structurediagramgeneratortest.java

化学图形处理软件

/* $Revision: 8312 $ $Author: egonw $ $Date: 2007-05-08 11:48:15 +0000 (Di, 08 Mai 2007) $
 *
 *  Copyright (C) 2003-2007  Christoph Steinbeck <[e-mail]>
 *
 *  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.
 *
 *  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.layout;

import java.io.InputStream;
import java.io.StringReader;
import java.util.List;

import javax.vecmath.Vector2d;

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

import org.openscience.cdk.Atom;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.swing.MoleculeListViewer;
import org.openscience.cdk.applications.swing.MoleculeViewer2D;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.CMLReader;
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.Mol2Reader;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.manipulator.ChemModelManipulator;

/**
 *  A set of test cases for the StructureDiagramGenerator
 *
 * @cdk.module test-extra
 *
 *@author     steinbeck
 *@cdk.created    August 29, 2003
 */
public class StructureDiagramGeneratorTest extends CDKTestCase
{

	MoleculeListViewer moleculeListViewer = null;
	boolean standAlone = false;


	/**
	 *  Constructor for the StructureDiagramGeneratorTest object
	 */
	public StructureDiagramGeneratorTest(String name)
	{
		super(name);
	}


	/**
	 *  The JUnit setup method
	 */
	public void setUp() 
	{ 
			
	}


	/**
	 *  A unit test suite for JUnit
	 *
	 *@return    The test suite
	 */
	public static Test suite()
	{
		return new TestSuite(StructureDiagramGeneratorTest.class);
	}

	public void runVisualTests() throws Exception
	{
		moleculeListViewer = new MoleculeListViewer();
		//MoleculeViewer2D.display(MoleculeFactory.loadMolecule("data/mdl/reserpine.mol"), true);
		/*showIt(MoleculeFactory.loadMolecule("data/mdl/reserpine.mol"), "Reserpine");
		showIt(MoleculeFactory.loadMolecule("data/mdl/four-ring-5x10.mol"), "5x10 condensed four membered rings");
		showIt(MoleculeFactory.loadMolecule("data/mdl/six-ring-4x4.mol"), "4x4 condensed six membered rings");
		showIt(MoleculeFactory.loadMolecule("data/mdl/polycarpol.mol")
		, "Polycarpol");*/
		showIt(MoleculeFactory.makeAlphaPinene(), "alpha-Pinene");
		showIt(MoleculeFactory.makeBiphenyl(), "Biphenyl");
		showIt(MoleculeFactory.make4x3CondensedRings(), "4x3CondensedRings");
		showIt(MoleculeFactory.makePhenylEthylBenzene(), "PhenylEthylBenzene");
		showIt(MoleculeFactory.makeSpiroRings(), "Spiro");
		showIt(MoleculeFactory.makeMethylDecaline(), "Methyldecaline");
		showIt(MoleculeFactory.makeBranchedAliphatic(), "Branched aliphatic");
		showIt(MoleculeFactory.makeDiamantane(), "Diamantane - Was A Problem! - Solved :-)");
		showIt(MoleculeFactory.makeEthylCyclohexane(), "Ethylcyclohexane");
		showIt(MoleculeFactory.makeBicycloRings(), "Bicyclo-[2.2.2]-octane");		
		//showIt(makeBug736137(), "Bug 736137");
		//showIt(makeBug891021(), "Bug 891021");
		showIt(makeJhao1(), "Bug jhao1");
		showIt(makeJhao2(), "Bug jhao2");
		showIt(makeJhao3(), "Bug jhao3");
		showIt(makeJhao4(), "Bug jhao4");
	}

	private boolean showIt(IMolecule molecule, String name) throws Exception
	{
		MoleculeViewer2D mv = new MoleculeViewer2D();
		mv.setAtomContainer(generateCoordinates(molecule));
		moleculeListViewer.addStructure(mv, name);
		return true;
	}

	public IAtomContainer generateCoordinates(IMolecule m) throws Exception
	{
		StructureDiagramGenerator sdg = new StructureDiagramGenerator();
		sdg.setMolecule(m);
		sdg.generateCoordinates(new Vector2d(0, 1));
		return sdg.getMolecule();
	}

	/**
	 * @cdk.bug 736137
	 */
	public void testBug736137() throws Exception
	{
		String filename = "data/mdl/bug736137.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLV2000Reader reader = new MDLV2000Reader(ins);
		ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
		IChemSequence chemSequence = chemFile.getChemSequence(0);
		IChemModel chemModel = chemSequence.getChemModel(0);
		List atomContainers = ChemModelManipulator.getAllAtomContainers(chemModel);
		assertEquals(1, atomContainers.size());
	}

	public void visualBugPMR() throws Exception
	{
                String filename = "data/SL0016a.cml";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		CMLReader reader = new CMLReader(ins);
		ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
		IChemSequence seq = chemFile.getChemSequence(0);
		IChemModel model = seq.getChemModel(0);
		IMolecule mol = model.getMoleculeSet().getMolecule(0);
		MoleculeViewer2D.display(mol, true);
		//logger.debug(new SmilesGenerator().createSMILES(mol));
	}
	
	
	
	/**
	 *  A unit test for JUnit
	 */
	public void testAlphaPinene() throws Exception
	{
		Molecule m = MoleculeFactory.makeAlphaPinene();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testBiphenyl() throws Exception
	{
		Molecule m = MoleculeFactory.makeBiphenyl();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void test4x3CondensedRings() throws Exception
	{
		Molecule m = MoleculeFactory.make4x3CondensedRings();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testPhenylEthylBenzene() throws Exception
	{
		Molecule m = MoleculeFactory.makePhenylEthylBenzene();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testSpiroRings() throws Exception
	{
		Molecule m = MoleculeFactory.makeSpiroRings();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
		if (standAlone)MoleculeViewer2D.display(new Molecule(ac), false);
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testMethylDecaline() throws Exception
	{
		Molecule m = MoleculeFactory.makeMethylDecaline();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */
	public void testBranchedAliphatic() throws Exception
	{
		Molecule m = MoleculeFactory.makeBranchedAliphatic();
		IAtomContainer ac = generateCoordinates(m);
        assertTrue(GeometryTools.has2DCoordinates(ac));
	}


	/**
	 *  A unit test for JUnit
	 */