hydrogenplacertest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-03-10 13:32:01 +0000 (Sa, 10 Mrz 2007) $
 * $Revision: 8072 $
 * 
 * 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.
 * 
 * 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.IOException;
import java.io.InputStream;

import javax.vecmath.Point2d;

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

import org.openscience.cdk.Atom;
import org.openscience.cdk.Bond;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.applications.swing.MoleculeViewer2D;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.GeometryToolsInternalCoordinates;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.layout.HydrogenPlacer;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;

/**
 * @cdk.module test-extra
 */
public class HydrogenPlacerTest extends CDKTestCase {
    
    public boolean standAlone = false;
    private LoggingTool logger = null;
    
    public HydrogenPlacerTest(String name) {
        super(name);
    }

    public void setUp() throws Exception
    {
        super.setUp();
        logger = new LoggingTool(this);
    }

    public static Test suite() {
        return new TestSuite(HydrogenPlacerTest.class);
    }
    
    public void testBug933572() throws IOException, ClassNotFoundException, CDKException{
        Molecule ac=new Molecule();
        ac.addAtom(new Atom("H"));
        ac.getAtom(0).setPoint2d(new Point2d(0,0));
        new HydrogenAdder().addExplicitHydrogensToSatisfyValency(ac);
        HydrogenPlacer hPlacer = new HydrogenPlacer();
        hPlacer.placeHydrogens2D(ac, 36);
        for(int i=0;i<ac.getAtomCount();i++){
            assertNotNull(ac.getAtom(i).getPoint2d());
        }
     }

    public void testPlaceHydrogens2D() throws Exception {
	    HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
        Molecule dichloromethane = new Molecule();
        Atom carbon = new Atom("C");
        Point2d carbonPos = new Point2d(0.0,0.0);
        carbon.setPoint2d(carbonPos);
        Atom h1 = new Atom("H");
        Atom h2 = new Atom("H");
        Atom cl1 = new Atom("Cl");
        Point2d cl1Pos = new Point2d(0.0,-1.0);
        cl1.setPoint2d(cl1Pos);
        Atom cl2 = new Atom("Cl");
        Point2d cl2Pos = new Point2d(-1.0,0.0);
        cl2.setPoint2d(cl2Pos);
        dichloromethane.addAtom(carbon);
        dichloromethane.addAtom(h1);
        dichloromethane.addAtom(h2);
        dichloromethane.addAtom(cl1);
        dichloromethane.addAtom(cl2);
        dichloromethane.addBond(new Bond(carbon, h1));
        dichloromethane.addBond(new Bond(carbon, h2));
        dichloromethane.addBond(new Bond(carbon, cl1));
        dichloromethane.addBond(new Bond(carbon, cl2));

        assertNull(h1.getPoint2d());
        assertNull(h2.getPoint2d());
        
        // generate new coords
        hydrogenPlacer.placeHydrogens2D(dichloromethane, carbon);
        if (standAlone) MoleculeViewer2D.display(dichloromethane, false);
        // check that previously set coordinates are kept
        assertEquals(carbonPos, carbon.getPoint2d(), 0.01);
        assertEquals(cl1Pos, cl1.getPoint2d(), 0.01);
        assertEquals(cl2Pos, cl2.getPoint2d(), 0.01);
        assertNotNull(h1.getPoint2d());
        assertNotNull(h2.getPoint2d());
    }
    
    /* This one tests adding hydrogens to all atoms of a molecule and doing the layout for them.
    *  It is intended for visually checking the work of HydrogenPlacer, not to be run
    *  as a JUnit test. Thus the name withouth "test".
    */
	public void visualFullMolecule2DEvaluation() throws Exception
	{
		HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
                String filename = "data/mdl/reserpine.mol";
		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
		MDLReader reader = new MDLReader(ins);
		ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
		org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
		org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
		org.openscience.cdk.interfaces.IMolecule mol = model.getMoleculeSet().getMolecule(0);
		double bondLength = GeometryToolsInternalCoordinates.getBondLengthAverage(mol);
		HydrogenAdder ha = new HydrogenAdder();
		logger.debug("Read Reserpine");
		logger.debug("Starting addition of H's");
		ha.addExplicitHydrogensToSatisfyValency(mol);
		logger.debug("ended addition of H's");
		hydrogenPlacer.placeHydrogens2D(mol, bondLength);
		if (standAlone) {
			MoleculeViewer2D.display(mol, false);
		}
	}

}