cmlroundtriptest.java

化学图形处理软件

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

import javax.vecmath.Point2d;
import javax.vecmath.Point3d;

import junit.framework.Test;
import junit.framework.TestSuite;
import nu.xom.Element;

import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.MoleculeSet;
import org.openscience.cdk.PseudoAtom;
import org.openscience.cdk.Reaction;
import org.openscience.cdk.SingleElectron;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
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.IMoleculeSet;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.libio.cml.Convertor;
import org.openscience.cdk.libio.cml.QSARCustomizer;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptor;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;

/**
 * TestCase for the reading CML 2 files using a few test files
 * in data/cmltest.
 *
 * @cdk.module  test-io
 * @cdk.require xom-1.0.jar
 * @cdk.require java1.5+
 */
public class CMLRoundTripTest extends CDKTestCase {

    private LoggingTool logger;
    private Convertor convertor;

    public CMLRoundTripTest(String name) {
        super(name);
        logger = new LoggingTool(this);
        convertor = new Convertor(false, "");
        convertor.registerCustomizer(new QSARCustomizer());
    }

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

    public void testAtom() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getSymbol(), roundTrippedAtom.getSymbol());
    }
    
    public void testAtomId() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        atom.setID("N1");
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getID(), roundTrippedAtom.getID());
    }
    
    public void testAtom2D() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        Point2d p2d = new Point2d(1.3, 1.4);
        atom.setPoint2d(p2d);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getPoint2d(), roundTrippedAtom.getPoint2d(), 0.00001);
    }
    
    public void testAtom3D() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        Point3d p3d = new Point3d(1.3, 1.4, 0.9);
        atom.setPoint3d(p3d);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getPoint3d(), roundTrippedAtom.getPoint3d(), 0.00001);
    }
    
    public void testAtom2DAnd3D() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        Point2d p2d = new Point2d(1.3, 1.4);
        atom.setPoint2d(p2d);
        Point3d p3d = new Point3d(1.3, 1.4, 0.9);
        atom.setPoint3d(p3d);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getPoint2d(), roundTrippedAtom.getPoint2d(), 0.00001);
        assertEquals(atom.getPoint3d(), roundTrippedAtom.getPoint3d(), 0.00001);
    }
    
    public void testAtomFract3D() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        Point3d p3d = new Point3d(0.3, 0.4, 0.9);
        atom.setFractionalPoint3d(p3d);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getFractionalPoint3d(), roundTrippedAtom.getFractionalPoint3d(), 0.00001);
    }
    
    public void testPseudoAtom() throws Exception {
        Molecule mol = new Molecule();
        PseudoAtom atom = new PseudoAtom("N");
        atom.setLabel("Glu55");
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertNotNull(roundTrippedAtom);
        assertTrue(roundTrippedAtom instanceof PseudoAtom);
        assertEquals("Glu55", ((PseudoAtom)roundTrippedAtom).getLabel());
    }
    
    /**
     * @cdk.bug 1455346
     */
    public void testChemModel() throws Exception {
    	ChemModel model = new ChemModel();
    	MoleculeSet moleculeSet = new MoleculeSet();
        Molecule mol = new Molecule();
        PseudoAtom atom = new PseudoAtom("N");
        mol.addAtom(atom);
        moleculeSet.addAtomContainer(mol);
        model.setMoleculeSet(moleculeSet);
        
        IChemModel roundTrippedModel = roundTripChemModel(model);
        
        IMoleculeSet roundTrippedMolSet = roundTrippedModel.getMoleculeSet(); 
        assertNotNull(roundTrippedMolSet);
        assertEquals(1, roundTrippedMolSet.getAtomContainerCount());
        IMolecule roundTrippedMolecule = roundTrippedMolSet.getMolecule(0);
        assertNotNull(roundTrippedMolecule);
        assertEquals(1, roundTrippedMolecule.getAtomCount());
    }
    
    public void testAtomFormalCharge() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        int formalCharge = +1;
        atom.setFormalCharge(formalCharge);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getFormalCharge(), roundTrippedAtom.getFormalCharge());
    }
    
    public void testAtomPartialCharge() throws Exception {
        if (true) return;
        fail("Have to figure out how to store partial charges in CML2");
        Molecule mol = new Molecule();
        Atom atom = new Atom("N");
        double partialCharge = 0.5;
        atom.setCharge(partialCharge);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getCharge(), roundTrippedAtom.getCharge(), 0.0001);
    }
    
    public void testAtomStereoParity() throws Exception {
        if (true) return;
        fail("Have to figure out how to store atom parity in CML2");
        Molecule mol = new Molecule();
        Atom atom = new Atom("C");
        int stereo = CDKConstants.STEREO_ATOM_PARITY_PLUS;
        atom.setStereoParity(stereo);
        mol.addAtom(atom);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getStereoParity(), roundTrippedAtom.getStereoParity());
    }
    
    public void testIsotope() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("C");
        atom.setMassNumber(13);
        mol.addAtom(atom);
        IMolecule roundTrippedMol = roundTripMolecule(mol);
        
        assertEquals(1, roundTrippedMol.getAtomCount());
        IAtom roundTrippedAtom = roundTrippedMol.getAtom(0);
        assertEquals(atom.getMassNumber(), roundTrippedAtom.getMassNumber());
    }
    
    public void testBond() throws Exception {
        Molecule mol = new Molecule();
        Atom atom = new Atom("C");
        Atom atom2 = new Atom("O");
        mol.addAtom(atom);
        mol.addAtom(atom2);
        Bond bond = new Bond(atom, atom2, 1.0);
        mol.addBond(bond);
        
        IMolecule roundTrippedMol = roundTripMolecule(mol);