Package org.openscience.cdk

Class AtomRef

java.lang.Object

org.openscience.cdk.AtomRef

All Implemented Interfaces:

Cloneable, IAtom, IAtomType, ICDKObject, IChemObject, IElement, IIsotope

public class AtomRef
extends Object
implements IAtom

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

Author:

John Mayfield

Nested Class Summary

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

IAtomType.Hybridization

Field Summary

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

Ac, Ag, Al, Am, Ar, As, At, Au, B, Ba, Be, Bh, Bi, Bk, Br, C, Ca, Cd, Ce, Cf, Cl, Cm, Cn, Co, Cr, Cs, Cu, Db, Ds, Dy, Er, Es, Eu, F, Fe, Fl, Fm, Fr, Ga, Gd, Ge, H, He, Hf, Hg, Ho, Hs, I, In, Ir, K, Kr, La, Li, Lr, Lu, Lv, Mc, Md, Mg, Mn, Mo, Mt, N, Na, Nb, Nd, Ne, Nh, Ni, No, Np, O, Og, Os, P, Pa, Pb, Pd, Pm, Po, Pr, Pt, Pu, Ra, Rb, Re, Rf, Rg, Rh, Rn, Ru, S, Sb, Sc, Se, Sg, Si, Sm, Sn, Sr, Ta, Tb, Tc, Te, Th, Ti, Tl, Tm, Ts, U, V, W, Wildcard, Xe, Y, Yb, Zn, Zr

Constructor Summary

Constructors

Constructor	Description
AtomRef(IAtom atom)	Create a pointer for the provided atom.

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)	Add properties to this object, duplicate keys will replace any existing value.
Iterable<IBond>	bonds()	Returns the bonds connected to this atom.
IAtom	clone()	Returns a deep clone of this IChemObject.
IAtom	deref()	Dereference the atom pointer once providing access to the base atom.
static IAtom	deref(IAtom atom)	Utility method to dereference an atom.
boolean	equals(Object obj)
Integer	getAtomicNumber()	Returns the atomic number of this element.
String	getAtomTypeName()	Gets the id attribute of the AtomType object.
IBond	getBond(IAtom atom)	Returns the bond connecting 'this' atom to the provided atom.
int	getBondCount()	Get the number of explicit bonds connected to this atom.
Double	getBondOrderSum()	Gets the bondOrderSum attribute of the AtomType object.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
Double	getCharge()	Returns the partial charge of this atom.
IAtomContainer	getContainer()	Access the IAtomContainer of which this atom is a member of.
Double	getCovalentRadius()	Returns the covalent radius for this AtomType.
Double	getExactMass()	Gets the ExactMass attribute of the Isotope object.
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.
Integer	getFormalCharge()	Returns the formal charge of this atom.
Integer	getFormalNeighbourCount()	Returns the formal neighbour count of this atom.
javax.vecmath.Point3d	getFractionalPoint3d()	Returns a point specifying the location of this atom in a Crystal unit cell.
IAtomType.Hybridization	getHybridization()	Returns the hybridization of this atom.
String	getID()	Returns the identifier (ID) of this object.
Integer	getImplicitHydrogenCount()	Returns the implicit hydrogen count of this atom.
int	getIndex()	Acces the index of an atom in the context of an IAtomContainer.
int	getListenerCount()	Returns the number of ChemObjectListeners registered with this object.
int	getMapIdx()	Access the map index for this atom.
Integer	getMassNumber()	Returns the atomic mass of this element.
IBond.Order	getMaxBondOrder()	Gets the MaxBondOrder attribute of the AtomType object.
Double	getNaturalAbundance()	Gets the NaturalAbundance attribute of the Isotope object.
boolean	getNotification()	Returns the flag that indicates whether notification messages are sent around.
javax.vecmath.Point2d	getPoint2d()	Returns a point specifying the location of this atom in a 2D space.
javax.vecmath.Point3d	getPoint3d()	Returns a point specifying the location of this atom in a 3D space.
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.
Integer	getStereoParity()	Returns the stereo parity of this atom.
String	getSymbol()	Returns the element symbol of this element.
Integer	getValency()	Gets the the exact electron valency of the AtomType object.
int	hashCode()
boolean	isAromatic()	Access whether this atom has been marked as aromatic.
boolean	isInRing()	Access whether this atom 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	setAtomicNumber(Integer atomicNumber)	Sets the atomic number of this element.
void	setAtomTypeName(String identifier)	Sets the if attribute of the AtomType object.
void	setBondOrderSum(Double bondOrderSum)	Sets the the exact bond order sum attribute of the AtomType object.
void	setCharge(Double charge)	Sets the partial charge of this atom.
void	setCovalentRadius(Double radius)	Sets the covalent radius for this AtomType.
void	setExactMass(Double exactMass)	Sets the ExactMass attribute of the Isotope object.
void	setFlag(int mask, boolean value)	Sets the value of some flag.
void	setFlags(boolean[] newFlags)	Sets the whole set of flags.
void	setFormalCharge(Integer charge)	Sets the formal charge of this atom.
void	setFormalNeighbourCount(Integer count)	Sets the formal neighbour count of this atom.
void	setFractionalPoint3d(javax.vecmath.Point3d point3d)	Sets a point specifying the location of this atom in a Crystal unit cell.
void	setHybridization(IAtomType.Hybridization hybridization)	Sets the hybridization of this atom.
void	setID(String identifier)	Sets the identifier (ID) of this object.
void	setImplicitHydrogenCount(Integer hydrogenCount)	Sets the implicit hydrogen count of this atom.
void	setIsAromatic(boolean arom)	Mark this atom as being aromatic.
void	setIsInRing(boolean ring)	Mark this atom as being in a ring.
void	setMapIdx(int mapidx)	Set the map index for this atom.
void	setMassNumber(Integer massNumber)	Sets the atomic mass of this element.
void	setMaxBondOrder(IBond.Order maxBondOrder)	Sets the MaxBondOrder attribute of the AtomType object.
void	setNaturalAbundance(Double naturalAbundance)	Sets the NaturalAbundance attribute of the Isotope object.
void	setNotification(boolean bool)	Set a flag to use or not use notification.
void	setPoint2d(javax.vecmath.Point2d point2d)	Sets a point specifying the location of this atom in a 2D space.
void	setPoint3d(javax.vecmath.Point3d point3d)	Sets a point specifying the location of this atom in 3D space.
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	setStereoParity(Integer stereoParity)	Sets the stereo parity for this atom.
void	setSymbol(String symbol)	Sets the element symbol of this element.
void	setValency(Integer valency)	Sets the the exact electron valency of the AtomType object.
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.ICDKObject

