Java Examples

• Molecule loader
• Exact match
• Similarity search
• SMARTS substructure search
• MOL file substructure search
• Conformer loader
• Shape search

The search examples require that test data has been loaded, and domain indexes have been built.

An example molecule loader:

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.Statement;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolistream;

import java.net.URL;

/***************************************************************************
MoleculeLoader demonstrate creating and loading molecules from a file
into a database table.
This test table is created prior to loading molecules from the input file.
The domain index is created after molecules are loaded.
***************************************************************************/

public class MoleculeLoader
{
    public static void moleculeLoader(oemolistream ifs,
                                      String password)
    {
      Connection        conn = null;
      Statement         stmt = null;
      PreparedStatement pstmt = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        // First, create the table.
        stmt = conn.createStatement();
        String sql = "create table test (title varchar2(100)," +
          "smiles varchar2(4000) not null,conf blob)";
        stmt.execute(sql);
        System.out.println("Created test table");

        // Next, load the molecules.
        sql = "insert into test(title, smiles) values (?, ?)";
        pstmt = conn.prepareStatement(sql);
        OEMolBase mol = new OEGraphMol();
        int count = 0;

        while (oechem.OEReadMolecule(ifs, mol))
        {
          String title = mol.GetTitle();
          String ism = oechem.OECreateIsoSmiString(mol);
          pstmt.setString(1, title);
          pstmt.setString(2, ism);
          pstmt.executeUpdate();
          count++;
          if (count % 1000 == 0)
          {
            conn.commit();
            System.out.print("Loaded " + count + " molecules (so far)\r");
            System.out.flush();
          }
        }

        conn.commit();

        System.out.println("Loaded " + count + " molecules (complete)");
        System.out.println("Building domain index");

        // Last, create the domain index.
        stmt = conn.createStatement();
        stmt.execute("create index test_structure_idx on test(smiles) " +
                     "indextype is c$arnachm1.structureIndexType");
        System.out.println("Created index test_structure_idx");
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(stmt);
        Util.closeStatement(pstmt);
      }
    }

    public static void main(String[] args)
    {
      URL fileURL = MoleculeLoader.class.getResource("MoleculeLoader.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal(
          "Unable to open interface file MoleculeLoader.txt");
      }

      oemolistream ifs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"MoleculeLoader", args);
        String inputFilename = itf.GetString("-i");
        String password = "";
        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        ifs = new oemolistream();
        if (!ifs.open(inputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for reading" +
                               inputFilename);
        }

        moleculeLoader(ifs,password);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ifs != null)
          ifs.close();
      }
    }
}

An example of an exact match search:

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolistream;
import openeye.oechem.oemolostream;

import java.net.URL;

/***************************************************************************
ExactMatch demonstrates exact match searching using the cartridge.
Takes a molecule file query_filename containing one or more query molecules
and searches the 'test' table for exact match molecules. The 'hit' molecules
are written to output_filename.

Assumes the test table and domain index have been created.
(see MoleculeLoader.java)
***************************************************************************/

public class ExactMatch
{
    public static void exactMatch(oemolistream ifs,
                                  oemolostream ofs,
                                  String password,
                                  String tableName,
                                  String columnName)
    {
      Connection conn = null;
      PreparedStatement pstmt = null;
      ResultSet rs = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        String sql = "select " + columnName + ",title from " + tableName +
          " where " + "c$arnachm1.exactMatch(" + columnName + ", ?, -1) = 1";
        pstmt = conn.prepareStatement(sql);

        OEMolBase mol = new OEGraphMol();

        int queryCount = 0;
        int hitCount = 0;

        while (oechem.OEReadMolecule(ifs, mol))
        {
          String query = oechem.OECreateIsoSmiString(mol);
          pstmt.setString(1, query);
          rs = pstmt.executeQuery();

          while (rs.next())
          {
            String smi = rs.getString(1);
            String title = rs.getString(2);
            mol.Clear();
            oechem.OESmilesToMol(mol,smi);
            mol.SetTitle(title);
            oechem.OEWriteMolecule(ofs, mol);
            hitCount++;
          }
          queryCount++;
        }

        System.out.println("Found " + hitCount + " exact matches for " +
                           queryCount + " queries");
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(pstmt);
      }
    }

    public static void main(String args[])
    {
      URL fileURL = ExactMatch.class.getResource("ExactMatch.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal("Unable to open interface file ExactMatch.txt");
      }

      oemolistream ifs = null;
      oemolostream ofs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"ExactMatch", args);
        String inputFilename = itf.GetString("-i");
        String outputFilename = itf.GetString("-o");
        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");
        String password = "";

