/*
* 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 Sep 12, 2007
*
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.*;
import java.util.ArrayList;
import java.util.List;
/** Converts full atom representations to Calpha only ones.
*
* @author Andreas Prlic
* @version %I% %G%
*/
public class CAConverter {
/** Convert a List of chain objects to another List of chains, containing C-alpha atoms only.
*
* @param chains list of chains
* @return a list of chains
* @deprecated Use the more generic {@link #getRepresentativeAtomsOnly(List)} instead
*/
@Deprecated
public static List<Chain> getCAOnly(List<Chain> chains){
List<Chain> newChains = new ArrayList<Chain>();
for (Chain chain : chains){
Chain newChain = getCAOnly(chain);
newChains.add(newChain);
}
return newChains;
}
/** Convert a List of chain objects to another List of chains, containing Representative atoms only.
*
* @param chains list of chains
* @return a list of chains
* @since Biojava 4.1.0
*/
public static List<Chain> getRepresentativeAtomsOnly(List<Chain> chains){
List<Chain> newChains = new ArrayList<Chain>();
for (Chain chain : chains){
Chain newChain = getRepresentativeAtomsOnly(chain);
newChains.add(newChain);
}
return newChains;
}
/**
* Convert a Chain to a new Chain containing C-alpha atoms only.
*
* @param chain to convert
* @return a new chain containing Amino acids with C-alpha only.
* @deprecated Use the more generic {@link #getRepresentativeAtomsOnly(Chain)} instead
*/
@Deprecated
public static Chain getCAOnly(Chain chain){
Chain newChain = new ChainImpl();
newChain.setChainID(chain.getChainID());
newChain.setEntityInfo(chain.getEntityInfo());
newChain.setSwissprotId(chain.getSwissprotId());
List<Group> groups = chain.getAtomGroups();
grouploop:
for (Group g: groups){
List<Atom> atoms = g.getAtoms();
if ( ! (g instanceof AminoAcid))
continue;
for (Atom a : atoms){
if ( a.getName().equals(StructureTools.CA_ATOM_NAME) && a.getElement()==Element.C){
// we got a CA atom in this group!
AminoAcid n = new AminoAcidImpl();
n.setPDBName(g.getPDBName());
n.setResidueNumber(g.getResidueNumber());
n.addAtom(a);
newChain.addGroup(n);
continue grouploop;
}
}
}
return newChain;
}
/**
* Convert a Chain to a new Chain containing C-alpha atoms only.
*
* @param chain to convert
* @return a new chain containing Amino acids with C-alpha only.
* @since Biojava 4.1.0
*/
public static Chain getRepresentativeAtomsOnly(Chain chain){
Chain newChain = new ChainImpl();
newChain.setId(chain.getId());
newChain.setName(chain.getName());
newChain.setEntityInfo(chain.getEntityInfo());
newChain.setSwissprotId(chain.getSwissprotId());
List<Group> groups = chain.getAtomGroups();
grouploop:
for (Group g: groups){
List<Atom> atoms = g.getAtoms();
if ( ! (g instanceof AminoAcid))
continue;
for (Atom a : atoms){
if ( a.getName().equals(StructureTools.CA_ATOM_NAME) && a.getElement()==Element.C){
// we got a CA atom in this group!
AminoAcid n = new AminoAcidImpl();
n.setPDBName(g.getPDBName());
n.setResidueNumber(g.getResidueNumber());
n.addAtom(a);
newChain.addGroup(n);
continue grouploop;
}
}
}
return newChain;
}
}