JChem Cartridge User defined function example

molconvert

The example can be found in the <JChem home>/examples/cartridge/user_def_func/molconvert directory.

Consider the MolConvert Java class that converts structures between various file types according to the parameters. We would like to covert structures comming from a database table into aromatized SMILES format using the MolConvert Java class.

First of all we have to create a PL/SQL operator and function that can be used in SQL select statements. The operator gets the structure from a table as a parameter and gets the format also as a parameter. For example aromatize structures:

SQL> select molconverter(cd_smiles, 'smiles:a') from jchemtable;

Now create the PL/SQL function and operator (molconvert_sql.sql):

SQL> CREATE FUNCTION molconverter_func(query VARCHAR2, type VARCHAR2) RETURN VARCHAR2 AS
  BEGIN
    RETURN jchem_core_pkg.send_user_func('MolConvert', '{delim}', query || '{delim}' || type);
  END;
/
show errors;

SQL> CREATE OPERATOR molconverter BINDING(VARCHAR2, VARCHAR2) RETURN VARCHAR2 
  USING molconverter_func;

The molconverter_func function sends its query and type parameters to the MolConvert external Java class using the send_user_func function.

The MolConvert class has to implement the JChemCartModul interface. It's doFunc function gets the parameters sent by the molconverter_func PL/SQL function (query and type).

ChemAxon's MolConvert tool is ideal to convert structures between various types thus we can use it. Let's see the MolConvert Java class (MolConvert.java):

import chemaxon.formats.MolConverter;
import java.io.*;	

public class MolConvert implements JChemCartModul {

    public Object doFunc(String[] args) throws Exception {
    	ByteArrayInputStream bis = new ByteArrayInputStream(args[0].getBytes());
    	ByteArrayOutputStream bout = new ByteArrayOutputStream();
    	MolConverter mc = new MolConverter(bis, bout, args[1], false);
    	mc.convert();
    	return new String(bout.toByteArray());
    }
}

Compile the java file and make sure that the JCART_XCLASSPATH variable includes the parent directory of the MolConvert.class file before starting JChem Server. Now our new function is ready to call from PL/SQL, for example:

SQL> select molconverter(cd_smiles, 'smiles:a') from jchemtable;