cml23fragmentstest.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.util.Enumeration;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.dict.DictRef;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.test.CDKTestCase;

/**
 * Atomic tests for the reading CML documents. All tested CML strings are valid CML 2.3,
 * as can be determined in cdk/src/org/openscience/cdk/test/io/cml/cml23TestFramework.xml.
 *
 * @cdk.module test-io
 *
 * @author Egon Willighagen <[e-mail]>
 */
public class CML23FragmentsTest extends CDKTestCase {

    public CML23FragmentsTest(String name) {
        super(name);
    }

    public static Test suite() {
        return new TestSuite(CML23FragmentsTest.class);
    }

    public void testAtomId() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/></atomArray></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(1, mol.getAtomCount());
        IAtom atom = mol.getAtom(0);
        assertEquals("a1", atom.getID());
    }
    
    
    public void testAtomId3() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2 a3'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(3, mol.getAtomCount());
        IAtom atom = mol.getAtom(1);
        assertEquals("a2", atom.getID());
    }

    
    public void testAtomElementType3() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1' elementType='C'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(1, mol.getAtomCount());
        IAtom atom = mol.getAtom(0);
        assertEquals("C", atom.getSymbol());
    }
    
    public void testBond() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(2, mol.getAtomCount());
        assertEquals(1, mol.getBondCount());
        org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
        assertEquals(2, bond.getAtomCount());
        IAtom atom1 = bond.getAtom(0);
        IAtom atom2 = bond.getAtom(1);
        assertEquals("a1", atom1.getID());
        assertEquals("a2", atom2.getID());
    }

    public void testBond4() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' bondID='b1 b2'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(3, mol.getAtomCount());
        assertEquals(2, mol.getBondCount());
        org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
        assertEquals(2, bond.getAtomCount());
        IAtom atom1 = bond.getAtom(0);
        IAtom atom2 = bond.getAtom(1);
        assertEquals("a1", atom1.getID());
        assertEquals("a2", atom2.getID());
        assertEquals("b2", mol.getBond(1).getID());
    }

    public void testBond5() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2 a3'/><bondArray atomRef1='a1 a1' atomRef2='a2 a3' order='1 1'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(3, mol.getAtomCount());
        assertEquals(2, mol.getBondCount());
        org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
        assertEquals(2, bond.getAtomCount());
        assertEquals(1.0, bond.getOrder(), 0.0001);
        bond = mol.getBond(1);
        assertEquals(2, bond.getAtomCount());
        assertEquals(1.0, bond.getOrder(), 0.0001);
    }

    public void testBondId() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(2, mol.getAtomCount());
        assertEquals(1, mol.getBondCount());
        org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
        assertEquals("b1", bond.getID());
    }

    public void testBondStereo() throws Exception {
    	String cmlString = "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'><bondStereo dictRef='cml:H'/></bond></bondArray></molecule>";
    	IChemFile chemFile = parseCMLString(cmlString);
    	IMolecule mol = checkForSingleMoleculeFile(chemFile);

    	assertEquals(2, mol.getAtomCount());
    	assertEquals(1, mol.getBondCount());
    	IBond bond = mol.getBond(0);
    	assertEquals(CDKConstants.STEREO_BOND_DOWN, bond.getStereo());
    }

  public void testBondAromatic() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2'/><bondArray atomRef1='a1' atomRef2='a2' order='A'/></molecule>";
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);

        assertEquals(2, mol.getAtomCount());
        assertEquals(1, mol.getBondCount());
        org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
        assertEquals(CDKConstants.BONDORDER_SINGLE, bond.getOrder(), 0.0001);
        assertEquals(true, bond.getFlag(CDKConstants.ISAROMATIC));
    }
    
  
  public void testBondAromatic2() throws Exception {
      String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2'/><bondArray><bond atomRefs='a1 a2' order='2'><bondType dictRef='cdk:aromaticBond'/></bond></bondArray></molecule>";
      IChemFile chemFile = parseCMLString(cmlString);
      IMolecule mol = checkForSingleMoleculeFile(chemFile);

      assertEquals(2, mol.getAtomCount());
      assertEquals(1, mol.getBondCount());
      org.openscience.cdk.interfaces.IBond bond = mol.getBond(0);
      assertEquals(CDKConstants.BONDORDER_DOUBLE, bond.getOrder(), 0.0001);
      assertEquals(true, bond.getFlag(CDKConstants.ISAROMATIC));
  }

  public void testList() throws Exception {
        String cmlString = 
          "<list>" + 
          "<molecule id='m1'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>" +
          "<molecule id='m2'><atomArray><atom id='a1'/><atom id='a2'/></atomArray><bondArray><bond id='b1' atomRefs2='a1 a2'/></bondArray></molecule>" +
          "</list>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        checkForXMoleculeFile(chemFile, 2);
    }

    public void testCoordinates2D() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' x2='0.0 0.1' y2='1.2 1.3'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals(2, mol.getAtomCount());
        assertNotNull(mol.getAtom(0).getPoint2d());
        assertNotNull(mol.getAtom(1).getPoint2d());
        assertNull(mol.getAtom(0).getPoint3d());
        assertNull(mol.getAtom(1).getPoint3d());
    }
  
    public void testCoordinates3D() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' x3='0.0 0.1' y3='1.2 1.3' z3='2.1 2.5'/></molecule>";
        
        IChemFile chemFile = parseCMLString(cmlString);
        IMolecule mol = checkForSingleMoleculeFile(chemFile);
        
        assertEquals(2, mol.getAtomCount());
        assertNull(mol.getAtom(0).getPoint2d());
        assertNull(mol.getAtom(1).getPoint2d());
        assertNotNull(mol.getAtom(0).getPoint3d());
        assertNotNull(mol.getAtom(1).getPoint3d());
    }
    
    public void testFractional3D() throws Exception {
        String cmlString = "<molecule id='m1'><atomArray atomID='a1 a2' xFract='0.0 0.1' yFract='1.2 1.3' zFract='2.1 2.5'/></molecule>";