/* 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.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
 */
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
     */
    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;
    }

    @Override
    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);
        }
    }
}
