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The protein structure modules of BioJava.
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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 * Created on 05.03.2004
 * @author Andreas Prlic
 *
 */
package org.biojava.nbio.structure;

/**
 * 
 * A {@link Group} that represents an AminoAcid.
 * 
 *
 * 
 * In PDB files information on AminoAcids can be observed in the SEQRES and in the ATOM records.
 * Since frequently coordinates for some of the amino acids are missing, during parsing of the PDB
 * files the SEQRES and the ATOM records are aligned and a whenever possible the AminoAcid objects
 * are combined. Access to the SEQRES and ATOM sequence is possible through the {@link Chain} object.
 * It is possible to distinguish between SEQRES and ATOM derived AminoAcids by {@link #getRecordType()}.
 * 
 *
 *
 *  AminoAcid inherits most from {@link HetatomImpl }.  Adds a few AminoAcid
 *  specific methods.
 *  
 *
 * @author Andreas Prlic
 * @since 1.4
 * @version %I% %G%
 *
 */
public interface AminoAcid extends Group {

	/**
	 * Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
	 *
	 */
	public static final String ATOMRECORD = "ATOM";

	/**
	 * Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
	 *
	 */
	public static final String SEQRESRECORD = "SEQRES";

	/**
	 * Get N atom.
	 *
	 * @return an Atom object or null if N atom does not exist
	 */
	public Atom getN()    ;

	/**
	 * Get CA atom.
	 * @return an Atom object or null if CA atom does not exist
	 */
	public Atom getCA()   ;

	/**
	 * Get C atom.
	 * @return an Atom object or null if C atom does not exist
	 */
	public Atom getC()    ;

	/**
	 * Get O atom.
	 * @return an Atom object or null if O atom does not exist
	 */
	public Atom getO()    ;

	/**
	 * Get CB atom.
	 * @return an Atom object or null if CB atom does not exist
	 */
	public Atom getCB()   ;

	/**
	 * Returns the name of the AA, in single letter code.
	 *
	 * @return a Character object representing the amino type value
	 * @see #setAminoType
	 */
	public  Character getAminoType() ;

	/**
	 * Set the name of the AA, in single letter code .
	 *
	 * @param aa  a Character object specifying the amino type value
	 * @see #getAminoType
	 */
	public void setAminoType(Character aa) ;

	/**
	 * Allows to distinguish between amino acids that are provided
	 * as ATOM records and a SEQRES records.
	 * @param recordName either ATOMRECORD or SEQRESRECORD
	 * @see #getRecordType()
	 */
	public void setRecordType(String recordName);

	/**
	 * Allows to distinguish between amino acids that are provided
	 * as ATOM records and a SEQRES records.
	 * @return the origin of this amino acid (ATOM or SEQRES records)
	 * @see #setRecordType(String)
	 */
	public String getRecordType();

}