mol2readertest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-05-08 11:48:15 +0000 (Di, 08 Mai 2007) $
 * $Revision: 8312 $
 *
 * 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;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.util.Iterator;
import java.util.List;
import java.util.zip.GZIPInputStream;

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

import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.ChemObject;
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.IChemModel;
import org.openscience.cdk.io.Mol2Reader;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

/**
 * TestCase for the reading SYBYL mol2 files using a test file.
 *
 * @cdk.module test-io
 *
 * @see org.openscience.cdk.io.Mol2Reader
 */
public class Mol2ReaderTest extends CDKTestCase {

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

    public Mol2ReaderTest(String name) {
        super(name);
        logger = new LoggingTool(this);
    }

    public static Test suite() {
        return new TestSuite(Mol2ReaderTest.class);
    }

    public void testAccepts() {
    	Mol2Reader reader = new Mol2Reader();
    	assertTrue(reader.accepts(ChemFile.class));
    	assertTrue(reader.accepts(ChemModel.class));
    }

    /**
     * Test example from website. See
     * <a href="http://www.tripos.com/custResources/mol2Files/mol2_format3.html">Tripos example</a>.
     */
    public void testExampleFromWebsite() throws Exception {
        String filename = "data/mol2/fromWebsite.mol2";
        logger.info("Testing: ", filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        Mol2Reader reader = new Mol2Reader(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(12, m.getAtomCount());
        assertEquals(12, m.getBondCount());

        assertEquals("C.ar", m.getAtom(0).getAtomTypeName());
        assertEquals("C", m.getAtom(0).getSymbol());
        assertEquals("H", m.getAtom(6).getAtomTypeName());
        assertEquals("H", m.getAtom(6).getSymbol());
    }

    
    /**
     * Tests the Mol2Reader with about 30% of the NCI molecules.
     * 
     * @throws IOException if an I/O error occurs
     * @throws CDKException if an CDK error occurs
     */
    public void testNCIfeb03_2D() throws Exception {
    	if (!runSlowTests()) fail("Not running time consuming test");
    	
        String filename = "data/mol2/NCI_feb03_2D.mol2.gz";
        InputStream in = new GZIPInputStream(Mol2ReaderTest.class.getClassLoader().getResourceAsStream(filename));
        BufferedReader br = new BufferedReader(new InputStreamReader(in));
        StringBuilder buf = new StringBuilder();
        String line;
        while ((line = br.readLine()) != null) {
            if (line.startsWith("@<TRIPOS>MOLECULE") && (buf.length() > 0)) {
                checkMol(buf);
                buf.delete(0, buf.length() - 1);
            }
            buf.append(line).append('\n');
        }
        if (buf.length() > 0) {
            checkMol(buf);
        }
    }
    
