/* * 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.bio.structure; import java.util.Map; /** *
* 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 distribguish AminoAcids that have been created from SEQRES records and ATOM records. * */ public static final String ATOMRECORD = "ATOM"; /** Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records. * */ public static final String SEQRESRECORD = "SEQRES"; /** * Specifies the secondary structure as a Map. * * @param secstr a Map object specifying the sec struc * @see #getSecStruc */ public void setSecStruc(Map