cml2test.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-05-05 12:00:36 +0000 (Sa, 05 Mai 2007) $
 * $Revision: 8301 $
 *
 * 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.cml;

import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.io.StringWriter;

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

import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBioPolymer;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.CMLWriter;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.PDBReader;
import org.openscience.cdk.nonotify.NNChemFile;
import org.openscience.cdk.protein.data.PDBPolymer;
import org.openscience.cdk.test.CDKTestCase;

/**
 * TestCase for the reading CML 2 files using a few test files
 * in data/cmltest.
 *
 * @cdk.module test-io
 * @cdk.require java1.5+
 */
public class CML2Test extends CDKTestCase {

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

    public CML2Test(String name) {
        super(name);
        logger = new org.openscience.cdk.tools.LoggingTool(this);
    }

    public static Test suite() {
        return new TestSuite(CML2Test.class);
    }

    public void testCOONa() throws Exception {
        String filename = "data/cml/COONa.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(4, mol.getAtomCount());
        assertEquals(2, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(!GeometryToolsInternalCoordinates.has2DCoordinates(mol));

        java.util.Iterator atoms = mol.atoms();
        while (atoms.hasNext()) {
        	org.openscience.cdk.interfaces.IAtom atom = (IAtom)atoms.next();
        	if (atom.getSymbol().equals("Na")) 
        		assertEquals(+1, atom.getFormalCharge()); 
        }
    }

    public void testNitrate() throws Exception {
        String filename = "data/cml/nitrate.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(4, mol.getAtomCount());
        assertEquals(3, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(!GeometryToolsInternalCoordinates.has2DCoordinates(mol));

        java.util.Iterator atoms = mol.atoms();
        while (atoms.hasNext()) {
        	org.openscience.cdk.interfaces.IAtom atom = (IAtom)atoms.next();
        	if (atom.getSymbol().equals("N")) 
        		assertEquals(+1, atom.getFormalCharge()); 
        }
    }

    public void testCMLOK1() throws Exception {
        String filename = "data/cml/cs2a.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(38, mol.getAtomCount());
        assertEquals(48, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK2() throws Exception {
        String filename = "data/cml/cs2a.mol.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(38, mol.getAtomCount());
        assertEquals(29, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK3() throws Exception {
        String filename = "data/cml/nsc2dmol.1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(13, mol.getAtomCount());
        assertEquals(12, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK4() throws Exception {
        String filename = "data/cml/nsc2dmol.2.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(13, mol.getAtomCount());
        assertEquals(12, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK5() throws Exception {
        String filename = "data/cml/nsc2dmol.a1.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(13, mol.getAtomCount());
        assertEquals(12, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK6() throws Exception {
        String filename = "data/cml/nsc2dmol.a2.cml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(13, mol.getAtomCount());
        assertEquals(12, mol.getBondCount());
        assertFalse(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertTrue(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK7() throws Exception {
        String filename = "data/cml/nsc3dcml.xml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);
        org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
        assertNotNull(seq);
        assertEquals(seq.getChemModelCount(), 1);
        org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
        assertNotNull(model);
        assertEquals(model.getMoleculeSet().getMoleculeCount(), 1);

        // test the molecule
        org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
        assertNotNull(mol);
        assertEquals(27, mol.getAtomCount());
        assertEquals(27, mol.getBondCount());
        assertTrue(GeometryToolsInternalCoordinates.has3DCoordinates(mol));
        assertFalse(GeometryToolsInternalCoordinates.has2DCoordinates(mol));
    }

    public void testCMLOK8() throws Exception {
        String filename = "data/cml/nsc2dcml.xml";
        logger.info("Testing: " + filename);
        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
        CMLReader reader = new CMLReader(ins);
        IChemFile chemFile = (IChemFile)reader.read(new org.openscience.cdk.ChemFile());

        // test the resulting ChemFile content
        assertNotNull(chemFile);
        assertEquals(chemFile.getChemSequenceCount(), 1);