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AtomTypeCharges.java

/*  $RCSfile$
 *  $Author: egonw $
 *  $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 *  $Revision: 7636 $
 *
 *  Copyright (C) 2005-2007  Christian Hoppe <chhoppe@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.interfaces.IAtomContainer;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.tools.HOSECodeGenerator;

/**
 * Assigns charges to atom types.
 *
 * @author      chhoppe
 * @cdk.created 2004-11-03
 * @cdk.module  charges
 */
00041 public class AtomTypeCharges {
      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
       */
00053       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
       */
00070       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
       */
00096       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(ac.getAtom(i).getFormalCharge());
                  }
            }
            return ac;
      }
}


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