public class DebugAtomContainer extends AtomContainer implements IAtomContainer
Constructor and Description |
---|
DebugAtomContainer() |
DebugAtomContainer(IAtomContainer container) |
DebugAtomContainer(int atomCount,
int bondCount,
int lonePairCount,
int singleElectronCount) |
Modifier and Type | Method and Description |
---|---|
void |
add(IAtomContainer atomContainer)
Adds all atoms and electronContainers of a given atomcontainer to this
container.
|
void |
addAtom(IAtom atom)
Adds an atom to this container.
|
void |
addBond(IBond bond)
Adds a Bond to this AtomContainer.
|
void |
addBond(int atom1,
int atom2,
IBond.Order order)
Adds a bond to this container.
|
void |
addBond(int atom1,
int atom2,
IBond.Order order,
IBond.Stereo stereo)
Adds a bond to this container.
|
void |
addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
addLonePair(int atomID)
Adds a LonePair to this Atom.
|
void |
addSingleElectron(int atomID)
Adds a LonePair to this Atom.
|
void |
addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
Iterable<IAtom> |
atoms()
Returns an Iterable for looping over all atoms in this container.
|
Iterable<IBond> |
bonds()
Returns an Iterable for looping over all bonds in this container.
|
IAtomContainer |
clone()
Clones this AtomContainer object and its content.
|
boolean |
contains(IAtom atom)
True, if the AtomContainer contains the given atom object.
|
boolean |
contains(IBond bond)
True, if the AtomContainer contains the given bond object.
|
boolean |
contains(IElectronContainer electronContainer)
True, if the AtomContainer contains the given ElectronContainer object.
|
boolean |
contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
Iterable<IElectronContainer> |
electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
IAtom |
getAtom(int number)
Get the atom at position
number in [0,..]. |
int |
getAtomCount()
Returns the number of Atoms in this Container.
|
int |
getAtomNumber(IAtom atom)
Returns the position of a given atom in the atoms array.
|
IBond |
getBond(IAtom atom1,
IAtom atom2)
Returns the bond that connects the two given atoms.
|
IBond |
getBond(int number)
Get the bond at position
number in [0,..]. |
int |
getBondCount()
Returns the number of Bonds in this Container.
|
int |
getBondNumber(IAtom atom1,
IAtom atom2)
Returns the position of the bond between two given atoms in the
electronContainers array.
|
int |
getBondNumber(IBond bond)
Returns the position of a given bond in the electronContainers array.
|
double |
getBondOrderSum(IAtom atom)
Returns the sum of the bond orders for a given Atom.
|
IChemObjectBuilder |
getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
int |
getConnectedAtomsCount(IAtom atom)
Returns the number of atoms connected to the given atom.
|
List |
getConnectedAtomsList(IAtom atom)
Returns an ArrayList of all atoms connected to the given atom.
|
int |
getConnectedBondsCount(IAtom atom)
Returns the number of Bonds for a given Atom.
|
List |
getConnectedBondsList(IAtom atom)
Returns an ArrayList of all Bonds connected to the given atom.
|
List |
getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
int |
getConnectedLonePairsCount(IAtom atom)
Returns the number of LonePairs for a given Atom.
|
List |
getConnectedLonePairsList(IAtom atom)
Returns the array of lone pairs connected to an atom.
|
int |
getConnectedSingleElectronsCount(IAtom atom)
Returns the sum of the SingleElectron for a given Atom.
|
List |
getConnectedSingleElectronsList(IAtom atom)
Returns an array of all SingleElectron connected to the given atom.
|
IElectronContainer |
getElectronContainer(int number)
Returns the ElectronContainer at position
number in the
container. |
int |
getElectronContainerCount()
Returns the number of ElectronContainers in this Container.
|
IAtom |
getFirstAtom()
Returns the atom at position 0 in the container.
|
boolean |
getFlag(int flag_type)
Returns the value of some flag.
|
boolean[] |
getFlags()
Returns the whole set of flags.
|
String |
getID()
Returns the identifier (ID) of this object.
|
IAtom |
getLastAtom()
Returns the atom at the last position in the container.
|
int |
getListenerCount()
Returns the number of ChemObjectListeners registered with this object.
|
ILonePair |
getLonePair(int number)
Get the lone pair at position
number in [0,..]. |
int |
getLonePairCount()
Returns the number of LonePairs in this Container.
