Package org.biojava.nbio.structure

Class NucleotideImpl

java.lang.Object

org.biojava.nbio.structure.HetatomImpl

org.biojava.nbio.structure.NucleotideImpl

All Implemented Interfaces:

Serializable, Group

public class NucleotideImpl
extends HetatomImpl

A nucleotide group is almost the same as a Hetatm group.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic

See Also:

• HetatomImpl
• AminoAcidImpl
• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class org.biojava.nbio.structure.HetatomImpl

HetatomImpl.PerformanceBehavior

Field Summary

Fields

Modifier and Type	Field	Description
static final GroupType	type	this is a "nucleotide", a special occurance of a Hetatom.

Fields inherited from class org.biojava.nbio.structure.HetatomImpl

atoms, chemComp, pdb_flag, pdb_name, residueNumber

Fields inherited from interface org.biojava.nbio.structure.Group

SEC_STRUC

Constructor Summary

Constructors

Constructor	Description
NucleotideImpl()

Method Summary

Modifier and Type	Method	Description
Object	clone()	returns and identical copy of this Group object .
Atom	getO3Prime()	Returns the O3' atom if present, otherwise null
Atom	getO5Prime()	Returns the O5' atom if present, otherwise null
Atom	getP()	Returns the P atom if present, otherwise null
GroupType	getType()	Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE
String	toString()

Methods inherited from class org.biojava.nbio.structure.HetatomImpl

addAltLoc, addAtom, clearAtoms, cloneAtomsAndBonds, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtoms, getChain, getChainId, getChemComp, getId, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isAminoAcid, isHetAtomInFile, isNucleotide, isPolymeric, isWater, iterator, setAtoms, setChain, setChemComp, setHetAtomInFile, setId, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, toSDF, trimToSize

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

type

public static final GroupType type

this is a "nucleotide", a special occurance of a Hetatom.

Constructor Details

NucleotideImpl

public NucleotideImpl()

Method Details

getType

public GroupType getType()

Description copied from class: HetatomImpl

Get Type of group, one of GroupType.AMINOACID, GroupType.HETATM or GroupType.NUCLEOTIDE

Specified by:

getType in interface Group

Overrides:

getType in class HetatomImpl

Returns:

a String representing the type value

toString

public String toString()

Overrides:

toString in class HetatomImpl

getO3Prime

public Atom getO3Prime()

Returns the O3' atom if present, otherwise null

Returns:

O3' atom or null

getO5Prime

public Atom getO5Prime()

Returns the O5' atom if present, otherwise null

Returns:

O5' atom or null

getP

public Atom getP()

Returns the P atom if present, otherwise null

Returns:

P atom or null

clone

public Object clone()

Description copied from class: HetatomImpl

returns and identical copy of this Group object .

Specified by:

clone in interface Group

Overrides:

clone in class HetatomImpl

Returns:

and identical copy of this Group object