Package org.openscience.cdk

Class AminoAcid

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainer

org.openscience.cdk.Monomer

org.openscience.cdk.AminoAcid

All Implemented Interfaces:

Serializable, Cloneable, IAminoAcid, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer

Direct Known Subclasses:

DebugAminoAcid

public class AminoAcid
extends Monomer
implements IAminoAcid, Serializable, Cloneable

A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.

Author:

Egon Willighagen <e.willighagen@science.ru.nl>

See Also:

• Serialized Form

Keywords:

amino acid

Created on:

2005-08-11

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
AminoAcid()	Constructs a new AminoAcid.

Method Summary

Modifier and Type	Method	Description
void	addCTerminus(IAtom atom)	Add an Atom and makes it the C-terminus atom.
void	addNTerminus(IAtom atom)	Add an Atom and makes it the N-terminus atom.
IAminoAcid	clone()	Clones this AminoAcid object.
IAtom	getCTerminus()	Retrieves the C-terminus atom.
IAtom	getNTerminus()	Retrieves the N-terminus atom.
String	toString()	Returns a one line description of this IChemObject.

Methods inherited from class org.openscience.cdk.Monomer

getMonomerName, getMonomerType, setMonomerName, setMonomerType

Methods inherited from class org.openscience.cdk.AtomContainer

add, addAtom, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, shallowCopy, singleElectrons, stateChanged, stereoElements

Methods inherited from class org.openscience.cdk.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.IAtomContainer

add, addAtom, addBond, addBond, addBond, addBond, addElectronContainer, addLonePair, addLonePair, addSingleElectron, addSingleElectron, addStereoElement, atoms, bonds, contains, contains, contains, contains, contains, electronContainers, getAtom, getAtomCount, getAtomNumber, getBond, getBond, getBondCount, getBondNumber, getBondNumber, getBondOrderSum, getConnectedAtomsCount, getConnectedAtomsList, getConnectedBondsCount, getConnectedBondsCount, getConnectedBondsList, getConnectedElectronContainersList, getConnectedLonePairsCount, getConnectedLonePairsList, getConnectedSingleElectronsCount, getConnectedSingleElectronsList, getElectronContainer, getElectronContainerCount, getFirstAtom, getLastAtom, getLonePair, getLonePairCount, getLonePairNumber, getMaximumBondOrder, getMinimumBondOrder, getSingleElectron, getSingleElectronCount, getSingleElectronNumber, getTitle, indexOf, indexOf, indexOf, indexOf, isEmpty, lonePairs, newAtom, newAtom, newAtom, newAtom, newBond, newBond, remove, removeAllBonds, removeAllElectronContainers, removeAllElements, removeAtom, removeAtom, removeAtomAndConnectedElectronContainers, removeAtomOnly, removeAtomOnly, removeBond, removeBond, removeBond, removeElectronContainer, removeElectronContainer, removeLonePair, removeLonePair, removeSingleElectron, removeSingleElectron, setAtom, setAtoms, setBonds, setStereoElements, setTitle, singleElectrons, stereoElements

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Methods inherited from interface org.openscience.cdk.interfaces.IChemObjectListener

stateChanged

Methods inherited from interface org.openscience.cdk.interfaces.IMonomer

getMonomerName, getMonomerType, setMonomerName, setMonomerType

Constructor Details

AminoAcid

public AminoAcid()

Constructs a new AminoAcid.

Method Details

getNTerminus

public IAtom getNTerminus()

Retrieves the N-terminus atom.

Specified by:

getNTerminus in interface IAminoAcid

Returns:

The Atom that is the N-terminus

See Also:

• addNTerminus(IAtom)

addNTerminus

public void addNTerminus(IAtom atom)

Add an Atom and makes it the N-terminus atom.

Specified by:

addNTerminus in interface IAminoAcid

Parameters:

atom - The Atom that is the N-terminus

See Also:

• getNTerminus()

getCTerminus

public IAtom getCTerminus()

Retrieves the C-terminus atom.

Specified by:

getCTerminus in interface IAminoAcid

Returns:

The Atom that is the C-terminus

See Also:

• addCTerminus(IAtom)

addCTerminus

public void addCTerminus(IAtom atom)

Add an Atom and makes it the C-terminus atom.

Specified by:

addCTerminus in interface IAminoAcid

Parameters:

atom - The Atom that is the C-terminus

See Also:

• getCTerminus()

clone

public IAminoAcid clone()
                 throws CloneNotSupportedException

Clones this AminoAcid object.

Specified by:

clone in interface IAminoAcid

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IMonomer

Overrides:

clone in class Monomer

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Description copied from class: AtomContainer

Returns a one line description of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Monomer

Returns:

a String representation of this object