public class DebugBond extends Bond implements IBond
IBond.Order, IBond.Stereo
Constructor and Description |
---|
DebugBond() |
DebugBond(IAtom[] atoms) |
DebugBond(IAtom[] atoms,
IBond.Order order) |
DebugBond(IAtom atom1,
IAtom atom2) |
DebugBond(IAtom atom1,
IAtom atom2,
IBond.Order order) |
DebugBond(IAtom atom1,
IAtom atom2,
IBond.Order order,
IBond.Stereo stereo) |
Modifier and Type | Method and Description |
---|---|
void |
addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
Iterable<IAtom> |
atoms()
Returns the Iterator to atoms making up this bond.
|
Object |
clone()
Clones this bond object, including clones of the atoms between which the
bond is defined.
|
boolean |
compare(Object object)
Compares a bond with this bond.
|
boolean |
contains(IAtom atom)
Returns true if the given atom participates in this bond.
|
javax.vecmath.Point2d |
get2DCenter()
Returns the geometric 2D center of the bond.
|
javax.vecmath.Point3d |
get3DCenter()
Returns the geometric 3D center of the bond.
|
IAtom |
getAtom(int position)
Returns an Atom from this bond.
|
int |
getAtomCount()
Returns the number of Atoms in this Bond.
|
IChemObjectBuilder |
getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
IAtom |
getConnectedAtom(IAtom atom)
Returns the atom connected to the given atom.
|
Integer |
getElectronCount()
Returns the number of electrons in this electron 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.
|
int |
getListenerCount()
Returns the number of ChemObjectListeners registered with this object.
|
IBond.Order |
getOrder()
Returns the bond order of this bond.
|
Map<Object,Object> |
getProperties()
Returns a Map with the IChemObject's properties.
|
Object |
getProperty(Object description)
Returns a property for the IChemObject.
|
IBond.Stereo |
getStereo()
Returns the stereo descriptor for this bond.
|
boolean |
isConnectedTo(IBond bond)
Checks whether a bond is connected to another one.
|
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 |
removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
removeProperty(Object description)
Removes a property for a IChemObject.
|
void |
setAtom(IAtom atom,
int position)
Sets an Atom in this bond.
|
void |
setAtoms(IAtom[] atoms)
Sets the array of atoms making up this bond.
|
void |
setElectronCount(Integer electronCount)
Sets the number of electrons in this electron container.
|
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 |
setOrder(IBond.Order order)
Sets the bond order of this bond.
|
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 |
setStereo(IBond.Stereo stereo)
Sets the stereo descriptor for this bond.
|
getConnectedAtoms, toString
getNotification, setNotification, shallowCopy
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
getConnectedAtoms
getNotification, setNotification, toString
public DebugBond()
public DebugBond(IAtom atom1, IAtom atom2, IBond.Order order)
public DebugBond(IAtom atom1, IAtom atom2, IBond.Order order, IBond.Stereo stereo)
public DebugBond(IAtom[] atoms)
public DebugBond(IAtom[] atoms, IBond.Order order)
public Integer getElectronCount()
ElectronContainer
getElectronCount
in interface IElectronContainer
getElectronCount
in class ElectronContainer
ElectronContainer.setElectronCount(java.lang.Integer)
public void setElectronCount(Integer electronCount)
ElectronContainer
setElectronCount
in interface IElectronContainer
setElectronCount
in class ElectronContainer
electronCount
- The number of electrons in this electron container.ElectronContainer.getElectronCount()
public 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 Object clone() throws CloneNotSupportedException
Bond
clone
in interface IChemObject
clone
in class Bond
CloneNotSupportedException
- if the IChemObject cannot be clonedpublic IChemObjectBuilder getBuilder()
ICDKObject
IChemObjectBuilder
for the data classes that extend
this class.getBuilder
in interface ICDKObject
getBuilder
in class ChemObject
IChemObjectBuilder
matching this ICDKObject
public Iterable<IAtom> atoms()
Bond
atoms
in interface IBond
atoms
in class Bond
Bond.setAtoms(org.openscience.cdk.interfaces.IAtom[])
public void setAtoms(IAtom[] atoms)
Bond
setAtoms
in interface IBond
setAtoms
in class Bond
atoms
- An array of atoms that forms this bondBond.atoms
public int getAtomCount()
Bond
getAtomCount
in interface IBond
getAtomCount
in class Bond
public IAtom getAtom(int position)
Bond
getAtom
in interface IBond
getAtom
in class Bond
position
- The position in this bond where the atom isBond.setAtom(org.openscience.cdk.interfaces.IAtom, int)
public IAtom getConnectedAtom(IAtom atom)
Bond
Bond.getConnectedAtoms(org.openscience.cdk.interfaces.IAtom)
getConnectedAtom
in interface IBond
getConnectedAtom
in class Bond
atom
- The atom the bond partner is searched ofBond.getConnectedAtoms(org.openscience.cdk.interfaces.IAtom)
public boolean contains(IAtom atom)
Bond
public void setAtom(IAtom atom, int position)
Bond
setAtom
in interface IBond
setAtom
in class Bond
atom
- The atom to be setposition
- The position in this bond where the atom is to be insertedBond.getAtom(int)
public IBond.Order getOrder()
Bond
getOrder
in interface IBond
getOrder
in class Bond
org.openscience.cdk.CDKConstants
for predefined values.
,
Bond.setOrder(org.openscience.cdk.interfaces.IBond.Order)
public void setOrder(IBond.Order order)
Bond
setOrder
in interface IBond
setOrder
in class Bond
order
- The bond order to be assigned to this bondorg.openscience.cdk.CDKConstants for predefined values.
,
Bond.getOrder()
public IBond.Stereo getStereo()
Bond
getStereo
in interface IBond
getStereo
in class Bond
Bond.setStereo(org.openscience.cdk.interfaces.IBond.Stereo)
,
for predefined values.
public void setStereo(IBond.Stereo stereo)
Bond
setStereo
in interface IBond
setStereo
in class Bond
stereo
- The stereo descriptor to be assigned to this bond.Bond.getStereo()
,
for predefined values.
public javax.vecmath.Point2d get2DCenter()
Bond
get2DCenter
in interface IBond
get2DCenter
in class Bond
public javax.vecmath.Point3d get3DCenter()
Bond
get3DCenter
in interface IBond
get3DCenter
in class Bond
public boolean compare(Object object)
Bond
public boolean isConnectedTo(IBond bond)
Bond
isConnectedTo
in interface IBond
isConnectedTo
in class Bond
bond
- The bond which is checked to be connect with this one