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 chainName = "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,chainName,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

Modifier and Type	Method	Description
Structure	mutate(Structure struc, String chainId, String pdbResnum, String newType)	creates a new structure which is identical with the original one.
AminoAcid	mutateResidue(AminoAcid oldAmino, 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,
                        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