mdlv2000readertest.java

化学图形处理软件

/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-08 23:35:55 +0000 (Do, 08 Feb 2007) $
 *
 * 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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * 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.io;

import java.io.InputStream;
import java.io.StringReader;
import java.util.List;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * TestCase for the reading MDL mol files using one test file.
 * A test case for SDF files is available as separate Class.
 *
 * @cdk.module test-io
 *
 * @see org.openscience.cdk.io.MDLV2000Reader
 * @see org.openscience.cdk.test.io.SDFReaderTest
 */
public class MDLV2000ReaderTest extends CDKTestCase {

    private org.openscience.cdk.tools.LoggingTool logger;

    public MDLV2000ReaderTest(String name) {
        super(name);
        logger = new org.openscience.cdk.tools.LoggingTool(this);
    }

    public static Test suite() {
        return new TestSuite(MDLV2000ReaderTest.class);
    }

    public void testAccepts() {
    	MDLV2000Reader reader = new MDLV2000Reader();
    	assertTrue(reader.accepts(ChemFile.class));
    	assertTrue(reader.accepts(ChemModel.class));
    	assertTrue(reader.accepts(Molecule.class));
    }
    
    /**
     * @cdk.bug 682233
     */
    public void testBug682233() throws Exception {
        String filename = "data/mdl/bug682233.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());

        assertNotNull(chemFile);
        assertEquals(1, chemFile.getChemSequenceCount());
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(1, seq.getChemModelCount());
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);

        org.openscience.cdk.interfaces.IMoleculeSet som = model.getMoleculeSet();
        assertNotNull(som);
        assertEquals(1, som.getMoleculeCount());
        org.openscience.cdk.interfaces.IMolecule m = som.getMolecule(0);
        assertNotNull(m);
        assertEquals(4, m.getAtomCount());
        assertEquals(2, m.getBondCount());

        // test reading of formal charges
        org.openscience.cdk.interfaces.IAtom a = m.getAtom(0);
        assertNotNull(a);
        assertEquals("Na", a.getSymbol());
        assertEquals(1, a.getFormalCharge());
        a = m.getAtom(2); 
        assertNotNull(a);
        assertEquals("O", a.getSymbol());
        assertEquals(-1, a.getFormalCharge());
    }

    public void testAPinene() throws Exception {
        String filename = "data/mdl/a-pinene.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }

    public void testReadTitle() throws Exception {
        String filename = "data/mdl/a-pinene.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        Molecule mol = (Molecule)reader.read(new Molecule());
        assertEquals("a-pinen.mol", mol.getProperty(CDKConstants.TITLE));
    }

    public void testFourRing() throws Exception {
        String filename = "data/mdl/four-ring-5x10.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }


    public void testHydrozyamino() throws Exception {
        String filename = "data/mdl/hydroxyamino.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }


    public void testMethylBenzol() throws Exception {
        String filename = "data/mdl/methylbenzol.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
        assertNotNull(chemFile);
        List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
        assertEquals(1, containersList.size());
        assertTrue(((IAtomContainer)containersList.get(0)).getAtomCount() > 0);
        assertTrue(((IAtomContainer)containersList.get(0)).getBondCount() > 0);
    }
    

    public void testPolycarpol() throws Exception {
        String filename = "data/mdl/polycarpol.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        MDLV2000Reader reader = new MDLV2000Reader(ins);
        ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());