org.biojava.nbio.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

Fields

Modifier and Type	Field and Description
static String	ATOMRECORD Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
static String	SEQRESRECORD Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.

Method Summary

Methods

Modifier and Type	Method and Description
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) Set the secondary structure as a Map.
String	toString() string representation.

Methods inherited from interface org.biojava.nbio.structure.Group

addAltLoc, addAtom, clearAtoms, clone, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtoms, getChain, getChainId, getChemComp, getPDBName, getProperties, getProperty, getResidueNumber, getType, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, trimToSize

Field Detail

ATOMRECORD

static final String ATOMRECORD

Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.

See Also:

Constant Field Values

SEQRESRECORD

static final String SEQRESRECORD

Field to distinguish 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)

Set 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<java.lang.String, java.lang.String>)

getN

Atom getN()

Get N atom.

Returns:

an Atom object or null if N atom does not exist

getCA

Atom getCA()

Get CA atom.

Returns:

an Atom object or null if CA atom does not exist

getC

Atom getC()

Get C atom.

Returns:

an Atom object or null if C atom does not exist

getO

Atom getO()

Get O atom.

Returns:

an Atom object or null if O atom does not exist

getCB

Atom getCB()

Get CB atom.

Returns:

an Atom object or null if CB atom does not exist

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