atomcontainertest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $    
 * $Date: 2007-02-08 23:35:55 +0000 (Do, 08 Feb 2007) $    
 * $Revision: 7921 $
 * 
 * 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;


import java.util.Iterator;
import java.util.List;

import javax.vecmath.Point2d;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomParity;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
import org.openscience.cdk.interfaces.IChemObjectListener;
import org.openscience.cdk.interfaces.IElectronContainer;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.ISingleElectron;

/**
 * Checks the funcitonality of the AtomContainer.
 *
 * @cdk.module test-data
 */
public class AtomContainerTest extends CDKTestCase {

	protected IChemObjectBuilder builder;
	
    public AtomContainerTest(String name) {
        super(name);
    }

    public void setUp() {
    	builder = DefaultChemObjectBuilder.getInstance();
    }

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

    public void testSetAtoms_arrayIAtom() {
        IAtom[] atoms = new IAtom[4];
        atoms[0] = builder.newAtom("C");
        atoms[1] = builder.newAtom("C");
        atoms[2] = builder.newAtom("C");
        atoms[3] = builder.newAtom("O");
        IAtomContainer ac = builder.newAtomContainer();
        ac.setAtoms(atoms);
        
        assertEquals(4, ac.getAtomCount());
        //assertEquals(4, ac.getAtoms().length);
    }

    /**
     * Only test wether the atoms are correctly cloned.
     */
	public void testClone() throws Exception {
        IAtomContainer molecule = builder.newAtomContainer();
        Object clone = molecule.clone();
        assertTrue(clone instanceof IAtomContainer);
    }    
        
    public void testClone_IAtom() throws Exception {
		IAtomContainer molecule = builder.newAtomContainer();
		molecule.addAtom(builder.newAtom("C")); // 1
		molecule.addAtom(builder.newAtom("C")); // 2
		molecule.addAtom(builder.newAtom("C")); // 3
		molecule.addAtom(builder.newAtom("C")); // 4

		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
		assertEquals(molecule.getAtomCount(), clonedMol.getAtomCount());
		for (int f = 0; f < molecule.getAtomCount(); f++) {
			for (int g = 0; g < clonedMol.getAtomCount(); g++) {
				assertNotNull(molecule.getAtom(f));
				assertNotNull(clonedMol.getAtom(g));
				assertNotSame(molecule.getAtom(f), clonedMol.getAtom(g));
			}
		}        
    }
    
	public void testClone_IAtom2() throws Exception {
		IMolecule molecule = builder.newMolecule();
        IAtom carbon = builder.newAtom("C");
        carbon.setPoint2d(new Point2d(2, 4));
		molecule.addAtom(carbon); // 1

        // test cloning of Atoms
		IMolecule clonedMol = (IMolecule)molecule.clone();
        carbon.setPoint2d(new Point2d(3, 1));
		assertEquals(clonedMol.getAtom(0).getPoint2d().x, 2.0, 0.001);
	}

    public void testClone_IBond() throws Exception {
		IAtomContainer molecule = builder.newAtomContainer();
		molecule.addAtom(builder.newAtom("C")); // 1
		molecule.addAtom(builder.newAtom("C")); // 2
		molecule.addAtom(builder.newAtom("C")); // 3
		molecule.addAtom(builder.newAtom("C")); // 4

		molecule.addBond(0, 1, 2.0); // 1
		molecule.addBond(1, 2, 1.0); // 2
		molecule.addBond(2, 3, 1.0); // 3
		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
		assertNotNull(clonedMol);
		assertEquals(molecule.getBondCount(), clonedMol.getBondCount());
		for (int f = 0; f < molecule.getElectronContainerCount(); f++) {
			for (int g = 0; g < clonedMol.getElectronContainerCount(); g++) {
				assertNotNull(molecule.getBond(f));
				assertNotNull(clonedMol.getBond(g));
				assertNotSame(molecule.getBond(f), clonedMol.getBond(g));
			}
		}
	}

    public void testClone_IBond2() throws Exception {
		IAtomContainer molecule = builder.newAtomContainer();
        IAtom atom1 = builder.newAtom("C");
        IAtom atom2 = builder.newAtom("C");
		molecule.addAtom(atom1); // 1
		molecule.addAtom(atom2); // 2
		molecule.addBond(builder.newBond(atom1, atom2, 2.0)); // 1
        
        // test cloning of atoms in bonds
		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
		assertNotNull(clonedMol);
        assertNotSame(atom1, clonedMol.getBond(0).getAtom(0));
        assertNotSame(atom2, clonedMol.getBond(0).getAtom(1));
	}

    public void testClone_IBond3() throws Exception {
		IAtomContainer molecule = builder.newAtomContainer();
        IAtom atom1 = builder.newAtom("C");
        IAtom atom2 = builder.newAtom("C");
		molecule.addAtom(atom1); // 1
		molecule.addAtom(atom2); // 2
		molecule.addBond(builder.newBond(atom1, atom2, 2.0)); // 1
        