        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        ifs = new oemolistream();
        if (!ifs.open(inputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for reading " +
                               inputFilename);
        }

        ofs = new oemolostream();
        if (!ofs.open(outputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for writing " +
                               outputFilename);
        }

        exactMatch(ifs,ofs,password,tableName,columnName);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ifs != null)
          ifs.close();
        if (ofs != null)
          ofs.close();
      }
    }
}

An example of a similarity search:

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolistream;
import openeye.oechem.oemolostream;

import java.net.URL;

/***************************************************************************
Similarity demonstrates similarity searching using the data cartridge.
This takes a molecule file containing one of more query molecules and
searches the 'test' table for similar molecules with a Tanimoto >= the
provided cutoff. Each set of results is written to a separate molecule file
in the working directory (sim-hits-XXX.sdf) and the similarity of the
molecules to the query is stored in an SD tag.
***************************************************************************/

public class Similarity
{

    public static void similarity(oemolistream ifs,
                                  double cutoff,
                                  String password,
                                  String tableName,
                                  String columnName)

    {
      Connection conn = null;
      PreparedStatement pstmt = null;
      ResultSet rs = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        pstmt = conn.prepareStatement("select " + columnName + ", title, " +
                                      "c$arnachm1.similarityScore(1) from " + tableName + " where " +
                                      "c$arnachm1.similarity(" + columnName + ", ?, ?, -1, 1) = 1");
        String foo = "select " + columnName + ", title, " +
          "c$arnachm1.similarityScore(1) from " + tableName + " where " +
          "c$arnachm1.similarity(" + columnName + ", ?, ?, -1, 1) = 1";

        System.out.println("sql = " + foo);

        int count = 1;
        String dir = System.getProperty("user.dir");
        OEGraphMol mol = new OEGraphMol();
        OEGraphMol outmol = new OEGraphMol();

        while (oechem.OEReadMolecule(ifs, mol))
        {
          String query = oechem.OECreateIsoSmiString(mol);
          pstmt.setString(1, query);
          pstmt.setDouble(2, cutoff);
          rs = pstmt.executeQuery();

          String outputFilename = dir +
            String.format("/sim-hits-%03d.sdf", (int)count);

          oemolostream oms = new oemolostream(outputFilename);
          int hitCount = 0;

          while (rs.next())
          {
            String smi = rs.getString(1);
            String title = rs.getString(2);
            if (title == null || title.equals(""))
              title = "Hit "+String.valueOf(hitCount+1);
            String tan = String.format("%.3f",rs.getDouble(3));
            outmol.Clear();
            oechem.OESmilesToMol(outmol,smi);
            outmol.SetTitle(title);
            oechem.OESetSDData(outmol,"Tanimoto",tan);
            oechem.OEWriteMolecule(oms, outmol);
            hitCount++;
          }

          System.out.println("Found " + hitCount + " molecules with sim >= " +
                             cutoff + " for query " + query + " output to " +
                             outputFilename);
          oms.close();
          count++;
        }
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(pstmt);
      }
    }


    public static void main(String[] args)
    {
      URL fileURL = Similarity.class.getResource("Similarity.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal("Unable to open interface file Similarity.txt");
      }

      oemolistream ifs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"Similarity", args);
        String inputFilename = itf.GetString("-i");
        double cutoff = itf.GetDouble("-c");
        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");
        String password = "";
        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        ifs = new oemolistream();
        if (!ifs.open(inputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for reading " +
                               inputFilename);
        }

        similarity(ifs,cutoff,password,tableName,columnName);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ifs != null)
          ifs.close();
      }
    }
}

A substructure search using a SMARTS query:

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolostream;

import java.net.URL;

/***************************************************************************
SubSearchSmarts demonstrates substructure searching using the data cartridge
where the query is an SMARTS string.  This read the query from the command
line and runs a substructure search against the test table. The hits are
written to an output file.
***************************************************************************/

public class SubSearchSmarts
{
    public static void subSearchSmarts(oemolostream ofs,
                                       String pattern,
                                       String password,
                                       String tableName,
                                       String columnName)
    {
      PreparedStatement pstmt = null;
      ResultSet rs = null;

