Package org.openscience.cdk.debug

Class DebugBond

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.ElectronContainer

org.openscience.cdk.Bond

org.openscience.cdk.debug.DebugBond

All Implemented Interfaces:

Serializable, Cloneable, IBond, ICDKObject, IChemObject, IElectronContainer

public class DebugBond
extends Bond
implements IBond

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Nested Class Summary

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

IBond.Display, IBond.Order, IBond.Stereo

Field Summary

Fields inherited from class org.openscience.cdk.Bond

atomCount, atoms, display, order

Fields inherited from class org.openscience.cdk.ElectronContainer

electronCount

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	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)

Method Summary

Modifier and Type	Method	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.

Methods inherited from class org.openscience.cdk.Bond

equals, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getIndex, hashCode, isAromatic, isInRing, setDisplay, setIsAromatic, setIsInRing, toString

Methods inherited from class org.openscience.cdk.ChemObject

clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, shallowCopy

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

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

getConnectedAtom, getConnectedAtom, getConnectedAtoms, getContainer, getDisplay, getIndex, isAromatic, isInRing, setDisplay, setIsAromatic, setIsInRing

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

clear, flags, getFlagValue, getNotification, getProperty, is, set, setNotification, setProperties, toString

Constructor Details

DebugBond

public DebugBond()

DebugBond

public DebugBond(IAtom atom1,
 IAtom atom2)

DebugBond

public DebugBond(IAtom atom1,
 IAtom atom2,
 IBond.Order order)

DebugBond

public DebugBond(IAtom atom1,
 IAtom atom2,
 IBond.Order order,
 IBond.Stereo stereo)

DebugBond

public DebugBond(IAtom[] atoms)

DebugBond

public DebugBond(IAtom[] atoms,
 IBond.Order order)

Method Details

getElectronCount

public Integer getElectronCount()

Returns the number of electrons in this electron container.

Specified by:

getElectronCount in interface IElectronContainer

Overrides:

getElectronCount in class ElectronContainer

Returns:

The number of electrons in this electron container.

See Also:

• ElectronContainer.setElectronCount(java.lang.Integer)

setElectronCount

public void setElectronCount(Integer electronCount)

Sets the number of electrons in this electron container.

Specified by:

setElectronCount in interface IElectronContainer

Overrides:

setElectronCount in class ElectronContainer

Parameters:

electronCount - The number of electrons in this electron container.

See Also:

• ElectronContainer.getElectronCount()

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

Overrides:

addListener in class ChemObject

Parameters:

col - the ChemObjectListener

See Also:

• ChemObject.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

Overrides:

getListenerCount in class ChemObject

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

Overrides:

removeListener in class ChemObject

Parameters:

col - The ChemObjectListener to be removed

See Also:

• ChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)

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

Overrides:

notifyChanged in class ChemObject

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

Overrides:

notifyChanged in class ChemObject

Parameters:

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

setProperty

public void setProperty(Object description,
 Object property)

Sets a property for a IChemObject.

Specified by:

setProperty in interface IChemObject

Overrides:

setProperty in class ChemObject

Parameters:

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

property - An object with the property itself

See Also:

• ChemObject.getProperty(java.lang.Object)
• ChemObject.removeProperty(java.lang.Object)

removeProperty

public void removeProperty(Object description)

Removes a property for a IChemObject.

Specified by:

removeProperty in interface IChemObject

Overrides:

removeProperty in class ChemObject

Parameters:

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

See Also:

• ChemObject.setProperty(java.lang.Object, java.lang.Object)
• ChemObject.getProperty(java.lang.Object)

getProperty

public <T> T getProperty(Object description)

Returns a property for the IChemObject.

Specified by:

getProperty in interface IChemObject

Overrides:

getProperty in class ChemObject

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 propert is not set.

See Also:

• ChemObject.setProperty(java.lang.Object, java.lang.Object)
• ChemObject.removeProperty(java.lang.Object)

getProperties

public Map<Object,Object> getProperties()

Returns a Map with the IChemObject's properties.

Specified by:

getProperties in interface IChemObject

Overrides:

getProperties in class ChemObject

Returns:

The object's properties as an Hashtable

See Also:

• ChemObject.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

Overrides:

getID in class ChemObject

Returns:

a String representing the ID value

See Also:

• ChemObject.setID(java.lang.String)

setID

public void setID(String identifier)

Sets the identifier (ID) of this object.

