AtomPlacer3DTest.java

/* $Revision: 12144 $ $Author: egonw $ $Date: 2008-09-02 21:53:30 +0100 (Tue, 02 Sep 2008) $
 *
 *  Copyright (C) 2005-2007  Christian Hoppe <chhoppe@users.sf.net>
 *
 *  Contact: cdk-devel@list.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.
 *
 *  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.modeling.builder3d;

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

import javax.vecmath.Point3d;

import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;


/**
 * Tests for AtomPlacer3D
 *
 * @cdk.module test-builder3d
 * @cdk.githash
 */
public class AtomPlacer3DTest extends CDKTestCase{

	boolean standAlone = false;


    /**
	 *  Sets the standAlone attribute 
	 *
	 *@param  standAlone  The new standAlone value
	 */
	public void setStandAlone(boolean standAlone)
	{
		this.standAlone = standAlone;
	}
	
	@Test
	public void testAllHeavyAtomsPlaced_IAtomContainer(){
		IAtomContainer ac=MoleculeFactory.makeAlphaPinene();
		Assert.assertFalse(new AtomPlacer3D().allHeavyAtomsPlaced(ac));
		for(IAtom atom : ac.atoms()){
			atom.setFlag(CDKConstants.ISPLACED,true);
		}
		Assert.assertTrue(new AtomPlacer3D().allHeavyAtomsPlaced(ac));
	}
	
	@Test
	public void testFindHeavyAtomsInChain_IAtomContainer_IAtomContainer() throws Exception{
    	String filename = "data/mdl/allmol232.mol";
    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
    	// TODO: shk3-cleanuptests: best to use the STRICT IO mode here
    	MDLV2000Reader reader = new MDLV2000Reader(ins);
    	ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
    	// TODO: shk3-cleanuptests: please make it a types list
    	List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
    	IMolecule ac = new NNMolecule((IAtomContainer)containersList.get(0));
    	addExplicitHydrogens(ac);
    	IAtomContainer chain=ac.getBuilder().newInstance(IAtomContainer.class);
    	for(int i=16;i<25;i++){
    		chain.addAtom(ac.getAtom(i));
    	}
    	chain.addAtom(ac.getAtom(29));
    	chain.addAtom(ac.getAtom(30));
    	int[] result=new AtomPlacer3D().findHeavyAtomsInChain(ac,chain);
    	Assert.assertEquals(16,result[0]);
    	Assert.assertEquals(11,result[1]);
	}
	
	@Test
	public void testNumberOfUnplacedHeavyAtoms_IAtomContainer(){
		IMolecule ac = MoleculeFactory.makeAlphaPinene();
		int count=new AtomPlacer3D().numberOfUnplacedHeavyAtoms(ac);
		Assert.assertEquals(10,count);
	}
	
	@Test
	public void testGetPlacedHeavyAtoms_IAtomContainer_IAtom(){
	    IMolecule ac = MoleculeFactory.makeAlphaPinene();
		IAtomContainer acplaced = new AtomPlacer3D().getPlacedHeavyAtoms(ac, ac.getAtom(0));
		Assert.assertEquals(0,acplaced.getAtomCount());
		ac.getAtom(1).setFlag(CDKConstants.ISPLACED, true);
		acplaced = new AtomPlacer3D().getPlacedHeavyAtoms(ac, ac.getAtom(0));
		Assert.assertEquals(1,acplaced.getAtomCount());
	}

	@Test
	public void testGetPlacedHeavyAtom_IAtomContainer_IAtom_IAtom(){
	    IMolecule ac = MoleculeFactory.makeAlphaPinene();
		IAtom acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0), ac.getAtom(1));
		Assert.assertNull(acplaced);
		ac.getAtom(1).setFlag(CDKConstants.ISPLACED, true);
		acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0),ac.getAtom(2));
		Assert.assertEquals(ac.getAtom(1),acplaced);
		acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0),ac.getAtom(1));
		Assert.assertNull(acplaced);
	}

	@Test
	public void testGetPlacedHeavyAtom_IAtomContainer_IAtom(){
	    IMolecule ac = MoleculeFactory.makeAlphaPinene();
		IAtom acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0));
		Assert.assertNull(acplaced);
		ac.getAtom(1).setFlag(CDKConstants.ISPLACED, true);
		acplaced = new AtomPlacer3D().getPlacedHeavyAtom(ac, ac.getAtom(0));
		Assert.assertEquals(ac.getAtom(1),acplaced);
	}
	
	@Test
	public void testGeometricCenterAllPlacedAtoms_IAtomContainer() throws Exception {
	    IMolecule ac = MoleculeFactory.makeAlphaPinene();
		for(int i=0;i<ac.getAtomCount();i++){
			ac.getAtom(i).setFlag(CDKConstants.ISPLACED, true);
		}
		ac.getAtom(0).setPoint3d(new Point3d(1.39,2.04,0));
		ac.getAtom(0).setPoint3d(new Point3d(2.02,2.28,-1.12));
		ac.getAtom(0).setPoint3d(new Point3d(3.44,2.80,-1.09));
		ac.getAtom(0).setPoint3d(new Point3d(3.91,2.97,0.35));
		ac.getAtom(0).setPoint3d(new Point3d(3.56,1.71,1.16));
		ac.getAtom(0).setPoint3d(new Point3d(2.14,2.31,1.29));
		ac.getAtom(0).setPoint3d(new Point3d(0,1.53,0));
		ac.getAtom(0).setPoint3d(new Point3d(2.83,3.69,1.17));
		ac.getAtom(0).setPoint3d(new Point3d(3.32,4.27,2.49));
		ac.getAtom(0).setPoint3d(new Point3d(2.02,4.68,0.35));
		Point3d center=new AtomPlacer3D().geometricCenterAllPlacedAtoms(ac);
		Assert.assertEquals(2.02, center.x,0.01);
		Assert.assertEquals(4.68, center.y,0.01);
		Assert.assertEquals(0.35, center.z,0.01);
	}
}