Package org.biojava.bio.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 bygetRecordType()
.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 java.lang.String
ATOMRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.static java.lang.String
SEQRESRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description 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 .void
setAminoType(java.lang.Character aa)
set the name of the AA, in single letter code .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)
Specifies the secondary structure as a Map.java.lang.String
toString()
string representation.-
Methods inherited from interface org.biojava.bio.structure.Group
addAtom, clearAtoms, clone, getAtom, getAtom, getAtoms, getParent, getPDBCode, getPDBName, getProperties, getProperty, getType, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, size
-
-
-
-
Field Detail
-
ATOMRECORD
static final java.lang.String ATOMRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.- See Also:
- Constant Field Values
-
SEQRESRECORD
static final java.lang.String SEQRESRECORD
Field to distribguish AminoAcids that have been created from SEQRES records and ATOM records.- See Also:
- Constant Field Values
-
-
Method Detail
-
setSecStruc
void setSecStruc(java.util.Map<java.lang.String,java.lang.String> secstr)
Specifies the secondary structure as a Map.- Parameters:
secstr
- a Map object specifying the sec struc- See Also:
getSecStruc()
-
getSecStruc
java.util.Map<java.lang.String,java.lang.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() throws StructureException
get N atom.- Returns:
- an Atom object
- Throws:
StructureException
- ...
-
getCA
Atom getCA() throws StructureException
get CA atom.- Returns:
- an Atom object
- Throws:
StructureException
- ...
-
getC
Atom getC() throws StructureException
get C atom.- Returns:
- an Atom object
- Throws:
StructureException
- ...
-
getO
Atom getO() throws StructureException
get O atom.- Returns:
- an Atom object
- Throws:
StructureException
- ...
-
getCB
Atom getCB() throws StructureException
get CB atom.- Returns:
- an Atom object
- Throws:
StructureException
- ...
-
getAminoType
java.lang.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(java.lang.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(java.lang.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
java.lang.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
java.lang.String toString()
string representation.- Overrides:
toString
in classjava.lang.Object
-
-