Specified by:

setID in interface IChemObject

Overrides:

setID in class ChemObject

Parameters:

identifier - a String representing the ID value

See Also:

• ChemObject.getID()

setFlag

public void setFlag(int flagType,
 boolean flagValue)

Sets the value of some flag. The flag is a mask from a given CDKConstant (e.g. IChemObject.AROMATIC or IChemObject.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

Overrides:

setFlag in class ChemObject

Parameters:

flagType - flag to set the value for

flagValue - value to assign to flag

See Also:

• IChemObject.getFlag(int)

getFlag

public boolean getFlag(int flagType)

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

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

Specified by:

getFlag in interface IChemObject

Overrides:

getFlag in class ChemObject

Parameters:

flagType - flag to retrieve the value of

Returns:

true if the flag flag_type is set

See Also:

• IChemObject.setFlag(int, boolean)

addProperties

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

Sets the properties of this object.

Specified by:

addProperties in interface IChemObject

Overrides:

addProperties in class ChemObject

Parameters:

properties - a Hashtable specifying the property values

See Also:

• ChemObject.getProperties()

setFlags

public void setFlags(boolean[] flagsNew)

Sets the whole set of flags.

Specified by:

setFlags in interface IChemObject

Overrides:

setFlags in class ChemObject

Parameters:

flagsNew - the new flags.

See Also:

• ChemObject.getFlags()

getFlags

public boolean[] getFlags()

Returns the whole set of flags.

Specified by:

getFlags in interface IChemObject

Overrides:

getFlags in class ChemObject

Returns:

the flags.

See Also:

• ChemObject.setFlags(boolean[])

clone

public IBond clone()
            throws CloneNotSupportedException

Clones this bond object, including clones of the atoms between which the bond is defined.

Specified by:

clone in interface IBond

Specified by:

clone in interface IChemObject

Overrides:

clone in class Bond

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

getBuilder

public IChemObjectBuilder getBuilder()

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

Specified by:

getBuilder in interface ICDKObject

Overrides:

getBuilder in class ChemObject

Returns:

The IChemObjectBuilder matching this ICDKObject

atoms

public Iterable<IAtom> atoms()

Returns the Iterator to atoms making up this bond. Iterator.remove() is not implemented.

Specified by:

atoms in interface IBond

Overrides:

atoms in class Bond

Returns:

An Iterator to atoms participating in this bond

See Also:

• Bond.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

Overrides:

setAtoms in class Bond

Parameters:

atoms - An array of atoms that forms this bond

See Also:

• Bond.atoms

getAtomCount

public int getAtomCount()

Returns the number of Atoms in this Bond.

Specified by:

getAtomCount in interface IBond

Overrides:

getAtomCount in class Bond

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

Overrides:

getAtom in class Bond

Parameters:

position - The position in this bond where the atom is

Returns:

The atom at the specified position, null if there are no atoms in the bond

See Also:

• Bond.setAtom(org.openscience.cdk.interfaces.IAtom, int)

getBegin

public IAtom getBegin()

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

Specified by:

getBegin in interface IBond

Overrides:

getBegin in class Bond

Returns:

the begin atom

getEnd

public IAtom getEnd()

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

Specified by:

getEnd in interface IBond

Overrides:

getEnd in class Bond

Returns:

the end atom

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

Overrides:

getOther in class Bond

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

contains

public boolean contains(IAtom atom)

Returns true if the given atom participates in this bond.

Specified by:

contains in interface IBond

Overrides:

contains in class Bond

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

Overrides:

setAtom in class Bond

Parameters:

atom - The atom to be set

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

See Also:

• Bond.getAtom(int)

getOrder

public IBond.Order getOrder()

Returns the bond order of this bond.

Specified by:

getOrder in interface IBond

Overrides:

getOrder in class Bond

Returns:

The bond order of this bond

See Also:

• org.openscience.cdk.CDKConstants for predefined values.
• Bond.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

Overrides:

setOrder in class Bond

Parameters:

order - The bond order to be assigned to this bond

See Also:

• org.openscience.cdk.CDKConstants for predefined values.
• Bond.getOrder()

getStereo

public IBond.Stereo getStereo()

Returns the stereo descriptor for this bond.

Specified by:

getStereo in interface IBond

Overrides:

getStereo in class Bond

Returns:

The stereo descriptor for this bond

See Also:

• Bond.setStereo(org.openscience.cdk.interfaces.IBond.Stereo)
• for predefined values.

setStereo

public void setStereo(IBond.Stereo stereo)

Sets the stereo descriptor for this bond.

Specified by:

setStereo in interface IBond

Overrides:

setStereo in class Bond

Parameters:

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

See Also:

• Bond.getStereo()
• for predefined values.

get2DCenter

public javax.vecmath.Point2d get2DCenter()

Returns the geometric 2D center of the bond.

Specified by:

get2DCenter in interface IBond

Overrides:

get2DCenter in class Bond

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

Overrides:

get3DCenter in class Bond

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

Overrides:

compare in class Bond

Parameters:

object - Object of type Bond

Returns:

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

Overrides:

isConnectedTo in class Bond

Parameters:

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

Returns:

true if the bonds share an atom, otherwise false