org.biojava.bio.structure
Class AminoAcid

java.lang.Object
  org.biojava.bio.structure.Hetatom
      org.biojava.bio.structure.AminoAcid

All Implemented Interfaces:

Group

public class AminoAcid

extends Hetatom

AminoAcid inherits most from Hetatom. Adds a few AminoAcid specific methods.

Field Summary

static String

type

Constructor Summary

AminoAcid()

Method Summary

Character	getAminoType() returns the name of the AA, in single letter code
Atom	getC() get C atom
Atom	getCA() get CA atom
Atom	getCB() get CB atom
Atom	getN() get N atom
Atom	getO() get O atom
HashMap	getSecStruc() get secondary structure data
String	getType() get Type of group, e.g.
void	setAminoType(Character aa) set the name of the AA, in single letter code
void	setSecStruc(HashMap secstr) set the secondary structure data for this amino acids the data is a HashMap with the following indeces (@see Secstruc)
String	toString() string representation

Methods inherited from class org.biojava.bio.structure.Hetatom

addAtom, getAtom, getAtom, getAtoms, getPDBCode, getPDBName, getProperties, getProperty, has3D, hasAminoAtoms, hasAtom, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, size

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

type

public static String type

Constructor Detail

AminoAcid

public AminoAcid()

Method Detail

getType

public String getType()

Description copied from interface: Group

get Type of group, e.g. amino, hetatom, nucleotide

Specified by:

getType in interface Group

Overrides:

getType in class Hetatom

setSecStruc

public void setSecStruc(HashMap secstr)

set the secondary structure data for this amino acids the data is a HashMap with the following indeces (@see Secstruc)

getSecStruc

public HashMap getSecStruc()

get secondary structure data

getN

public Atom getN()
          throws StructureException

get N atom

Throws:

StructureException

getCA

public Atom getCA()
           throws StructureException

get CA atom

Throws:

StructureException

getC

public Atom getC()
          throws StructureException

get C atom

Throws:

StructureException

getO

public Atom getO()
          throws StructureException

get O atom

Throws:

StructureException

getCB

public Atom getCB()
           throws StructureException

get CB atom

Throws:

StructureException

getAminoType

public Character getAminoType()

returns the name of the AA, in single letter code

setAminoType

public void setAminoType(Character aa)

set the name of the AA, in single letter code

toString

public String toString()

string representation

Overrides:

toString in class Hetatom