ghemicalreadertest.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) 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.StringReader;

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

import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.io.GhemicalMMReader;
import org.openscience.cdk.test.CDKTestCase;

/**
 * TestCase for the reading Ghemical molecular dynamics files using one test file.
 *
 * @cdk.module test-io
 *
 * @see org.openscience.cdk.io.GhemicalReader
 */
public class GhemicalReaderTest extends CDKTestCase {

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

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

    public void testAccepts() {
    	GhemicalMMReader reader = new GhemicalMMReader();
    	assertTrue(reader.accepts(ChemModel.class));
    }

    public void testExample() throws Exception {
        String testfile =
"!Header mm1gp 100\n" +
"!Info 1\n" +
"!Atoms 6\n" +
"0 6 \n" +
"1 6 \n" +
"2 1 \n" +
"3 1 \n" +
"4 1 \n" +
"5 1 \n" +
"!Bonds 5\n" +
"1 0 D \n" +
"2 0 S \n" +
"3 0 S \n" +
"4 1 S \n" +
"5 1 S \n" +
"!Coord\n" +
"0 0.06677 -0.00197151 4.968e-07 \n" +
"1 -0.0667699 0.00197154 -5.19252e-07 \n" +
"2 0.118917 -0.097636 2.03406e-06 \n" +
"3 0.124471 0.0904495 -4.84021e-07 \n" +
"4 -0.118917 0.0976359 -2.04017e-06 \n" +
"5 -0.124471 -0.0904493 5.12591e-07 \n" +
"!Charges\n" +
"0 -0.2\n" +
"1 -0.2\n" +
"2 0.1\n" +
"3 0.1\n" +
"4 0.1\n" +
"5 0.1\n" +
"!End";
        StringReader stringReader = new StringReader(testfile);
        GhemicalMMReader reader = new GhemicalMMReader(stringReader);
        ChemModel model = (ChemModel)reader.read((ChemObject)new ChemModel());

        assertNotNull(model);
        assertNotNull(model.getMoleculeSet());
        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(6, m.getAtomCount());
        assertEquals(5, m.getBondCount());

        // test reading of formal charges
        org.openscience.cdk.interfaces.IAtom a = m.getAtom(0);
        assertNotNull(a);
        assertEquals(6, a.getAtomicNumber());
        assertEquals(-0.2, a.getCharge(), 0.01);
        assertEquals(0.06677, a.getPoint3d().x, 0.01);
    }

}