Package org.biojava.bio.structure
Class AminoAcidImpl
- java.lang.Object
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- org.biojava.bio.structure.HetatomImpl
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- org.biojava.bio.structure.AminoAcidImpl
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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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
type
this is an Amino acid.-
Fields inherited from interface org.biojava.bio.structure.AminoAcid
ATOMRECORD, SEQRESRECORD
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Constructor Summary
Constructors Constructor Description AminoAcidImpl()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
addAtom, clearAtoms, getAtom, getAtom, getAtoms, getId, getParent, getPDBCode, getPDBName, getProperties, getProperty, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setId, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, size
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
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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
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Field Detail
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type
public static final java.lang.String type
this is an Amino acid. type is "amino".- See Also:
- Constant Field Values
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Method Detail
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getType
public java.lang.String getType()
Description copied from class:HetatomImpl
Returns the type value.- Specified by:
getType
in interfaceGroup
- Overrides:
getType
in classHetatomImpl
- Returns:
- a String representing the type value
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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 interfaceAminoAcid
- Parameters:
secstr
- a Map object specifying the sec struc value- See Also:
getSecStruc()
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getSecStruc
public java.util.Map<java.lang.String,java.lang.String> getSecStruc()
get secondary structure data .- Specified by:
getSecStruc
in interfaceAminoAcid
- Returns:
- a Map object representing the sec struc value
- See Also:
setSecStruc(java.util.Map<java.lang.String, java.lang.String>)
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getN
public Atom getN() throws StructureException
get N atom.- Specified by:
getN
in interfaceAminoAcid
- Returns:
- an Atom object
- Throws:
StructureException
- ...
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getCA
public Atom getCA() throws StructureException
get CA atom.- Specified by:
getCA
in interfaceAminoAcid
- Returns:
- an Atom object
- Throws:
StructureException
- ...
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getC
public Atom getC() throws StructureException
get C atom.- Specified by:
getC
in interfaceAminoAcid
- Returns:
- an Atom object
- Throws:
StructureException
- ...
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getO
public Atom getO() throws StructureException
get O atom.- Specified by:
getO
in interfaceAminoAcid
- Returns:
- an Atom object
- Throws:
StructureException
- ...
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getCB
public Atom getCB() throws StructureException
get CB atom.- Specified by:
getCB
in interfaceAminoAcid
- Returns:
- an Atom object
- Throws:
StructureException
- ...
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getAminoType
public java.lang.Character getAminoType()
returns the name of the AA, in single letter code.- Specified by:
getAminoType
in interfaceAminoAcid
- Returns:
- a Character object representing the amino type value
- See Also:
setAminoType(java.lang.Character)
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setAminoType
public void setAminoType(java.lang.Character aa)
set the name of the AA, in single letter code .- Specified by:
setAminoType
in interfaceAminoAcid
- Parameters:
aa
- a Character object specifying the amino type value- See Also:
getAminoType()
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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 interfaceAminoAcid
- Parameters:
recordName
- either ATOMRECORD or SEQRESRECORD- See Also:
AminoAcid.getRecordType()
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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 interfaceAminoAcid
- Returns:
- the origin of this amino acid (ATOM or SEQRES records)
- See Also:
AminoAcid.setRecordType(String)
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toString
public java.lang.String toString()
string representation.- Specified by:
toString
in interfaceAminoAcid
- Overrides:
toString
in classHetatomImpl
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setPDBName
public void setPDBName(java.lang.String s) throws PDBParseException
set three character name of AminoAcid.- Specified by:
setPDBName
in interfaceGroup
- Overrides:
setPDBName
in classHetatomImpl
- Parameters:
s
- a String specifying the PDBName value- Throws:
PDBParseException
- ...- See Also:
HetatomImpl.getPDBName()
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clone
public java.lang.Object clone()
returns and identical copy of this Group object .- Specified by:
clone
in interfaceGroup
- Overrides:
clone
in classHetatomImpl
- Returns:
- and identical copy of this Group object
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