      Connection conn = null;
      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);
        pstmt = conn.prepareStatement("select " + columnName +
                                      ", title from " + tableName +
                                      " where " + "c$arnachm1.substructure(" +
                                      columnName + ", ?, -1) = 1");
        pstmt.setString(1, pattern);
        rs = pstmt.executeQuery();

        OEMolBase mol = new OEGraphMol();
        int hitCount = 0;

        while (rs.next())
        {
          String smi = rs.getString(1);
          String title = rs.getString(2);
          mol.Clear();
          oechem.OESmilesToMol(mol,smi);
          mol.SetTitle(title);
          oechem.OEWriteMolecule(ofs, mol);
          hitCount++;
        }

        System.out.println("Found " + hitCount + " hits.");
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(pstmt);
        Util.closeResultSet(rs);
      }
    }


    public static void main(String[] args)
    {
      URL fileURL = SubSearchSmarts.class.getResource("SubSearchSmarts.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal(
          "Unable to open interface file SubSearchSmarts.txt");
      }

      oemolostream ofs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"SubSearchSmarts", args);
        String pattern = itf.GetString("-s");
        String outputFilename = itf.GetString("-o");
        String password = "";
        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");

        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        ofs = new oemolostream();
        if (!ofs.open(outputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for writing " +
                               outputFilename);
        }

        subSearchSmarts(ofs,pattern,password,tableName,columnName);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ofs != null)
          ofs.close();
      }
    }
}

A substructure search using a MOL file query:

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.sql.Clob;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolostream;

import oracle.sql.CLOB;
import java.net.URL;

/***************************************************************************
SubSearchMdl demonstrates substructure searching using the data cartridge
where the query is an MDL query.  This read the query from a file and runs
a substructure search against the test table. The hits are written to an
output file.
***************************************************************************/

public class SubSearchMDL
{
    private static String readMDLQuery(String filename) throws IOException
    {
      BufferedReader reader = null;
      try
      {
        reader = new BufferedReader(new FileReader(filename));
        String line = null;
        StringBuilder stringBuilder = new StringBuilder();
        String ls = System.getProperty("line.separator");
        while ((line = reader.readLine()) != null)
        {
          stringBuilder.append(line);
          stringBuilder.append(ls);
        }
        return stringBuilder.toString();
      }
      finally
      {
        if (reader != null)
          reader.close();
      }
    }

    private static void subSearchMDL(String mdl,
                                     oemolostream ofs,
                                     String password,
                                     String tableName,
                                     String columnName)
    {
      Connection conn = null;
      PreparedStatement pstmt = null;
      ResultSet rs = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        pstmt = conn.prepareStatement("select " + columnName +
                                      ", title from " + tableName +
                                      " where " +
                                      "c$arnachm1.mdl_clob_substructure(" +
                                      columnName + ", ?, -1) = 1");

// Set parameters on prepared statement. In this case it is slightly
// complicated as we have to create a Clob first, set the string on that,
// then set that as the parameter on the prepared statement. This is often
// database dependent.

        Clob clob = oracle.sql.CLOB.createTemporary(conn, false,
                                                    oracle.sql.CLOB.DURATION_SESSION);
        clob.setString(1, mdl);
        pstmt.setClob(1, clob);

        rs = pstmt.executeQuery();

        OEMolBase mol = new OEGraphMol();
        int hitCount = 0;

        while (rs.next())
        {
          String smi = rs.getString(1);
          String title = rs.getString(2);
          mol.Clear();
          oechem.OESmilesToMol(mol,smi);
          mol.SetTitle(title);
          oechem.OEWriteMolecule(ofs, mol);
          hitCount++;
        }
        ofs.close();

        System.out.println("Found " + hitCount + " hits.");

        // Important to free the Oracle CLOB.
        ((CLOB) clob).freeTemporary();

      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(pstmt);
      }
    }

    public static void main(String[] args)
    {
      URL fileURL = SubSearchMDL.class.getResource("SubSearchMDL.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal("Unable to open interface file SubSearchMDL.txt");
      }

      oemolostream ofs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"SubSearchMDL", args);
        String inputFilename = itf.GetString("-i");
        String outputFilename = itf.GetString("-o");
        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");
        String password = "";

        String mdl = readMDLQuery(inputFilename);

