ambit2.core.groups

Class SuppleAtomContainer

java.lang.Object

org.openscience.cdk.ChemObject

ambit2.core.groups.SuppleAtomContainer

All Implemented Interfaces:

IFiltered<org.openscience.cdk.interfaces.IAtom>, Serializable, Cloneable, org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.ICDKObject, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObjectListener

public class SuppleAtomContainer
extends org.openscience.cdk.ChemObject
implements org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObjectListener, Serializable, Cloneable, IFiltered<org.openscience.cdk.interfaces.IAtom>

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected FilteredList<org.openscience.cdk.interfaces.IAtom>	atoms
protected FilteredList<org.openscience.cdk.interfaces.IBond>	bonds
protected List<org.openscience.cdk.interfaces.ILonePair>	lonePairs
protected List<org.openscience.cdk.interfaces.ISingleElectron>	singleElectrons Internal array of single electrons.
protected Set<org.openscience.cdk.interfaces.IStereoElement>	stereoElements Internal list of atom parities.

Constructor Summary

Constructors

Constructor and Description
SuppleAtomContainer()

Method Summary

Modifier and Type	Method and Description
void	add(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
void	addAtom(org.openscience.cdk.interfaces.IAtom atom)
void	addBond(org.openscience.cdk.interfaces.IBond bond)
void	addBond(int atom1, int atom2, org.openscience.cdk.interfaces.IBond.Order order)
void	addBond(int atom1, int atom2, org.openscience.cdk.interfaces.IBond.Order order, org.openscience.cdk.interfaces.IBond.Stereo stereo)
void	addElectronContainer(org.openscience.cdk.interfaces.IElectronContainer electronContainer)
void	addGroupAtom(ISGroup group, org.openscience.cdk.interfaces.IAtom atom)
void	addGroupBond(ISGroup group, org.openscience.cdk.interfaces.IBond bond)
void	addLonePair(org.openscience.cdk.interfaces.ILonePair lonePair)
void	addLonePair(int atomID)
void	addSingleElectron(int atomID)
void	addSingleElectron(org.openscience.cdk.interfaces.ISingleElectron singleElectron)
void	addStereoElement(org.openscience.cdk.interfaces.IStereoElement element)
void	addToFilter(org.openscience.cdk.interfaces.IAtom atom)
void	addToFilter(org.openscience.cdk.interfaces.IBond bond)
Iterable<org.openscience.cdk.interfaces.IAtom>	atoms()
Iterable<org.openscience.cdk.interfaces.IBond>	bonds()
void	clearFilter()
org.openscience.cdk.interfaces.IAtomContainer	clone()
boolean	contains(org.openscience.cdk.interfaces.IAtom atom)
boolean	contains(org.openscience.cdk.interfaces.IBond bond)
boolean	contains(org.openscience.cdk.interfaces.IElectronContainer electronContainer)
boolean	contains(org.openscience.cdk.interfaces.ILonePair lonePair)
boolean	contains(org.openscience.cdk.interfaces.ISingleElectron singleElectron)
Iterable<org.openscience.cdk.interfaces.IElectronContainer>	electronContainers()
org.openscience.cdk.interfaces.IAtom	getAtom(int index)
int	getAtomCount()
int	getAtomNumber(org.openscience.cdk.interfaces.IAtom atom)
org.openscience.cdk.interfaces.IBond	getBond(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2)
org.openscience.cdk.interfaces.IBond	getBond(int arg0)
int	getBondCount()
int	getBondNumber(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2)
int	getBondNumber(org.openscience.cdk.interfaces.IBond bond)
double	getBondOrderSum(org.openscience.cdk.interfaces.IAtom atom)
int	getConnectedAtomsCount(org.openscience.cdk.interfaces.IAtom atom)
List<org.openscience.cdk.interfaces.IAtom>	getConnectedAtomsList(org.openscience.cdk.interfaces.IAtom atom)
int	getConnectedBondsCount(org.openscience.cdk.interfaces.IAtom atom)
int	getConnectedBondsCount(int atomNumber)
List<org.openscience.cdk.interfaces.IBond>	getConnectedBondsList(org.openscience.cdk.interfaces.IAtom atom)
