Package org.openscience.cdk.interfaces

Interface IAminoAcid

All Superinterfaces:

Cloneable, IAtomContainer, ICDKObject, IChemObject, IChemObjectListener, IMonomer

All Known Implementing Classes:

AminoAcid, AminoAcid, DebugAminoAcid

public interface IAminoAcid
extends IMonomer

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

Author:

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

Keywords:

amino acid

Created on:

2005-12-05

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

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()	Returns a deep clone of this IChemObject.
IAtom	getCTerminus()	Retrieves the C-terminus atom.
IAtom	getNTerminus()	Retrieves the N-terminus atom.

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, toString

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

stateChanged

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

getMonomerName, getMonomerType, setMonomerName, setMonomerType

Method Details

getNTerminus

IAtom getNTerminus()

Retrieves the N-terminus atom.

Returns:

The Atom that is the N-terminus

See Also:

• addNTerminus(IAtom)

addNTerminus

void addNTerminus(IAtom atom)

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

Parameters:

atom - The Atom that is the N-terminus

See Also:

• getNTerminus()

getCTerminus

IAtom getCTerminus()

Retrieves the C-terminus atom.

Returns:

The Atom that is the C-terminus

See Also:

• addCTerminus(IAtom)

addCTerminus

void addCTerminus(IAtom atom)

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

Parameters:

atom - The Atom that is the C-terminus

See Also:

• getCTerminus()

clone

IAminoAcid clone()
          throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtomContainer

Specified by:

clone in interface IChemObject

Specified by:

clone in interface IMonomer

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned