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.
Modifier and Type | Field and 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.
|
Modifier and Type | Method and 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.
|
addAtom, clearAtoms, clone, getAtom, getAtom, getAtoms, getParent, getPDBCode, getPDBName, getProperties, getProperty, getType, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, size
static final java.lang.String ATOMRECORD
static final java.lang.String SEQRESRECORD
void setSecStruc(java.util.Map<java.lang.String,java.lang.String> secstr)
secstr
- a Map object specifying the sec strucgetSecStruc()
java.util.Map<java.lang.String,java.lang.String> getSecStruc()
setSecStruc(java.util.Map<java.lang.String, java.lang.String>)
Atom getN() throws StructureException
StructureException
- ...Atom getCA() throws StructureException
StructureException
- ...Atom getC() throws StructureException
StructureException
- ...Atom getO() throws StructureException
StructureException
- ...Atom getCB() throws StructureException
StructureException
- ...java.lang.Character getAminoType()
setAminoType(java.lang.Character)
void setAminoType(java.lang.Character aa)
aa
- a Character object specifying the amino type valuegetAminoType()
void setRecordType(java.lang.String recordName)
recordName
- either ATOMRECORD or SEQRESRECORDgetRecordType()
java.lang.String getRecordType()
setRecordType(String)
java.lang.String toString()
toString
in class java.lang.Object