ForceField.java

/* $Revision$ $Author$ $Date$
 *
 * Copyright (C) 2005-2007  Violeta Labarta <vlabarta@users.sf.net>
 *
 * 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.
 *
 * 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.forcefield;

import javax.vecmath.GVector;

import org.openscience.cdk.Molecule;
import org.openscience.cdk.graph.ConnectivityChecker;

/**
 *  To work with the coordinates of the molecule, like get the 3d coordinates of the atoms or 
 *  calculate the distance between two atoms.
 *@author     vlabarta
 *@cdk.module     forcefield
 * @cdk.githash
 *
 */
public class ForceField extends GeometricMinimizer{
	
	private String potentialFunction="mmff94";
	
	boolean sdm_flag=true;
        boolean cgm_flag=true;
        boolean nrm_flag=true;
	
	/**
	 *  Constructor for the ForceField object
	 */
	public ForceField() {}
	
	public ForceField(Molecule molecule) throws Exception {
		setMolecule(molecule, false);
	}


	public void setPotentialFunction(String potentialName){
		potentialFunction=potentialName;
	}
	
        public void setUsedGMMethods(boolean sdm, boolean cgm,boolean nrm){
	       sdm_flag=sdm;
               cgm_flag=cgm;
               nrm_flag=nrm;
        }
	
	public void minimize( ) throws Exception{
        if (!ConnectivityChecker.isConnected(molecule)) {
			throw new Exception("CDKError: Molecule is NOT connected,could not layout.");
		}
		GVector moleculeCoords = new GVector(3);
		MMFF94EnergyFunction mmff94PF=null;
		if (potentialFunction.equals("mmff94")){
		    //logger.debug("SET POTENTIAL FUNCTION TO MMFF94");
		    setMMFF94Tables(molecule);
		    mmff94PF=new MMFF94EnergyFunction(molecule,getPotentialParameterSet());
			//logger.debug("PotentialFunction set:"+potentialFunction+", Hashtable:" +getPotentialParameterSet().size());
		}
		moleculeCoords.setSize(molecule.getAtomCount() * 3);
		moleculeCoords.set(ForceFieldTools.getCoordinates3xNVector(molecule));
		
		//logger.debug("PotentialFunction set:"+potentialFunction+" Molecule Coords set:"+moleculeCoords.getSize()+" Hashtable:"+getPotentialParameterSet().size());
		//logger.debug(moleculeCoords.toString());
        //logger.debug("Starting minmization at " + start);
		if (sdm_flag) steepestDescentsMinimization(moleculeCoords,mmff94PF);

		if (cgm_flag)conjugateGradientMinimization(moleculeCoords, mmff94PF);
		//conjugateGradientMinimization(moleculeCoords, tpf);
        //logger.debug("Finished minmization at " + stop);
		//if ((stop - start)/1000 < 60) {
			//logger.debug("Time for minimization: " + (stop - start)/1000 + " sec");
		//}
		//	logger.debug("Time for minimization: " + (stop - start)/60000 + " min");

		//}
		//logger.debug("Minimization READY");
		//ForceFieldTools.assignCoordinatesToMolecule(moleculeCoords, (AtomContainer) molecule); 
	}
			



}