org.biojava.bio.structure
Class Mutator

java.lang.Object
  extended by org.biojava.bio.structure.Mutator

public class Mutator
extends java.lang.Object

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();
  } 
  

Since:
1.5
Version:
%I% %G%
Author:
Andreas Prlic

Constructor Summary
Mutator()
           
 
Method Summary
 Structure mutate(Structure struc, java.lang.String chainId, java.lang.String pdbResnum, java.lang.String newType)
          creates a new structure which is identical with the original one.
 AminoAcid mutateResidue(AminoAcid oldAmino, java.lang.String newType)
          create a new residue which is of the new type.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Mutator

public Mutator()
Method Detail

mutate

public Structure mutate(Structure struc,
                        java.lang.String chainId,
                        java.lang.String pdbResnum,
                        java.lang.String newType)
                 throws PDBParseException
creates a new structure which is identical with the original one. only one amino acid will be different.

Parameters:
struc - the structure object that is the container for the residue to be mutated
chainId - the id (name) of the chain to be mutated. @see Chain.getName()
pdbResnum - the PDB residue number of the residue
newType - the new residue type (3 characters)
Returns:
a structure object where one residue has been modified
Throws:
PDBParseException

mutateResidue

public AminoAcid mutateResidue(AminoAcid oldAmino,
                               java.lang.String newType)
                        throws PDBParseException
create a new residue which is of the new type. Only the atoms N, Ca, C, O, Cb will be considered.

Parameters:
oldAmino -
newType -
Returns:
a new, mutated, residue
Throws:
PDBParseException