org.biojava.bio.structure

Class AminoAcidImpl

java.lang.Object

org.biojava.bio.structure.HetatomImpl

org.biojava.bio.structure.AminoAcidImpl

All Implemented Interfaces:

java.io.Serializable, AminoAcid, Group

public class AminoAcidImpl
extends HetatomImpl
implements AminoAcid, java.io.Serializable

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

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Jules Jacobsen

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	type this is an Amino acid.

Fields inherited from class org.biojava.bio.structure.HetatomImpl

atoms, pdb_flag, pdb_name, residueNumber

Fields inherited from interface org.biojava.bio.structure.AminoAcid

ATOMRECORD, SEQRESRECORD

Constructor Summary

Constructors

Constructor and Description
AminoAcidImpl()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Object	clone() returns and identical copy of this Group object .
java.lang.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.
java.lang.String	getRecordType() Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
java.util.Map<java.lang.String,java.lang.String>	getSecStruc() get secondary structure data .
java.lang.String	getType() Returns the type value.
void	setAminoType(java.lang.Character aa) set the name of the AA, in single letter code .
void	setPDBName(java.lang.String s) set three character name of AminoAcid.
void	setRecordType(java.lang.String recordName) Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.
void	setSecStruc(java.util.Map<java.lang.String,java.lang.String> secstr) set the secondary structure data for this amino acid.
java.lang.String	toString() string representation.

Methods inherited from class org.biojava.bio.structure.HetatomImpl

addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtomByPDBname, getAtoms, getChain, getChainId, getChemComp, getId, getParent, getPDBCode, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setId, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, setResidueNumber, setResidueNumber, size, trimToSize

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtomByPDBname, getAtoms, getChain, getChainId, getChemComp, getParent, getPDBCode, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, setResidueNumber, setResidueNumber, size, trimToSize

Field Detail

type

public static final java.lang.String type

this is an Amino acid. type is "amino".

See Also:

Constant Field Values

Constructor Detail

AminoAcidImpl

public AminoAcidImpl()

Method Detail

getType

public java.lang.String getType()

Description copied from class: HetatomImpl

Returns the type value.

Specified by:

getType in interface Group

Overrides:

getType in class HetatomImpl

Returns:

a String representing the type value

setSecStruc

public void setSecStruc(java.util.Map<java.lang.String,java.lang.String> secstr)

set the secondary structure data for this amino acid. the data is a Map with the following indeces (@see Secstruc)

Specified by:

setSecStruc in interface AminoAcid

Parameters:

secstr - a Map object specifying the sec struc value

See Also:

getSecStruc()

getSecStruc

public java.util.Map<java.lang.String,java.lang.String> getSecStruc()

get secondary structure data .

Specified by:

getSecStruc in interface AminoAcid

Returns:

a Map object representing the sec struc value

See Also:

setSecStruc(java.util.Map<java.lang.String, java.lang.String>)

getN

public Atom getN()
          throws StructureException

get N atom.

Specified by:

getN in interface AminoAcid

Returns:

an Atom object

Throws:

StructureException - ...

getCA

public Atom getCA()
           throws StructureException

get CA atom.

Specified by:

getCA in interface AminoAcid

Returns:

an Atom object

Throws:

StructureException - ...

getC

public Atom getC()
          throws StructureException

get C atom.

Specified by:

getC in interface AminoAcid

Returns:

an Atom object

Throws:

StructureException - ...

getO

public Atom getO()
          throws StructureException

get O atom.

Specified by:

getO in interface AminoAcid

Returns:

an Atom object

Throws:

StructureException - ...

getCB

public Atom getCB()
           throws StructureException

get CB atom.

Specified by:

getCB in interface AminoAcid

Returns:

an Atom object

Throws:

StructureException - ...

getAminoType

public java.lang.Character getAminoType()

returns the name of the AA, in single letter code.

Specified by:

getAminoType in interface AminoAcid

Returns:

a Character object representing the amino type value

See Also:

setAminoType(java.lang.Character)

setAminoType

public void setAminoType(java.lang.Character aa)

set the name of the AA, in single letter code .

Specified by:

setAminoType in interface AminoAcid

Parameters:

aa - a Character object specifying the amino type value

See Also:

getAminoType()

setRecordType

public void setRecordType(java.lang.String recordName)

Description copied from interface: AminoAcid

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

Specified by:

setRecordType in interface AminoAcid

Parameters:

recordName - either ATOMRECORD or SEQRESRECORD

See Also:

AminoAcid.getRecordType()

getRecordType

public java.lang.String getRecordType()

Description copied from interface: AminoAcid

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

Specified by:

getRecordType in interface AminoAcid

Returns:

the origin of this amino acid (ATOM or SEQRES records)

See Also:

AminoAcid.setRecordType(String)

toString

public java.lang.String toString()

string representation.

Specified by:

toString in interface AminoAcid

Overrides:

toString in class HetatomImpl

setPDBName

public void setPDBName(java.lang.String s)
                throws PDBParseException

set three character name of AminoAcid.

Specified by:

setPDBName in interface Group

Overrides:

setPDBName in class HetatomImpl

Parameters:

s - a String specifying the PDBName value

Throws:

PDBParseException - ...

See Also:

HetatomImpl.getPDBName()

clone

public java.lang.Object clone()

returns and identical copy of this Group object .

Specified by:

clone in interface Group

Overrides:

clone in class HetatomImpl

Returns:

and identical copy of this Group object