Package org.biojava.nbio.structure
Interface AminoAcid
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- All Superinterfaces:
Group
,java.io.Serializable
- 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
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
ATOMRECORD
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.static java.lang.String
SEQRESRECORD
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.
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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.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.-
Methods inherited from interface org.biojava.nbio.structure.Group
addAltLoc, addAtom, clearAtoms, clone, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtoms, getChain, getChainId, getChemComp, getPDBName, getProperties, getProperty, getResidueNumber, getType, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isAminoAcid, isHetAtomInFile, isNucleotide, isPolymeric, isWater, iterator, setAtoms, setChain, setChemComp, setHetAtomInFile, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, toSDF, trimToSize
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Field Detail
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ATOMRECORD
static final java.lang.String ATOMRECORD
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.- See Also:
- Constant Field Values
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SEQRESRECORD
static final java.lang.String SEQRESRECORD
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.- See Also:
- Constant Field Values
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Method Detail
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getN
Atom getN()
Get N atom.- Returns:
- an Atom object or null if N atom does not exist
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getCA
Atom getCA()
Get CA atom.- Returns:
- an Atom object or null if CA atom does not exist
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getC
Atom getC()
Get C atom.- Returns:
- an Atom object or null if C atom does not exist
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getO
Atom getO()
Get O atom.- Returns:
- an Atom object or null if O atom does not exist
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getCB
Atom getCB()
Get CB atom.- Returns:
- an Atom object or null if CB atom does not exist
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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)
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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()
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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()
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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)
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