public class DebugBond extends Bond implements IBond
IBond.Display, IBond.Order, IBond.Stereo
electronCount
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.
|
void |
addProperties(Map<Object,Object> properties)
Sets the properties of this object.
|
Iterable<IAtom> |
atoms()
Returns the Iterator to atoms making up this bond.
|
IBond |
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.
|
IAtom |
getBegin()
Access the begin (or first) atom of the bond.
|
IChemObjectBuilder |
getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
Integer |
getElectronCount()
Returns the number of electrons in this electron container.
|
IAtom |
getEnd()
Access the end (or second) atom of the bond.
|
boolean |
getFlag(int flagType)
Returns the value of a given 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.
|
IAtom |
getOther(IAtom atom)
Returns the other atom in the bond, the atom is connected to the given atom.This
method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined
and the more correct
IBond.getConnectedAtoms(IAtom) should be used. |
Map<Object,Object> |
getProperties()
Returns a Map with the IChemObject's properties.
|
<T> T |
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 flagType,
boolean flagValue)
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 |
setProperty(Object description,
Object property)
Sets a property for a IChemObject.
|
void |
setStereo(IBond.Stereo stereo)
Sets the stereo descriptor for this bond.
|
equals, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getIndex, hashCode, isAromatic, isInRing, setDisplay, setIsAromatic, setIsInRing, toString
getFlagValue, getNotification, getProperty, setNotification, setProperties, shallowCopy
finalize, getClass, notify, notifyAll, wait, wait, wait
getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getIndex, isAromatic, isInRing, setDisplay, setIsAromatic, setIsInRing
getFlagValue, getNotification, getProperty, setNotification, setProperties, 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()
getElectronCount
in interface IElectronContainer
getElectronCount
in class ElectronContainer
ElectronContainer.setElectronCount(java.lang.Integer)
public void setElectronCount(Integer electronCount)
setElectronCount
in interface IElectronContainer
setElectronCount
in class ElectronContainer
electronCount
- The number of electrons in this electron container.ElectronContainer.getElectronCount()
public void addListener(IChemObjectListener col)
addListener
in interface IChemObject
addListener
in class ChemObject
col
- the ChemObjectListenerChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)
public int getListenerCount()
getListenerCount
in interface IChemObject
getListenerCount
in class ChemObject
public void removeListener(IChemObjectListener col)
removeListener
in interface IChemObject
removeListener
in class ChemObject
col
- The ChemObjectListener to be removedChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)
public void notifyChanged()
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
public void notifyChanged(IChemObjectChangeEvent evt)
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
evt
- A ChemObjectChangeEvent pointing to the source of where
the change happenedpublic void setProperty(Object description, Object property)
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)
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 <T> T getProperty(Object description)
getProperty
in interface IChemObject
getProperty
in class ChemObject
T
- generic return typedescription
- 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()
getProperties
in interface IChemObject
getProperties
in class ChemObject
ChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)
public String getID()
getID
in interface IChemObject
getID
in class ChemObject
ChemObject.setID(java.lang.String)
public void setID(String identifier)
setID
in interface IChemObject
setID
in class ChemObject
identifier
- a String representing the ID valueChemObject.getID()
public void setFlag(int flagType, boolean flagValue)
CDKConstants.ISAROMATIC
or CDKConstants.VISITED
). The flags are
intrinsic internal properties and should not be used to store custom
values, please use IChemObject.setProperty(Object, Object)
.
// set this chem object to be aromatic
chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
// ...
// indicate we have visited this chem object
chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
setFlag
in interface IChemObject
setFlag
in class ChemObject
flagType
- flag to set the value forflagValue
- value to assign to flagIChemObject.getFlag(int)
,
CDKConstants
public boolean getFlag(int flagType)
CDKConstants.ISAROMATIC
).
if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
// handle aromatic flag on this chem object
}
getFlag
in interface IChemObject
getFlag
in class ChemObject
flagType
- flag to retrieve the value offlag_type
is setIChemObject.setFlag(int, boolean)
,
CDKConstants
public void addProperties(Map<Object,Object> properties)
addProperties
in interface IChemObject
addProperties
in class ChemObject
properties
- a Hashtable specifying the property valuesChemObject.getProperties()
public void setFlags(boolean[] flagsNew)
setFlags
in interface IChemObject
setFlags
in class ChemObject
flagsNew
- the new flags.ChemObject.getFlags()
public boolean[] getFlags()
getFlags
in interface IChemObject
getFlags
in class ChemObject
ChemObject.setFlags(boolean[])
public IBond clone() throws CloneNotSupportedException
clone
in interface IBond
clone
in interface IChemObject
clone
in class Bond
CloneNotSupportedException
- if the IChemObject cannot be clonedpublic IChemObjectBuilder getBuilder()
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()
atoms
in interface IBond
atoms
in class Bond
Bond.setAtoms(org.openscience.cdk.interfaces.IAtom[])
public void setAtoms(IAtom[] atoms)
setAtoms
in interface IBond
setAtoms
in class Bond
atoms
- An array of atoms that forms this bondBond.atoms
public int getAtomCount()
getAtomCount
in interface IBond
getAtomCount
in class Bond
public IAtom getAtom(int position)
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 getBegin()
public IAtom getEnd()
public IAtom getOther(IAtom atom)
IBond.getConnectedAtoms(IAtom)
should be used.
IAtom beg = bond.getBegin();
IAtom end = bond.getEnd();
// bond.getOther(beg) == end
// bond.getOther(end) == beg
public boolean contains(IAtom atom)
public void setAtom(IAtom atom, int position)
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()
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)
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()
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)
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()
get2DCenter
in interface IBond
get2DCenter
in class Bond
public javax.vecmath.Point3d get3DCenter()
get3DCenter
in interface IBond
get3DCenter
in class Bond
public boolean compare(Object object)
public boolean isConnectedTo(IBond bond)
isConnectedTo
in interface IBond
isConnectedTo
in class Bond
bond
- The bond which is checked to be connect with this oneCopyright © 2021. All rights reserved.