radicalsiteinitiationhreactiontest.java

化学图形处理软件

/* $RCSfile$
 * $Author: miguelrojasch $
 * $Date: 2006-05-11 14:25:07 +0200 (Do, 11 Mai 2006) $
 * $Revision: 6221 $
 *
 *  Copyright (C) 2004-2007  Miguel Rojas <[e-mail]>
 * 
 * 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.reaction.type;


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

import org.openscience.cdk.Atom;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.RadicalSiteInitiationHReaction;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;

/**
 * TestSuite that runs a test for the RadicalSiteInitiationHReactionTest.
 * Generalized Reaction: [A*]-B-H => A=B + [H*].
 *
 * @cdk.module test-reaction
 */
public class RadicalSiteInitiationHReactionTest extends CDKTestCase {
	
	private IReactionProcess type;
	/**
	 * Constructror of the RadicalSiteInitiationHReactionTest object
	 *
	 */
	public  RadicalSiteInitiationHReactionTest() {
		type  = new RadicalSiteInitiationHReaction();
	}
    
	public static Test suite() {
		return new TestSuite(RadicalSiteInitiationHReactionTest.class);
	}
	/**
	 * A unit test suite for JUnit. Reaction: [C*]([H])([H])C([H])([H])[H] => C=C +[H*]
	 * Automatic sarch of the centre active.
	 *
	 * @return    The test suite
	 */
	public void testAutomaticSearchCentreActiveExample1() throws ClassNotFoundException, CDKException, java.lang.Exception {
        
		/*[C*]-C-C*/
		IMolecule molecule = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]([H])([H])C([H])([H])[H]");
        IAtom atom =  molecule.getAtom(0);
        molecule.addSingleElectron(new SingleElectron(atom));
        atom.setFormalCharge(0);
		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
		setOfReactants.addMolecule(molecule);
		
        Object[] params = {Boolean.FALSE};
        type.setParameters(params);
        IReactionSet setOfReactions = type.initiate(setOfReactants, null);
        
        Assert.assertEquals(1, setOfReactions.getReactionCount());
        Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());

        
        IMolecule product1 = setOfReactions.getReaction(0).getProducts().getMolecule(0);
		
        /*C=C*/
        IMolecule molecule2 = (new SmilesParser(org.openscience.cdk.DefaultChemObjectBuilder.getInstance())).parseSmiles("C([H])([H])=C([H])[H]");
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product1);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
		IMolecule product2 = setOfReactions.getReaction(0).getProducts().getMolecule(1);
		
        /*[H*]*/
		molecule2 = (Molecule) molecule2.getBuilder().newMolecule();
		molecule2.addAtom(new Atom("H"));
        molecule2.addSingleElectron(new SingleElectron(molecule2.getAtom(0)));
        		
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product2);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));

		Assert.assertEquals(4,setOfReactions.getReaction(0).getMappingCount());
		IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(4));
		assertEquals(mappedProductA1, product2.getAtom(0));
        IBond mappedProductB1 = (IBond)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getBond(2));
        assertEquals(mappedProductB1, product1.getBond(2));
        IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
        assertEquals(mappedProductA2, product1.getAtom(0));
        IAtom mappedProductA3 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(3));
        assertEquals(mappedProductA3, product1.getAtom(3));
       
	}
}