org.openscience.cdk

Class BondRef

java.lang.Object

org.openscience.cdk.BondRef

All Implemented Interfaces:

Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer

public class BondRef
extends Object
implements IBond

A bond ref, references a CDK IBond indirectly. All methods are passed through to the referenced bond. The reference can be used to override the behaviour of the base bond.

Author:

John Mayfield

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IBond

IBond.Display, IBond.Order, IBond.Stereo

Constructor Summary

Constructors

Constructor and Description
BondRef(IBond bond) Create a pointer for the provided bond.

Method Summary

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) Add properties to this object, duplicate keys will replace any existing value.
Iterable<IAtom>	atoms() Returns the Iterable to atoms making up this bond.
IBond	clone() Returns a deep clone of this IChemObject.
boolean	compare(Object object) Compares a bond with this bond.
boolean	contains(IAtom atom) Returns true if the given atom participates in this bond.
IBond	deref() Dereference the bond pointer once providing access to the base bond.
static IBond	deref(IBond bond) Utility method to dereference an bond pointer.
boolean	equals(Object obj)
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.
IAtom	getConnectedAtom(IAtom atom) Returns the other atom in the bond, the atom is connected to the given atom.
IAtom[]	getConnectedAtoms(IAtom atom) Returns all the atoms in the bond connected to the given atom.
IAtomContainer	getContainer()
IBond.Display	getDisplay() Access the bond display style.
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 mask) Returns the value of a given flag.
boolean[]	getFlags() Returns the whole set of flags.
Number	getFlagValue() Access the internal value used to store the flags.
String	getID() Returns the identifier (ID) of this object.
int	getIndex()
int	getListenerCount() Returns the number of ChemObjectListeners registered with this object.
boolean	getNotification() Returns the flag that indicates whether notification messages are sent around.
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 - the object is automatically cast to the required type.
<T> T	getProperty(Object description, Class<T> c) Access a property of the given description and cast the specified class.
IBond.Stereo	getStereo() Returns the stereo descriptor for this bond.
int	hashCode()
boolean	isAromatic() Access whether this bond has been marked as aromatic.
boolean	isConnectedTo(IBond bond) Checks whether a bond is connected to another one.
boolean	isInRing() Access whether this bond has been flagged as in a ring.
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	setDisplay(IBond.Display display) Set the bond display style.
void	setElectronCount(Integer count) Sets the number of electrons in this electron container.
void	setFlag(int mask, boolean value) Sets the value of some flag.
void	setFlags(boolean[] newFlags) Sets the whole set of flags.
void	setID(String identifier) Sets the identifier (ID) of this object.
void	setIsAromatic(boolean arom) Mark this bond as being aromatic.
void	setIsInRing(boolean ring) Mark this bond as being in a ring.
void	setNotification(boolean bool) Set a flag to use or not use notification.
void	setOrder(IBond.Order order) Sets the bond order of this bond.
void	setProperties(Map<Object,Object> properties) Set the properties of this object to the provided map (shallow copy).
void	setProperty(Object description, Object property) Sets a property for a IChemObject.
void	setStereo(IBond.Stereo stereo) Sets the stereo descriptor for this bond.
String	toString() Returns a one line description of this IChemObject.

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, 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

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

getBuilder

Constructor Detail

BondRef

public BondRef(IBond bond)

Create a pointer for the provided bond.

Parameters:

bond - the bond to reference

Method Detail

deref

public static IBond deref(IBond bond)

Utility method to dereference an bond pointer. If the bond is not an BondRef it simply returns the input.

Parameters:

bond - the bond

Returns:

non-pointer bond

deref

public IBond deref()

Dereference the bond pointer once providing access to the base bond.

Returns:

the bond pointed to

getElectronCount

public Integer getElectronCount()

Returns the number of electrons in this electron container.

Specified by:

getElectronCount in interface IElectronContainer

Returns:

The number of electrons in this electron container.

See Also:

IElectronContainer.setElectronCount(java.lang.Integer)

setElectronCount

public void setElectronCount(Integer count)

Sets the number of electrons in this electron container.

Specified by:

setElectronCount in interface IElectronContainer

Parameters:

count - The number of electrons in this electron container.

See Also:

IElectronContainer.getElectronCount()

atoms

public Iterable<IAtom> atoms()

Returns the Iterable to atoms making up this bond.

