How to generate fingerprints for similarity screening

FingerprintGenerator.java

package org.theplateisbad.fp;

import java.io.IOException;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.BitSet;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.aromaticity.Aromaticity;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.fingerprint.IBitFingerprint;
import org.openscience.cdk.fingerprint.PubchemFingerprinter;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;

public class FingerprintGenerator {

	static {
		try {
			Class.forName("org.postgresql.Driver");
		} catch (ClassNotFoundException e) {
			e.printStackTrace();
		}
	}

	public static void main(String[] args) throws CDKException, CloneNotSupportedException, IOException, SQLException {
		String url = "jdbc:postgresql://localhost/chemistry?user=postgres&password=";
		CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
		SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());

		PubchemFingerprinter fpr = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());

		try (Connection conn = DriverManager.getConnection(url);
				Statement query = conn.createStatement(ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY);
				PreparedStatement update = conn.prepareStatement(
						"UPDATE cdk.externalfp SET pubchemfp = ?::bit varying, cardinality = ? WHERE id = ?",
						ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_UPDATABLE)) {
			
			conn.setAutoCommit(false);

			query.setFetchSize(10000);

			ResultSet rows = query.executeQuery("SELECT id, smiles FROM cdk.externalfp");

			while (rows.next()) {
				int id = rows.getInt(1);
				String smiles = rows.getString(2);
				System.out.println(id + ":" + smiles);
				IAtomContainer mol = smilesParser.parseSmiles(smiles);
				AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
				adder.addImplicitHydrogens(mol);
				AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
				Aromaticity.cdkLegacy().apply(mol);
				IBitFingerprint fp = fpr.getBitFingerprint(mol);
				String bitstring = fingerprint2bitString(fp);
				update.setString(1, bitstring);
				update.setInt(2, fp.cardinality());
				update.setInt(3, id);
				update.executeUpdate();
			}

			conn.commit();
			rows.close();
			conn.setAutoCommit(true);
		}
	}

	private static String fingerprint2bitString(final IBitFingerprint fp) {
		StringBuilder res = new StringBuilder();
		BitSet fpBits = fp.asBitSet();

		for (long i = 0; i < fp.size(); i++) {
			if (true == fpBits.get((int) i)) {
				res.append('1');
			} else {
				res.append('0');
			}
		}

		return res.toString();
	}
}