java.lang.Object

org.biojava.nbio.structure.HetatomImpl

org.biojava.nbio.structure.AminoAcidImpl

All Implemented Interfaces:: Serializable, AminoAcid, Group

public class AminoAcidImpl extends HetatomImpl implements AminoAcid, 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

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.HetatomImpl
HetatomImpl.PerformanceBehavior
Field Summary

Fields

Modifier and Type

Field

Description

static final GroupType

type

this is an Amino acid.

Fields inherited from class org.biojava.nbio.structure.HetatomImpl
atoms, chemComp, pdb_flag, pdb_name, performanceBehavior, residueNumber

Fields inherited from interface org.biojava.nbio.structure.AminoAcid
ATOMRECORD, SEQRESRECORD

Fields inherited from interface org.biojava.nbio.structure.Group
SEC_STRUC
Constructor Summary

Constructors

Constructor

Description

AminoAcidImpl()

inherits most from Hetero and has just a few extensions.
Method Summary

Modifier and Type

Method

Description

Object

clone()

returns and identical copy of this Group object .

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.

GroupType

getType()

Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE

void

setAminoType(Character aa)

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

void

setPDBName(String s)

set three character name of AminoAcid.

void

setRecordType(String recordName)

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

String

toString()

string representation.

Methods inherited from class org.biojava.nbio.structure.HetatomImpl
addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtoms, getChain, getChainId, getChemComp, getId, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setId, setPDBFlag, setProperties, setProperty, setResidueNumber, setResidueNumber, size, toSDF, trimToSize

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.nbio.structure.Group
addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtoms, getChain, getChainId, getChemComp, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setPDBFlag, setProperties, setProperty, setResidueNumber, setResidueNumber, size, toSDF, trimToSize

Field Details
- type
  
  public static final GroupType type
  
  this is an Amino acid. type is "amino".
Constructor Details
- AminoAcidImpl
  
  public AminoAcidImpl()
  
  inherits most from Hetero and has just a few extensions.
Method Details
- getType
  
  public GroupType getType()
  
  Description copied from class: HetatomImpl
  
  Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
  
  Specified by:
  
  getType in interface Group
  
  Overrides:
  
  getType in class HetatomImpl
  
  Returns:
  
  a String representing the type value
- getN
  
  public Atom getN()
  
  Get N atom.
  
  Specified by:
  
  getN in interface AminoAcid
  
  Returns:
  
  an Atom object or null if N atom does not exist
- getCA
  
  public Atom getCA()
  
  Get CA atom.
  
  Specified by:
  
  getCA in interface AminoAcid
  
  Returns:
  
  an Atom object or null if CA atom does not exist
- getC
  
  public Atom getC()
  
  Get C atom.
  
  Specified by:
  
  getC in interface AminoAcid
  
  Returns:
  
  an Atom object or null if C atom does not exist
- getO
  
  public Atom getO()
  
  Get O atom.
  
  Specified by:
  
  getO in interface AminoAcid
  
  Returns:
  
  an Atom object or null if O atom does not exist
- getCB
  
  public Atom getCB()
  
  Get CB atom.
  
  Specified by:
  
  getCB in interface AminoAcid
  
  Returns:
  
  an Atom object or null if CB atom does not exist
- getAminoType
  
  public 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:
  
  AminoAcid.setAminoType(java.lang.Character)
- setAminoType
  
  public void setAminoType(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:
  
  AminoAcid.getAminoType()
- setRecordType
  
  public void setRecordType(String recordName)
  
  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 String getRecordType()
  
  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 String toString()
  
  string representation.
  
  Overrides:
  
  toString in class HetatomImpl
- setPDBName
  
  public void setPDBName(String s)
  
  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
  
  See Also:
  
  HetatomImpl.getPDBName()
- clone
  
  public 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

Class AminoAcidImpl

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.HetatomImpl

Field Summary

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

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

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Details

type

Constructor Details

AminoAcidImpl

Method Details

getType

getN

getCA

getC

getO

getCB

getAminoType

setAminoType

setRecordType

getRecordType

toString

setPDBName

clone