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AtomType.java

/* $RCSfile$
 * $Author$    
 * $Date$    
 * $Revision$
 *
 *  Copyright (C) 2001-2007  Christoph Steinbeck <steinbeck@users.sf.net>
 *
 *  Contact: cdk-devel@lists.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.
 *  All we ask is that proper credit is given for our work, which includes
 *  - but is not limited to - adding the above copyright notice to the beginning
 *  of your source code files, and to any copyright notice that you may distribute
 *  with programs based on this work.
 *
 *  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;

import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IElement;

import java.io.Serializable;

/**
 * The base class for atom types. Atom types are typically used to describe the
 * behaviour of an atom of a particular element in different environment like 
 * sp<sup>3</sup>
 * hybridized carbon C3, etc., in some molecular modelling applications.
 *
 * @author       steinbeck
 * @cdk.created  2001-08-08
 * @cdk.module   data
 * @cdk.githash
 * @cdk.keyword  atom, type
 */
00049 public class AtomType extends Isotope implements IAtomType, Serializable, Cloneable
{

      /**
     * Determines if a de-serialized object is compatible with this class.
     *
     * This value must only be changed if and only if the new version
     * of this class is incompatible with the old version. See Sun docs
     * for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
     * /serialization/spec/version.doc.html>details</a>.
       */
00060       private static final long serialVersionUID = -7950397716808229972L;

      /**
       *  The maximum bond order allowed for this atom type.
       */
00065       IBond.Order maxBondOrder = null;
      /**
       *  The maximum sum of all bond orders allowed for this atom type.
       */
00069       Double bondOrderSum = (Double) CDKConstants.UNSET;

    /**
     * The covalent radius of this atom type.
     */
00074     Double covalentRadius = (Double) CDKConstants.UNSET;
    
    /**
     *  The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6.
     * 
     *  Note that some constructors ({@link #AtomType(String)} and
     * {@link #AtomType(String, String)} ) will explicitly set this field to 0
     */
00082     protected Integer formalCharge = (Integer) CDKConstants.UNSET;

    /**
     * The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET
     * as default.
     */
00088     protected IAtomType.Hybridization hybridization = (Hybridization) CDKConstants.UNSET;

    /**
     *  The electron Valency of this atom with CDKConstants.UNSET as default.
     */
00093     protected Integer electronValency = (Integer) CDKConstants.UNSET;

    /**
     * The formal number of neighbours this atom type can have with CDKConstants_UNSET
     * as default. This includes explicitely and implicitely connected atoms, including
     * implicit hydrogens.
     */
00100     protected Integer formalNeighbourCount = (Integer) CDKConstants.UNSET;

    /**
     * String representing the identifier for this atom type with null as default.
     */
00105     private String identifier;
    
    /**
       * Constructor for the AtomType object. Defaults to a zero formal charge.
     *
     * @param elementSymbol  Symbol of the atom
       */
00112       public AtomType(String elementSymbol) {
            super(elementSymbol);
            this.identifier = null;
            this.formalNeighbourCount = 0;
            this.electronValency = 0;
            this.formalCharge = 0;
      }


      /**
       * Constructor for the AtomType object. Defaults to a zero formal charge.
       *
       * @param  identifier     An id for this atom type, like C3 for sp3 carbon
       * @param  elementSymbol  The element symbol identifying the element to which this atom type applies
       */
00127       public AtomType(String identifier, String elementSymbol)
      {
            this(elementSymbol);
            this.identifier = identifier;
      }

      /**
       * Constructs an isotope by copying the symbol, atomic number,
       * flags, identifier, exact mass, natural abundance and mass 
       * number from the given IIsotope. It does not copy the
       * listeners and properties. If the element is an instanceof
       * IAtomType, then the maximum bond order, bond order sum,
       * van der Waals and covalent radii, formal charge, hybridization,
       * electron valency, formal neighbour count and atom type name
       * are copied too.
       * 
       * @param element IIsotope to copy information from
       */
00145       public AtomType(IElement element) {
            super(element);
            if (element instanceof IAtomType) {
                  this.maxBondOrder = ((IAtomType)element).getMaxBondOrder();
                  this.bondOrderSum = ((IAtomType)element).getBondOrderSum();
                  this.covalentRadius = ((IAtomType)element).getCovalentRadius();
                  this.formalCharge = ((IAtomType)element).getFormalCharge();
                  this.hybridization = ((IAtomType)element).getHybridization();
                  this.electronValency = ((IAtomType)element).getValency();
                  this.formalNeighbourCount = ((IAtomType)element).getFormalNeighbourCount();
                  this.identifier = ((IAtomType)element).getAtomTypeName();
            }
      }

      /**
       *  Sets the if attribute of the AtomType object.
       *
       * @param  identifier  The new AtomTypeID value. Null if unset.
     *
     * @see    #getAtomTypeName
       */
00166       public void setAtomTypeName(String identifier)
      {
            this.identifier = identifier;
            notifyChanged();
      }


      /**
       *  Sets the MaxBondOrder attribute of the AtomType object.
       *
       * @param  maxBondOrder  The new MaxBondOrder value
     *
     * @see       #getMaxBondOrder
       */
00180       public void setMaxBondOrder(IBond.Order maxBondOrder)
      {
            this.maxBondOrder = maxBondOrder;
            notifyChanged();
      }


