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IBioPolymer.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;
import java.util.Map;

/**
 * A BioPolymer is a subclass of a Polymer which is supposed to store
 * additional informations about the Polymer which are connected to BioPolymers.
 *
 * @cdk.module  interfaces
 *
 * @author      Edgar Luttmann <edgar@uni-paderborn.de>
 * @cdk.created 2001-08-06 
 *
 * @cdk.keyword polymer
 * @cdk.keyword biopolymer
 */
00045 public interface IBioPolymer extends IPolymer {

      /**
       * Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the
       * atom to this AtomContainer, but not to a certain Strand or Monomer (intended
       * e.g. for HETATMs).
       *
       * @param oAtom  The atom to add
       */
      public void addAtom(IAtom oAtom);
      
      /**
       * Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence
       * the atom will be added to a Monomer of type UNKNOWN in the specified Strand.
       *
       * @param oAtom   The atom to add
       * @param oStrand The strand the atom belongs to
       */
      public void addAtom(IAtom oAtom, IStrand oStrand);
      
      /**
       * Adds the atom to a specified Strand and a specified Monomer.
       * 
       * @param oAtom    The atom to add
       * @param oMonomer The monomer the atom belongs to
       * @param oStrand  The strand the atom belongs to
       */
      public void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand);
      
      /**
       * Return the number of monomers present in BioPolymer.
       *
       * @return number of monomers
       */
      public int getMonomerCount();
      
      /**
       * Retrieve a <code>Monomer</code> object by specifying its name.
       * 
       * <p>You have to specify the strand to enable
       * monomers with the same name in different strands. There is at least one such case: every
       * strand contains a monomer called "".
       *
       * @param  monName    The name of the monomer to look for
       * @param  strandName The name of the strand to look for
       * @return            The Monomer object which was asked for
       */
      public IMonomer getMonomer(String monName, String strandName);
            
      /**
       * Returns a collection of the names of all <code>Monomer</code>s in this
       * BioPolymer.
       *
       * @return a <code>Collection</code> of all the monomer names.
       */
      public Collection getMonomerNames();
      
      /**
       * Return the number of strands present in the BioPolymer.
       *
       * @return number of strands
       */
      public int getStrandCount();
      
      /**
       * 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 IStrand getStrand(String cName);
      
      /**
       * Returns a collection of the names of all <code>Strand</code>s in this
       * BioPolymer.
       *
       * @return a <code>Collection</code> of all the strand names.
       */
      public Collection getStrandNames();
      
      /**
       * Removes a particular strand, specified by its name.
       * 
       * @param name  The name of the strand to remove
       */
      public void removeStrand(String name);
      
      /**
       * Returns a Hashtable containing the strands in the Polymer.
       * 
       * @return hashtable containing the strands in the Polymer
       */
      public Map getStrands();
      
}

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