Package org.biojava.nbio.structure

Interface AminoAcid

All Superinterfaces:

Group, Serializable

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	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.

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

SEC_STRUC

Method Summary

Modifier and Type	Method	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.
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.

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, isAminoAcid, isHetAtomInFile, isNucleotide, isPolymeric, isWater, iterator, setAtoms, setChain, setChemComp, setHetAtomInFile, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, toSDF, 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

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)