List<org.openscience.cdk.interfaces.IElectronContainer>	getConnectedElectronContainersList(org.openscience.cdk.interfaces.IAtom atom)
int	getConnectedLonePairsCount(org.openscience.cdk.interfaces.IAtom atom)
List<org.openscience.cdk.interfaces.ILonePair>	getConnectedLonePairsList(org.openscience.cdk.interfaces.IAtom atom)
int	getConnectedSingleElectronsCount(org.openscience.cdk.interfaces.IAtom atom)
List<org.openscience.cdk.interfaces.ISingleElectron>	getConnectedSingleElectronsList(org.openscience.cdk.interfaces.IAtom atom)
org.openscience.cdk.interfaces.IElectronContainer	getElectronContainer(int number)
int	getElectronContainerCount()
org.openscience.cdk.interfaces.IAtom	getFirstAtom()
org.openscience.cdk.interfaces.IAtom	getLastAtom()
org.openscience.cdk.interfaces.ILonePair	getLonePair(int number)
int	getLonePairCount()
int	getLonePairNumber(org.openscience.cdk.interfaces.ILonePair lonePair)
org.openscience.cdk.interfaces.IBond.Order	getMaximumBondOrder(org.openscience.cdk.interfaces.IAtom atom)
org.openscience.cdk.interfaces.IBond.Order	getMinimumBondOrder(org.openscience.cdk.interfaces.IAtom atom)
org.openscience.cdk.interfaces.ISingleElectron	getSingleElectron(int index)
int	getSingleElectronCount()
int	getSingleElectronNumber(org.openscience.cdk.interfaces.ISingleElectron singleElectron)
String	getTitle()
int	indexOf(org.openscience.cdk.interfaces.IAtom arg0)
int	indexOf(org.openscience.cdk.interfaces.IBond arg0)
int	indexOf(org.openscience.cdk.interfaces.ILonePair arg0)
int	indexOf(org.openscience.cdk.interfaces.ISingleElectron arg0)
protected void	init()
boolean	isEmpty()
boolean	isFiltered()
boolean	isFiltered(org.openscience.cdk.interfaces.IAtom atom)
boolean	isFiltered(org.openscience.cdk.interfaces.IBond bond)
boolean	isVisible(org.openscience.cdk.interfaces.IAtom atom)
Iterable<org.openscience.cdk.interfaces.ILonePair>	lonePairs()
void	remove(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
void	removeAllBonds()
void	removeAllElectronContainers()
void	removeAllElements()
void	removeAtom(org.openscience.cdk.interfaces.IAtom atom)
void	removeAtom(int position)
void	removeAtomAndConnectedElectronContainers(org.openscience.cdk.interfaces.IAtom atom)
void	removeAtomOnly(org.openscience.cdk.interfaces.IAtom arg0)
void	removeAtomOnly(int arg0)
org.openscience.cdk.interfaces.IBond	removeBond(org.openscience.cdk.interfaces.IAtom atom1, org.openscience.cdk.interfaces.IAtom atom2)
void	removeBond(org.openscience.cdk.interfaces.IBond bond)
org.openscience.cdk.interfaces.IBond	removeBond(int position)
void	removeElectronContainer(org.openscience.cdk.interfaces.IElectronContainer electronContainer)
org.openscience.cdk.interfaces.IElectronContainer	removeElectronContainer(int number)
void	removeFromFilter(org.openscience.cdk.interfaces.IAtom atom)
void	removeFromFilter(org.openscience.cdk.interfaces.IBond bond)
void	removeLonePair(org.openscience.cdk.interfaces.ILonePair lp)
org.openscience.cdk.interfaces.ILonePair	removeLonePair(int position)
org.openscience.cdk.interfaces.ISingleElectron	removeSingleElectron(int position)
void	removeSingleElectron(org.openscience.cdk.interfaces.ISingleElectron se)
void	setAtom(int number, org.openscience.cdk.interfaces.IAtom atom)
void	setAtoms(org.openscience.cdk.interfaces.IAtom[] newatoms)
void	setBonds(org.openscience.cdk.interfaces.IBond[] newbonds)
void	setFiltered(boolean filtered)
void	setStereoElements(List<org.openscience.cdk.interfaces.IStereoElement> elements)
void	setTitle(String arg0)
Iterable<org.openscience.cdk.interfaces.ISingleElectron>	singleElectrons()
void	stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
Iterable<org.openscience.cdk.interfaces.IStereoElement>	stereoElements()