|
int |
getLonePairNumber(ILonePair lp)
Returns the position of a given lone pair in the lone pair array.
|
IBond.Order |
getMaximumBondOrder(IAtom atom)
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
|
IBond.Order |
getMinimumBondOrder(IAtom atom)
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
|
Map<Object,Object> |
getProperties()
Returns a Map with the IChemObject's properties.
|
Object |
getProperty(Object description)
Returns a property for the IChemObject.
|
ISingleElectron |
getSingleElectron(int number)
Get the single electron at position
number in [0,..]. |
int |
getSingleElectronCount()
Returns the number of the single electrons in this container,
|
int |
getSingleElectronNumber(ISingleElectron se)
Returns the position of a given single electron in the single electron array.
|
boolean |
isEmpty()
Indicates whether this container is empty.
|
Iterable<ILonePair> |
lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
void |
notifyChanged()
This should be triggered by an method that changes the content of an object
to that the registered listeners can react to it.
|
void |
notifyChanged(IChemObjectChangeEvent evt)
This should be triggered by an method that changes the content of an object
to that the registered listeners can react to it.
|
void |
remove(IAtomContainer atomContainer)
Removes all atoms and electronContainers of a given atomcontainer from this
container.
|
void |
removeAllBonds()
Removes all Bonds from this container.
|
void |
removeAllElectronContainers()
Removes electronContainers from this container.
|
void |
removeAllElements()
Removes all atoms, bonds and stereo elements from this container.
|
void |
removeAtom(IAtom atom)
Removes the given atom from the AtomContainer.
|
void |
removeAtom(int position)
Removes the atom at the given position from the AtomContainer.
|
void |
removeAtomAndConnectedElectronContainers(IAtom atom)
Removes the given atom and all connected electronContainers from the
AtomContainer.
|
IBond |
removeBond(IAtom atom1,
IAtom atom2)
Removes the bond that connects the two given atoms.
|
void |
removeBond(IBond bond)
Removes the bond from this container.
|
IBond |
removeBond(int pos)
Removes the bond at the given position from the AtomContainer.
|
void |
removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
IElectronContainer |
removeElectronContainer(int position)
Removes the bond at the given position from this container.
|
void |
removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
ILonePair |
removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
void |
removeProperty(Object description)
Removes a property for a IChemObject.
|
ISingleElectron |
removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
void |
removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
setAtom(int number,
IAtom atom)
Sets the atom at position
number in [0,..]. |
void |
setAtoms(IAtom[] atoms)
Sets the array of atoms of this AtomContainer.
|
void |
setFlag(int flag_type,
boolean flag_value)
Sets the value of some flag.
|
void |
setFlags(boolean[] flagsNew)
Sets the whole set of flags.
|
void |
setID(String identifier)
Sets the identifier (ID) of this object.
|
void |
setProperties(Map<Object,Object> properties)
Sets the properties of this object.
|
void |
setProperty(Object description,
Object property)
Sets a property for a IChemObject.
|
void |
setStereoElements(List<IStereoElement> elements)
Set the stereo elements - this will replace the existing instance
with a new instance.
|
Iterable<ISingleElectron> |
singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<IStereoElement> |
stereoElements()
Returns the stereo elements defined for this atom container.
