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 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 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