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Viewing changes to src/org/openscience/cdk/charges/AtomTypeCharges.java

  • Committer: Bazaar Package Importer
  • Author(s): Paul Cager
  • Date: 2008-04-09 21:17:53 UTC
  • Revision ID: james.westby@ubuntu.com-20080409211753-46lmjw5z8mx5pd8d
Tags: upstream-1.0.2
Import upstream version 1.0.2

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src/org/openscience/cdk/charges/AtomTypeCharges.java
 
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/*  $RCSfile$
 
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 *  $Author: egonw $
 
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 *  $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 
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 *  $Revision: 7636 $
 
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 *
 
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 *  Copyright (C) 2005-2007  Christian Hoppe <chhoppe@users.sf.net>
 
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 *
 
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 *  Contact: cdk-devel@list.sourceforge.net
 
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 *
 
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 *  This program is free software; you can redistribute it and/or
 
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 *  modify it under the terms of the GNU Lesser General Public License
 
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 *  as published by the Free Software Foundation; either version 2.1
 
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 *  of the License, or (at your option) any later version.
 
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 *
 
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 *  This program is distributed in the hope that it will be useful,
 
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 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 
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 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 
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 *  GNU Lesser General Public License for more details.
 
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 *
 
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 *  You should have received a copy of the GNU Lesser General Public License
 
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 *  along with this program; if not, write to the Free Software
 
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 *  Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 
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 */
 
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package org.openscience.cdk.charges;
 
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import java.util.regex.Matcher;
 
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import java.util.regex.Pattern;
 
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import org.openscience.cdk.interfaces.IAtomContainer;
 
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import org.openscience.cdk.exception.CDKException;
 
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import org.openscience.cdk.tools.HOSECodeGenerator;
 
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/**
 
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 * Assigns charges to atom types.
 
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 *
 
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 * @author      chhoppe
 
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 * @cdk.created 2004-11-03
 
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 * @cdk.module  charges
 
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 */
 
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public class AtomTypeCharges {
 
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        HOSECodeGenerator hcg = new HOSECodeGenerator();
 
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        Pattern pOC = Pattern.compile("O-[1][-];=?+C[(]=?+O.*+");
 
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        Pattern pOP = Pattern.compile("O-[1][-];=?+P.*+");
 
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        Pattern pOS = Pattern.compile("O-[1][-];=?+S.*+");
 
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        Pattern p_p = Pattern.compile("[A-Za-z]{1,2}+[-][0-6].?+[+].*+");
 
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        Pattern p_n = Pattern.compile("[A-Za-z]{1,2}+[-][0-6].?+[-].*+");
 
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        /**
 
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         *  Constructor for the AtomTypeCharges object
 
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         */
 
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        AtomTypeCharges() { }
 
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        /**
 
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         *  Sets initial charges for atom types
 
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         * +1 for cationic atom types
 
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         * -1 for anionic atom types
 
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         * carboxylic oxygen -0.5
 
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         * phosphorylic oxygen -0.66
 
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         * sulfanilic oxygen -0.5
 
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         * or to formal charge (which must be determined elsewhere or set manually)
 
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         * polycations are not handled by this approach
 
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         *
 
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         *@param  atomContainer  AtomContainer
 
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         *@return                AtomContainer with set charges
 
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         *@exception  Exception  Description of the Exception
 
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         */
 
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        public IAtomContainer setCharges(IAtomContainer atomContainer) throws Exception {
 
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                atomContainer = setInitialCharges(atomContainer);
 
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                return atomContainer;
 
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        }
 
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        private String removeAromaticityFlagsFromHoseCode(String hoseCode){
 
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                //clean hosecode
 
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                String hosecode="";
 
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                for (int i=0;i<hoseCode.length();i++){
 
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                        if (hoseCode.charAt(i)== '*'){
 
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                        }else{
 
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                                hosecode=hosecode+hoseCode.charAt(i);
 
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                        }
 
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                }
 
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                return hosecode;
 
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        }
 
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        /**
 
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         *  Sets the initialCharges attribute of the AtomTypeCharges object
 
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         *
 
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         *@param  ac                AtomContainer
 
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         *@return                   AtomContainer with (new) partial charges
 
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         *@exception  CDKException  Description of the Exception
 
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         */
 
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        private IAtomContainer setInitialCharges(IAtomContainer ac) throws CDKException {
 
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                Matcher matOC = null;
 
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                Matcher matOP = null;
 
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                Matcher matOS = null;
 
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                Matcher mat_p = null;
 
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                Matcher mat_n = null;
 
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                String hoseCode = "";
 
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                for (int i = 0; i < ac.getAtomCount(); i++) {
 
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                        try {
 
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                                hoseCode = hcg.getHOSECode(ac, ac.getAtom(i), 3);
 
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                        } catch (CDKException ex1) {
 
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                                throw new CDKException("Could not build HOSECode from atom " + i + " due to " + ex1.toString(), ex1);
 
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                        }
 
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                        hoseCode=removeAromaticityFlagsFromHoseCode(hoseCode);
 
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                        matOC = pOC.matcher(hoseCode);
 
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                        matOP = pOP.matcher(hoseCode);
 
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                        matOS = pOS.matcher(hoseCode);
 
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                        mat_p = p_p.matcher(hoseCode);
 
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                        mat_n = p_n.matcher(hoseCode);
 
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                        if (matOC.matches()) {
 
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                                ac.getAtom(i).setCharge(-0.500);
 
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                        } else if (matOP.matches()) {
 
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                                ac.getAtom(i).setCharge(-0.666);
 
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                        } else if (matOS.matches()) {
 
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                                ac.getAtom(i).setCharge(-0.500);
 
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                        } else if (mat_p.matches()) {
 
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                                ac.getAtom(i).setCharge(+1.000);
 
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                        } else if (mat_n.matches()) {
 
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                                ac.getAtom(i).setCharge(-1.000);
 
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                        } else {
 
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                                ac.getAtom(i).setCharge(ac.getAtom(i).getFormalCharge());
 
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                        }
 
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                }
 
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                return ac;
 
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        }
 
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}
 
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