hydrogenaddertest.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: shk3 $
 *  $Date: 2007-05-29 11:30:16 +0000 (Di, 29 Mai 2007) $
 *  $Revision: 8337 $
 *
 *  Copyright (C) 2003-2007  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.tools;

import java.io.InputStream;

import javax.vecmath.Point2d;

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

import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.Molecule;
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.io.MDLReader;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.MFAnalyser;
import org.openscience.cdk.tools.SaturationChecker;

/**
 * Tests CDK's hydrogen adding capabilities in terms of
 * example molecules.
 *
 * @cdk.module test-valencycheck
 *
 * @author     egonw
 * @cdk.created    2003-06-18
 */
public class HydrogenAdderTest extends CDKTestCase {

    protected HydrogenAdder adder = null;

    public HydrogenAdderTest(String name) {
        super(name);
    }

    /**
     * The JUnit setup method
     */
    public void setUp() throws Exception {
        adder = new HydrogenAdder();
    }

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

    public void testProton() throws Exception {
        Molecule mol = new Molecule();
        Atom proton = new Atom("H");
        proton.setFormalCharge(+1);
        mol.addAtom(proton);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(1, mol.getAtomCount());
        assertEquals(1, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(0, mol.getConnectedBondsCount(proton));
        assertEquals(0, proton.getHydrogenCount());
    }
    
    public void testHydrogen() throws Exception {
        Molecule mol = new Molecule();
        Atom proton = new Atom("H");
        mol.addAtom(proton);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(2, mol.getAtomCount());
        assertEquals(2, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(1, mol.getConnectedBondsCount(proton));
        assertEquals(0, proton.getHydrogenCount());
    }
    
    public void testMethane() throws Exception {
        Molecule mol = new Molecule();
        Atom carbon = new Atom("C");
        mol.addAtom(carbon);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(5, mol.getAtomCount());
        assertEquals(4, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(4, mol.getConnectedBondsCount(carbon));
    }
    
    public void testAminomethane() throws Exception 
    {
        Molecule aminomethane = new Molecule();
        Atom carbon = new Atom("C");
        Point2d carbonPos = new Point2d(0.0,0.0);
        carbon.setPoint2d(carbonPos);
        Atom nitrogen = new Atom("N");
        Point2d nitrogenPos = new Point2d(1.0,1.0);
        nitrogen.setPoint2d(nitrogenPos);
        aminomethane.addAtom(carbon);
        aminomethane.addAtom(nitrogen);
        aminomethane.addBond(new Bond(carbon, nitrogen));
        
        adder.addExplicitHydrogensToSatisfyValency(aminomethane);

        assertEquals(7, aminomethane.getAtomCount());
	
    }    

    public void testAmmonia() throws Exception {
        Molecule mol = new Molecule();
        Atom nitrogen = new Atom("N");
        mol.addAtom(nitrogen);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(4, mol.getAtomCount());
        assertEquals(3, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(3, mol.getConnectedBondsCount(nitrogen));
    }

    public void testAmmonium() throws Exception {
        Molecule mol = new Molecule();
        Atom nitrogen = new Atom("N");
        nitrogen.setFormalCharge(+1);
        mol.addAtom(nitrogen);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(5, mol.getAtomCount());
        assertEquals(4, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(4, mol.getConnectedBondsCount(nitrogen));
    }

    public void testWater() throws Exception {
        Molecule mol = new Molecule();
        Atom oxygen = new Atom("O");
        mol.addAtom(oxygen);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(3, mol.getAtomCount());
        assertEquals(2, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(2, mol.getConnectedBondsCount(oxygen));
    }

    public void testHydroxyl() throws Exception {
        Molecule mol = new Molecule();
        Atom oxygen = new Atom("O");
        oxygen.setFormalCharge(-1);
        mol.addAtom(oxygen);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(2, mol.getAtomCount());
        assertEquals(1, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(1, mol.getConnectedBondsCount(oxygen));
    }

    public void testHydroxonium() throws Exception {
        Molecule mol = new Molecule();
        Atom oxygen = new Atom("O");
        oxygen.setFormalCharge(+1);
        mol.addAtom(oxygen);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(4, mol.getAtomCount());
        assertEquals(3, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(3, mol.getConnectedBondsCount(oxygen));
    }
    
    public void testHalogens() throws Exception {
        halogenTest("I");
        halogenTest("F");
        halogenTest("Cl");
        halogenTest("Br");
    }
    
    private void halogenTest(String halogen) throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom(halogen);
        mol.addAtom(atom);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(2, mol.getAtomCount());
        assertEquals(1, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(1, mol.getConnectedBondsCount(atom));
    }
    
    public void testSulphur() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("S");
        mol.addAtom(atom);
        
        adder.addExplicitHydrogensToSatisfyValency(mol);
        
        assertEquals(3, mol.getAtomCount());
        assertEquals(2, new MFAnalyser(mol).getAtomCount("H"));
        assertEquals(2, mol.getConnectedBondsCount(atom));
    }
    
    public void testSulfite() throws Exception {
        Molecule mol = new Molecule();
        Atom s = new Atom("S");
        Atom o1 = new Atom("O");
        Atom o2 = new Atom("O");
        Atom o3 = new Atom("O");
        mol.addAtom(s);
        mol.addAtom(o1);
        mol.addAtom(o2);
        mol.addAtom(o3);
        Bond b1 = new Bond(s, o1, 1.0);
        Bond b2 = new Bond(s, o2, 1.0);
        Bond b3 = new Bond(s, o3, 2.0);