org.biojava.bio.structure

Class NucleotideImpl

java.lang.Object

org.biojava.bio.structure.HetatomImpl

org.biojava.bio.structure.NucleotideImpl

All Implemented Interfaces:

java.io.Serializable, Group

public class NucleotideImpl
extends HetatomImpl
implements Group, java.io.Serializable

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

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	type this is a "nucleotide", a special occurance of a Hetatom.

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

atoms, pdb_flag, pdb_name, residueNumber

Constructor Summary

Constructors

Constructor and Description
NucleotideImpl()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.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
java.lang.String	getType() Returns the type value.
java.lang.String	toString()

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

addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtomByPDBname, getAtoms, getChain, getChainId, getChemComp, getId, getParent, getPDBCode, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setId, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, trimToSize

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.bio.structure.Group

addAltLoc, addAtom, clearAtoms, getAltLocGroup, getAltLocs, getAtom, getAtom, getAtomByPDBname, getAtoms, getChain, getChainId, getChemComp, getParent, getPDBCode, getPDBName, getProperties, getProperty, getResidueNumber, has3D, hasAltLoc, hasAminoAtoms, hasAtom, isWater, iterator, setAtoms, setChain, setChemComp, setParent, setPDBCode, setPDBFlag, setPDBName, setProperties, setProperty, setResidueNumber, setResidueNumber, size, trimToSize

Field Detail

type

public static final java.lang.String type

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

See Also:

Constant Field Values

Constructor Detail

NucleotideImpl

public NucleotideImpl()

Method Detail

getType

public java.lang.String getType()

Description copied from class: HetatomImpl

Returns the type value.

Specified by:

getType in interface Group

Overrides:

getType in class HetatomImpl

Returns:

a String representing the type value

toString

public java.lang.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 java.lang.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