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Polarizability.java

/*  $RCSfile$
 *  $Author: sea36 $
 *  $Date: 2007-03-07 22:47:48 +0100 (Wed, 07 Mar 2007) $
 *  $Revision: 8045 $
 *
 *  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.Vector;

import org.openscience.cdk.Atom;
import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.Bond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.graph.PathTools;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.tools.HydrogenAdder;
import org.openscience.cdk.tools.LoggingTool;

/**
 * Calculation of the polarizability of a molecule by the method of Kang and
 * Jhon and Gasteiger based on {@cdk.cite KJ81} and {@cdk.cite GH82}
 * Limitations in parameterization of atoms:
 * H, Csp3, Csp2, Csp2arom, Csp3, Nsp3, Nsp2, Nsp3,
 * P, Osp3 and Osp2. Aromaticity must be calculated on beforehand.
 *
 * @author         chhoppe
 * @cdk.created    2004-11-03
 */
00048 public class Polarizability {
    private LoggingTool logger;

    /**
     * Constructor for the Polarizability object
     */
00054     public Polarizability() {
        logger = new LoggingTool(this);
    }


    /**
     *  Gets the polarizabilitiyFactorForAtom
     *
     *@param  atomContainer    AtomContainer
     *@param  atom  atom for which the factor should become known
     *@return       The polarizabilitiyFactorForAtom value
     */
00066     public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer,
                                                  org.openscience.cdk.interfaces.IAtom atom) {
        AtomContainer acH = new org.openscience.cdk.AtomContainer(atomContainer);
        try {
            HydrogenAdder hAdder = new HydrogenAdder();
            hAdder.addExplicitHydrogensToSatisfyValency(acH);
        } catch (Exception ex1) {
            logger.debug("Error in hydrogen addition");
        }
        return getKJPolarizabilityFactor(acH, atom);
    }


    /**
     *  calculates the mean molecular polarizability as described in paper of Kang and Jhorn
     *
     *@param  atomContainer  AtomContainer
     *@return     polarizabilitiy
     */
00085     public double calculateKJMeanMolecularPolarizability(IAtomContainer atomContainer) {
        double polarizabilitiy = 0;
        Molecule acH = new Molecule(atomContainer);
        try {
            HydrogenAdder hAdder = new HydrogenAdder();
            hAdder.addExplicitHydrogensToSatisfyValency(acH);
        } catch (Exception ex1) {
            logger.debug("Error in hydrogen addition");
        }
        for (int i = 0; i < acH.getAtomCount(); i++) {
            polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i));
        }
        return polarizabilitiy;
    }


    /**
     *  calculate effective atom polarizability
     *
     *@param  atomContainer                     IAtomContainer
     *@param  atom                   atom for which effective atom polarizability should be calculated
     *@param  influenceSphereCutOff  cut off for spheres whoch should taken into account for calculation
     *@return                        polarizabilitiy
     */
00109     public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContainer,
                                                         org.openscience.cdk.interfaces.IAtom atom,
                                                         int influenceSphereCutOff) {
        double polarizabilitiy = 0;
        Molecule acH = new Molecule(atomContainer);
        Vector startAtom = new Vector(1);
        startAtom.add(0, (Atom) atom);
        double bond;
        try {
            HydrogenAdder hAdder = new HydrogenAdder();
            hAdder.addExplicitHydrogensToSatisfyValency(acH);
        } catch (Exception ex1) {
            logger.debug("Error in hydrogen addition");
        }
        polarizabilitiy += getKJPolarizabilityFactor(acH, atom);
        for (int i = 0; i < acH.getAtomCount(); i++) {
            if (acH.getAtom(i) != atom) {
                bond = PathTools.breadthFirstTargetSearch(acH,
                        startAtom, acH.getAtom(i), 0, influenceSphereCutOff);
                if (bond == 1) {
                    polarizabilitiy += getKJPolarizabilityFactor(acH, acH.getAtom(i));
                } else {
                    polarizabilitiy += (Math.pow(0.5, bond - 1) * getKJPolarizabilityFactor(acH, acH.getAtom(i)));
                }//if bond==0
            }//if !=atom
        }//for
        return polarizabilitiy;
    }


    /**
     *  calculate bond polarizability
     *
     *@param  atomContainer    AtomContainer
     *@param  bond  Bond bond for which the polarizabilitiy should be calculated
     *@return       polarizabilitiy
     */
00146     public double calculateBondPolarizability(IAtomContainer atomContainer, Bond bond) {
        double polarizabilitiy = 0;
        Molecule acH = new Molecule(atomContainer);
        try {
            HydrogenAdder hAdder = new HydrogenAdder();
            hAdder.addExplicitHydrogensToSatisfyValency(acH);
        } catch (Exception ex1) {
            logger.debug("Error in hydrogen addition");
        }
        if (bond.getAtomCount() == 2) {
            polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getAtom(0));
            polarizabilitiy += getKJPolarizabilityFactor(acH, bond.getAtom(1));
        }
        return (polarizabilitiy / 2);
    }


    /**
     *  Method which assigns the polarizabilitiyFactors
     *
     *@param  atomContainer    AtomContainer
     *@param  atom  Atom
     *@return       double polarizabilitiyFactor
     */
00170     private double getKJPolarizabilityFactor(IAtomContainer atomContainer, org.openscience.cdk.interfaces.IAtom atom) {
        double polarizabilitiyFactor = 0;
        String AtomSymbol;
        AtomSymbol = atom.getSymbol();
        if (AtomSymbol.equals("H")) {
            polarizabilitiyFactor = 0.387;
        } else if (AtomSymbol.equals("C")) {
            if (atomContainer.getMaximumBondOrder(atom) == 1) {
                polarizabilitiyFactor = 1.064;/*1.064*/
            } else if (atomContainer.getMaximumBondOrder(atom) == 1.5 || atom.getFlag(CDKConstants.ISAROMATIC)) {
                polarizabilitiyFactor = 1.230;
            } else if (atomContainer.getMaximumBondOrder(atom) == 2) {
                if (getNumberOfHydrogen(atomContainer, atom) == 0) {
                    polarizabilitiyFactor = 1.382;
                } else {
                    polarizabilitiyFactor = 1.37;
                }
            } else if (atomContainer.getMaximumBondOrder(atom) >= 3) {
                polarizabilitiyFactor = 1.279;
            }
        } else if (AtomSymbol.equals("N")) {
            if (atom.getCharge() < 0) {
                polarizabilitiyFactor = 1.090;
            } else if (atomContainer.getMaximumBondOrder(atom) == 1) {
                polarizabilitiyFactor = 1.094;
            } else if (atomContainer.getMaximumBondOrder(atom) > 1 && atomContainer.getMaximumBondOrder(atom) < 3) {
                polarizabilitiyFactor = 1.030;
            } else if (atomContainer.getMaximumBondOrder(atom) >= 3) {
                polarizabilitiyFactor = 0.852;
            }
        } else if (AtomSymbol.equals("O")) {
            if (atom.getCharge() == -1) {
                polarizabilitiyFactor = 1.791;
            } else if (atom.getCharge() == 1) {
                polarizabilitiyFactor = 0.422;
            } else if (atomContainer.getMaximumBondOrder(atom) == 1) {
                polarizabilitiyFactor = 0.664;
            } else if (atomContainer.getMaximumBondOrder(atom) == 2) {
                polarizabilitiyFactor = 0.460;
            }
        } else if (AtomSymbol.equals("P")) {
            if (atomContainer.getConnectedBondsCount(atom) == 4 && atomContainer.getMaximumBondOrder(atom) == 2) {
                polarizabilitiyFactor = 0;
            }
        } else if (AtomSymbol.equals("S")) {
            if (atomContainer.getMaximumBondOrder(atom) == 1) {
                polarizabilitiyFactor = 3.20;/*3.19*/
            } else if (atomContainer.getMaximumBondOrder(atom) == 1.5 || atom.getFlag(CDKConstants.ISAROMATIC)) {
                polarizabilitiyFactor = 3.38;
            } else if (atomContainer.getMaximumBondOrder(atom) == 2) {
                if (getNumberOfHydrogen(atomContainer, atom) == 0) {
                    polarizabilitiyFactor = 3.51;
                } else {
                    polarizabilitiyFactor = 3.50;
                }
            } else if (atomContainer.getMaximumBondOrder(atom) >= 3) {
                polarizabilitiyFactor = 3.42;
            }
        }else if (AtomSymbol.equals("F")) {
            polarizabilitiyFactor = 0.296;
        }else if (AtomSymbol.equals("Cl")) {
            polarizabilitiyFactor = 2.343;
        } else if (AtomSymbol.equals("Br")) {
            polarizabilitiyFactor = 3.5;
        } else if (AtomSymbol.equals("I")) {
            polarizabilitiyFactor = 5.79;
        }
        return polarizabilitiyFactor;
    }


    /**
     *  Gets the numberOfHydrogen attribute of the Polarizability object
     *
     *@param  atomContainer    Description of the Parameter
     *@param  atom  Description of the Parameter
     *@return       The numberOfHydrogen value
     */
00248     private int getNumberOfHydrogen(IAtomContainer atomContainer, org.openscience.cdk.interfaces.IAtom atom) {
        java.util.List bonds = atomContainer.getConnectedBondsList(atom);
        org.openscience.cdk.interfaces.IAtom connectedAtom;
        int hCounter = 0;
        for (int i = 0; i < bonds.size(); i++) {
            connectedAtom = ((org.openscience.cdk.interfaces.IBond)bonds.get(i)).getConnectedAtom(atom);
            if (connectedAtom.getSymbol().equals("H")) {
                hCounter += 1;
            }
        }
        return hCounter;
    }
}


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