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Polymer.java
/* $RCSfile$
 * $Author$
 * $Date$
 * $Revision$
 * 
 * Copyright (C) 2001-2007  Edgar Luttmann <edgar@uni-paderborn.de>
 * 
 * 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.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ILonePair;
import org.openscience.cdk.interfaces.IMonomer;
import org.openscience.cdk.interfaces.IPolymer;
import org.openscience.cdk.interfaces.ISingleElectron;

import java.util.Collection;
import java.util.Hashtable;
import java.util.Map;

/**
 * Subclass of Molecule to store Polymer specific attributes that a Polymer has.
 *
 * @cdk.module data
 * @cdk.githash
 *
 * @author      Edgar Luttmann <edgar@uni-paderborn.de>
 * @author      Martin Eklund <martin.eklund@farmbio.uu.se>
 * @cdk.created 2001-08-06
 * @cdk.keyword polymer
 */
00052 public class Polymer extends Molecule implements java.io.Serializable, IPolymer
{ 
      /**
     * 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>.
       */
00061       private static final long serialVersionUID = -2596790658835319339L;

    private Map<String, IMonomer> monomers;     // the list of all the contained Monomers.
      
      /**
       * Constructs a new Polymer to store the Monomers.
       */   
00068       public Polymer() {
            super();
            monomers = new Hashtable<String, IMonomer>();
      }
      
      /**
       * Adds the atom oAtom to a specified Monomer.
       *
       * @param oAtom  The atom to add
       * @param oMonomer  The monomer the atom belongs to
       */
00079       public void addAtom(IAtom oAtom, IMonomer oMonomer) {
            
            if(!contains(oAtom))    {
                  super.addAtom(oAtom);
                  
                  if(oMonomer != null)    {     // Not sure what's better here...throw nullpointer exception?
                        oMonomer.addAtom(oAtom);                        
                        if (! monomers.containsKey(oMonomer.getMonomerName())) {
                              monomers.put(oMonomer.getMonomerName(), oMonomer);
                        }
                  }
            }
            /* notifyChanged() is called by addAtom in
             AtomContainer */
      }
      
      /**
       * Returns the number of monomers present in the Polymer.
       *
       * @return number of monomers
       */
00100       public int getMonomerCount() {
            return monomers.size();
      }
      
      /**
       * Retrieves a Monomer object by specifying its name.
       *
       * @param cName  The name of the monomer to look for
       * @return The Monomer object which was asked for
       */
00110       public IMonomer getMonomer(String cName) {
            return monomers.get(cName);
      }
      
      /**
       * Returns a collection of the names of all <code>Monomer</code>s in this
       * polymer.
       *
       * @return a <code>Collection</code> of all the monomer names.
       */
00120       public Collection<String> getMonomerNames() {
            return monomers.keySet();
      }
      
      /**
       * Removes a particular monomer, specified by its name.
       * 
       * @param name The name of the monomer to remove
       */
00129       public void removeMonomer(String name)    {
            if (monomers.containsKey(name))     {
                  Monomer monomer = (Monomer)monomers.get(name);
                  this.remove(monomer);
                  monomers.remove(name);
            }
      }

00137     public String toString() {
        StringBuffer stringContent = new StringBuffer();
        stringContent.append("Polymer(");
        stringContent.append(this.hashCode()).append(", ");
        stringContent.append(super.toString());
        stringContent.append(')');
        return stringContent.toString();
    }

  /*
  TODO it's not clear why we need to remove all elements after the clone
  Looks like we should only clone the monomer related stuff
   */
00150     public Object clone() throws CloneNotSupportedException {
      Polymer clone = (Polymer)super.clone();
        clone.removeAllElements();
        clone.monomers = new Hashtable<String, IMonomer>();
        for (String monomerName : getMonomerNames()) {
            Monomer monomerClone = (Monomer) getMonomer(monomerName).clone();
            for (IAtom atomInMonomer : monomerClone.atoms()) {
                clone.addAtom(atomInMonomer, monomerClone);
            }
        }

        // now consider atoms that are not associated with any monomer
        for (IAtom atom : atoms()) {
            if (!atomIsInMonomer(atom))
                clone.addAtom((IAtom) atom.clone());
        }

        // since we already removed bonds we'll have to add them back
            IBond newBond;
            for (IBond bond : bonds()) {
                  newBond = (IBond)bond.clone();
                  IAtom[] newAtoms = new IAtom[bond.getAtomCount()];
                  for (int j = 0; j < bond.getAtomCount(); ++j) {
                        newAtoms[j] = clone.getAtom(getAtomNumber(bond.getAtom(j)));
                  }
                  newBond.setAtoms(newAtoms);
            clone.addBond(newBond);
        }

        // put back lone pairs
        ILonePair lp;
        ILonePair newLp;
        for (int i = 0; i < getLonePairCount(); ++i) {
            lp = getLonePair(i);
            newLp = (ILonePair) lp.clone();
            if (lp.getAtom() != null) {
                newLp.setAtom(clone.getAtom(getAtomNumber(lp.getAtom())));
            }
            clone.addLonePair(newLp);
        }

        // put back single electrons
        ISingleElectron singleElectron;
        ISingleElectron newSingleElectron;
        for (int i = 0; i < getSingleElectronCount(); ++i) {
            singleElectron = getSingleElectron(i);
            newSingleElectron = (ISingleElectron) singleElectron.clone();
            if (singleElectron.getAtom() != null) {
                newSingleElectron.setAtom(clone.getAtom(getAtomNumber(singleElectron.getAtom())));
            }
            clone.addSingleElectron(newSingleElectron);
        }

        return clone;
    }

    private boolean atomIsInMonomer(IAtom atom) {
        for (String monomerName : getMonomerNames()) {
            IMonomer monomer = getMonomer(monomerName);
            if (monomer.contains(atom)) return true;
        }
        return false;
    }
}

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