Package org.biojava.nbio.structure
Interface AminoAcid
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- All Superinterfaces:
Group
,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 String
ATOMRECORD
Field to distinguish AminoAcids that have been created from SEQRES records and ATOM records.static 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 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.String
getRecordType()
Allows to distinguish between amino acids that are provided as ATOM records and a SEQRES records.void
setAminoType(Character aa)
Set the name of the AA, in single letter code .void
setRecordType(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 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 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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getAminoType
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(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(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
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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