breakingbondreactiontest.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.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
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.BreakingBondReaction;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LonePairElectronChecker;
import org.openscience.cdk.tools.manipulator.ReactionManipulator;

/**
 * TestSuite that runs a test for the BreakingBondReactionTest.
 * Generalized Reaction: A=B => [A-]-[B+] + [A+]-[B-].
 *
 * @cdk.module test-reaction
 */
public class BreakingBondReactionTest extends CDKTestCase {
	
	private IReactionProcess type;

	/**
	 * Constructror of the BreakingBondReactionTest object
	 *
	 */
	public  BreakingBondReactionTest() {
		type  = new BreakingBondReaction();
	}
    
	public static Test suite() {
		return new TestSuite(BreakingBondReactionTest.class);
	}

	/**
	 * A unit test suite for JUnit. Reaction: 
	 * C(H)(H)=O => [C+](H)(H)-[O-] + [C+](H)=O +  
	 * Automatic sarch of the centre active.
	 *
	 * @return    The test suite
	 */
	public void testBB_AutomaticSearchCentreActiveFormaldehyde() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
		
		/*C=O*/
		IMolecule molecule = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("C=O");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addExplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(molecule);
		setOfReactants.addMolecule(molecule);
		
		/*automatic search of the centre active*/
        Object[] params = {Boolean.FALSE};
        type.setParameters(params);
        
        /* iniciate */
        IReactionSet setOfReactions = type.initiate(setOfReactants, null);
        
        Assert.assertEquals(5, setOfReactions.getReactionCount());
        Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());
        Assert.assertEquals(2, setOfReactions.getReaction(1).getProductCount());

        IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
        /*[C+]-[O-]*/
		IMolecule molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]-[O-]");
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(0, 2, 1);
	    molecule2.addBond(0, 3, 1);
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
		product = setOfReactions.getReaction(1).getProducts().getMolecule(0);
        /*[H-] + [C+](H)=O*/
		molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("C=O");
		molecule2.getAtom(0).setFormalCharge(+1);
		molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(0, 2, 1);
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
		product = setOfReactions.getReaction(2).getProducts().getMolecule(0);
        /*[H+] + [C-](H)=O*/
		molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("C=O");
		molecule2.getAtom(0).setFormalCharge(-1);
		molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(0, 2, 1);
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
		
	}
	/**
	 * A unit test suite for JUnit. Reaction: C=O => [C+]-[O-]
	 * Manually put of the centre active.
	 *
	 * @return    The test suite
	 */
	public void testBB_ManuallyPutCentreActiveFormaldehyde() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();

		/*C=O*/
		IMolecule molecule = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("C=O");
	    HydrogenAdder adder = new HydrogenAdder();
	    adder.addExplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(molecule);
		setOfReactants.addMolecule(molecule);
		
		/*manually put the centre active*/
		molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
		
        Object[] params = {Boolean.TRUE};
        type.setParameters(params);
        
        /* iniciate */
        IReactionSet setOfReactions = type.initiate(setOfReactants, null);
        
        Assert.assertEquals(1, setOfReactions.getReactionCount());
        Assert.assertEquals(1, setOfReactions.getReaction(0).getProductCount());

        IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
        /*[C+]-[O-]*/
		IMolecule molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]-[O-]");
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(0, 2, 1);
	    molecule2.addBond(0, 3, 1);
        QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
        		
	}
	/**
	 * A unit test suite for JUnit. Reaction: C=O => [C+]-[O-] + [C-]-[O+]
	 * Test of mapped between the reactant and product. Only is mapped the centre active.
	 *
	 * @return    The test suite
	 */
	public void testBB_MappingFormaldehyde() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
		/*C=O*/
		IMolecule molecule = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("C=O");
	    HydrogenAdder adder = new HydrogenAdder();
	    adder.addExplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(molecule);
		setOfReactants.addMolecule(molecule);
		
		/*automatic search of the centre active*/
        Object[] params = {Boolean.FALSE};
        type.setParameters(params);
        
        /* iniciate */
        IReactionSet setOfReactions = type.initiate(setOfReactants, null);
        
        IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(0);

        Assert.assertEquals(3,setOfReactions.getReaction(0).getMappingCount());
        IAtom mappedProductA1 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(0));
        assertEquals(mappedProductA1, product.getAtom(0));
        IAtom mappedProductA2 = (IAtom)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getAtom(1));
        assertEquals(mappedProductA2, product.getAtom(1));
        IBond mappedProductB1 = (IBond)ReactionManipulator.getMappedChemObject(setOfReactions.getReaction(0), molecule.getBond(0));
        assertEquals(mappedProductB1, product.getBond(0));
        
	}
	/**
	 * A unit test suite for JUnit. Reaction: 
	 * F-CC => [F-] + [C+]C  
	 *
	 * @return    The test suite
	 */
	public void testBB_1() throws ClassNotFoundException, CDKException, java.lang.Exception {
		IMoleculeSet setOfReactants = DefaultChemObjectBuilder.getInstance().newMoleculeSet();
		/*FCC*/
		IMolecule molecule = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("FCC");
	    HydrogenAdder adder = new HydrogenAdder();
        adder.addExplicitHydrogensToSatisfyValency(molecule);
        LonePairElectronChecker lpcheck = new LonePairElectronChecker();
		lpcheck.newSaturate(molecule);
		setOfReactants.addMolecule(molecule);
		
		/*manually put the centre active*/
		molecule.getAtom(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getAtom(1).setFlag(CDKConstants.REACTIVE_CENTER,true);
		molecule.getBond(0).setFlag(CDKConstants.REACTIVE_CENTER,true);
		
        Object[] params = {Boolean.TRUE};
        type.setParameters(params);
        
        /* iniciate */
        IReactionSet setOfReactions = type.initiate(setOfReactants, null);
        
        Assert.assertEquals(1, setOfReactions.getReactionCount());
        Assert.assertEquals(2, setOfReactions.getReaction(0).getProductCount());

        IMolecule product = setOfReactions.getReaction(0).getProducts().getMolecule(1);
        /*[C+]C*/
		IMolecule molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("[C+]C");
		molecule2.addAtom(new Atom("H"));
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(0, 2, 1);
	    molecule2.addBond(0, 3, 1);
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addAtom(new Atom("H"));
	    molecule2.addBond(1, 4, 1);
	    molecule2.addBond(1, 5, 1);
	    molecule2.addBond(1, 6, 1);
		
		QueryAtomContainer qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
		product = setOfReactions.getReaction(0).getProducts().getMolecule(0);
        /*F-]*/
		molecule2 = (new SmilesParser(DefaultChemObjectBuilder.getInstance())).parseSmiles("[F-]");
        qAC = QueryAtomContainerCreator.createSymbolAndChargeQueryContainer(product);
		Assert.assertTrue(UniversalIsomorphismTester.isIsomorph(molecule2,qAC));
		
	}
}