org.biojava.bio.structure
Class Mutator
java.lang.Object
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
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 |
Mutator
public Mutator()
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 mutatedchainId
- the id (name) of the chain to be mutated. @see Chain.getName()pdbResnum
- the PDB residue number of the residuenewType
- 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