Methods inherited from class org.openscience.cdk.ChemObject

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

Methods inherited from class java.lang.Object

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

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

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

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

getBuilder

Field Detail

atoms

protected FilteredList<org.openscience.cdk.interfaces.IAtom> atoms

bonds

protected FilteredList<org.openscience.cdk.interfaces.IBond> bonds

lonePairs

protected List<org.openscience.cdk.interfaces.ILonePair> lonePairs

singleElectrons

protected List<org.openscience.cdk.interfaces.ISingleElectron> singleElectrons

Internal array of single electrons.

stereoElements

protected Set<org.openscience.cdk.interfaces.IStereoElement> stereoElements

Internal list of atom parities.

Constructor Detail

SuppleAtomContainer

public SuppleAtomContainer()

Method Detail

init

protected void init()

add

public void add(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Specified by:

add in interface org.openscience.cdk.interfaces.IAtomContainer

addAtom

public void addAtom(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

addAtom in interface org.openscience.cdk.interfaces.IAtomContainer

addStereoElement

public void addStereoElement(org.openscience.cdk.interfaces.IStereoElement element)

Specified by:

addStereoElement in interface org.openscience.cdk.interfaces.IAtomContainer

setStereoElements

public void setStereoElements(List<org.openscience.cdk.interfaces.IStereoElement> elements)

Specified by:

setStereoElements in interface org.openscience.cdk.interfaces.IAtomContainer

stereoElements

public Iterable<org.openscience.cdk.interfaces.IStereoElement> stereoElements()

Specified by:

stereoElements in interface org.openscience.cdk.interfaces.IAtomContainer

addBond

public void addBond(org.openscience.cdk.interfaces.IBond bond)

Specified by:

addBond in interface org.openscience.cdk.interfaces.IAtomContainer

addBond

public void addBond(int atom1,
                    int atom2,
                    org.openscience.cdk.interfaces.IBond.Order order,
                    org.openscience.cdk.interfaces.IBond.Stereo stereo)

Specified by:

addBond in interface org.openscience.cdk.interfaces.IAtomContainer

addBond

public void addBond(int atom1,
                    int atom2,
                    org.openscience.cdk.interfaces.IBond.Order order)

Specified by:

addBond in interface org.openscience.cdk.interfaces.IAtomContainer

addElectronContainer

public void addElectronContainer(org.openscience.cdk.interfaces.IElectronContainer electronContainer)

Specified by:

addElectronContainer in interface org.openscience.cdk.interfaces.IAtomContainer

addLonePair

public void addLonePair(org.openscience.cdk.interfaces.ILonePair lonePair)

Specified by:

addLonePair in interface org.openscience.cdk.interfaces.IAtomContainer

addLonePair

public void addLonePair(int atomID)

Specified by:

addLonePair in interface org.openscience.cdk.interfaces.IAtomContainer

addSingleElectron

public void addSingleElectron(org.openscience.cdk.interfaces.ISingleElectron singleElectron)

Specified by:

addSingleElectron in interface org.openscience.cdk.interfaces.IAtomContainer

addSingleElectron

public void addSingleElectron(int atomID)

Specified by:

addSingleElectron in interface org.openscience.cdk.interfaces.IAtomContainer

atoms

public Iterable<org.openscience.cdk.interfaces.IAtom> atoms()

Specified by:

atoms in interface org.openscience.cdk.interfaces.IAtomContainer

bonds

public Iterable<org.openscience.cdk.interfaces.IBond> bonds()

Specified by:

bonds in interface org.openscience.cdk.interfaces.IAtomContainer

contains

public boolean contains(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

contains in interface org.openscience.cdk.interfaces.IAtomContainer

contains

public boolean contains(org.openscience.cdk.interfaces.IBond bond)

Specified by:

contains in interface org.openscience.cdk.interfaces.IAtomContainer

contains

public boolean contains(org.openscience.cdk.interfaces.ILonePair lonePair)

Specified by:

contains in interface org.openscience.cdk.interfaces.IAtomContainer

contains

public boolean contains(org.openscience.cdk.interfaces.ISingleElectron singleElectron)