        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        ofs = new oemolostream();
        if (!ofs.open(outputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open " + outputFilename +
                               " for writing" +
                               outputFilename);
        }

        subSearchMDL(mdl,ofs,password,tableName,columnName);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ofs != null)
          ofs.close();
      }
    }
}

An example of populating a blob column with conformers stored in an OEBinary array:

import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.Statement;
import java.sql.ResultSet;
import java.sql.Blob;
import java.io.Console;
import java.io.InputStream;
import java.io.ByteArrayInputStream;

import openeye.oechem.OEMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.OEFormat;
import openeye.oechem.oechem;
import openeye.oechem.oemolistream;
import openeye.oechem.oemolostream;
import openeye.oechem.OEBinaryIOHandlerBase;

import java.net.URL;

/***************************************************************************
ConformerLoader demonstrates loading conformers from an OEBinary file
into a database table.  This target table must be created prior to
loading molecules from the input file.  The domain index is created
after molecules are loaded.
***************************************************************************/

public class ConformerLoader
{
    public static void conformerLoader(oemolistream ifs,
                                       String password,
                                       String tableName,
                                       String columnName)
    {
      Connection        conn = null;
      Statement         stmt = null;
      PreparedStatement pstmt = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        int count = 0;
        OEMol mol = new OEMol();
        oemolostream ofs = new oemolostream();
        ofs.SetFormat(OEFormat.OEB);

        String sql = "update " + tableName +
          " set " + columnName + " = ? where title = ?";

        pstmt = conn.prepareStatement(sql);

        while (oechem.OEReadMolecule(ifs, mol))
        {
          ofs.openstring();
          oechem.OEWriteMolecule(ofs,mol);
          ofs.close();
          byte [] inputBytes = ofs.getByteArray();

          InputStream is = new ByteArrayInputStream(inputBytes);

          String title = mol.GetTitle();
          pstmt.setBinaryStream(1, is, inputBytes.length);
          pstmt.setString(2, title);

          if (pstmt.executeUpdate() == 1)
            count++;
          else
            System.out.println("Molecule '" + mol.GetTitle() + "' not found");

          if (count % 10 == 0)
          {
            conn.commit();
            System.out.print("Loaded " + count + " molecules (so far)\r");
            System.out.flush();
          }
        }

        conn.commit();
        System.out.println("\rLoaded " + count + " molecules (complete)");

        stmt = conn.createStatement();
        sql = "create index test_conf_idx on " +
          tableName + "(" + columnName + ") indextype is c$arnachm1.fastrocsIndexType";
        stmt.execute(sql);
        System.out.println("Created index test_conf_idx");
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(stmt);
        Util.closeStatement(pstmt);
      }
    }

    public static void main(String[] args)
    {
      URL fileURL = ConformerLoader.class.getResource("ConformerLoader.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal(
          "Unable to open interface file MoleculeLoader.txt");
      }

      oemolistream ifs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"MoleculeLoader", args);
        String inputFilename = itf.GetString("-i");
        String password = "";
        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");

        ifs = new oemolistream();
        if (!ifs.open(inputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open %s for reading" +
                               inputFilename);
        }
        OEBinaryIOHandlerBase hand = ifs.GetBinaryIOHandler();
        hand.Clear();
        oechem.OEInitHandler(hand,
                             oechem.OEBRotCompressOpts(),
                             oechem.OEBDefaultOpts());

        conformerLoader(ifs,password,tableName,columnName);
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ifs != null)
          ifs.close();
      }
    }
}

A shape similarity search example:

import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.sql.Clob;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.io.Console;

import openeye.oechem.OEGraphMol;
import openeye.oechem.OEMol;
import openeye.oechem.OEMolBase;
import openeye.oechem.OEInterface;
import openeye.oechem.oechem;
import openeye.oechem.oemolistream;
import openeye.oechem.oemolostream;
import openeye.oechem.OEFormat;

import oracle.sql.CLOB;
import java.net.URL;

/***************************************************************************
Runs a FastROCS search against the test table using the input query.
This fetches the hits from the database and outputs
the molecules to <output_filename>.
***************************************************************************/

public class ShapeSearch
{
    private static void shapeSearch(OEMolBase query,
                                    oemolostream ofs,
                                    String password,
                                    String tableName,
                                    String columnName,
                                    float tanCutoff,
                                    int maxHits)
    {
      Connection        conn = null;
      PreparedStatement pstmt = null;
      ResultSet         rs = null;

      try
      {
        String ORACLE_SID = null;
        String ORACLE_HOST = "localhost";
        String ORACLE_PORT = "1521";
        String ORACLE_USER = "arnachm1_test";
        if (System.getenv("ORACLE_SID") != null)
          ORACLE_SID = System.getenv("ORACLE_SID");
        if (System.getenv("ORACLE_HOST") != null)
          ORACLE_HOST = System.getenv("ORACLE_HOST");
        if (System.getenv("ORACLE_USER") != null)
          ORACLE_USER = System.getenv("ORACLE_USER");

