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java.lang.Objectorg.biojava.bio.structure.HetatomImpl
org.biojava.bio.structure.AminoAcidImpl
public class AminoAcidImpl
AminoAcid inherits most from Hetatom. Adds a few AminoAcid specific methods.
Field Summary | |
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static java.lang.String |
type
this is an Amino acid. |
Fields inherited from interface org.biojava.bio.structure.AminoAcid |
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ATOMRECORD, SEQRESRECORD |
Constructor Summary | |
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AminoAcidImpl()
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Method Summary | |
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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 |
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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 |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface org.biojava.bio.structure.Group |
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addAtom, clearAtoms, getAtom, getAtom, getAtoms, getParent, getPDBCode, getPDBName, getProperties, getProperty, has3D, hasAminoAtoms, hasAtom, iterator, setAtoms, setParent, setPDBCode, setPDBFlag, setProperties, setProperty, size |
Field Detail |
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public static final java.lang.String type
Constructor Detail |
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public AminoAcidImpl()
Method Detail |
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public java.lang.String getType()
HetatomImpl
getType
in interface Group
getType
in class HetatomImpl
public void setSecStruc(java.util.Map<java.lang.String,java.lang.String> secstr)
setSecStruc
in interface AminoAcid
secstr
- a Map object specifying the sec struc valuegetSecStruc()
public java.util.Map<java.lang.String,java.lang.String> getSecStruc()
getSecStruc
in interface AminoAcid
setSecStruc(java.util.Map)
public Atom getN() throws StructureException
getN
in interface AminoAcid
StructureException
- ...public Atom getCA() throws StructureException
getCA
in interface AminoAcid
StructureException
- ...public Atom getC() throws StructureException
getC
in interface AminoAcid
StructureException
- ...public Atom getO() throws StructureException
getO
in interface AminoAcid
StructureException
- ...public Atom getCB() throws StructureException
getCB
in interface AminoAcid
StructureException
- ...public java.lang.Character getAminoType()
getAminoType
in interface AminoAcid
setAminoType(java.lang.Character)
public void setAminoType(java.lang.Character aa)
setAminoType
in interface AminoAcid
aa
- a Character object specifying the amino type valuegetAminoType()
public void setRecordType(java.lang.String recordName)
AminoAcid
setRecordType
in interface AminoAcid
recordName
- either ATOMRECORD or SEQRESRECORDAminoAcid.getRecordType()
public java.lang.String getRecordType()
AminoAcid
getRecordType
in interface AminoAcid
AminoAcid.setRecordType(String)
public java.lang.String toString()
toString
in interface AminoAcid
toString
in class HetatomImpl
public void setPDBName(java.lang.String s) throws PDBParseException
setPDBName
in interface Group
setPDBName
in class HetatomImpl
s
- a String specifying the PDBName value
PDBParseException
- ...HetatomImpl.getPDBName()
public java.lang.Object clone()
clone
in interface Group
clone
in class HetatomImpl
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