?? mol2readertest.java
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/* $RCSfile$ * $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: cdk-devel@slists.sourceforge.net * * 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"?? 快捷鍵說明
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