/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2007 Ola Spjuth <ospjuth@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.libio.md;
import java.util.ArrayList;
import java.util.List;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.interfaces.IAtomContainer;
/**
* @cdk.module libiomd
* @cdk.githash
*/
public class MDMolecule extends Molecule{
/**
*
*/
private static final long serialVersionUID = -3129626782945020908L;
//List of Residues
private List residues;
//List of ChargeGroups
private List chargeGroups;
public MDMolecule() {
super();
}
public MDMolecule(IAtomContainer container) {
super(container);
}
public List getResidues() {
return residues;
}
public void setResidues(List residues) {
this.residues = residues;
}
/**
* Add a Residue to the MDMolecule if not already present
* @param residue Residue to add
*/
public void addResidue(Residue residue){
if (residues==null) residues=new ArrayList();
//Check if exists
if (residues.contains(residue)){
System.out.println("Residue: " + residue.getName() + " already present in molecule: " + getID());
return;
}
residues.add(residue);
}
public List getChargeGroups() {
return chargeGroups;
}
public void setChargeGroups(List chargeGroups) {
this.chargeGroups = chargeGroups;
}
/**
* Add a ChargeGroup to the MDMolecule if not already present
*
* @param chargeGroup {@link ChargeGroup} to add
*/
public void addChargeGroup(ChargeGroup chargeGroup){
if (chargeGroups==null) chargeGroups=new ArrayList();
//Check if exists
if (chargeGroups.contains(chargeGroup)){
System.out.println("Charge group: " + chargeGroup.getNumber() + " already present in molecule: " + getID());
return;
}
chargeGroups.add(chargeGroup);
}
}