hueckelaromaticitydetectortest.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-04-21 00:23:13 +0000 (Sa, 21 Apr 2007) $
 *  $Revision: 8225 $
 *
 *  Copyright (C) 1997-2007  The Chemistry Development Kit (CDK) 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.
 *
 *  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.aromaticity;

import java.io.InputStream;

import javax.vecmath.Point2d;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;

/**
 *  Description of the Class
 *
 * @cdk.module test-standard
 *
 *@author     steinbeck
 *@cdk.created    2002-10-06
 */
public class HueckelAromaticityDetectorTest extends CDKTestCase
{
	boolean standAlone = false;
	private static LoggingTool logger = new LoggingTool(HueckelAromaticityDetectorTest.class);

	/**
	 *  Constructor for the HueckelAromaticityDetectorTest object
	 *
	 *@param  name  Description of the Parameter
	 */
	public HueckelAromaticityDetectorTest(String name)
	{
		super(name);
	}


	/**
	 *  A unit test suite for JUnit
	 *
	 *@return    The test suite
	 */
	public static Test suite()
	{
		return new TestSuite(HueckelAromaticityDetectorTest.class);
	}


	/**
	 *  Sets the standAlone attribute of the HueckelAromaticityDetectorTest object
	 *
	 *@param  standAlone  The new standAlone value
	 */
	public void setStandAlone(boolean standAlone)
	{
		this.standAlone = standAlone;
	}

	public void testDetectAromaticity_IAtomContainer() throws Exception
	{
		IMolecule mol = makeAromaticMolecule();

		HueckelAromaticityDetector.detectAromaticity(mol);

		int numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(6, numberOfAromaticAtoms);

		int numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(6, numberOfAromaticBonds);
			
	}
	
	public void testDetectAromaticity_IAtomContainer_IRingSet() throws Exception
	{
		
		IMolecule mol = makeAromaticMolecule();

		IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
		HueckelAromaticityDetector.detectAromaticity(mol, rs);

		int numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(6, numberOfAromaticAtoms);

		int numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(6, numberOfAromaticBonds);
			
	}
	
	public void testDetectAromaticity_IAtomContainer_boolean() throws Exception
	{
		
		IMolecule mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		HueckelAromaticityDetector.detectAromaticity(mol, false);

		int numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(10, numberOfAromaticAtoms);

		int numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(11, numberOfAromaticBonds);
			
		mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		HueckelAromaticityDetector.detectAromaticity(mol, true);

		numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(6, numberOfAromaticAtoms);

		numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(6, numberOfAromaticBonds);
			
	}
	
	public void testDetectAromaticity_IAtomContainer_boolean_AllRingsFinder() throws Exception
	{
		IMolecule mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		HueckelAromaticityDetector.detectAromaticity(mol, false, new AllRingsFinder());

		int numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(10, numberOfAromaticAtoms);

		int numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(11, numberOfAromaticBonds);
			
		mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		HueckelAromaticityDetector.detectAromaticity(mol, true, new AllRingsFinder());

		numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(6, numberOfAromaticAtoms);

		numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(6, numberOfAromaticBonds);
			
	}
	
	public void testDetectAromaticity_IAtomContainer_IRingSet_boolean() throws Exception
	{
		IMolecule mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
		HueckelAromaticityDetector.detectAromaticity(mol, rs, false);

		int numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(10, numberOfAromaticAtoms);

		int numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(11, numberOfAromaticBonds);
			
		mol = makeAromaticMolecule();
		for (int i = 0; i < mol.getAtomCount(); ++i) mol.getAtom(i).setFlag(CDKConstants.ISAROMATIC, true);
		rs = (new AllRingsFinder()).findAllRings(mol);
		HueckelAromaticityDetector.detectAromaticity(mol, rs, true);

		numberOfAromaticAtoms = 0;
		for (int i = 0; i < mol.getAtomCount(); i++) {
			if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticAtoms++;
		}
		assertEquals(6, numberOfAromaticAtoms);

		numberOfAromaticBonds= 0;
		for (int i = 0; i < mol.getBondCount(); i++) {
			if (((IBond)mol.getBond(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticBonds++;
		}
		assertEquals(6, numberOfAromaticBonds);
			