Specified by:

atoms in interface IBond

Returns:

An Iterable to atoms participating in this bond

See Also:

IBond.setAtoms(org.openscience.cdk.interfaces.IAtom[])

setAtoms

public void setAtoms(IAtom[] atoms)

Sets the array of atoms making up this bond.

Specified by:

setAtoms in interface IBond

Parameters:

atoms - An array of atoms that forms this bond

See Also:

IBond.atoms()

getBegin

public IAtom getBegin()

Access the begin (or first) atom of the bond.

Specified by:

getBegin in interface IBond

Returns:

the begin atom

getEnd

public IAtom getEnd()

Access the end (or second) atom of the bond.

Specified by:

getEnd in interface IBond

Returns:

the end atom

getIndex

public int getIndex()

Specified by:

getIndex in interface IBond

getContainer

public IAtomContainer getContainer()

Specified by:

getContainer in interface IBond

getAtomCount

public int getAtomCount()

Returns the number of Atoms in this Bond.

Specified by:

getAtomCount in interface IBond

Returns:

The number of Atoms in this Bond

getAtom

public IAtom getAtom(int position)

Returns an Atom from this bond.

Specified by:

getAtom in interface IBond

Parameters:

position - The position in this bond where the atom is

Returns:

The atom at the specified position

See Also:

IBond.setAtom(org.openscience.cdk.interfaces.IAtom, int)

getConnectedAtom

public IAtom getConnectedAtom(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.

 IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getConnectedAtom(beg) == end
 // bond.getConnectedAtom(end) == beg
 

Specified by:

getConnectedAtom in interface IBond

Parameters:

atom - The atom the bond partner is searched of

Returns:

the connected atom or null if the given atom is not part of the bond

getOther

public 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.

 IAtom beg = bond.getBegin();
 IAtom end = bond.getEnd();
 // bond.getOther(beg) == end
 // bond.getOther(end) == beg
 

Specified by:

getOther in interface IBond

Parameters:

atom - The atom the bond partner is searched of

Returns:

the connected atom or null if the given atom is not part of the bond

getConnectedAtoms

public IAtom[] getConnectedAtoms(IAtom atom)

Returns all the atoms in the bond connected to the given atom.

Specified by:

getConnectedAtoms in interface IBond

Parameters:

atom - The atoms the bond partner is searched of

Returns:

the connected atoms or null if the given atom is not part of the bond

contains

public boolean contains(IAtom atom)

Returns true if the given atom participates in this bond.

Specified by:

contains in interface IBond

Parameters:

atom - The atom to be tested if it participates in this bond

Returns:

true if the atom participates in this bond

setAtom

public void setAtom(IAtom atom,
                    int position)

Sets an Atom in this bond.

Specified by:

setAtom in interface IBond

Parameters:

atom - The atom to be set

position - The position in this bond where the atom is to be inserted

See Also:

IBond.getAtom(int)

getOrder

public IBond.Order getOrder()

Returns the bond order of this bond.

Specified by:

getOrder in interface IBond

Returns:

The bond order of this bond

See Also:

org.openscience.cdk.CDKConstants for predefined values., IBond.setOrder(org.openscience.cdk.interfaces.IBond.Order)

setOrder

public void setOrder(IBond.Order order)

Sets the bond order of this bond.

Specified by:

setOrder in interface IBond

Parameters:

order - The bond order to be assigned to this bond

See Also:

for predefined values., IBond.getOrder()

getStereo

public IBond.Stereo getStereo()

Returns the stereo descriptor for this bond.

Specified by:

getStereo in interface IBond

Returns:

The stereo descriptor for this bond

See Also:

IBond.setStereo(org.openscience.cdk.interfaces.IBond.Stereo)

setStereo

public void setStereo(IBond.Stereo stereo)

Sets the stereo descriptor for this bond. Note this function will also modify the bond display style.

Specified by:

setStereo in interface IBond

Parameters:

stereo - The stereo descriptor to be assigned to this bond.

See Also:

IBond.getStereo(), IBond.setDisplay(Display)

getDisplay

public IBond.Display getDisplay()

Access the bond display style.

Specified by:

getDisplay in interface IBond

Returns:

the bond display

setDisplay

public void setDisplay(IBond.Display display)

Set the bond display style.

Specified by:

setDisplay in interface IBond

Parameters:

display - the display

get2DCenter

public javax.vecmath.Point2d get2DCenter()

Returns the geometric 2D center of the bond.

Specified by:

get2DCenter in interface IBond

Returns:

The geometric 2D center of the bond

get3DCenter

public javax.vecmath.Point3d get3DCenter()

Returns the geometric 3D center of the bond.

