Package org.biojava.nbio.structure

Class Mutator

java.lang.Object
org.biojava.nbio.structure.Mutator
public class Mutator extends 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 outputfile =  "/Users/ap3/WORK/PDB/mutated.pdb" ;

Structure struc = StructureIO.getStructure("5pti");
System.out.println(struc);

String chainId = "A";
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();
Since:
1.5
Version:
%I% %G%
Author:
Andreas Prlic

  • Constructor Details

    • Mutator

      public Mutator()

  • Method Details

    • mutate

      public Structure mutate(Structure struc, String chainId, String pdbResnum, 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, 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