tanimototest.java

化学图形处理软件

/*
 * $RCSfile$    
 * $Author: egonw $    
 * $Date: 2007-04-21 00:25:12 +0000 (Sa, 21 Apr 2007) $    
 * $Revision: 8226 $
 * 
 * Copyright (C) 1997-2007  The Chemistry Development Kit (CKD) project
 * 
 * Contact: [e-mail]
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All I ask is that proper credit is given for my work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. 
 * 
 */

package org.openscience.cdk.test.similarity;

import java.util.BitSet;

import junit.framework.Test;
import junit.framework.TestSuite;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.swing.MoleculeListViewer;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.similarity.Tanimoto;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.test.CDKTestCase;

/**
 * @cdk.module test-extra
 */
public class TanimotoTest extends CDKTestCase
{
	
	boolean standAlone = false;
	//private static LoggingTool logger = new LoggingTool(TanimotoTest.class);
	
	public TanimotoTest(String name)
	{
		super(name);
	}

	public static Test suite() {
		return new TestSuite(TanimotoTest.class);
	}

	public void testTanimoto1() throws java.lang.Exception
	{
		Molecule mol1 = MoleculeFactory.makeIndole();
		Molecule mol2 = MoleculeFactory.makePyrrole();
		Fingerprinter fingerprinter = new Fingerprinter();
		BitSet bs1 = fingerprinter.getFingerprint(mol1);
		BitSet bs2 = fingerprinter.getFingerprint(mol2);
		float tanimoto = Tanimoto.calculate(bs1, bs2);
		if (standAlone) System.out.println("Tanimoto: " + tanimoto);
		if (!standAlone) assertEquals(0.40625, tanimoto, 0.01);
	}
	public void testTanimoto2() throws java.lang.Exception
	{
		Molecule mol1 = MoleculeFactory.makeIndole();
		Molecule mol2 = MoleculeFactory.makeIndole();
		Fingerprinter fingerprinter = new Fingerprinter();
		BitSet bs1 = fingerprinter.getFingerprint(mol1);
		BitSet bs2 = fingerprinter.getFingerprint(mol2);
		float tanimoto = Tanimoto.calculate(bs1, bs2);
		if (standAlone) System.out.println("Tanimoto: " + tanimoto);
		if (!standAlone) assertEquals(1.0, tanimoto, 0.001);
	}
	
        public void testTanimoto3() throws java.lang.Exception
        {
            double[] f1 = {1,2,3,4,5,6,7};
            double[] f2 = {1,2,3,4,5,6,7};
            float tanimoto = Tanimoto.calculate(f1,f2);
            if (standAlone) System.out.println("Tanimoto: " + tanimoto);
            if (!standAlone) assertEquals(1.0, tanimoto, 0.001);
        }

    	public void visualTestR00258() throws java.lang.Exception
    	{
    		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
    		String smiles1 = "O=C(O)CCC(=O)C(=O)O";
    		String smiles2 = "O=C(O)C(N)CCC(=O)O";
    		String smiles3 = "O=C(O)C(N)C";
    		String smiles4 = "CC(=O)C(=O)O";
    		IMolecule molecule1 = sp.parseSmiles(smiles1);
    		MoleculeListViewer listviewer = new MoleculeListViewer();
    		listviewer.addStructure(molecule1, "Smiles-1");
    		IMolecule molecule2 = sp.parseSmiles(smiles2);
    		listviewer.addStructure(molecule2, "Smiles-2");
    		IMolecule molecule3 = sp.parseSmiles(smiles3);
    		listviewer.addStructure(molecule3, "Smiles-3");
    		IMolecule molecule4 = sp.parseSmiles(smiles4);
    		listviewer.addStructure(molecule4, "Smiles-4");
    		Fingerprinter fingerprinter = new Fingerprinter(1024, 6);
    		BitSet bs1 = fingerprinter.getFingerprint(molecule1);
    		BitSet bs2 = fingerprinter.getFingerprint(molecule2);
    		BitSet bs3 = fingerprinter.getFingerprint(molecule3);
    		BitSet bs4 = fingerprinter.getFingerprint(molecule4);
    		float tanimoto1 = Tanimoto.calculate(bs1, bs2);
    		float tanimoto2 = Tanimoto.calculate(bs1, bs3);
    		float tanimoto3 = Tanimoto.calculate(bs1, bs4);
    		float tanimoto4 = Tanimoto.calculate(bs2, bs3);
    		float tanimoto5 = Tanimoto.calculate(bs2, bs4);
    		float tanimoto6 = Tanimoto.calculate(bs3, bs4);
    		//logger.debug("Similarity " + smiles1 + " vs. " + smiles2 + ": " + tanimoto1);
    		//logger.debug("Similarity " + smiles1 + " vs. " + smiles3 + ": " + tanimoto2);
    		//logger.debug("Similarity " + smiles1 + " vs. " + smiles4 + ": " + tanimoto3);
    		//logger.debug("Similarity " + smiles2 + " vs. " + smiles3 + ": " + tanimoto4);
    		//logger.debug("Similarity " + smiles2 + " vs. " + smiles4 + ": " + tanimoto5);
    		//logger.debug("Similarity " + smiles3 + " vs. " + smiles4 + ": " + tanimoto6);
    		System.out.println("Similarity 1 vs. 2: " + tanimoto1);
    		System.out.println("Similarity 1 vs. 3: " + tanimoto2);
    		System.out.println("Similarity 1 vs. 4: " + tanimoto3);
    		System.out.println("Similarity 2 vs. 3: " + tanimoto4);
    		System.out.println("Similarity 2 vs. 4: " + tanimoto5);
    		System.out.println("Similarity 3 vs. 4: " + tanimoto6);

    		
    		
    	}

}