org.biojava.bio.structure
Interface AminoAcid

All Superinterfaces:
Group
All Known Implementing Classes:
AminoAcidImpl

public interface AminoAcid
extends Group

A Group that represents an AminoAcid.

In PDB files information on AminoAcids can be observed in the SEQRES and in the ATOM records. Since frequently coordinates for some of the amino acids are missing, during parsing of the PDB files the SEQRES and the ATOM records are aligned and a whenever possible the AminoAcid objects are combined. Access to the SEQRES and ATOM sequence is possible through the Chain object. It is possible to distinguish between SEQRES and ATOM derived AminoAcids by getRecordType().

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

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

Field Summary
static String ATOMRECORD
          Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
static String SEQRESRECORD
          Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
 
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.
 String getRecordType()
          Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
 Map<String,String> getSecStruc()
          get secondary structure data .
 void setAminoType(Character aa)
          set the name of the AA, in single letter code .
 void setRecordType(String recordName)
          Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
 void setSecStruc(Map<String,String> secstr)
          Specifies the secondary structure as a Map.
 String toString()
          string representation.
 
Methods inherited from interface org.biojava.bio.structure.Group
addAltLoc, addAtom, clearAtoms, clone, getAltLocs, getAtom, getAtom, getAtomByPDBname, getAtoms, getChain, getChainId, getChemComp, getParent, getPDBCode, getPDBName, getProperties, getProperty, getResidueNumber, getType, has3D, hasAltLoc, hasAminoAtoms, hasAtom, iterator, setAtoms, setChain, setChemComp, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size
 

Field Detail

ATOMRECORD

static final String ATOMRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.

See Also:
Constant Field Values

SEQRESRECORD

static final String SEQRESRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.

See Also:
Constant Field Values
Method Detail

setSecStruc

void setSecStruc(Map<String,String> secstr)
Specifies the secondary structure as a Map.

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

getSecStruc

Map<String,String> 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()

setRecordType

void setRecordType(String recordName)
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

Parameters:
recordName - either ATOMRECORD or SEQRESRECORD
See Also:
getRecordType()

getRecordType

String getRecordType()
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.

Returns:
the origin of this amino acid (ATOM or SEQRES records)
See Also:
setRecordType(String)

toString

String toString()
string representation.

Overrides:
toString in class Object