org.biojava.bio.structure
Interface AminoAcid

All Superinterfaces:
Group
All Known Implementing Classes:
AminoAcidImpl

public interface AminoAcid
extends Group

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

Since:
1.4
Version:
%I% %G%
Author:
Andreas Prlic

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.
 Map getSecStruc()
          get secondary structure data .
 void setAminoType(Character aa)
          set the name of the AA, in single letter code .
 void setSecStruc(Map secstr)
          Specifies the secondary structure as a Map.
 String toString()
          string representation.
 
Methods inherited from interface org.biojava.bio.structure.Group
addAtom, clearAtoms, clone, getAtom, getAtom, getAtoms, getParent, getPDBCode, getPDBName, getProperties, getProperty, getType, has3D, hasAminoAtoms, hasAtom, iterator, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, size
 

Method Detail

setSecStruc

void setSecStruc(Map secstr)
Specifies the secondary structure as a Map.

Parameters:
secstr - a Map object specifying the sec struc
See Also:
getSecStruc()

getSecStruc

Map getSecStruc()
get secondary structure data .

Returns:
a Map object representing the sec struc value
See Also:
setSecStruc(java.util.Map)

getN

Atom getN()
          throws StructureException
get N atom.

Returns:
an Atom object
Throws:
StructureException - ...

getCA

Atom getCA()
           throws StructureException
get CA atom.

Returns:
an Atom object
Throws:
StructureException - ...

getC

Atom getC()
          throws StructureException
get C atom.

Returns:
an Atom object
Throws:
StructureException - ...

getO

Atom getO()
          throws StructureException
get O atom.

Returns:
an Atom object
Throws:
StructureException - ...

getCB

Atom getCB()
           throws StructureException
get CB atom.

Returns:
an Atom object
Throws:
StructureException - ...

getAminoType

Character getAminoType()
returns the name of the AA, in single letter code.

Returns:
a Character object representing the amino type value
See Also:
setAminoType(java.lang.Character)

setAminoType

void setAminoType(Character aa)
set the name of the AA, in single letter code .

Parameters:
aa - a Character object specifying the amino type value
See Also:
getAminoType()

toString

String toString()
string representation.

Overrides:
toString in class Object