Specified by:

contains in interface org.openscience.cdk.interfaces.IAtomContainer

contains

public boolean contains(org.openscience.cdk.interfaces.IElectronContainer electronContainer)

Specified by:

contains in interface org.openscience.cdk.interfaces.IAtomContainer

electronContainers

public Iterable<org.openscience.cdk.interfaces.IElectronContainer> electronContainers()

Specified by:

electronContainers in interface org.openscience.cdk.interfaces.IAtomContainer

getAtom

public org.openscience.cdk.interfaces.IAtom getAtom(int index)

Specified by:

getAtom in interface org.openscience.cdk.interfaces.IAtomContainer

getAtomCount

public int getAtomCount()

Specified by:

getAtomCount in interface org.openscience.cdk.interfaces.IAtomContainer

getAtomNumber

public int getAtomNumber(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getAtomNumber in interface org.openscience.cdk.interfaces.IAtomContainer

getBond

public org.openscience.cdk.interfaces.IBond getBond(int arg0)

Specified by:

getBond in interface org.openscience.cdk.interfaces.IAtomContainer

getBond

public org.openscience.cdk.interfaces.IBond getBond(org.openscience.cdk.interfaces.IAtom atom1,
                                                    org.openscience.cdk.interfaces.IAtom atom2)

Specified by:

getBond in interface org.openscience.cdk.interfaces.IAtomContainer

getBondCount

public int getBondCount()

Specified by:

getBondCount in interface org.openscience.cdk.interfaces.IAtomContainer

getBondNumber

public int getBondNumber(org.openscience.cdk.interfaces.IBond bond)

Specified by:

getBondNumber in interface org.openscience.cdk.interfaces.IAtomContainer

getBondNumber

public int getBondNumber(org.openscience.cdk.interfaces.IAtom atom1,
                         org.openscience.cdk.interfaces.IAtom atom2)

Specified by:

getBondNumber in interface org.openscience.cdk.interfaces.IAtomContainer

getBondOrderSum

public double getBondOrderSum(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getBondOrderSum in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedAtomsCount

public int getConnectedAtomsCount(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedAtomsCount in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedAtomsList

public List<org.openscience.cdk.interfaces.IAtom> getConnectedAtomsList(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedAtomsList in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedBondsCount

public int getConnectedBondsCount(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedBondsCount in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedBondsCount

public int getConnectedBondsCount(int atomNumber)

Specified by:

getConnectedBondsCount in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedBondsList

public List<org.openscience.cdk.interfaces.IBond> getConnectedBondsList(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedBondsList in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedElectronContainersList

public List<org.openscience.cdk.interfaces.IElectronContainer> getConnectedElectronContainersList(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedElectronContainersList in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedLonePairsCount

public int getConnectedLonePairsCount(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedLonePairsCount in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedLonePairsList

public List<org.openscience.cdk.interfaces.ILonePair> getConnectedLonePairsList(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedLonePairsList in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedSingleElectronsCount

public int getConnectedSingleElectronsCount(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedSingleElectronsCount in interface org.openscience.cdk.interfaces.IAtomContainer

getConnectedSingleElectronsList

public List<org.openscience.cdk.interfaces.ISingleElectron> getConnectedSingleElectronsList(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getConnectedSingleElectronsList in interface org.openscience.cdk.interfaces.IAtomContainer

getElectronContainer

public org.openscience.cdk.interfaces.IElectronContainer getElectronContainer(int number)

Specified by:

getElectronContainer in interface org.openscience.cdk.interfaces.IAtomContainer

getElectronContainerCount

public int getElectronContainerCount()

Specified by:

getElectronContainerCount in interface org.openscience.cdk.interfaces.IAtomContainer

getFirstAtom

public org.openscience.cdk.interfaces.IAtom getFirstAtom()

Specified by:

getFirstAtom in interface org.openscience.cdk.interfaces.IAtomContainer

getLastAtom

public org.openscience.cdk.interfaces.IAtom getLastAtom()

Specified by:

getLastAtom in interface org.openscience.cdk.interfaces.IAtomContainer

getLonePair

public org.openscience.cdk.interfaces.ILonePair getLonePair(int number)

Specified by:

getLonePair in interface org.openscience.cdk.interfaces.IAtomContainer

getLonePairCount

public int getLonePairCount()

