forcefieldtests.java

化学图形处理软件

/* $Revision: 8201 $ $Author: egonw $ $Date: 2007-04-16 08:40:19 +0000 (Mo, 16 Apr 2007) $
 *
 *  Copyright (C) 2005-2007  Violeta Labarta Beceiro <[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.modeling.forcefield;

import java.io.FileWriter;
import java.io.InputStream;
import java.util.Hashtable;

import javax.vecmath.GVector;
import javax.vecmath.Point3d;

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

import org.openscience.cdk.RingSet;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator;
import org.openscience.cdk.modeling.forcefield.AngleBending;
import org.openscience.cdk.modeling.forcefield.BondStretching;
import org.openscience.cdk.modeling.forcefield.ElectrostaticInteractions;
import org.openscience.cdk.modeling.forcefield.ForceField;
import org.openscience.cdk.modeling.forcefield.ForceFieldTools;
import org.openscience.cdk.modeling.forcefield.GeometricMinimizer;
import org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction;
import org.openscience.cdk.modeling.forcefield.SmoothingFunctions;
import org.openscience.cdk.modeling.forcefield.StretchBendInteractions;
import org.openscience.cdk.modeling.forcefield.Torsions;
import org.openscience.cdk.modeling.forcefield.VanDerWaalsInteractions;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.LoggingTool;



/**
 *  Check forcefield package using some examples.
 *
 *@author         vlabarta
 *@cdk.module     test-forcefield
 *@cdk.created    2005-01-17
 */
public class ForceFieldTests extends CDKTestCase {

	IMolecule molecule = null;
	IAtomContainer ac = null;
	GVector moleculeCoordinates = null;
	GeometricMinimizer gm = new GeometricMinimizer();
	Hashtable mmff94Tables = null;
	MMFF94EnergyFunction mmff94Energy = null;

	double[] molecule3Coord = {9, 9, 0};
	GVector molecule3Coordinates = new GVector(molecule3Coord);

	TestPotentialFunction tpf = new TestPotentialFunction();
	double[] testResult3C = {0, 0, 0};
	
	String input;

	private LoggingTool logger;
	private boolean standAlone = false;

	/**
	 *  Constructor for ForceFieldTests object
	 */
	public ForceFieldTests() {
		logger = new LoggingTool(this);
	}
	
	public void setUp() throws Exception {
		input = "Ethane-TestFF";
		InputStream is = this.getClass().getClassLoader().getResourceAsStream("data/mdl/" + input + ".mol");
		MDLReader mdlReader = new MDLReader(is);
		molecule = (IMolecule)mdlReader.read(new org.openscience.cdk.Molecule());
		mdlReader.close();
		//logger.debug("molecule: " +  molecule);

		gm.setMMFF94Tables(molecule);
		mmff94Tables = gm.getPotentialParameterSet();

		moleculeCoordinates = ForceFieldTools.getCoordinates3xNVector(molecule);
	}


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


	/**
	 *  Get MMFF94 energy of a molecule (methylbenzol).
	 */
	public void testGetMMFF94EnergyOfAMolecule() throws Exception {
		
		double testResult_mmff94Energy = 92473.5759007652; //(methylbenzol)
		
		//logger.debug("");
		//logger.debug("FORCEFIELDTESTS Get MMFF94 energy of a molecule (methylbenzol)");

		double energy = 0;
		String localInput = "methylbenzol";
		
		InputStream is = this.getClass().getClassLoader().getResourceAsStream("data/mdl/" + localInput + ".mol");
		//FileReader fileReader = new FileReader("data/mdl/" + localInput + ".mol");
		MDLReader mdlReader = new MDLReader(is);
		molecule = (IMolecule)mdlReader.read(new org.openscience.cdk.Molecule());
		mdlReader.close();
		//logger.debug("molecule: " +  molecule);


		ForceFieldConfigurator ffc = new ForceFieldConfigurator();
		ffc.setForceFieldConfigurator("mmff94");
		RingSet rs = (RingSet) ffc.assignAtomTyps((IMolecule) molecule);
		mmff94Tables = ffc.getParameterSet();

		mmff94Energy = new MMFF94EnergyFunction(molecule, mmff94Tables);
		energy = mmff94Energy.energyFunctionOfAMolecule(molecule);

		//logger.debug("molecule energy = " + energy);


		assertEquals(testResult_mmff94Energy, energy, 0.00001);

	}

	
	/**
	 *  A unit test for JUnit (Steepest Descents Method minimization)
	 */
	public void testSteepestDescentsMinimization() throws Exception {
		//logger.debug("");
		//logger.debug("FORCEFIELDTESTS with Steepest Descents Minimization");

		gm.setConvergenceParametersForSDM(100, 0.00001);
		gm.steepestDescentsMinimization(molecule3Coordinates, tpf);

		for (int i = 0; i < molecule3Coordinates.getSize(); i++) {
			assertEquals(testResult3C[i], gm.getSteepestDescentsMinimum().getElement(i), 0.0001);
		}
	}


 	/**
	 *  A unit test for JUnit (Conjugate Gradient Method minimization)
	 */
	public void testConjugateGradientMinimization() throws Exception {
		//logger.debug("");
		//logger.debug("FORCEFIELDTESTS with Conjugate Gradient Minimization");

		gm.setConvergenceParametersForCGM(100, 0.00001);
		gm.conjugateGradientMinimization(molecule3Coordinates, tpf);

		for (int i = 0; i < molecule3Coordinates.getSize(); i++) {
			assertEquals(testResult3C[i], gm.getConjugateGradientMinimum().getElement(i), 0.00001);
		}
	}


	/**
	 *  A unit test for JUnit (Newton-Raphson Method minimization)
	 */
	public void testNewtonRaphsonMinimization() {
		//logger.debug("");
		//logger.debug("FORCEFIELDTESTS with Newton-Raphson Minimization");

		gm.setConvergenceParametersForNRM(1000, 0.00001);
		gm.newtonRaphsonMinimization(molecule3Coordinates, tpf);

		for (int i = 0; i < molecule3Coordinates.getSize(); i++) {
			assertEquals(testResult3C[i], gm.getNewtonRaphsonMinimum().getElement(i), 0.00001);
		}
	}