      /**
       *  Sets the the exact bond order sum attribute of the AtomType object.
       *
       * @param  bondOrderSum  The new bondOrderSum value
     *
     * @see       #getBondOrderSum
       */
00194       public void setBondOrderSum(Double bondOrderSum)
      {
            this.bondOrderSum = bondOrderSum;
            notifyChanged();
      }


      /**
       *  Gets the id attribute of the AtomType object.
       *
       * @return    The id value
     *
     * @see       #setAtomTypeName
       */
00208       public String getAtomTypeName()
      {
            return this.identifier;
      }


      /**
       *  Gets the MaxBondOrder attribute of the AtomType object.
       *
       * @return    The MaxBondOrder value
     *
     * @see       #setMaxBondOrder
       */
00221       public IBond.Order getMaxBondOrder()
      {
            return maxBondOrder;
      }


      /**
       *  Gets the bondOrderSum attribute of the AtomType object.
       *
       * @return    The bondOrderSum value
     *
     * @see       #setBondOrderSum
       */
00234       public Double getBondOrderSum()
      {
            return bondOrderSum;
      }

    /**
     *  Sets the formal charge of this atom.
     *
     * @param  charge  The formal charge
     *
     * @see    #getFormalCharge
     */
00246     public void setFormalCharge(Integer charge) {
      this.formalCharge = charge;
      notifyChanged();
    }
    
    /**
     *  Returns the formal charge of this atom.
     *
     * @return the formal charge of this atom
     *
     * @see    #setFormalCharge
     */
00258     public Integer getFormalCharge() {
        return this.formalCharge;
    }
    
    /**
     * Sets the formal neighbour count of this atom.
     *
     * @param  count  The neighbour count
     *
     * @see    #getFormalNeighbourCount
     */
00269     public void setFormalNeighbourCount(Integer count) {
        this.formalNeighbourCount = count;
      notifyChanged();
    }
    
    /**
     * Returns the formal neighbour count of this atom.
     *
     * @return the formal neighbour count of this atom
     *
     * @see    #setFormalNeighbourCount
     */
00281     public Integer getFormalNeighbourCount() {
        return this.formalNeighbourCount;
    }
    
    /**
     *  Sets the hybridization of this atom.
     *
     * @param  hybridization  The hybridization
     *
     * @see    #getHybridization
     */
00292     public void setHybridization(IAtomType.Hybridization hybridization) {
        this.hybridization = hybridization;
        notifyChanged();
    }
    
    /**
     *  Returns the hybridization of this atom.
     *
     * @return the hybridization of this atom
     *
     * @see    #setHybridization
     */
00304     public IAtomType.Hybridization getHybridization() {
        return this.hybridization;
    }
    
    /**
     * Compares a atom type with this atom type.
     *
     * @param  object Object of type AtomType
     * @return        true if the atom types are equal
     */
00314     public boolean compare(Object object) {
        if (!(object instanceof IAtomType)) {
            return false;
        }
        if (!super.compare(object)) {
            return false;
        }
        AtomType type = (AtomType) object;
        return (getAtomTypeName() == type.getAtomTypeName()) &&
                (maxBondOrder == type.maxBondOrder) &&
                (bondOrderSum == type.bondOrderSum);
    }

    /**
     * Sets the covalent radius for this AtomType.
     *
     * @param radius The covalent radius for this AtomType
     * @see    #getCovalentRadius
     */
00333     public void setCovalentRadius(Double radius) {
        this.covalentRadius = radius;
      notifyChanged();
    }
    
    /**
     * Returns the covalent radius for this AtomType.
     *
     * @return The covalent radius for this AtomType
     * @see    #setCovalentRadius
     */
00344     public Double getCovalentRadius() {
        return this.covalentRadius;
    }
    
      /**
       *  Sets the the exact electron valency of the AtomType object.
       *
       * @param  valency  The new valency value
       * @see #getValency
       *
       */
00355       public void setValency(Integer valency)
      {
            this.electronValency = valency;
            notifyChanged();
      }

      /**
       *  Gets the the exact electron valency of the AtomType object.
       *
       * @return The valency value
       * @see #setValency
       *
       */
00368       public Integer getValency()
      {
            return this.electronValency;
      }

00373     public Object clone() throws CloneNotSupportedException {
        return super.clone();
    }
      
00377     public String toString() {
        StringBuffer resultString = new StringBuffer(64);
        resultString.append("AtomType(").append(hashCode());
        if (getAtomTypeName() != null) {
            resultString.append(", N:").append(getAtomTypeName());
        }
        if (getMaxBondOrder() != null) {
            resultString.append(", MBO:").append(getMaxBondOrder());
        }
        if (getBondOrderSum() != null) {
            resultString.append(", BOS:").append(getBondOrderSum());
        }
        if (getFormalCharge() != null) {
            resultString.append(", FC:").append(getFormalCharge());
        }
        if (getHybridization() != null) {
            resultString.append(", H:").append(getHybridization());
        }
        if (getFormalNeighbourCount() != null) {
            resultString.append(", NC:").append(getFormalNeighbourCount());
        }
        if (getCovalentRadius() != null) {
            resultString.append(", CR:").append(getCovalentRadius());
        }        
        if (getValency() != null) {
            resultString.append(", EV:").append(getValency());
        }
        resultString.append(", ").append(super.toString());
        resultString.append(')');
        return resultString.toString(); 
    }
}


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