iteratingmdlreadertest.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) 2004-2007  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.iterator;

import java.io.InputStream;

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.io.formats.MDLV2000Format;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;

/**
 * TestCase for the reading MDL mol files using one test file.
 *
 * @cdk.module test-io
 *
 * @see org.openscience.cdk.io.MDLReader
 */
public class IteratingMDLReaderTest extends CDKTestCase {

    private LoggingTool logger;

    public IteratingMDLReaderTest(String name) {
        super(name);
        logger = new LoggingTool(this);
    }

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

    public void testSDF() throws Exception {
        String filename = "data/mdl/test2.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());

        int molCount = 0;
        while (reader.hasNext()) {
        	Object object = reader.next();
        	assertNotNull(object);
        	assertTrue(object instanceof Molecule);
        	molCount++;
        	assertEquals("Molecule # was not in MDL V2000 format: " + molCount,
        			MDLV2000Format.getInstance(), reader.getFormat());
        }

        assertEquals(6, molCount);
    }

    public void testReadTitle() throws Exception {
        String filename = "data/mdl/test.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());

        //int molCount = 0;
        assertTrue(reader.hasNext());
        Object object = reader.next();
        assertNotNull(object);
        assertTrue(object instanceof Molecule);
        assertEquals("2-methylbenzo-1,4-quinone", ((Molecule)object).getProperty(CDKConstants.TITLE));
        assertEquals(MDLV2000Format.getInstance(), reader.getFormat());
    }

    public void testReadDataItems() throws Exception {
        String filename = "data/mdl/test.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());

        //int molCount = 0;
        assertTrue(reader.hasNext());
        Object object = reader.next();
        assertNotNull(object);
        assertTrue(object instanceof Molecule);
        Molecule m = (Molecule)object;
        assertEquals("1", m.getProperty("E_NSC"));
        assertEquals("553-97-9", m.getProperty("E_CAS"));
    }

    public void testOnMDLMolfile() throws Exception {
        String filename = "data/mdl/bug682233.mol";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());

        int molCount = 0;
        while (reader.hasNext()) {
        	Object object = reader.next();
        	assertNotNull(object);
        	assertTrue(object instanceof Molecule);
        	molCount++;
        }

        assertEquals(1, molCount);
    }

    public void testOnSingleEntrySDFile() throws Exception {
        String filename = "data/mdl/singleMol.sdf";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        IteratingMDLReader reader = new IteratingMDLReader(ins, DefaultChemObjectBuilder.getInstance());

        int molCount = 0;
        while (reader.hasNext()) {
        	Object object = reader.next();
        	assertNotNull(object);
        	assertTrue(object instanceof Molecule);
        	molCount++;
        }

        assertEquals(1, molCount);
    }

}