mmff94partialcharges.java

化学图形处理软件

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 *  $Revision: 7636 $
 *
 *  Copyright (C) 2004-2007  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.charges;

import java.util.Hashtable;
import java.util.Vector;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator;
/**
 *  The calculation of the MMFF94 partial charges.
 *  Charges are stored as atom properties:
 *  for an AtomContainer ac, values are calculated with:
 *  <pre>
 *  HydrogenAdder hAdder = new HydrogenAdder();
 *  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
 *  IAtomContainer ac = sp.parseSmiles("CC");
 *  hAdder.addExplicitHydrogensToSatisfyValency((Molecule)ac);
 *  MMFF94PartialCharges mmff = new MMFF94PartialCharges();
 *  mmff.assignMMFF94PartialCharges(ac);
 *  </pre>
 *  and for each atom, the value is given by:
 *  <pre>
 *  ( (Double)atom.getProperty("MMFF94charge") ).doubleValue().
 *  </pre>
 *
 * @author      mfe4
 * @author chhoppe
 * @cdk.created 2004-11-03
 * @cdk.module  forcefield
 */
public class MMFF94PartialCharges {

	
	/**
	 *  Constructor for the MMFF94PartialCharges object
	 */
	public MMFF94PartialCharges() { }
	
	
	
	/**
	 *  Main method which assigns MMFF94 partial charges
	 *
	 *@param  ac             AtomContainer
	 *@return                AtomContainer with MMFF94 partial charges as atom properties
	 *@exception  Exception  Possible Exceptions
	 */
	public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws Exception {
		ForceFieldConfigurator ffc = new ForceFieldConfigurator();
		ffc.setForceFieldConfigurator("mmff94");
		ffc.assignAtomTyps((IMolecule)ac);
		Hashtable parameterSet = ffc.getParameterSet();
		// for this calculation,
		// we need some values stored in the vector "data" in the
		// hashtable of these atomTypes:		
		double charge = 0;
		double formalCharge = 0;
		double formalChargeNeigh = 0;
		double theta = 0;
		double sumOfFormalCharges = 0;
		double sumOfBondIncrements = 0;
		org.openscience.cdk.interfaces.IAtom thisAtom = null;
		java.util.List neighboors = null;
		Vector data = null;
		Vector bondData = null;
		Vector dataNeigh = null;
		java.util.Iterator atoms = ac.atoms();
		while(atoms.hasNext()) {
			//logger.debug("ATOM "+i+ " " +atoms[i].getSymbol());
			thisAtom = (org.openscience.cdk.interfaces.IAtom)atoms.next();
			data = (Vector) parameterSet.get("data"+thisAtom.getAtomTypeName());
			neighboors = ac.getConnectedAtomsList(thisAtom);
			formalCharge = thisAtom.getCharge();
			theta = ((Double)data.get(5)).doubleValue();
			charge = formalCharge * (1 - (neighboors.size() * theta));
			sumOfFormalCharges = 0;
			sumOfBondIncrements = 0;
			for(int n = 0; n < neighboors.size(); n++) {
				org.openscience.cdk.interfaces.IAtom neighbour = (org.openscience.cdk.interfaces.IAtom)neighboors.get(n);
				dataNeigh = (Vector) parameterSet.get("data"+neighbour.getAtomTypeName());
				if (parameterSet.containsKey("bond"+thisAtom.getAtomTypeName()+";"+neighbour.getAtomTypeName())) {
					bondData = (Vector) parameterSet.get("bond"+thisAtom.getAtomTypeName()+";"+neighbour.getAtomTypeName());
					sumOfBondIncrements -= ((Double) bondData.get(4)).doubleValue();
				}
				else if (parameterSet.containsKey("bond"+neighbour.getAtomTypeName()+";"+thisAtom.getAtomTypeName())) {
					bondData = (Vector) parameterSet.get("bond"+neighbour.getAtomTypeName()+";"+thisAtom.getAtomTypeName());
					sumOfBondIncrements += ((Double) bondData.get(4)).doubleValue();
				}
				else {
					// Maybe not all bonds have pbci in mmff94.prm, i.e. C-N
					sumOfBondIncrements += ( theta - ((Double)dataNeigh.get(5)).doubleValue() );
				}
				
				
				dataNeigh = (Vector) parameterSet.get("data"+neighbour.getID());
				formalChargeNeigh = neighbour.getCharge();
				sumOfFormalCharges += formalChargeNeigh;
			}
			charge += sumOfFormalCharges * theta;
			charge += sumOfBondIncrements;
			thisAtom.setProperty("MMFF94charge", new Double(charge));
			//logger.debug( "CHARGE :"+thisAtom.getProperty("MMFF94charge") );
		}
		return ac;
	}
}