mmff94atomtypematchertest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-05-01 12:48:26 +0000 (Di, 01 Mai 2007) $
 * $Revision: 8283 $
 * 
 * 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.atomtype;

import java.io.InputStream;
import java.io.InputStreamReader;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher;
import org.openscience.cdk.config.Elements;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.AtomTypeTools;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;

/**
 * Checks the functionality of the AtomType-MMFF94AtomTypeMatcher.
 *
 * @cdk.module test-extra
 *
 * @see org.openscience.cdk.atomtype.MMFF94AtomTypeMatcher
 */
public class MMFF94AtomTypeMatcherTest extends CDKTestCase {

	private LoggingTool logger;
	private final IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
	private HydrogenAdder haad=new HydrogenAdder();
	
	private static IMolecule testMolecule = null;
	
	public MMFF94AtomTypeMatcherTest(String name) {
        super(name);
    }

    public void setUp() throws Exception {
    	logger = new LoggingTool(this);
    }
    
    public void setUpTestMolecule() throws Exception {
    	if (testMolecule == null) {
        	//logger.debug("**** START ATOMTYPE TEST ******");
        	AtomTypeTools att=new AtomTypeTools();
            MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
            InputStream ins=this.getClass().getClassLoader().getResourceAsStream("data/mdl/mmff94AtomTypeTest_molecule.mol");
            MDLReader mdl=new MDLReader(new InputStreamReader(ins));
            testMolecule=(Molecule)mdl.read(new NNMolecule());
           
            att.assignAtomTypePropertiesToAtom(testMolecule);
            for (int i=0;i<testMolecule.getAtomCount();i++){
            	logger.debug("atomNr:" + testMolecule.getAtom(i).toString());
            	IAtomType matched = atm.findMatchingAtomType(testMolecule, testMolecule.getAtom(i));
            	assertNotNull(matched);
            	AtomTypeManipulator.configure(testMolecule.getAtom(i), matched);       
            }
            
            logger.debug("MMFF94 Atom 0:"+testMolecule.getAtom(0).getAtomTypeName());
    	}
    }

    public static Test suite() {
        return new TestSuite(MMFF94AtomTypeMatcherTest.class);
    }
    
    public void testMMFF94AtomTypeMatcher() throws ClassNotFoundException, CDKException, java.lang.Exception {
    	MMFF94AtomTypeMatcher matcher = new MMFF94AtomTypeMatcher();
	    assertNotNull(matcher);
	    
    }
    
    public void testFindMatchingAtomType_IAtomContainer_IAtom() throws ClassNotFoundException, CDKException, java.lang.Exception {
    	setUpTestMolecule();
    	for (int i=0;i<testMolecule.getAtomCount();i++) {
    		assertNotNull(testMolecule.getAtom(i).getAtomTypeName());
    		assertTrue(testMolecule.getAtom(i).getAtomTypeName().length() > 0);
    	}
    }
    
    // FIXME: Below should be tests for *all* atom types in the MM2 atom type specificiation
    
    public void testSthi() throws Exception {
    	setUpTestMolecule();
    	assertEquals("Sthi",testMolecule.getAtom(0).getAtomTypeName());
    }
    public void testCsp2() throws Exception {
    	setUpTestMolecule();
    	assertEquals("Csp2",testMolecule.getAtom(7).getAtomTypeName());
    }
    public void testCsp() throws Exception {
    	setUpTestMolecule();
        assertEquals("Csp",testMolecule.getAtom(51).getAtomTypeName());
    }
    public void testNdbO() throws Exception {
    	setUpTestMolecule();
        assertEquals("N=O",testMolecule.getAtom(148).getAtomTypeName());
    }
    public void testOar() throws Exception {
    	setUpTestMolecule();
        assertEquals("Oar",testMolecule.getAtom(198).getAtomTypeName());
    }
    public void testN2OX() throws Exception {
    	setUpTestMolecule();
        assertEquals("N2OX",testMolecule.getAtom(233).getAtomTypeName());
    }
    public void testNAZT() throws Exception {
    	setUpTestMolecule();
        assertEquals("NAZT",testMolecule.getAtom(256).getAtomTypeName());
    }
    
    // Other tests
    
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Methanol() throws ClassNotFoundException, CDKException, java.lang.Exception {

//		logger.debug("**** START ATOMTYPE Methanol TEST ******");
		//System.out.println("**** START ATOMTYPE Methanol TEST ******");  
        IMolecule mol = builder.newMolecule();
		IAtom carbon = builder.newAtom(Elements.CARBON);
		IAtom oxygen = builder.newAtom(Elements.OXYGEN);
		// making sure the order matches the test results
		mol.addAtom(carbon); 
		mol.addAtom(oxygen);
		mol.addBond(builder.newBond(carbon, oxygen, CDKConstants.BONDORDER_SINGLE));
		
		haad.addExplicitHydrogensToSatisfyValency(mol);
        
		String [] testResult={"C","O","HC","HC","HC","HO"};
		AtomTypeTools att=new AtomTypeTools();
        MMFF94AtomTypeMatcher atm= new MMFF94AtomTypeMatcher();
		att.assignAtomTypePropertiesToAtom(mol,false);
        for (int i=0;i<mol.getAtomCount();i++){
        	logger.debug("atomNr:" + mol.getAtom(i).toString());
        	IAtomType matched = atm.findMatchingAtomType(mol, mol.getAtom(i));
        	assertNotNull(matched);
        	AtomTypeManipulator.configure(mol.getAtom(i), matched);       
        }
        for (int i=0; i<testResult.length;i++){
        	assertEquals(testResult[i],mol.getAtom(i).getAtomTypeName());
        }
        
        //System.out.println("MMFF94 Atom 0:"+mol.getAtom(0).getAtomTypeName());       
	}
	/**
	 *  A unit test for JUnit with Methylamine
	 */
	public void testFindMatchingAtomType_IAtomContainer_IAtom_Methylamine() throws ClassNotFoundException, CDKException, java.lang.Exception {
		//System.out.println("**** START ATOMTYPE Methylamine TEST ******");	
		IMolecule mol = builder.newMolecule();
		IAtom carbon = builder.newAtom(Elements.CARBON);
		IAtom nitrogen = builder.newAtom(Elements.NITROGEN);
		// making sure the order matches the test results
		mol.addAtom(carbon); 
		mol.addAtom(nitrogen);
		mol.addBond(builder.newBond(carbon, nitrogen, CDKConstants.BONDORDER_SINGLE));