org.biojava.bio.structure
Class AminoAcidImpl

java.lang.Object
  extended by org.biojava.bio.structure.HetatomImpl
      extended by org.biojava.bio.structure.AminoAcidImpl
All Implemented Interfaces:
AminoAcid, Group

public class AminoAcidImpl
extends HetatomImpl
implements AminoAcid

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

Since:
1.4
Version:
%I% %G%
Author:
Andreas Prlic, Jules Jacobsen

Field Summary
static String type
          this is an Amino acid.
 
Fields inherited from interface org.biojava.bio.structure.AminoAcid
ATOMRECORD, SEQRESRECORD
 
Constructor Summary
AminoAcidImpl()
           
 
Method Summary
 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.
 Map<String,String> getSecStruc()
          get secondary structure data .
 String getType()
          Returns the type value.
 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.
 void setSecStruc(Map<String,String> secstr)
          set the secondary structure data for this amino acid.
 String toString()
          string representation.
 
Methods inherited from class org.biojava.bio.structure.HetatomImpl
addAtom, clearAtoms, getAtom, getAtom, getAtoms, getId, getParent, getPDBCode, getPDBName, getProperties, getProperty, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setId, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, size
 
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
addAtom, clearAtoms, getAtom, getAtom, getAtoms, getParent, getPDBCode, getPDBName, getProperties, getProperty, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, size
 

Field Detail

type

public static final String type
this is an Amino acid. type is "amino".

See Also:
Constant Field Values
Constructor Detail

AminoAcidImpl

public AminoAcidImpl()
Method Detail

getType

public 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(Map<String,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 Map<String,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)

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 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(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(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 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 String toString()
string representation.

Specified by:
toString in interface AminoAcid
Overrides:
toString in class HetatomImpl

setPDBName

public void setPDBName(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 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