/*
* 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/
*/
package org.biojava.bio.structure;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import org.biojava.bio.structure.io.PDBParseException;
/** A class that can change one amino acid to another. Side chain atoms are neglected, only the Cb atom is kept.
*
*
* example usage:
*
String filename = "/Users/ap3/WORK/PDB/5pti.pdb" ;
String outputfile = "/Users/ap3/WORK/PDB/mutated.pdb" ;
PDBFileReader pdbreader = new PDBFileReader();
try{
Structure struc = pdbreader.getStructure(filename);
System.out.println(struc);
String chainId = " ";
String pdbResnum = "3";
String newType = "ARG";
// mutate the original structure and create a new one.
Mutator m = new Mutator();
Structure newstruc = m.mutate(struc,chainId,pdbResnum,newType);
FileOutputStream out= new FileOutputStream(outputfile);
PrintStream p = new PrintStream( out );
p.println (newstruc.toPDB());
p.close();
} catch (Exception e) {
e.printStackTrace();
}
* @author Andreas Prlic
* @since 1.5
* @version %I% %G%
*/
public class Mutator{
List supportedAtoms;
public Mutator(){
supportedAtoms = new ArrayList();
supportedAtoms.add("N");
supportedAtoms.add("CA");
supportedAtoms.add("C");
supportedAtoms.add("O");
supportedAtoms.add("CB");
}
/** creates a new structure which is identical with the original one.
* only one amino acid will be different.
*
*
*
*
* @param struc the structure object that is the container for the residue to be mutated
* @param chainId the id (name) of the chain to be mutated. @see Chain.getName()
* @param pdbResnum the PDB residue number of the residue
* @param newType the new residue type (3 characters)
* @return a structure object where one residue has been modified
* @throws PDBParseException
*/
public Structure mutate(Structure struc, String chainId, String pdbResnum, String newType)
throws PDBParseException{
// create a container for the new structure
Structure newstruc = new StructureImpl();
// first we need to find our corresponding chain
// get the chains for model nr. 0
// if structure is xray there will be only one "model".
List chains = struc.getChains(0);
// iterate over all chains.
Iterator iter = chains.iterator();
while (iter.hasNext()){
Chain c = (Chain)iter.next();
if (c.getName().equals(chainId)) {
// here is our chain!
Chain newchain = new ChainImpl();
newchain.setName(c.getName());
List groups = c.getAtomGroups();
// now iterate over all groups in this chain.
// in order to find the amino acid that has this pdbRenum.
Iterator giter = groups.iterator();
while (giter.hasNext()){
Group g = (Group) giter.next();
String rnum = g.getPDBCode();
// we only mutate amino acids
// and ignore hetatoms and nucleotides in this case
if (rnum.equals(pdbResnum) && (g.getType().equals("amino"))){
// create the mutated amino acid and add it to our new chain
AminoAcid newgroup = mutateResidue((AminoAcid)g,newType);
newchain.addGroup(newgroup);
}
else {
// add the group to the new chain unmodified.
newchain.addGroup(g);
}
}
// add the newly constructed chain to the structure;
newstruc.addChain(newchain);
} else {
// this chain is not requested, add it to the new structure unmodified.
newstruc.addChain(c);
}
}
return newstruc;
}
/** create a new residue which is of the new type.
* Only the atoms N, Ca, C, O, Cb will be considered.
* @param oldAmino
* @param newType
* @return a new, mutated, residue
* @throws PDBParseException
*/
public AminoAcid mutateResidue(AminoAcid oldAmino, String newType)
throws PDBParseException {
AminoAcid newgroup = new AminoAcidImpl();
newgroup.setPDBCode(oldAmino.getPDBCode());
newgroup.setPDBName(newType);
AtomIterator aiter =new AtomIterator(oldAmino);
while (aiter.hasNext()){
Atom a = (Atom)aiter.next();
if ( supportedAtoms.contains(a.getName())){
newgroup.addAtom(a);
}
}
return newgroup;
}
}