|
getConnectedBondsCount, setBonds, stateChanged, toString
compare, getNotification, setNotification, shallowCopy
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
getConnectedBondsCount, setBonds
getNotification, setNotification, toString
stateChanged
public DebugAtomContainer()
public DebugAtomContainer(int atomCount, int bondCount, int lonePairCount, int singleElectronCount)
public DebugAtomContainer(IAtomContainer container)
public void addStereoElement(IStereoElement parity)
AtomContainer
addStereoElement
in interface IAtomContainer
addStereoElement
in class AtomContainer
parity
- The new IStereoElement
for this containerIAtomContainer.stereoElements()
public void setStereoElements(List<IStereoElement> elements)
IAtomContainer
setStereoElements
in interface IAtomContainer
setStereoElements
in class AtomContainer
elements
- the new stereo elementspublic Iterable<IStereoElement> stereoElements()
AtomContainer
stereoElements
in interface IAtomContainer
stereoElements
in class AtomContainer
Iterable
of IStereoElement
s.IAtomContainer.addStereoElement(IStereoElement)
public void setAtoms(IAtom[] atoms)
AtomContainer
setAtoms
in interface IAtomContainer
setAtoms
in class AtomContainer
atoms
- The array of atoms to be assigned to this AtomContainerAtomContainer.getAtom(int)
public void setAtom(int number, IAtom atom)
AtomContainer
number
in [0,..].setAtom
in interface IAtomContainer
setAtom
in class AtomContainer
number
- The position of the atom to be set.atom
- The atom to be stored at position number
AtomContainer.getAtom(int)
public IAtom getAtom(int number)
AtomContainer
number
in [0,..].getAtom
in interface IAtomContainer
getAtom
in class AtomContainer
number
- The position of the atom to be retrieved.AtomContainer.setAtom(int, org.openscience.cdk.interfaces.IAtom)
,
AtomContainer.setAtoms(org.openscience.cdk.interfaces.IAtom[])
public IBond getBond(int number)
AtomContainer
number
in [0,..].getBond
in interface IAtomContainer
getBond
in class AtomContainer
number
- The position of the bond to be retrieved.public ILonePair getLonePair(int number)
AtomContainer
number
in [0,..].getLonePair
in interface IAtomContainer
getLonePair
in class AtomContainer
number
- The position of the LonePair to be retrieved.public ISingleElectron getSingleElectron(int number)
AtomContainer
number
in [0,..].getSingleElectron
in interface IAtomContainer
getSingleElectron
in class AtomContainer
number
- The position of the SingleElectron to be retrieved.public Iterable<IAtom> atoms()
AtomContainer
atoms
in interface IAtomContainer
atoms
in class AtomContainer
public Iterable<IBond> bonds()
AtomContainer
bonds
in interface IAtomContainer
bonds
in class AtomContainer
public Iterable<ILonePair> lonePairs()
AtomContainer
lonePairs
in interface IAtomContainer
lonePairs
in class AtomContainer
public Iterable<ISingleElectron> singleElectrons()
AtomContainer
singleElectrons
in interface IAtomContainer
singleElectrons
in class AtomContainer
public Iterable<IElectronContainer> electronContainers()
AtomContainer
electronContainers
in interface IAtomContainer
electronContainers
in class AtomContainer
public IAtom getFirstAtom()
AtomContainer
getFirstAtom
in interface IAtomContainer
getFirstAtom
in class AtomContainer
public IAtom getLastAtom()
AtomContainer
getLastAtom
in interface IAtomContainer
getLastAtom
in class AtomContainer
public int getAtomNumber(IAtom atom)
AtomContainer
getAtomNumber
in interface IAtomContainer
getAtomNumber
in class AtomContainer
atom
- The atom to be soughtpublic int getBondNumber(IAtom atom1, IAtom atom2)
AtomContainer
getBondNumber
in interface IAtomContainer
getBondNumber
in class AtomContainer
atom1
- The first atomatom2
- The second atompublic int getBondNumber(IBond bond)
AtomContainer
getBondNumber
in interface IAtomContainer
getBondNumber
in class AtomContainer
bond
- The bond to be soughtpublic int getLonePairNumber(ILonePair lp)
AtomContainer
getLonePairNumber
in interface IAtomContainer
getLonePairNumber
in class AtomContainer
lp
- The lone pair to be soughtpublic int getSingleElectronNumber(ISingleElectron se)
AtomContainer
getSingleElectronNumber
in interface IAtomContainer
getSingleElectronNumber
in class AtomContainer
se
- The single electron to be soughtpublic IElectronContainer getElectronContainer(int number)
AtomContainer
number
in the
container.getElectronContainer
in interface IAtomContainer
getElectronContainer