getBuilder

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

Constructor Detail

AtomRef

public AtomRef(IAtom atom)

Create a pointer for the provided atom.

Parameters:

atom - the atom to reference

Method Detail

deref

public static IAtom deref(IAtom atom)

Utility method to dereference an atom. If the atom is not an AtomRef it simply returns the input.

Parameters:

atom - the atom

Returns:

non-pointer atom

deref

public IAtom deref()

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

Returns:

the atom pointed to

getCharge

public Double getCharge()

Returns the partial charge of this atom.

Specified by:

getCharge in interface IAtom

Returns:

the charge of this atom

See Also:

IAtom.setCharge(java.lang.Double)

setCharge

public void setCharge(Double charge)

Sets the partial charge of this atom.

Specified by:

setCharge in interface IAtom

Parameters:

charge - The partial charge

See Also:

IAtom.getCharge()

getAtomicNumber

public Integer getAtomicNumber()

Returns the atomic number of this element.

Once instantiated all field not filled by passing parameters to the constructor are null. Elements can be configured by using the IsotopeFactory.configure() method:

   Element element = new Element("C");
   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
   if.configure(element);
 

Specified by:

getAtomicNumber in interface IElement

Returns:

The atomic number of this element

See Also:

IElement.setAtomicNumber(java.lang.Integer)

setAtomicNumber

public void setAtomicNumber(Integer atomicNumber)

Sets the atomic number of this element.

Specified by:

setAtomicNumber in interface IElement

Parameters:

atomicNumber - The atomic mass to be assigned to this element

See Also:

IElement.getAtomicNumber()

getNaturalAbundance

public Double getNaturalAbundance()

Gets the NaturalAbundance attribute of the Isotope object. Returns null when unconfigured.

Specified by:

getNaturalAbundance in interface IIsotope

Returns:

The NaturalAbundance value

See Also:

IIsotope.setNaturalAbundance(java.lang.Double)

setNaturalAbundance

public void setNaturalAbundance(Double naturalAbundance)

Sets the NaturalAbundance attribute of the Isotope object.

