.UpdateHandler.execute(UpdateHandler.java:2200)

please see attachments.

save function as:

Connection conn = this.getConnection();
  String structureTableName = Constants.STRUCTURE_TABLE_NAME;
  ConnectionHandler ch = new ConnectionHandler();
  UpdateHandler uh = null;
     try {
       ch.setConnection(conn);
       uh = new UpdateHandler(ch, isInsert ? UpdateHandler.INSERT : UpdateHandler.UPDATE,structureTableName, "");
       uh.setDuplicateFiltering(true);
       uh.setStructure(molfile);
       uh.setEmptyStructuresAllowed(true);
       uh.setDuplicateFiltering(false);
       if (!isInsert) { uh.setID(cdId); }
       return uh.execute(true);
     } catch (Exception e) {
      e.printStackTrace();
     } finally {
      try {
        uh.close();
      } catch (Exception e) {
       e.printStackTrace();
      }
     }

Any suggestions? thanks in advance.

 

Hi,

I tried to import the molfile which you sent, and it inserted successfully.

I have some questions:
- which  was the table type? The specified structure can be inserted to any, markush or query table type.
- Is it possible that the user tried to import  the structure as an image or a binary format? It is not clear from your code snipplet what is the source of the uh.setStructure(molfile)

Regards, Edvard

I test it in mysql, it works ok, but when i use sql server 2008, it can't work well. the structure table was created by jchemmanager with default setting. the attachment is the screen of jchemproperties table value.

Hi,

I will try to reproduce it with MS SQL 2008. I will inform you soon.

Regards, Edvard

Hi,

It is successfully imported to the MS SQL 2005 with Jchem 5.2.6 and other later versions.
It seems the type of the table where you tried to import the compound is a molecule table. The specified structure can be inserted to any,
markush or query table type.

Regards, Edvard