Specified by:

getLonePairCount in interface org.openscience.cdk.interfaces.IAtomContainer

getLonePairNumber

public int getLonePairNumber(org.openscience.cdk.interfaces.ILonePair lonePair)

Specified by:

getLonePairNumber in interface org.openscience.cdk.interfaces.IAtomContainer

getMaximumBondOrder

public org.openscience.cdk.interfaces.IBond.Order getMaximumBondOrder(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getMaximumBondOrder in interface org.openscience.cdk.interfaces.IAtomContainer

getMinimumBondOrder

public org.openscience.cdk.interfaces.IBond.Order getMinimumBondOrder(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

getMinimumBondOrder in interface org.openscience.cdk.interfaces.IAtomContainer

getSingleElectron

public org.openscience.cdk.interfaces.ISingleElectron getSingleElectron(int index)

Specified by:

getSingleElectron in interface org.openscience.cdk.interfaces.IAtomContainer

getSingleElectronCount

public int getSingleElectronCount()

Specified by:

getSingleElectronCount in interface org.openscience.cdk.interfaces.IAtomContainer

getSingleElectronNumber

public int getSingleElectronNumber(org.openscience.cdk.interfaces.ISingleElectron singleElectron)

Specified by:

getSingleElectronNumber in interface org.openscience.cdk.interfaces.IAtomContainer

lonePairs

public Iterable<org.openscience.cdk.interfaces.ILonePair> lonePairs()

Specified by:

lonePairs in interface org.openscience.cdk.interfaces.IAtomContainer

remove

public void remove(org.openscience.cdk.interfaces.IAtomContainer atomContainer)

Specified by:

remove in interface org.openscience.cdk.interfaces.IAtomContainer

removeAllBonds

public void removeAllBonds()

Specified by:

removeAllBonds in interface org.openscience.cdk.interfaces.IAtomContainer

removeAllElectronContainers

public void removeAllElectronContainers()

Specified by:

removeAllElectronContainers in interface org.openscience.cdk.interfaces.IAtomContainer

removeAllElements

public void removeAllElements()

Specified by:

removeAllElements in interface org.openscience.cdk.interfaces.IAtomContainer

removeAtom

public void removeAtom(int position)

Specified by:

removeAtom in interface org.openscience.cdk.interfaces.IAtomContainer

removeAtom

public void removeAtom(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

removeAtom in interface org.openscience.cdk.interfaces.IAtomContainer

removeAtomAndConnectedElectronContainers

public void removeAtomAndConnectedElectronContainers(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

removeAtomAndConnectedElectronContainers in interface org.openscience.cdk.interfaces.IAtomContainer

removeBond

public org.openscience.cdk.interfaces.IBond removeBond(int position)

Specified by:

removeBond in interface org.openscience.cdk.interfaces.IAtomContainer

removeBond

public void removeBond(org.openscience.cdk.interfaces.IBond bond)

Specified by:

removeBond in interface org.openscience.cdk.interfaces.IAtomContainer

removeBond

public org.openscience.cdk.interfaces.IBond removeBond(org.openscience.cdk.interfaces.IAtom atom1,
                                                       org.openscience.cdk.interfaces.IAtom atom2)

Specified by:

removeBond in interface org.openscience.cdk.interfaces.IAtomContainer

removeElectronContainer

public org.openscience.cdk.interfaces.IElectronContainer removeElectronContainer(int number)

Specified by:

removeElectronContainer in interface org.openscience.cdk.interfaces.IAtomContainer

removeElectronContainer

public void removeElectronContainer(org.openscience.cdk.interfaces.IElectronContainer electronContainer)

Specified by:

removeElectronContainer in interface org.openscience.cdk.interfaces.IAtomContainer

removeLonePair

public org.openscience.cdk.interfaces.ILonePair removeLonePair(int position)

Specified by:

removeLonePair in interface org.openscience.cdk.interfaces.IAtomContainer

removeLonePair

public void removeLonePair(org.openscience.cdk.interfaces.ILonePair lp)

Specified by:

removeLonePair in interface org.openscience.cdk.interfaces.IAtomContainer

removeSingleElectron

public org.openscience.cdk.interfaces.ISingleElectron removeSingleElectron(int position)