in class AtomContainer
number
- The position of the ElectronContainer to be returned.number
.IAtomContainer.addElectronContainer(IElectronContainer)
public IBond getBond(IAtom atom1, IAtom atom2)
AtomContainer
getBond
in interface IAtomContainer
getBond
in class AtomContainer
atom1
- The first atomatom2
- The second atompublic int getAtomCount()
AtomContainer
getAtomCount
in interface IAtomContainer
getAtomCount
in class AtomContainer
public int getBondCount()
AtomContainer
getBondCount
in interface IAtomContainer
getBondCount
in class AtomContainer
public int getLonePairCount()
AtomContainer
getLonePairCount
in interface IAtomContainer
getLonePairCount
in class AtomContainer
public int getSingleElectronCount()
AtomContainer
getSingleElectronCount
in interface IAtomContainer
getSingleElectronCount
in class AtomContainer
public int getElectronContainerCount()
AtomContainer
getElectronContainerCount
in interface IAtomContainer
getElectronContainerCount
in class AtomContainer
public List getConnectedAtomsList(IAtom atom)
AtomContainer
getConnectedAtomsList
in interface IAtomContainer
getConnectedAtomsList
in class AtomContainer
atom
- The atom the bond partners are searched of.public List getConnectedBondsList(IAtom atom)
AtomContainer
getConnectedBondsList
in interface IAtomContainer
getConnectedBondsList
in class AtomContainer
atom
- The atom the connected bonds are searched ofpublic List getConnectedLonePairsList(IAtom atom)
AtomContainer
getConnectedLonePairsList
in interface IAtomContainer
getConnectedLonePairsList
in class AtomContainer
atom
- The atom for which to get lone pairsAtomContainer.getElectronContainer(int)
,
AtomContainer.electronContainers()
,
AtomContainer.getBond(int)
public List getConnectedSingleElectronsList(IAtom atom)
AtomContainer
getConnectedSingleElectronsList
in interface IAtomContainer
getConnectedSingleElectronsList
in class AtomContainer
atom
- The atom on which the single electron is locatedpublic List getConnectedElectronContainersList(IAtom atom)
AtomContainer
getConnectedElectronContainersList
in interface IAtomContainer
getConnectedElectronContainersList
in class AtomContainer
atom
- The atom the connected electronContainers are searched ofpublic int getConnectedAtomsCount(IAtom atom)
AtomContainer
getConnectedAtomsCount
in interface IAtomContainer
getConnectedAtomsCount
in class AtomContainer
atom
- The atom the number of bond partners are searched of.public int getConnectedBondsCount(IAtom atom)
AtomContainer
getConnectedBondsCount
in interface IAtomContainer
getConnectedBondsCount
in class AtomContainer
atom
- The atompublic int getConnectedLonePairsCount(IAtom atom)
AtomContainer
getConnectedLonePairsCount
in interface IAtomContainer
getConnectedLonePairsCount
in class AtomContainer
atom
- The atompublic int getConnectedSingleElectronsCount(IAtom atom)
AtomContainer
getConnectedSingleElectronsCount
in interface IAtomContainer
getConnectedSingleElectronsCount
in class AtomContainer
atom
- The atom on which the single electron is locatedpublic double getBondOrderSum(IAtom atom)
AtomContainer
getBondOrderSum
in interface IAtomContainer
getBondOrderSum
in class AtomContainer
atom
- The atompublic IBond.Order getMaximumBondOrder(IAtom atom)
AtomContainer
getMaximumBondOrder
in interface IAtomContainer
getMaximumBondOrder
in class AtomContainer
atom
- The atompublic IBond.Order getMinimumBondOrder(IAtom atom)
AtomContainer
getMinimumBondOrder
in interface IAtomContainer
getMinimumBondOrder
in class AtomContainer
atom
- The atompublic void add(IAtomContainer atomContainer)
AtomContainer
add
in interface IAtomContainer
add
in class AtomContainer
atomContainer
- The atomcontainer to be addedpublic void addAtom(IAtom atom)
AtomContainer
addAtom
in interface IAtomContainer
addAtom
in class AtomContainer
atom
- The atom to be added to this containerpublic void addBond(IBond bond)
AtomContainer
addBond
in interface IAtomContainer
addBond
in class AtomContainer
bond
- The bond to added to this containerpublic void addLonePair(ILonePair ec)
AtomContainer
addLonePair
in interface IAtomContainer
addLonePair
in class AtomContainer
ec
- The LonePair to added to this containerpublic void addSingleElectron(ISingleElectron ec)
AtomContainer
addSingleElectron
in interface IAtomContainer
addSingleElectron
in class AtomContainer
ec
- The SingleElectron to added to this containerpublic void addElectronContainer(IElectronContainer electronContainer)