Specified by:

get3DCenter in interface IBond

Returns:

The geometric 3D center of the bond

compare

public boolean compare(Object object)

Compares a bond with this bond.

Specified by:

compare in interface IBond

Parameters:

object - Object of type Bond

Returns:

Return true, if the bond is equal to this bond

isConnectedTo

public boolean isConnectedTo(IBond bond)

Checks whether a bond is connected to another one. This can only be true if the bonds have an Atom in common.

Specified by:

isConnectedTo in interface IBond

Parameters:

bond - The bond which is checked to be connect with this one

Returns:

True, if the bonds share an atom, otherwise false

isAromatic

public boolean isAromatic()

Access whether this bond has been marked as aromatic. The default value is false and you must explicitly perceive aromaticity with one of the available models.

Specified by:

isAromatic in interface IBond

Returns:

aromatic status

See Also:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

public void setIsAromatic(boolean arom)

Mark this bond as being aromatic.

Specified by:

setIsAromatic in interface IBond

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

isInRing

public boolean isInRing()

Access whether this bond has been flagged as in a ring. The default value is false and you must explicitly find rings first.

Specified by:

isInRing in interface IBond

Returns:

ring status

See Also:

IChemObject.getFlag(int), RingSearch

setIsInRing

public void setIsInRing(boolean ring)

Mark this bond as being in a ring.

Specified by:

setIsInRing in interface IBond

Parameters:

ring - ring status

See Also:

IChemObject.setFlag(int, boolean)

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

clone

public IBond clone()
            throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IBond

Specified by:

clone in interface IChemObject

Returns:

Object the clone of this IChemObject.

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

toString

public String toString()

Description copied from interface: IChemObject

Returns a one line description of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

a String representation of this object

getBuilder

public IChemObjectBuilder getBuilder()

Returns a IChemObjectBuilder for the data classes that extend this class.

Specified by:

getBuilder in interface ICDKObject

Returns:

The IChemObjectBuilder matching this ICDKObject

addListener

public void addListener(IChemObjectListener col)

Use this to add yourself to this IChemObject as a listener. In order to do so, you must implement the ChemObjectListener Interface.

Specified by:

addListener in interface IChemObject

Parameters:

col - the ChemObjectListener

See Also:

IChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)

getListenerCount

public int getListenerCount()

Returns the number of ChemObjectListeners registered with this object.

Specified by:

getListenerCount in interface IChemObject

Returns:

the number of registered listeners.

removeListener

public void removeListener(IChemObjectListener col)

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject. It will then not be notified of change in this object anymore.

Specified by:

removeListener in interface IChemObject

Parameters:

col - The ChemObjectListener to be removed

See Also:

IChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)

setNotification

public void setNotification(boolean bool)

Set a flag to use or not use notification. By default it should be set to true.

Specified by:

setNotification in interface IChemObject

Parameters:

bool - if true, then notification messages are sent.

See Also:

IChemObject.getNotification()

getNotification

public boolean getNotification()

Returns the flag that indicates whether notification messages are sent around.

Specified by:

getNotification in interface IChemObject

Returns:

true if messages are sent.

See Also:

IChemObject.setNotification(boolean)

notifyChanged

public 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.

Specified by:

notifyChanged in interface IChemObject

notifyChanged

public 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. This is a version of notifyChanged() which allows to propagate a change event while preserving the original origin.

Specified by:

notifyChanged in interface IChemObject

Parameters:

evt - A ChemObjectChangeEvent pointing to the source of where the change happend

setProperty

public void setProperty(Object description,
                        Object property)

Sets a property for a IChemObject.

Specified by:

setProperty in interface IChemObject

Parameters:

description - An object description of the property (most likely a unique string)

property - An object with the property itself

See Also:

IChemObject.getProperty(java.lang.Object), IChemObject.removeProperty(java.lang.Object)

removeProperty

public void removeProperty(Object description)

Removes a property for a IChemObject.

Specified by:

removeProperty in interface IChemObject

Parameters:

description - The object description of the property (most likely a unique string)

See Also:

IChemObject.setProperty(java.lang.Object, java.lang.Object), IChemObject.getProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description)

Returns a property for the IChemObject - the object is automatically cast to the required type. This does however mean if the wrong type is provided then a runtime ClassCastException will be thrown.

