/* $RCSfile$ * $Author: egonw $ * $Date: 2007-03-16 14:40:56 +0000 (Fr, 16 Mrz 2007) $ * $Revision: 8132 $ * * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project *  * Contact: cdk-devel@lists.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.cml;import java.io.StringWriter;import javax.vecmath.Point3d;import javax.vecmath.Vector3d;import junit.framework.Test;import junit.framework.TestSuite;import org.openscience.cdk.Atom;import org.openscience.cdk.CDKConstants;import org.openscience.cdk.Crystal;import org.openscience.cdk.Molecule;import org.openscience.cdk.Reaction;import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;import org.openscience.cdk.config.Elements;import org.openscience.cdk.interfaces.IMolecule;import org.openscience.cdk.interfaces.IReaction;import org.openscience.cdk.io.CMLWriter;import org.openscience.cdk.libio.cml.PDBAtomCustomizer;import org.openscience.cdk.libio.cml.QSARCustomizer;import org.openscience.cdk.nonotify.NNMolecule;import org.openscience.cdk.protein.data.PDBAtom;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 java1.5+ */public class CML2WriterTest extends CDKTestCase {    private LoggingTool logger;    public CML2WriterTest(String name) {        super(name);        logger = new LoggingTool(this);    }    public static Test suite() {        return new TestSuite(CML2WriterTest.class);    }	public void testCMLWriterBenzene() throws Exception {		StringWriter writer = new StringWriter();        Molecule molecule = MoleculeFactory.makeBenzene();        HueckelAromaticityDetector.detectAromaticity(molecule);        CMLWriter cmlWriter = new CMLWriter(writer);                cmlWriter.write(molecule);		logger.debug("****************************** testCMLWriterBenzene()");        logger.debug(writer.toString());		logger.debug("******************************");        assertTrue(writer.toString().indexOf("</molecule>") != -1);	}		/**	 * Test example with one explicit carbon, and four implicit hydrogens.	 * 	 * @cdk.bug 1655045	 */	public void testHydrogenCount() throws Exception {		StringWriter writer = new StringWriter();		IMolecule molecule = new NNMolecule(); // methane		molecule.addAtom(molecule.getBuilder().newAtom(Elements.CARBON));		molecule.getAtom(0).setHydrogenCount(4);        CMLWriter cmlWriter = new CMLWriter(writer);                cmlWriter.write(molecule);		logger.debug("****************************** testHydrogenCount()");        logger.debug(writer.toString());		logger.debug("******************************");        assertTrue(writer.toString().indexOf("hydrogenCount=\"4\"") != -1);	}		/**	 * Test example with one explicit carbon, and one implicit hydrogen, and three implicit hydrogens.	 * 	 * @cdk.bug 1655045	 */	public void testHydrogenCount_2() throws Exception {		StringWriter writer = new StringWriter();		IMolecule molecule = new NNMolecule(); // methane		molecule.addAtom(molecule.getBuilder().newAtom(Elements.CARBON));		molecule.addAtom(molecule.getBuilder().newAtom(Elements.HYDROGEN));		molecule.getAtom(0).setHydrogenCount(3);		molecule.addBond(0,1,CDKConstants.BONDORDER_SINGLE);        CMLWriter cmlWriter = new CMLWriter(writer);                cmlWriter.write(molecule);		logger.debug("****************************** testHydrogenCount_2()");        logger.debug(writer.toString());		logger.debug("******************************");        assertTrue(writer.toString().indexOf("hydrogenCount=\"4\"") != -1);	}		public void testCMLCrystal() throws Exception {		StringWriter writer = new StringWriter();        Crystal crystal = new Crystal();        Atom silicon = new Atom("Si");        silicon.setFractionalPoint3d(        	new Point3d(0.0, 0.0, 0.0)        );        crystal.addAtom(silicon);        crystal.setA(new Vector3d(1.5, 0.0, 0.0));        crystal.setB(new Vector3d(0.0, 2.0, 0.0));        crystal.setC(new Vector3d(0.0, 0.0, 1.5));        CMLWriter cmlWriter = new CMLWriter(writer);                cmlWriter.write(crystal);        String cmlContent = writer.toString();		logger.debug("****************************** testCMLCrystal()");        logger.debug(cmlContent);		logger.debug("******************************");        assertTrue(cmlContent.indexOf("</crystal>") != -1); // the cystal info has to be present        assertTrue(cmlContent.indexOf("<atom") != -1); // an Atom has to be present	}	    public void testQSARCustomization() throws Exception {        StringWriter writer = new StringWriter();        Molecule molecule = MoleculeFactory.makeBenzene();        IMolecularDescriptor descriptor = new WeightDescriptor();        CMLWriter cmlWriter = new CMLWriter(writer);        cmlWriter.registerCustomizer(new QSARCustomizer());        DescriptorValue value = descriptor.calculate(molecule);        molecule.setProperty(value.getSpecification(), value);        cmlWriter.write(molecule);        String cmlContent = writer.toString();        logger.debug("****************************** testQSARCustomization()");        logger.debug(cmlContent);        logger.debug("******************************");        assertTrue(cmlContent.indexOf("<property") != -1 &&        		   cmlContent.indexOf("xmlns:qsar") != -1);        assertTrue(cmlContent.indexOf("#weight\"") != -1);    }        public void testReactionCustomization() throws Exception {    	StringWriter writer = new StringWriter();        IReaction reaction = new Reaction();        reaction.setID("reaction1");        IMolecule reactant = reaction.getBuilder().newMolecule();        reactant.setID("react");        IMolecule product = reaction.getBuilder().newMolecule();        product.setID("product");        IMolecule agent = reaction.getBuilder().newMolecule();        agent.setID("agent");                reaction.addReactant(reactant);        reaction.addProduct(product);        reaction.addAgent(agent);                CMLWriter cmlWriter = new CMLWriter(writer);        cmlWriter.write(reaction);        String cmlContent = writer.toString();        logger.debug("****************************** testReactionCustomization()");        logger.debug(cmlContent);        logger.debug("******************************");        assertTrue(cmlContent.indexOf("<reaction id=\"reaction1") != -1);        assertTrue(cmlContent.indexOf("<molecule id=\"react") != -1);        assertTrue(cmlContent.indexOf("<molecule id=\"product") != -1);        assertTrue(cmlContent.indexOf("<molecule id=\"agent") != -1);    }        public void testPDBAtomCustomization() throws Exception {        StringWriter writer = new StringWriter();        Molecule molecule = new Molecule();        PDBAtom atom = new PDBAtom("C");        atom.setName("CA");        atom.setResName("PHE");        molecule.addAtom(atom);                CMLWriter cmlWriter = new CMLWriter(writer);        cmlWriter.registerCustomizer(new PDBAtomCustomizer());        cmlWriter.write(molecule);        String cmlContent = writer.toString();        logger.debug("****************************** testPDBAtomCustomization()");        logger.debug(cmlContent);        logger.debug("******************************");        assertTrue(cmlContent.indexOf("<scalar dictRef=\"pdb:resName") != -1);    }    }