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