    public void testBug1714794() throws Exception {
        String problematicMol2 = "@<TRIPOS>MOLECULE\n"
            + "mol_197219.smi\n"
            + " 129 135 0 0 0\n"
            + "SMALL\n"
            + "GASTEIGER\n"
            + "Energy = 0\n"
            + "\n"
            + "@<TRIPOS>ATOM\n"
            + "      1 N1          0.0000    0.0000    0.0000 N.am    1  <1>        -0.2782\n"
            + "      2 H1          0.0000    0.0000    0.0000 H       1  <1>         0.1552\n"
            + "      3 C1          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0886\n"
            + "      4 C2          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1500\n"
            + "      5 C3          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0714\n"
            + "      6 C4          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0456\n"
            + "      7 C5          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0788\n"
            + "      8 C6          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1435\n"
            + "      9 C7          0.0000    0.0000    0.0000 C.ar    1  <1>         0.0342\n"
            + "     10 C8          0.0000    0.0000    0.0000 C.ar    1  <1>         0.1346\n"
            + "     11 O1          0.0000    0.0000    0.0000 O.3     1  <1>        -0.5057\n"
            + "     12 H2          0.0000    0.0000    0.0000 H       1  <1>         0.2922\n"
            + "     13 C9          0.0000    0.0000    0.0000 C.3     1  <1>        -0.0327\n"
            + "     14 H3          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     15 H4          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     16 H5          0.0000    0.0000    0.0000 H       1  <1>         0.0280\n"
            + "     17 O2          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4436\n"
            + "     18 C10         0.0000    0.0000    0.0000 C.3     1  <1>         0.3143\n"
            + "     19 O3          0.0000    0.0000    0.0000 O.2     1  <1>        -0.4528\n"
            + "     20 C11         0.0000    0.0000    0.0000 C.2     1  <1>         0.0882\n"
            + "     21 H6          0.0000    0.0000    0.0000 H       1  <1>         0.1022\n"
            + "     22 C12         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0208\n"
            + "     23 H7          0.0000    0.0000    0.0000 H       1  <1>         0.0628\n"
            + "     24 C13         0.0000    0.0000    0.0000 C.3     1  <1>         0.0854\n"
            + "     25 H8          0.0000    0.0000    0.0000 H       1  <1>         0.0645\n"
            + "     26 C14         0.0000    0.0000    0.0000 C.3     1  <1>         0.0236\n"
            + "     27 H9          0.0000    0.0000    0.0000 H       1  <1>         0.0362\n"
            + "     28 C15         0.0000    0.0000    0.0000 C.3     1  <1>         0.1131\n"
            + "     29 H10         0.0000    0.0000    0.0000 H       1  <1>         0.0741\n"
            + "     30 C16         0.0000    0.0000    0.0000 C.3     1  <1>         0.0200\n"
            + "     31 H11         0.0000    0.0000    0.0000 H       1  <1>         0.0359\n"
            + "     32 C17         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n"
            + "     33 H12         0.0000    0.0000    0.0000 H       1  <1>         0.0600\n"
            + "     34 C18         0.0000    0.0000    0.0000 C.3     1  <1>         0.0091\n"
            + "     35 H13         0.0000    0.0000    0.0000 H       1  <1>         0.0348\n"
            + "     36 C19         0.0000    0.0000    0.0000 C.3     1  <1>         0.0661\n"
            + "     37 H14         0.0000    0.0000    0.0000 H       1  <1>         0.0602\n"
            + "     38 C20         0.0000    0.0000    0.0000 C.3     1  <1>         0.0009\n"
            + "     39 H15         0.0000    0.0000    0.0000 H       1  <1>         0.0365\n"
            + "     40 C21         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0787\n"
            + "     41 H16         0.0000    0.0000    0.0000 H       1  <1>         0.0576\n"
            + "     42 C22         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0649\n"
            + "     43 H17         0.0000    0.0000    0.0000 H       1  <1>         0.0615\n"
            + "     44 C23         0.0000    0.0000    0.0000 C.2     1  <1>        -0.0542\n"
            + "     45 H18         0.0000    0.0000    0.0000 H       1  <1>         0.0622\n"
            + "     46 C24         0.0000    0.0000    0.0000 C.2     1  <1>         0.0115\n"
            + "     47 C25         0.0000    0.0000    0.0000 C.2     1  <1>         0.2441\n"
            + "     48 O4          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2702\n"
            + "     49 C26         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0348\n"
            + "     50 H19         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     51 H20         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     52 H21         0.0000    0.0000    0.0000 H       1  <1>         0.0279\n"
            + "     53 C27         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0566\n"
            + "     54 H22         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     55 H23         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     56 H24         0.0000    0.0000    0.0000 H       1  <1>         0.0236\n"
            + "     57 O5          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3909\n"
            + "     58 H25         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n"
            + "     59 C28         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0577\n"
            + "     60 H26         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     61 H27         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     62 H28         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     63 O6          0.0000    0.0000    0.0000 O.3     1  <1>        -0.3910\n"
            + "     64 H29         0.0000    0.0000    0.0000 H       1  <1>         0.2098\n"
            + "     65 C29         0.0000    0.0000    0.0000 C.3     1  <1>        -0.0567\n"
            + "     66 H30         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     67 H31         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     68 H32         0.0000    0.0000    0.0000 H       1  <1>         0.0234\n"
            + "     69 O7          0.0000    0.0000    0.0000 O.3     1  <1>        -0.4608\n"
            + "     70 C30         0.0000    0.0000    0.0000 C.2     1  <1>         0.3042\n"
            + "     71 O8          0.0000    0.0000    0.0000 O.2     1  <1>        -0.2512\n"
            + "     72 C31         0.0000    0.0000    0.0000 C.3     1  <1>         0.0332\n"
            + "     73 H33         0.0000    0.0000    0.0000 H       1  <1>         0.0342\n"