AtomContainer
addElectronContainer
in interface IAtomContainer
addElectronContainer
in class AtomContainer
electronContainer
- The ElectronContainer to added to this containerpublic void remove(IAtomContainer atomContainer)
AtomContainer
remove
in interface IAtomContainer
remove
in class AtomContainer
atomContainer
- The atomcontainer to be removedpublic IElectronContainer removeElectronContainer(int position)
AtomContainer
removeElectronContainer
in interface IAtomContainer
removeElectronContainer
in class AtomContainer
position
- The position of the bond in the electronContainers arraypublic void removeElectronContainer(IElectronContainer electronContainer)
AtomContainer
removeElectronContainer
in interface IAtomContainer
removeElectronContainer
in class AtomContainer
electronContainer
- The electronContainer to be removedpublic void removeAtom(int position)
AtomContainer
removeAtom
in interface IAtomContainer
removeAtom
in class AtomContainer
position
- The position of the atom to be removed.public void removeAtom(IAtom atom)
AtomContainer
removeAtom
in interface IAtomContainer
removeAtom
in class AtomContainer
atom
- The atom to be removedpublic IBond removeBond(int pos)
AtomContainer
removeBond
in interface IAtomContainer
removeBond
in class AtomContainer
pos
- The position of the bond to be removed.public IBond removeBond(IAtom atom1, IAtom atom2)
AtomContainer
removeBond
in interface IAtomContainer
removeBond
in class AtomContainer
atom1
- The first atomatom2
- The second atompublic void removeBond(IBond bond)
AtomContainer
removeBond
in interface IAtomContainer
removeBond
in class AtomContainer
bond
- The bond to be removed.public ILonePair removeLonePair(int pos)
AtomContainer
removeLonePair
in interface IAtomContainer
removeLonePair
in class AtomContainer
pos
- The position of the LonePair to be removed.public void removeLonePair(ILonePair ec)
AtomContainer
removeLonePair
in interface IAtomContainer
removeLonePair
in class AtomContainer
ec
- The LonePair to be removed.public ISingleElectron removeSingleElectron(int pos)
AtomContainer
removeSingleElectron
in interface IAtomContainer
removeSingleElectron
in class AtomContainer
pos
- The position of the SingleElectron to be removed.public void removeSingleElectron(ISingleElectron ec)
AtomContainer
removeSingleElectron
in interface IAtomContainer
removeSingleElectron
in class AtomContainer
ec
- The SingleElectron to be removed.public void removeAtomAndConnectedElectronContainers(IAtom atom)
AtomContainer
removeAtomAndConnectedElectronContainers
in interface IAtomContainer
removeAtomAndConnectedElectronContainers
in class AtomContainer
atom
- The atom to be removedpublic void removeAllElements()
IAtomContainer
removeAllElements
in interface IAtomContainer
removeAllElements
in class AtomContainer
public void removeAllElectronContainers()
AtomContainer
removeAllElectronContainers
in interface IAtomContainer
removeAllElectronContainers
in class AtomContainer
public void removeAllBonds()
AtomContainer
removeAllBonds
in interface IAtomContainer
removeAllBonds
in class AtomContainer
public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo)
AtomContainer
addBond
in interface IAtomContainer
addBond
in class AtomContainer
atom1
- Id of the first atom of the Bond in [0,..]atom2
- Id of the second atom of the Bond in [0,..]order
- Bondorderstereo
- Stereochemical orientationpublic void addBond(int atom1, int atom2, IBond.Order order)
AtomContainer
addBond
in interface IAtomContainer
addBond
in class AtomContainer
atom1
- Id of the first atom of the Bond in [0,..]atom2
- Id of the second atom of the Bond in [0,..]order
- Bondorderpublic void addLonePair(int atomID)
AtomContainer
addLonePair
in interface IAtomContainer
addLonePair
in class AtomContainer
atomID
- The atom number to which the LonePair is added in [0,..]public void addSingleElectron(int atomID)
AtomContainer
addSingleElectron
in interface IAtomContainer
addSingleElectron
in class AtomContainer
atomID
- The atom number to which the LonePair is added in [0,..]public boolean contains(IAtom atom)
AtomContainer
contains
in interface IAtomContainer
contains
in class AtomContainer
atom
- the atom this AtomContainer is searched forpublic boolean contains(IBond bond)
AtomContainer
contains
in interface IAtomContainer
contains
in class AtomContainer
bond
- the bond this AtomContainer is searched forpublic boolean contains(ILonePair ec)