     IAtom atom = new Atom("C");
     atom.setProperty("number", 1); // set an integer property

     // access the property and automatically cast to an int
     Integer number = atom.getProperty("number");

     // if the method is in a chain or needs to be nested the type
     // can be provided
     methodAcceptingInt(atom.getProperty("number", Integer.class));

     // the type cannot be checked and so...
     String number = atom.getProperty("number"); // ClassCastException

     // if the type is provided a more meaningful error is thrown
     atom.getProperty("number", String.class); // IllegalArgumentException

 

Specified by:

getProperty in interface IChemObject

Type Parameters:

T - generic return type

Parameters:

description - An object description of the property (most likely a unique string)

Returns:

The object containing the property. Returns null if property is not set.

See Also:

IChemObject.setProperty(java.lang.Object, java.lang.Object), IChemObject.getProperty(Object, Class), IChemObject.removeProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description,
                         Class<T> c)

Access a property of the given description and cast the specified class.

     IAtom atom = new Atom("C");
     atom.setProperty("number", 1); // set an integer property

     // access the property and automatically cast to an int
     Integer number = atom.getProperty("number");

     // if the method is in a chain or needs to be nested the type
     // can be provided
     methodAcceptingInt(atom.getProperty("number", Integer.class));

     // the type cannot be checked and so...
     String number = atom.getProperty("number"); // ClassCastException

     // if the type is provided a more meaningful error is thrown
     atom.getProperty("number", String.class); // IllegalArgumentException

 

Specified by:

getProperty in interface IChemObject

Type Parameters:

T - generic type (of provided class)

Parameters:

description - description of a property (normally a string)

c - type of the value to be returned

Returns:

the value stored for the specified description.

See Also:

IChemObject.getProperty(Object), IChemObject.addProperties(java.util.Map)

getProperties

public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Specified by:

getProperties in interface IChemObject

Returns:

The object's properties as an Map

See Also:

IChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)

getID

public String getID()

Returns the identifier (ID) of this object.

Specified by:

getID in interface IChemObject

Returns:

a String representing the ID value

See Also:

IChemObject.setID(java.lang.String)

setID

public void setID(String identifier)

Sets the identifier (ID) of this object.

Specified by:

setID in interface IChemObject

Parameters:

identifier - a String representing the ID value

See Also:

IChemObject.getID()

setFlag

public void setFlag(int mask,
                    boolean value)

Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. 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);
 

Specified by:

setFlag in interface IChemObject

Parameters:

mask - flag to set the value for

value - value to assign to flag

See Also:

IChemObject.getFlag(int), CDKConstants

getFlag

public boolean getFlag(int mask)

Returns the value of a given flag. The flag is a mask from a given CDKConstant (e.g. CDKConstants.ISAROMATIC).

 if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
     // handle aromatic flag on this chem object
 }
 

Specified by:

getFlag in interface IChemObject

Parameters:

mask - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

IChemObject.setFlag(int, boolean), CDKConstants

setProperties

public void setProperties(Map<Object,Object> properties)

Set the properties of this object to the provided map (shallow copy). Any existing properties are removed.

Specified by:

setProperties in interface IChemObject

Parameters:

properties - map key-value pairs

addProperties

public void addProperties(Map<Object,Object> properties)

Add properties to this object, duplicate keys will replace any existing value.

Specified by:

addProperties in interface IChemObject

Parameters:

properties - a Map specifying the property values

See Also:

IChemObject.getProperties()

setFlags

public void setFlags(boolean[] newFlags)

Sets the whole set of flags. This set will iteratively invoke IChemObject.setFlag(int, boolean) for each value in the array and use CDKConstants.FLAG_MASKS to look up the correct mask. If only a single flag is being set it is a lot faster to use IChemObject.setFlag(int, boolean).

Specified by:

setFlags in interface IChemObject

Parameters:

newFlags - the new flags to set.

See Also:

IChemObject.setFlag(int, boolean), IChemObject.getFlags()

getFlags

public boolean[] getFlags()

Returns the whole set of flags. This method will create a new array on each invocation and it is recommend you use IChemObject.getFlagValue() if you need all the flags. For individual flags please use IChemObject.getFlag(int)

Specified by:

getFlags in interface IChemObject

Returns:

the flags.

See Also:

IChemObject.setFlags(boolean[]), IChemObject.getFlag(int), IChemObject.getFlagValue()

getFlagValue

public Number getFlagValue()

Access the internal value used to store the flags. The flags are stored on a single numeric value and are set/cleared.

Specified by:

getFlagValue in interface IChemObject

Returns:

numeric representation of the flags