        // test that cloned bonds contain atoms from cloned atomcontainer
		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
		assertNotNull(clonedMol);
        assertTrue(clonedMol.contains(clonedMol.getBond(0).getAtom(0)));
        assertTrue(clonedMol.contains(clonedMol.getBond(0).getAtom(1)));
	}

    public void testClone_ILonePair() throws Exception {
		IAtomContainer molecule = builder.newAtomContainer();
        IAtom atom1 = builder.newAtom("C");
        IAtom atom2 = builder.newAtom("C");
		molecule.addAtom(atom1); // 1
		molecule.addAtom(atom2); // 2
		molecule.addLonePair(0); 
        
        // test that cloned bonds contain atoms from cloned atomcontainer
		IAtomContainer clonedMol = (IAtomContainer)molecule.clone();
		assertNotNull(clonedMol);
        assertEquals(1, clonedMol.getConnectedLonePairsCount(clonedMol.getAtom(0)));
	}

    public void testGetConnectedElectronContainersList_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(1, acetone.getConnectedElectronContainersList(o).size());
        assertEquals(3, acetone.getConnectedElectronContainersList(c1).size());
        assertEquals(1, acetone.getConnectedElectronContainersList(c2).size());
        assertEquals(1, acetone.getConnectedElectronContainersList(c3).size());
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);

        assertEquals(3, acetone.getConnectedElectronContainersList(o).size());
        assertEquals(3, acetone.getConnectedElectronContainersList(c1).size());
        assertEquals(1, acetone.getConnectedElectronContainersList(c2).size());
        assertEquals(1, acetone.getConnectedElectronContainersList(c3).size());

    }

    public void testGetConnectedBondsList_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(1, acetone.getConnectedBondsList(o).size());
        assertEquals(3, acetone.getConnectedBondsList(c1).size());
        assertEquals(1, acetone.getConnectedBondsList(c2).size());
        assertEquals(1, acetone.getConnectedBondsList(c3).size());
        
        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);

        assertEquals(1, acetone.getConnectedBondsList(o).size());
        assertEquals(3, acetone.getConnectedBondsList(c1).size());
        assertEquals(1, acetone.getConnectedBondsList(c2).size());
        assertEquals(1, acetone.getConnectedBondsList(c3).size());
    }

//    public void testGetConnectedBonds_IAtom() {
//        // acetone molecule
//        IMolecule acetone = builder.newMolecule();
//        
//        IAtom c1 = builder.newAtom("C");
//        IAtom c2 = builder.newAtom("C");
//        IAtom o = builder.newAtom("O");
//        IAtom c3 = builder.newAtom("C");
//        acetone.addAtom(c1);
//        acetone.addAtom(c2);
//        acetone.addAtom(c3);
//        acetone.addAtom(o);
//        IBond b1 = builder.newBond(c1, c2,1);
//        IBond b2 = builder.newBond(c1, o, 2);
//        IBond b3 = builder.newBond(c1, c3,1);
//        acetone.addBond(b1);
//        acetone.addBond(b2);
//        acetone.addBond(b3);
//        
//        assertEquals(1, acetone.getConnectedBondsVector(o).size());
//        assertEquals(3, acetone.getConnectedBondsVector(c1).size());
//        assertEquals(1, acetone.getConnectedBondsVector(c2).size());
//        assertEquals(1, acetone.getConnectedBondsVector(c3).size());
//        
//        // add lone pairs on oxygen
//        ILonePair lp1 = builder.newLonePair(o);
//        ILonePair lp2 = builder.newLonePair(o);
//        acetone.addElectronContainer(lp1);
//        acetone.addElectronContainer(lp2);
//
//        assertEquals(1, acetone.getConnectedBondsVector(o).size());
//        assertEquals(3, acetone.getConnectedBondsVector(c1).size());
//        assertEquals(1, acetone.getConnectedBondsVector(c2).size());
//        assertEquals(1, acetone.getConnectedBondsVector(c3).size());
//    }

    public void testGetConnectedLonePairsList_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        assertEquals(0, acetone.getConnectedLonePairsList(o).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c1).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c2).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c3).size());

        // add lone pairs on oxygen
        ILonePair lp1 = builder.newLonePair(o);
        ILonePair lp2 = builder.newLonePair(o);
        acetone.addLonePair(lp1);
        acetone.addLonePair(lp2);

        assertEquals(2, acetone.getConnectedLonePairsList(o).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c1).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c2).size());
        assertEquals(0, acetone.getConnectedLonePairsList(c3).size());

    }

    
    public void testRemoveAtomAndConnectedElectronContainers_IAtom() {
        // acetone molecule
        IMolecule acetone = builder.newMolecule();
        
        IAtom c1 = builder.newAtom("C");
        IAtom c2 = builder.newAtom("C");
        IAtom o = builder.newAtom("O");
        IAtom c3 = builder.newAtom("C");
        acetone.addAtom(c1);
        acetone.addAtom(c2);
        acetone.addAtom(c3);
        acetone.addAtom(o);
        IBond b1 = builder.newBond(c1, c2,1);
        IBond b2 = builder.newBond(c1, o, 2);
        IBond b3 = builder.newBond(c1, c3,1);
        acetone.addBond(b1);
        acetone.addBond(b2);
        acetone.addBond(b3);
        
        // add lone pairs on oxygen