Specified by:

setNaturalAbundance in interface IIsotope

Parameters:

naturalAbundance - The new NaturalAbundance value

See Also:

IIsotope.getNaturalAbundance()

getImplicitHydrogenCount

public Integer getImplicitHydrogenCount()

Returns the implicit hydrogen count of this atom.

Specified by:

getImplicitHydrogenCount in interface IAtom

Returns:

The hydrogen count of this atom.

See Also:

IAtom.setImplicitHydrogenCount(java.lang.Integer)

setImplicitHydrogenCount

public void setImplicitHydrogenCount(Integer hydrogenCount)

Sets the implicit hydrogen count of this atom.

Specified by:

setImplicitHydrogenCount in interface IAtom

Parameters:

hydrogenCount - The number of hydrogen atoms bonded to this atom.

See Also:

IAtom.getImplicitHydrogenCount()

getExactMass

public Double getExactMass()

Gets the ExactMass attribute of the Isotope object. Returns null when unconfigured.

Specified by:

getExactMass in interface IIsotope

Returns:

The ExactMass value

See Also:

IIsotope.setExactMass(java.lang.Double)

setExactMass

public void setExactMass(Double exactMass)

Sets the ExactMass attribute of the Isotope object.

Specified by:

setExactMass in interface IIsotope

Parameters:

exactMass - The new ExactMass value

See Also:

IIsotope.getExactMass()

getSymbol

public String getSymbol()

Returns the element symbol of this element.

Specified by:

getSymbol in interface IElement

Returns:

The element symbol of this element. Null if unset.

See Also:

IElement.setSymbol(java.lang.String)

setSymbol

public void setSymbol(String symbol)

Sets the element symbol of this element.

Specified by:

setSymbol in interface IElement

Parameters:

symbol - The element symbol to be assigned to this atom

See Also:

IElement.getSymbol()

getMassNumber

public Integer getMassNumber()

Returns the atomic mass of this element. Returns null when unconfigured.

Specified by:

getMassNumber in interface IIsotope

Returns:

The atomic mass of this element

See Also:

IIsotope.setMassNumber(Integer)

setMassNumber

public void setMassNumber(Integer massNumber)

Sets the atomic mass of this element.

Specified by:

setMassNumber in interface IIsotope

Parameters:

massNumber - The atomic mass to be assigned to this element

See Also:

IIsotope.getMassNumber()

getAtomTypeName

public String getAtomTypeName()

Gets the id attribute of the AtomType object.

Specified by:

getAtomTypeName in interface IAtomType

Returns:

The id value

See Also:

IAtomType.setAtomTypeName(java.lang.String)

setAtomTypeName

public void setAtomTypeName(String identifier)

Sets the if attribute of the AtomType object.

Specified by:

setAtomTypeName in interface IAtomType

Parameters:

identifier - The new AtomTypeID value. Null if unset.

See Also:

IAtomType.getAtomTypeName()

getMaxBondOrder

public IBond.Order getMaxBondOrder()

Gets the MaxBondOrder attribute of the AtomType object.

Specified by:

getMaxBondOrder in interface IAtomType

Returns:

The MaxBondOrder value

See Also:

IAtomType.setMaxBondOrder(org.openscience.cdk.interfaces.IBond.Order)

setMaxBondOrder

public void setMaxBondOrder(IBond.Order maxBondOrder)

Sets the MaxBondOrder attribute of the AtomType object.

Specified by:

setMaxBondOrder in interface IAtomType

Parameters:

maxBondOrder - The new MaxBondOrder value

See Also:

IAtomType.getMaxBondOrder()

getBondOrderSum

public Double getBondOrderSum()

Gets the bondOrderSum attribute of the AtomType object.

Specified by:

getBondOrderSum in interface IAtomType

Returns:

The bondOrderSum value

See Also:

IAtomType.setBondOrderSum(java.lang.Double)

setBondOrderSum

public void setBondOrderSum(Double bondOrderSum)

Sets the the exact bond order sum attribute of the AtomType object.

Specified by:

setBondOrderSum in interface IAtomType

Parameters:

bondOrderSum - The new bondOrderSum value

See Also:

IAtomType.getBondOrderSum()

getPoint2d

public javax.vecmath.Point2d getPoint2d()

Returns a point specifying the location of this atom in a 2D space.

Specified by:

getPoint2d in interface IAtom

Returns:

A point in a 2D plane. Null if unset.