Specified by:

removeSingleElectron in interface org.openscience.cdk.interfaces.IAtomContainer

removeSingleElectron

public void removeSingleElectron(org.openscience.cdk.interfaces.ISingleElectron se)

Specified by:

removeSingleElectron in interface org.openscience.cdk.interfaces.IAtomContainer

setAtom

public void setAtom(int number,
                    org.openscience.cdk.interfaces.IAtom atom)

Specified by:

setAtom in interface org.openscience.cdk.interfaces.IAtomContainer

setAtoms

public void setAtoms(org.openscience.cdk.interfaces.IAtom[] newatoms)

Specified by:

setAtoms in interface org.openscience.cdk.interfaces.IAtomContainer

setBonds

public void setBonds(org.openscience.cdk.interfaces.IBond[] newbonds)

Specified by:

setBonds in interface org.openscience.cdk.interfaces.IAtomContainer

singleElectrons

public Iterable<org.openscience.cdk.interfaces.ISingleElectron> singleElectrons()

Specified by:

singleElectrons in interface org.openscience.cdk.interfaces.IAtomContainer

stateChanged

public void stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)

Specified by:

stateChanged in interface org.openscience.cdk.interfaces.IChemObjectListener

clone

public org.openscience.cdk.interfaces.IAtomContainer clone()
                                                    throws CloneNotSupportedException

Specified by:

clone in interface org.openscience.cdk.interfaces.IAtomContainer

Specified by:

clone in interface org.openscience.cdk.interfaces.IChemObject

Overrides:

clone in class org.openscience.cdk.ChemObject

Throws:

CloneNotSupportedException

addToFilter

public void addToFilter(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

addToFilter in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

addToFilter

public void addToFilter(org.openscience.cdk.interfaces.IBond bond)

clearFilter

public void clearFilter()

Specified by:

clearFilter in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

isVisible

public boolean isVisible(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

isVisible in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

isFiltered

public boolean isFiltered(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

isFiltered in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

isFiltered

public boolean isFiltered(org.openscience.cdk.interfaces.IBond bond)

removeFromFilter

public void removeFromFilter(org.openscience.cdk.interfaces.IAtom atom)

Specified by:

removeFromFilter in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

removeFromFilter

public void removeFromFilter(org.openscience.cdk.interfaces.IBond bond)

isFiltered

public boolean isFiltered()

Specified by:

isFiltered in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

setFiltered

public void setFiltered(boolean filtered)

Specified by:

setFiltered in interface IFiltered<org.openscience.cdk.interfaces.IAtom>

addGroupAtom

public void addGroupAtom(ISGroup group,
                         org.openscience.cdk.interfaces.IAtom atom)

addGroupBond

public void addGroupBond(ISGroup group,
                         org.openscience.cdk.interfaces.IBond bond)

isEmpty

public boolean isEmpty()

Specified by:

isEmpty in interface org.openscience.cdk.interfaces.IAtomContainer

indexOf

public int indexOf(org.openscience.cdk.interfaces.IAtom arg0)

Specified by:

indexOf in interface org.openscience.cdk.interfaces.IAtomContainer

indexOf

public int indexOf(org.openscience.cdk.interfaces.IBond arg0)

Specified by:

indexOf in interface org.openscience.cdk.interfaces.IAtomContainer

indexOf

public int indexOf(org.openscience.cdk.interfaces.ISingleElectron arg0)

Specified by:

indexOf in interface org.openscience.cdk.interfaces.IAtomContainer

indexOf

public int indexOf(org.openscience.cdk.interfaces.ILonePair arg0)

Specified by:

indexOf in interface org.openscience.cdk.interfaces.IAtomContainer

getTitle

public String getTitle()

Specified by:

getTitle in interface org.openscience.cdk.interfaces.IAtomContainer

removeAtomOnly

public void removeAtomOnly(int arg0)

Specified by:

removeAtomOnly in interface org.openscience.cdk.interfaces.IAtomContainer

removeAtomOnly

public void removeAtomOnly(org.openscience.cdk.interfaces.IAtom arg0)

Specified by:

removeAtomOnly in interface org.openscience.cdk.interfaces.IAtomContainer

setTitle

public void setTitle(String arg0)

Specified by:

setTitle in interface org.openscience.cdk.interfaces.IAtomContainer