/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2005-2007 Egon Willighagen <e.willighagen@science.ru.nl>
*
* 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 java.io.Serializable;
import org.openscience.cdk.interfaces.IAminoAcid;
import org.openscience.cdk.interfaces.IAtom;
/**
* A AminoAcid is Monomer which stores additional amino acid specific
* informations, like the N-terminus atom.
*
* @cdk.module data
* @cdk.githash
*
* @author Egon Willighagen <e.willighagen@science.ru.nl>
* @cdk.created 2005-08-11
* @cdk.keyword amino acid
*/
public class AminoAcid extends Monomer implements IAminoAcid, Serializable, Cloneable {
/**
* Determines if a de-serialized object is compatible with this class.
*
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for <a href=http://java.sun.com/products/jdk/1.1/docs/guide
* /serialization/spec/version.doc.html>details</a>.
*/
private static final long serialVersionUID = -5032283549467862509L;
/** The atom that constitutes the N-terminus. */
private IAtom nTerminus;
/** The atom that constitutes the C-terminus. */
private IAtom cTerminus;
/**
* Constructs a new AminoAcid.
*/
public AminoAcid() {
super();
}
/**
* Retrieves the N-terminus atom.
*
* @return The Atom that is the N-terminus
*
* @see #addNTerminus(IAtom)
*/
public IAtom getNTerminus() {
return nTerminus;
}
/**
* Add an Atom and makes it the N-terminus atom.
*
* @param atom The Atom that is the N-terminus
*
* @see #getNTerminus
*/
public void addNTerminus(IAtom atom) {
super.addAtom(atom);
nTerminus = atom;
}
/**
* Marks an Atom as being the N-terminus atom. It assumes that the Atom
* is already added to the AminoAcid.
*
* @param atom The Atom that is the N-terminus
*
* @see #addNTerminus
*/
private void setNTerminus(IAtom atom) {
nTerminus = atom;
}
/**
* Retrieves the C-terminus atom.
*
* @return The Atom that is the C-terminus
*
* @see #addCTerminus(IAtom)
*/
public IAtom getCTerminus() {
return cTerminus;
}
/**
* Add an Atom and makes it the C-terminus atom.
*
* @param atom The Atom that is the C-terminus
*
* @see #getCTerminus
*/
public void addCTerminus(IAtom atom) {
super.addAtom(atom);
setCTerminus(atom);
}
/**
* Marks an Atom as being the C-terminus atom. It assumes that the Atom
* is already added to the AminoAcid.
*
* @param atom The Atom that is the C-terminus
*
* @see #addCTerminus
*/
private void setCTerminus(IAtom atom) {
cTerminus = atom;
}
/**
* Clones this AminoAcid object.
*
* @return The cloned object
*/
public Object clone() throws CloneNotSupportedException {
AminoAcid clone = (AminoAcid) super.clone();
// copying the new N-terminus and C-terminus pointers
if (getNTerminus() != null)
clone.setNTerminus(clone.getAtom(getAtomNumber(getNTerminus())));
if (getCTerminus() != null)
clone.setCTerminus(clone.getAtom(getAtomNumber(getCTerminus())));
return clone;
}
public String toString() {
StringBuffer stringContent = new StringBuffer(32);
stringContent.append("AminoAcid(");
stringContent.append(this.hashCode());
if (nTerminus != null) {
stringContent.append(", N:").append(nTerminus.toString());
}
if (cTerminus != null) {
stringContent.append(", C:").append(cTerminus.toString());
}
stringContent.append(", ").append(super.toString());
stringContent.append(')');
return stringContent.toString();
}
}