How to screen for chemical similarity using binary fingerprints

FindBySimilarity.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.Types;
import java.util.BitSet;
import java.util.LinkedList;
import java.util.Scanner;

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;

import java.util.List;

public class FindBySimilarity {

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

	public static void main(String[] args) throws CDKException, CloneNotSupportedException, IOException, SQLException {
		try (Scanner scan = new Scanner(System.in)) {
			while (true) {
				System.out.println("Enter SMILES:");
				String SMILES = scan.next();
				System.out.println("Enter >= threshold:");
				float threshold = scan.nextFloat();
				System.out.println("Enter top N:");
				int topN = scan.nextInt();

				System.out.println("\nPos.\tTanimoto\tTarget");
				System.out.println("--------------------------------------------------------------------------------");
				for (String result : find(SMILES, threshold, topN)) {
					System.out.println(result);
				}
				System.out.println();
			}
		}
	}

	private static List<String> find(final String SMILES, final float threshold, final int topN)
			throws SQLException, CDKException {
		String url = "jdbc:postgresql://localhost/chemistry?user=postgres&password=";
		List<String> res = new LinkedList<String>();

		try (Connection conn = DriverManager.getConnection(url);
				PreparedStatement query = conn.prepareStatement(
						"SELECT id, smiles, cdk.tanimoto(?::bit varying, pubchemfp) AS tanimoto FROM cdk.externalfp WHERE cdk.tanimoto_c(?::bit varying, pubchemfp) >= ? AND cardinality BETWEEN ? AND ? ORDER BY tanimoto DESC FETCH FIRST ? ROWS ONLY",
						ResultSet.TYPE_FORWARD_ONLY, ResultSet.CONCUR_READ_ONLY)) {
			
			conn.setAutoCommit(false);

			IBitFingerprint fp = fingerprint(SMILES);

			//int[] lohi = swamidassBaldiLimitsForTanimoto(fp.cardinality(), threshold);
			int[] lohi = {0, Integer.MAX_VALUE};

			String bitstring = fingerprint2bitString(fp);
			query.setString(1, bitstring);
			query.setString(2, bitstring);
			query.setFloat(3, threshold);
			query.setInt(4, lohi[0]);
			query.setInt(5, lohi[1]);

			if (topN < 1) {
				query.setNull(6, Types.BIGINT);
				query.setFetchSize(1000);
			} else {
				query.setInt(6, topN);
				query.setFetchSize(topN);
			}

			long start = System.currentTimeMillis();
			ResultSet result = query.executeQuery();
			long end = System.currentTimeMillis();
			int pos = 1;

			while (result.next()) {
				res.add(pos++ + "\t" + String.format("%f", result.getFloat(3)) + "\t" + result.getInt(1) + ":"
						+ result.getString(2));
			}
			
			res.add("Found in " + (end - start) / 1000f + " s");

			result.close();
			conn.setAutoCommit(true);
		}

		return res;
	}

	private static IBitFingerprint fingerprint(final String SMILES) throws CDKException {
		CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance());
		SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());
		PubchemFingerprinter fpr = new PubchemFingerprinter(DefaultChemObjectBuilder.getInstance());
		IAtomContainer mol = smilesParser.parseSmiles(SMILES);
		AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
		adder.addImplicitHydrogens(mol);
		AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
		Aromaticity.cdkLegacy().apply(mol);

		return fpr.getBitFingerprint(mol);
	}

	/*
	 * "Bounds and algorithms for fast exact searches of chemical fingerprints in
	 * linear and sublinear time." Swamidass S.J., Baldi P. J Chem Inf Model. 2007
	 * Mar-Apr;47(2):302-17. Epub 2007 Feb 28.
	 * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527184/
	 */
	private static int[] swamidassBaldiLimitsForTanimoto(final int cardinality, final double threshold) {
		int[] lohi = { 0, Integer.MAX_VALUE };

		lohi[0] = (int) Math.floor(cardinality * threshold);
		lohi[1] = (int) Math.ceil(cardinality / threshold);

		return lohi;
	}

	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();
	}
}