AtomContainer
contains
in interface IAtomContainer
contains
in class AtomContainer
ec
- the LonePair this AtomContainer is searched forpublic boolean contains(ISingleElectron ec)
AtomContainer
contains
in interface IAtomContainer
contains
in class AtomContainer
ec
- the LonePair this AtomContainer is searched forpublic boolean contains(IElectronContainer electronContainer)
AtomContainer
contains
in interface IAtomContainer
contains
in class AtomContainer
electronContainer
- ElectronContainer that is searched forpublic void addListener(IChemObjectListener col)
ChemObject
addListener
in interface IChemObject
addListener
in class ChemObject
col
- the ChemObjectListenerChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)
public int getListenerCount()
ChemObject
getListenerCount
in interface IChemObject
getListenerCount
in class ChemObject
public void removeListener(IChemObjectListener col)
ChemObject
removeListener
in interface IChemObject
removeListener
in class ChemObject
col
- The ChemObjectListener to be removedChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)
public void notifyChanged()
ChemObject
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
public void notifyChanged(IChemObjectChangeEvent evt)
ChemObject
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
evt
- A ChemObjectChangeEvent pointing to the source of where
the change happendpublic void setProperty(Object description, Object property)
ChemObject
setProperty
in interface IChemObject
setProperty
in class ChemObject
description
- An object description of the property (most likely a
unique string)property
- An object with the property itselfChemObject.getProperty(java.lang.Object)
,
ChemObject.removeProperty(java.lang.Object)
public void removeProperty(Object description)
ChemObject
removeProperty
in interface IChemObject
removeProperty
in class ChemObject
description
- The object description of the property (most likely a
unique string)ChemObject.setProperty(java.lang.Object, java.lang.Object)
,
ChemObject.getProperty(java.lang.Object)
public Object getProperty(Object description)
ChemObject
getProperty
in interface IChemObject
getProperty
in class ChemObject
description
- An object description of the property (most likely a
unique string)ChemObject.setProperty(java.lang.Object, java.lang.Object)
,
ChemObject.removeProperty(java.lang.Object)
public Map<Object,Object> getProperties()
ChemObject
getProperties
in interface IChemObject
getProperties
in class ChemObject
ChemObject.setProperties(java.util.Map<java.lang.Object, java.lang.Object>)
public String getID()
ChemObject
getID
in interface IChemObject
getID
in class ChemObject
ChemObject.setID(java.lang.String)
public void setID(String identifier)
ChemObject
setID
in interface IChemObject
setID
in class ChemObject
identifier
- a String representing the ID valueChemObject.getID()
public void setFlag(int flag_type, boolean flag_value)
ChemObject
setFlag
in interface IChemObject
setFlag
in class ChemObject
flag_type
- Flag to setflag_value
- Value to assign to flagChemObject.getFlag(int)
public boolean getFlag(int flag_type)
ChemObject
getFlag
in interface IChemObject
getFlag
in class ChemObject
flag_type
- Flag to retrieve the value offlag_type
is setChemObject.setFlag(int, boolean)
public void setProperties(Map<Object,Object> properties)
ChemObject
setProperties
in interface IChemObject
setProperties
in class ChemObject
properties
- a Hashtable specifying the property valuesChemObject.getProperties()
public void setFlags(boolean[] flagsNew)
ChemObject
setFlags
in interface IChemObject
setFlags
in class ChemObject
flagsNew
- the new flags.ChemObject.getFlags()
public boolean[] getFlags()
ChemObject
getFlags
in interface IChemObject
getFlags
in class ChemObject
ChemObject.setFlags(boolean[])
public IAtomContainer clone() throws CloneNotSupportedException
AtomContainer
clone
in interface IAtomContainer
clone
in interface IChemObject
clone
in class AtomContainer
CloneNotSupportedException
- if the IChemObject cannot be clonedChemObject.shallowCopy()
public IChemObjectBuilder getBuilder()
ICDKObject
IChemObjectBuilder
for the data classes that extend
this class.getBuilder
in interface ICDKObject
getBuilder
in class ChemObject
IChemObjectBuilder
matching this ICDKObject
@TestMethod(value="testIsEmpty") public boolean isEmpty()
IAtomContainer
isEmpty
in interface IAtomContainer
isEmpty
in class AtomContainer