/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2001-2008 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.protein.data;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.openscience.cdk.BioPolymer;
import org.openscience.cdk.interfaces.IMonomer;
import org.openscience.cdk.interfaces.IPDBAtom;
import org.openscience.cdk.interfaces.IPDBPolymer;
import org.openscience.cdk.interfaces.IPDBStructure;
import org.openscience.cdk.interfaces.IStrand;
/**
* An entry in the PDB database. It is not just a regular protein, but the
* regular PDB mix of protein or protein complexes, ligands, water molecules
* and other species.
*
* @cdk.module data
* @cdk.githash
*
* @author Egon Willighagen
* @cdk.created 2006-04-19
* @cdk.keyword polymer
*/
public class PDBPolymer extends BioPolymer implements Cloneable, IPDBPolymer{
private static final long serialVersionUID = 4173552834313952358L;
List<String> sequentialListOfMonomers;
List<IPDBStructure> secondaryStructures;
/**
* Constructs a new Polymer to store the {@link IMonomer}s.
*/
public PDBPolymer() {
super();
sequentialListOfMonomers = new ArrayList<String>();
secondaryStructures = new ArrayList<IPDBStructure>();
}
public void addStructure(IPDBStructure structure) {
secondaryStructures.add(structure);
}
public Collection<IPDBStructure> getStructures() {
// don't return the original
return new ArrayList<IPDBStructure>(secondaryStructures);
}
/**
* Adds the atom oAtom without specifying a {@link IMonomer} or a Strand. Therefore the
* atom to this AtomContainer, but not to a certain Strand or {@link IMonomer} (intended
* e.g. for HETATMs).
*
* @param oAtom The {@link IPDBAtom} to add
*/
public void addAtom(IPDBAtom oAtom){
super.addAtom(oAtom);
}
/**
* Adds the atom oAtom to a specified Monomer. Additionally, it keeps
* record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer) {
super.addAtom(oAtom, oMonomer);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}
/**
* Adds the IPDBAtom oAtom to a specified Monomer of a specified Strand.
* Additionally, it keeps record of the iCode.
*
* @param oAtom The IPDBAtom to add
* @param oMonomer The monomer the atom belongs to
*/
public void addAtom(IPDBAtom oAtom, IMonomer oMonomer, IStrand oStrand) {
super.addAtom(oAtom, oMonomer, oStrand);
if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName()))
sequentialListOfMonomers.add(oMonomer.getMonomerName());
}
/**
* Returns the monomer names in the order in which they were added.
*
* @see org.openscience.cdk.interfaces.IPolymer#getMonomerNames()
*/
public Collection<String> getMonomerNamesInSequentialOrder() {
// don't return the original
return new ArrayList<String>(sequentialListOfMonomers);
}
public String toString() {
StringBuffer stringContent = new StringBuffer();
stringContent.append("PDBPolymer(");
stringContent.append(this.hashCode()).append(", ");
stringContent.append(super.toString());
stringContent.append(")");
return stringContent.toString();
}
}