JCB FAQ

    • General

      The most probable causes:

        • Incorrect URL to the database (it may occur during login)

          • Inappropriate username / password (it may occur during login)

          • Faulty JDBC or ODBC driver. Try a different one.

      • I get exception when I start JChemManager using Oracle's JDBC thin driver.

      Make sure that the URL is appropriate (e.g: jdbc:oracle:thin:@myhost:1521:mySID). Check if all needed services run (the listener service is necessary).

      • JChem Manager and chemaxon.jchem.db.Importer fails to import date formats into PostgreSQL tables which otherwise work with psql or other non-JDBC-based clients

      If this is a date or time stamp format which works using psql or other non-JDBC-based database clients, you have likely run into this PostgreSQL JDBC issue:

      The work-around is to to append stringtype=unspecified to the connection.jdbcUrl:

                      connection.jdbcUrl=jdbc\:postgresql\://localhost\:5432/jcbtest?stringtype=unspecified
      • Integration
        • How can I use the JChem API from my favorite programming language (C++, C#, .NET, Python, Javascript, Perl)?

      For users of the .NET API, the JChem API can be integrated into .NET applications by the .NET Packages. Other web service compatible languages (including C++ and C#) can use JChem Web Services.

      • How can I use the JChem tools as a web service?

      Many of the JChem tools are available as web services. See the JChem Web Services Server for more information

      • Examples

        • Where can I find examples for using JChem?

          • A JSP (Java Server Pages) and ASP examples can be found in the examples directory. Please see {{<jchem dir>/examples/index.html}} for a description.

        • How should I set the connection string in the case of ASP or other ADO capable environment?

      If you would like to call SQL statements using ADO, you may choose between ODBC and OLEDB connections. (ADO can not contact to the databases through JDBC drivers.)

      • Example for an ODBC connection
          var adoConnectionString=
    "DSN="+MyDSN+";"+
    "UID="+username+";"+
    "PWD="+password;
      • Example for an OLEDB connection to Oracle
          var adoConnectionString=
    "Provider=MSDAORA.1;"+
    "Data Source="+myServiceName+";"+
    "User ID="+username+";"+
    "Password="+password;

      (The above examples use the JavaScript syntax)

      In the case of Oracle, if an error occurs, please see HOWTO: Troubleshoot an ASP-to-Oracle Connectivity Problem

        • Copy/paste doesn't work with a certain Look and Feel.

          Keyboard shortcuts for Copy/Paste/Cut functions may vary by Look and Feel. For example in the case of Windows Look and Feel these are CTRL+C,CTRL+V, and CTRL+X, respectively. In the case of Motif LF the shortcuts for the same commands are: CTRL+INS,SHIFT+INS, and SHIFT+DEL.

      • Common issues
        • I get the following exception using MySQL: com.mysql.jdbc.PacketTooBigException: Packet for query is too large

      Please increase the value of the "max_allowed_packet" variable for MySQL. The following line should be added to the configuration file "my.ini" under the [mysqld] section :

       max_allowed_packet = 100M
      • For some structures the database field "cd_smiles" is null . Why?

      JChem works with the standardized form of imported structures stored in ChemAxon Extended SMILES format. This extended format can represent a wider range of structures than SMILES, but there are still some cases, when this format is not applicable. In these cases the "cd_smiles" field is null , and JChem uses the "cd_structure" field for these rows. (The "cd_structure" represents the structures in the original input format)

      Currently the cd_smiles is null in the following cases:

      • Structure contains radicals

      • Structure contains R-groups

      • the SMILES would be too long for the database field (very large molecules).

      In these cases the search is slower, since the target structures have to be standardized on the fly.

      Note: For most databases the size of the "cd_smiles" field can be increased at the table creation dialog (in the SQL text). The increased length is automatically utilized. This can speed up the search if a high percentage of the structures are huge.

      • I get the following error message : " The structure table contains obsolete data. Please regenerate the table. " What does it mean ?

        Sometimes there are some changes in the data structure of JChem, which are incompatible with earlier versions. To obtain correct search result, the regeneration of the old structure tables is necessary. For more information and instructions please see the administration guide.

      • In DB2 databases, row length of JChem structure tables has been increased

        Please, be aware of the increased (by about 1K) row lengths of the JChem structure tables from JChem 6.1.2. It's possible that the new row length will reach the maximum row length allowed in your database. In this case the extended row size support must be enabled or the page size of the tablespace must be increased manually.

      • How to check for duplicates in duplicate filtered tables

        Because of a bug - fixed in JChem version 17.29.0 - duplicates could have been inserted in tables with duplicate filtering set on if there were too many structures with the same hash code already in the database. Starting from JChem version 18.1.0, a command line tool duplicatecheck is provided for finding the duplicates in a JChem table. This tool is available in the bin folder of JChem. For detailed help please run:

        
duplicatecheck -help