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>, java.io.Serializable, java.lang.Cloneable, org.openscience.cdk.interfaces.IAtomContainer, org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObjectListener, org.openscience.cdk.interfaces.IMolecule
public class SuppleAtomContainer
- extends org.openscience.cdk.ChemObject
- implements org.openscience.cdk.interfaces.IMolecule, org.openscience.cdk.interfaces.IChemObjectListener, java.io.Serializable, java.lang.Cloneable, IFiltered<org.openscience.cdk.interfaces.IAtom>
- See Also:
- Serialized Form
Field Summary |
protected java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtomParity> |
atomParities
Internal list of atom parities. |
protected FilteredList<org.openscience.cdk.interfaces.IAtom> |
atoms
|
protected FilteredList<org.openscience.cdk.interfaces.IBond> |
bonds
|
protected java.util.List<org.openscience.cdk.interfaces.ILonePair> |
lonePairs
|
protected java.util.List<org.openscience.cdk.interfaces.ISingleElectron> |
singleElectrons
Internal array of single electrons. |
Method Summary |
void |
add(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
|
void |
addAtom(org.openscience.cdk.interfaces.IAtom atom)
|
void |
addAtomParity(org.openscience.cdk.interfaces.IAtomParity parity)
|
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,
int 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 |
addToFilter(org.openscience.cdk.interfaces.IAtom atom)
|
void |
addToFilter(org.openscience.cdk.interfaces.IBond bond)
|
java.util.Iterator<org.openscience.cdk.interfaces.IAtom> |
atoms()
|
java.util.Iterator<org.openscience.cdk.interfaces.IBond> |
bonds()
|
void |
clearFilter()
|
java.lang.Object |
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)
|
java.util.Iterator<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.IAtomParity |
getAtomParity(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)
|
java.util.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)
|
java.util.List<org.openscience.cdk.interfaces.IBond> |
getConnectedBondsList(org.openscience.cdk.interfaces.IAtom atom)
|
java.util.List<org.openscience.cdk.interfaces.IElectronContainer> |
getConnectedElectronContainersList(org.openscience.cdk.interfaces.IAtom atom)
|
int |
getConnectedLonePairsCount(org.openscience.cdk.interfaces.IAtom atom)
|
java.util.List<org.openscience.cdk.interfaces.ILonePair> |
getConnectedLonePairsList(org.openscience.cdk.interfaces.IAtom atom)
|
int |
getConnectedSingleElectronsCount(org.openscience.cdk.interfaces.IAtom atom)
|
java.util.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)
|
protected void |
init()
|
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)
|
java.util.Iterator<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)
|
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)
|
java.util.Iterator<org.openscience.cdk.interfaces.ISingleElectron> |
singleElectrons()
|
void |
stateChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent event)
|
Methods inherited from class org.openscience.cdk.ChemObject |
addListener, compare, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, 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, getBuilder, getFlag, getFlags, getID, getListenerCount, getNotification, getProperties, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString |
atoms
protected FilteredList<org.openscience.cdk.interfaces.IAtom> atoms
bonds
protected FilteredList<org.openscience.cdk.interfaces.IBond> bonds
lonePairs
protected java.util.List<org.openscience.cdk.interfaces.ILonePair> lonePairs
singleElectrons
protected java.util.List<org.openscience.cdk.interfaces.ISingleElectron> singleElectrons
- Internal array of single electrons.
atomParities
protected java.util.Map<org.openscience.cdk.interfaces.IAtom,org.openscience.cdk.interfaces.IAtomParity> atomParities
- Internal list of atom parities.
SuppleAtomContainer
public SuppleAtomContainer()
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
addAtomParity
public void addAtomParity(org.openscience.cdk.interfaces.IAtomParity parity)
- Specified by:
addAtomParity
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,
int 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 java.util.Iterator<org.openscience.cdk.interfaces.IAtom> atoms()
- Specified by:
atoms
in interface org.openscience.cdk.interfaces.IAtomContainer
bonds
public java.util.Iterator<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 java.util.Iterator<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
getAtomParity
public org.openscience.cdk.interfaces.IAtomParity getAtomParity(org.openscience.cdk.interfaces.IAtom atom)
- Specified by:
getAtomParity
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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.Iterator<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 java.util.Iterator<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 java.lang.Object clone()
throws java.lang.CloneNotSupportedException
- Specified by:
clone
in interface org.openscience.cdk.interfaces.IChemObject
- Overrides:
clone
in class org.openscience.cdk.ChemObject
- Throws:
java.lang.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)