AtomTypeCharges.java

/*  $Revision$ $Author$ $Date$
 *
 *  Copyright (C) 2005-2007  Christian Hoppe <chhoppe@users.sf.net>
 *                     2008  Egon Willighagen <egonw@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.charges;

import java.util.regex.Matcher;
import java.util.regex.Pattern;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.tools.HOSECodeGenerator;

/**
 * Assigns charges to atom types.
 *
 * @author      chhoppe
 * @cdk.created 2004-11-03
 * @cdk.module  charges
 * @cdk.githash
 */
@TestClass("org.openscience.cdk.charges.AtomTypeChargesTest")
public class AtomTypeCharges implements IChargeCalculator {
	
	HOSECodeGenerator hcg = new HOSECodeGenerator();
	Pattern pOC = Pattern.compile("O-[1][-];=?+C[(]=?+O.*+");
	Pattern pOP = Pattern.compile("O-[1][-];=?+P.*+");
	Pattern pOS = Pattern.compile("O-[1][-];=?+S.*+");
	Pattern p_p = Pattern.compile("[A-Za-z]{1,2}+[-][0-6].?+[+].*+");
	Pattern p_n = Pattern.compile("[A-Za-z]{1,2}+[-][0-6].?+[-].*+");


	/**
	 *  Constructor for the AtomTypeCharges object
	 */
	AtomTypeCharges() { }


	/**
	 *  Sets initial charges for atom types
	 * +1 for cationic atom types
	 * -1 for anionic atom types
	 * carboxylic oxygen -0.5
	 * phosphorylic oxygen -0.66
	 * sulfanilic oxygen -0.5
	 * or to formal charge (which must be determined elsewhere or set manually)
	 * polycations are not handled by this approach
	 *
	 *@param  atomContainer  AtomContainer
	 *@return                AtomContainer with set charges
	 *@exception  Exception  Description of the Exception
	 */
	@TestMethod("testCharges_pOC,testCharges_pOP,testCharges_pOS,testCharges_p_p,testCharges_p_n")
	public IAtomContainer setCharges(IAtomContainer atomContainer) throws Exception {
		
		atomContainer = setInitialCharges(atomContainer);
		return atomContainer;
	}


	private String removeAromaticityFlagsFromHoseCode(String hoseCode){
		//clean hosecode
		String hosecode="";
		for (int i=0;i<hoseCode.length();i++){
			if (hoseCode.charAt(i)== '*'){
			}else{
				hosecode=hosecode+hoseCode.charAt(i);
			}
		}
		return hosecode;
	}
	
	/**
	 *  Sets the initialCharges attribute of the AtomTypeCharges object
	 *
	 *@param  ac                AtomContainer
	 *@return                   AtomContainer with (new) partial charges
	 *@exception  CDKException  Description of the Exception
	 */
	private IAtomContainer setInitialCharges(IAtomContainer ac) throws CDKException {
		Matcher matOC = null;
		Matcher matOP = null;
		Matcher matOS = null;
		Matcher mat_p = null;
		Matcher mat_n = null;
		String hoseCode = "";

		for (int i = 0; i < ac.getAtomCount(); i++) {
			try {
				hoseCode = hcg.getHOSECode(ac, ac.getAtom(i), 3);
			} catch (CDKException ex1) {
				throw new CDKException("Could not build HOSECode from atom " + i + " due to " + ex1.toString(), ex1);
			}
			hoseCode=removeAromaticityFlagsFromHoseCode(hoseCode);

			matOC = pOC.matcher(hoseCode);
			matOP = pOP.matcher(hoseCode);
			matOS = pOS.matcher(hoseCode);
			mat_p = p_p.matcher(hoseCode);
			mat_n = p_n.matcher(hoseCode);

			if (matOC.matches()) {
				ac.getAtom(i).setCharge(-0.500);
			} else if (matOP.matches()) {
				ac.getAtom(i).setCharge(-0.666);
			} else if (matOS.matches()) {
				ac.getAtom(i).setCharge(-0.500);
			} else if (mat_p.matches()) {
				ac.getAtom(i).setCharge(+1.000);
			} else if (mat_n.matches()) {
				ac.getAtom(i).setCharge(-1.000);
			} else {
				ac.getAtom(i).setCharge(new Double(ac.getAtom(i).getFormalCharge()));
			}
		}
		return ac;
	}

	@TestMethod("testCharges_pOC,testCharges_pOP,testCharges_pOS," +
			"testCharges_p_p,testCharges_p_n")
    public void calculateCharges(IAtomContainer container) throws CDKException {
    	try {
	        this.setInitialCharges(container);
        } catch (Exception exception) {
	        throw new CDKException(
	        	"Could not calculate Gasteiger-Marsili PEPE charges: " +
	        	exception.getMessage(), exception
	        );
        }
    }
}