	}
	
	/**
	 *  A unit test for JUnit
	 */
	public void testSetRingFlags_IRingSet() throws Exception
	{

		IMolecule mol = makeAromaticMolecule();
		IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
		HueckelAromaticityDetector.detectAromaticity(mol, rs, true);

		IRingSet ringset = (new SSSRFinder(mol)).findSSSR();
		HueckelAromaticityDetector.setRingFlags(ringset);

		int numberOfAromaticRings = 0;
		for (int i = 0; i < ringset.getAtomContainerCount(); i++) {
			if (((Ring)ringset.getAtomContainer(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticRings++;
		}
		assertEquals(numberOfAromaticRings, 1);
	}
	
	public void testGetRingSet() throws Exception
	{
		IMolecule mol = makeAromaticMolecule();

		HueckelAromaticityDetector.detectAromaticity(mol);
		IRingSet rs = HueckelAromaticityDetector.getRingSet();
		assertEquals(3, rs.getAtomContainerCount());
			
	}
	
	public void testSetTimeout_long() throws Exception
	{
		HueckelAromaticityDetector.setTimeout(1);
		IMolecule mol = makeAromaticMolecule();
		try {
			HueckelAromaticityDetector.detectAromaticity(mol);
			int numberOfAromaticAtoms = 0;
			for (int i = 0; i < mol.getAtomCount(); i++) {
				if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
					numberOfAromaticAtoms++;
			}
			fail("Should have failed with an time out exception");
			
		} catch (Exception exc)
		{
			if (exc.getMessage().equals("Timeout for AllringsFinder exceeded")) {
				HueckelAromaticityDetector.setTimeout(5000); // reset timeout to default
				return;
			}
			throw exc;
		}
	}
	
//	public void testSetRingFinder_AllRingsFinder()
//	{
//		// Will fail because it never uses the instance of HAD (static method)
//		AllRingsFinder finder = new AllRingsFinder();
//		finder.setTimeout(0);
//		HueckelAromaticityDetector detector = new HueckelAromaticityDetector(); 
//		detector.setRingFinder(finder);
//		IMolecule mol = makeAromaticMolecule();
//		try {
//			detector.detectAromaticity(mol);
//			int numberOfAromaticAtoms = 0;
//			for (int i = 0; i < mol.getAtomCount(); i++) {
//				if (((IAtom)mol.getAtom(i)).getFlag(CDKConstants.ISAROMATIC))
//					numberOfAromaticAtoms++;
//			}
//			assertEquals(0, numberOfAromaticAtoms);
//			
//		} catch (Exception exc)
//		{
//			if (exc.getMessage().equals("Timeout for AllringsFinder exceeded")) {
//				return;
//			}
//			if (standAlone)
//			{
//				exc.printStackTrace();
//			}
//			fail(exc.toString());
//		}
//	}
	
	public void testHueckelAromaticityDetector()
	{
		// For autogenerated constructor
		HueckelAromaticityDetector detector = new HueckelAromaticityDetector(); 
		assertNotNull(detector);
	}
	
	public void testPyridine() throws Exception
	{
		SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());

		IMolecule mol = sp.parseSmiles("c1ccncc1");
		IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
		HueckelAromaticityDetector.detectAromaticity(mol, rs, true);

		IRingSet ringset = (new SSSRFinder(mol)).findSSSR();
		HueckelAromaticityDetector.setRingFlags(ringset);

		int numberOfAromaticRings = 0;
		for (int i = 0; i < ringset.getAtomContainerCount(); i++) {
			if (((Ring)ringset.getAtomContainer(i)).getFlag(CDKConstants.ISAROMATIC))
				numberOfAromaticRings++;
		}
		assertEquals(numberOfAromaticRings, 1);
	}
	
	
	/**
	 *  A unit test for JUnit The special difficulty with Azulene is that only the
	 *  outermost larger 10-ring is aromatic according to Hueckel rule.
	 */
	public void testAzulene() throws Exception
	{
		boolean[] testResult =
				{true,
				true,
				true,
				true,
				true,
				true,
				true,
				true,
				true,