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IPolymer.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-04 18:46:10 +0100 (Thu, 04 Jan 2007) $
 * $Revision: 7636 $
 * 
 * Copyright (C) 2006-2007  Egon Willighagen <egonw@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.interfaces;

import java.util.Collection;

/**
 * Subclass of Molecule to store Polymer specific attributes that a Polymer has.
 *
 * @cdk.module  interfaces
 *
 * @author      Edgar Luttmann <edgar@uni-paderborn.de>
 * @author      Martin Eklund <martin.eklund@farmbio.uu.se>
 * @cdk.created 2001-08-06
 * @cdk.keyword polymer
 */
00042 public interface IPolymer extends IMolecule {
      
      /**
       * Adds the atom oAtom without specifying a Monomer. Therefore the
       * atom to this AtomContainer, but not to a certain Monomer (intended
       * e.g. for HETATMs).
       *
       * @param oAtom  The atom to add
       */
      public void addAtom(IAtom oAtom);
      
      /**
       * Adds the atom oAtom to a specified Monomer.
       *
       * @param oAtom  The atom to add
       * @param oMonomer  The monomer the atom belongs to
       */
      public void addAtom(IAtom oAtom, IMonomer oMonomer);
      
      /**
       * Return the number of monomers present in the Polymer.
       *
       * @return number of monomers
       */
      public int getMonomerCount();
      
      /**
       * Retrieve 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
       */
      public IMonomer getMonomer(String 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.
       */
      public Collection getMonomerNames();
      
      /**
       * Removes a particular monomer, specified by its name.
       * 
       * @param name The name of the monomer to be removed
       */
      public void removeMonomer(String name);

}

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