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FragmentAtom.java

/* $Revision$ $Author$$Date$
 *
 * Copyright (C) 2006-2007  Egon Willighagen <ewilligh@uni-koeln.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.IAtomContainer;
import org.openscience.cdk.interfaces.IFragmentAtom;

/**
 * Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
 * like the MDL Molfile <code>Group</code> concept.
 * 
 * @cdk.module data
 * @cdk.githash
 * 
 * @author egonw
 */
00040 public class FragmentAtom extends PseudoAtom implements IFragmentAtom {

00042       private static final long serialVersionUID = -6144605920605752463L;

      private IAtomContainer fragment;
      private boolean isExpanded;

      public FragmentAtom() {
            fragment = this.getBuilder().newAtomContainer();
            isExpanded = false;
      }
      
00052       public boolean isExpanded() {
            return isExpanded;
      }

      public void setExpanded(boolean bool) {
            this.isExpanded = bool;
      }

00060       public IAtomContainer getFragment() {
            return fragment;
      }

00064       public void setFragment(IAtomContainer fragment) {
            this.fragment = fragment;
      }

00068       public void setExactMass(Double mass) {
          throw new IllegalAccessError("Cannot set the mass of a IFragmentAtom.");
      }

      /**
       * The exact mass of an FragmentAtom is defined as the sum of exact masses
       * of the IAtom's in the fragment.
       */
00076       public Double getExactMass() {
            double totalMass = 0.0;
        for (IAtom atom : fragment.atoms()) {
            totalMass += atom.getExactMass();
        }
            return totalMass;
      }

00084       public String toString() {
            StringBuffer buffer = new StringBuffer();
            buffer.append("FragmentAtom{").append(hashCode());
            buffer.append(", A=").append(super.toString());
            if (fragment != null) {
                  buffer.append(", F=").append(fragment.toString());
            }
            buffer.append('}');
            return buffer.toString();
      }
      
}

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