Class 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

      Constructors 
      Constructor Description
      Mutator()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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