        String connectURL = "jdbc:oracle:thin:@" + ORACLE_HOST + ":" +
          ORACLE_PORT + ":" + ORACLE_SID;
        conn = Util.createConnection(connectURL,ORACLE_USER,password);

        pstmt = conn.prepareStatement("select " +
                                      "c$arnachm1.fastrocs_conformation(1) from " + tableName +
                                      " where c$arnachm1.fastrocs(" +
                                      columnName + ", ?, ?, ?, 1) = 1");
        String molstr = "";

        int dimension = query.GetDimension();
        if (dimension == 3)
        {
          oemolostream qfs = new oemolostream();
          qfs.SetFormat(OEFormat.SDF);
          qfs.openstring();
          oechem.OEWriteMolecule(qfs,query);
          qfs.close();
          molstr = qfs.GetString();
        }
        else
        {
          molstr = oechem.OEMolToSmiles(query);
        }

        Clob clob = oracle.sql.CLOB.createTemporary(conn, false,
                                                    oracle.sql.CLOB.DURATION_SESSION);

        pstmt.setFloat(2, tanCutoff);
        pstmt.setInt(3, maxHits);

        if (dimension == 3)
        {
          clob.setString(1, molstr);
          pstmt.setClob(1, clob);
        }
        else
        {
          pstmt.setString(1,molstr);
        }

        rs = pstmt.executeQuery();

        OEGraphMol mol = new OEGraphMol();
        int hitCount = 0;

        oemolistream resfs = new oemolistream();
        resfs.SetFormat(OEFormat.SDF);

        while (rs.next())
        {
          resfs.openstring(rs.getString(1));
          if (oechem.OEReadMolecule(resfs,mol))
          {
            oechem.OEWriteMolecule(ofs,mol);
          }
          else
          {
            oechem.OEThrow.Warning("Unable to read result molecule");
          }

          mol.Clear();
          hitCount++;
        }

        // Important to free the Oracle CLOB.
        ((CLOB) clob).freeTemporary();
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        Util.closeConnnection(conn);
        Util.closeStatement(pstmt);
      }
    }

    public static void main(String[] args)
    {
      URL fileURL = ShapeSearch.class.getResource("ShapeSearch.txt");
      if (fileURL == null)
      {
        oechem.OEThrow.Fatal("Unable to open interface file ShapeSearch.txt");
      }

      oemolostream ofs = null;
      oemolistream ifs = null;
      try
      {
        OEInterface itf = new OEInterface(fileURL,"ShapeSearch", args);

        String password = "";
        if (itf.HasString("-p"))
        {
          password = itf.GetString("-p");
        }
        else //prompt for password
        {
          Console cons;
          char [] tmp;
          if ((cons = System.console()) != null &&
              (tmp = cons.readPassword("Password: ")) != null)
          {
            password = new String(tmp);
          }
        }

        String outputFilename = itf.GetString("-o");
        ofs = new oemolostream();
        if (!ofs.open(outputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open " + outputFilename +
                               " for writing");
        }

        String inputFilename = itf.GetString("-i");
        ifs = new oemolistream();
        if (!ifs.open(inputFilename))
        {
          oechem.OEThrow.Fatal("Unable to open input file %s " + inputFilename);
        }

        String tableName = itf.GetString("-tname");
        String columnName = itf.GetString("-cname");
        int maxHits = itf.GetInt("-max_hits");
        float tanCutoff = itf.GetFloat("-tcut");

        OEMol mol = new OEMol();
        while (oechem.OEReadMolecule(ifs,mol))
        {
          shapeSearch(mol,ofs,password,tableName,
                      columnName,tanCutoff,maxHits);
        }
      }
      catch (Exception exception)
      {
        exception.printStackTrace();
      }
      finally
      {
        if (ofs != null)
          ofs.close();
        if (ifs != null)
          ifs.close();
      }
    }
}