MolfileReaderTest.java

/*
 * MX Cheminformatics Tools for Java
 * 
 * Copyright (c) 2007, 2008 Metamolecular, LLC
 * 
 * http://metamolecular.com
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */

package com.chemhack.jsMolEditor.client.test;

import com.chemhack.jsMolEditor.client.io.mdl.MolfileReader;
import com.chemhack.jsMolEditor.client.model.Molecule;
import com.chemhack.jsMolEditor.client.model.DefaultMolecule;
import com.chemhack.jsMolEditor.client.model.Atom;
import com.google.gwt.junit.client.GWTTestCase;

/**
 * @author Richard L. Apodaca
 *         Duan Lian
 */
public class MolfileReaderTest extends GWTTestCase {
    private String TEMPO = "[NO NAME]\n  CHEMWRIT          2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 11 11  0  0  0  0  0  0  0  0  0 V2000\n    7.3600   -6.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.2260   -7.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.0921   -6.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.0921   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.2260   -5.1800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    7.3600   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    9.5921   -4.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n   10.0921   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.8600   -4.8140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    6.3600   -5.6800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.2260   -4.1800    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n  1  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  3  4  1  0  0  0  0\n  4  5  1  0  0  0  0\n  5  6  1  0  0  0  0\n  6  1  1  0  0  0  0\n  4  7  1  0  0  0  0\n  4  8  1  0  0  0  0\n  6  9  1  0  0  0  0\n  6 10  1  0  0  0  0\n  5 11  1  0  0 \nM  RAD  1  11   1\nM  END";

    private String methylRadical = "[NO NAME]\n  CHEMWRIT          2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n  1  0  0  0  0  0  0  0  0  0  0 V2000\n    6.4000   -6.2000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\nM  RAD  1   1   1\nM  END";

    private MolfileReader reader = new MolfileReader();

    public String getModuleName() {
        return "com.chemhack.jsMolEditor.Editor";
    }


    public void testItShouldReadSingletMethylRadical() {
        Molecule mr = new DefaultMolecule();

        reader.read(mr, methylRadical);

        assertEquals(1, mr.countAtoms());
        assertEquals(1, mr.getAtom(0).getRadical());
    }

    public void testItShouldReadTheOxygenCenteredRadicalInNMO() {
        Molecule tempo = new DefaultMolecule();

        reader.read(tempo, TEMPO);

        Atom o = null;

        for (int i = 0; i < tempo.countAtoms(); i++) {
            Atom test = tempo.getAtom(i);

            if (test.getSymbol().equals("O")) {
                o = test;

                break;
            }
        }

        assertNotNull(o);
        assertEquals(1, o.getRadical());
    }
}