Package org.biojava.nbio.structure
Class Mutator
- java.lang.Object
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- org.biojava.nbio.structure.Mutator
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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
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Constructor Summary
Constructors Constructor Description Mutator()
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Method Summary
All Methods Instance Methods Concrete Methods 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.
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Constructor Detail
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Mutator
public Mutator()
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Method Detail
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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 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
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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
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