See Also:

IAtom.setPoint2d(javax.vecmath.Point2d)

setPoint2d

public void setPoint2d(javax.vecmath.Point2d point2d)

Sets a point specifying the location of this atom in a 2D space.

Specified by:

setPoint2d in interface IAtom

Parameters:

point2d - A point in a 2D plane

See Also:

IAtom.getPoint2d()

getPoint3d

public javax.vecmath.Point3d getPoint3d()

Returns a point specifying the location of this atom in a 3D space.

Specified by:

getPoint3d in interface IAtom

Returns:

A point in 3-dimensional space. Null if unset.

See Also:

IAtom.setPoint3d(javax.vecmath.Point3d)

setPoint3d

public void setPoint3d(javax.vecmath.Point3d point3d)

Sets a point specifying the location of this atom in 3D space.

Specified by:

setPoint3d in interface IAtom

Parameters:

point3d - A point in a 3-dimensional space

See Also:

IAtom.getPoint3d()

getFormalCharge

public Integer getFormalCharge()

Returns the formal charge of this atom.

Specified by:

getFormalCharge in interface IAtomType

Returns:

the formal charge of this atom

See Also:

IAtomType.setFormalCharge(java.lang.Integer)

setFormalCharge

public void setFormalCharge(Integer charge)

Sets the formal charge of this atom.

Specified by:

setFormalCharge in interface IAtomType

Parameters:

charge - The formal charge

See Also:

IAtomType.getFormalCharge()

getFractionalPoint3d

public javax.vecmath.Point3d getFractionalPoint3d()

Returns a point specifying the location of this atom in a Crystal unit cell.

Specified by:

getFractionalPoint3d in interface IAtom

Returns:

A point in 3d fractional unit cell space. Null if unset.

See Also:

IAtom.setFractionalPoint3d(javax.vecmath.Point3d), for predefined values.

setFractionalPoint3d

public void setFractionalPoint3d(javax.vecmath.Point3d point3d)

Sets a point specifying the location of this atom in a Crystal unit cell.

Specified by:

setFractionalPoint3d in interface IAtom

Parameters:

point3d - A point in a 3d fractional unit cell space

See Also:

IAtom.getFractionalPoint3d(), Crystal

getFormalNeighbourCount

public Integer getFormalNeighbourCount()

Returns the formal neighbour count of this atom.

Specified by:

getFormalNeighbourCount in interface IAtomType

Returns:

the formal neighbour count of this atom

See Also:

IAtomType.setFormalNeighbourCount(java.lang.Integer)

setFormalNeighbourCount

public void setFormalNeighbourCount(Integer count)

Sets the formal neighbour count of this atom.

Specified by:

setFormalNeighbourCount in interface IAtomType

Parameters:

count - The neighbour count

See Also:

IAtomType.getFormalNeighbourCount()

getStereoParity

public Integer getStereoParity()

Returns the stereo parity of this atom. It uses the predefined values found in CDKConstants.

Specified by:

getStereoParity in interface IAtom

Returns:

The stereo parity for this atom

See Also:

CDKConstants, IAtom.setStereoParity(java.lang.Integer)

setStereoParity

public void setStereoParity(Integer stereoParity)

Sets the stereo parity for this atom.

Specified by:

setStereoParity in interface IAtom

Parameters:

stereoParity - The stereo parity for this atom

See Also:

for predefined values., IAtom.getStereoParity()

getHybridization

public IAtomType.Hybridization getHybridization()

Returns the hybridization of this atom.

Specified by:

getHybridization in interface IAtomType

Returns:

the hybridization of this atom

See Also:

IAtomType.setHybridization(org.openscience.cdk.interfaces.IAtomType.Hybridization)

setHybridization

public void setHybridization(IAtomType.Hybridization hybridization)

Sets the hybridization of this atom.

Specified by:

setHybridization in interface IAtomType

Parameters:

hybridization - The hybridization

See Also:

IAtomType.getHybridization()

getCovalentRadius

public Double getCovalentRadius()

Returns the covalent radius for this AtomType.

Specified by:

getCovalentRadius in interface IAtomType

Returns:

The covalent radius for this AtomType

See Also:

IAtomType.setCovalentRadius(java.lang.Double)

setCovalentRadius

public void setCovalentRadius(Double radius)

Sets the covalent radius for this AtomType.

Specified by:

setCovalentRadius in interface IAtomType

Parameters:

radius - The covalent radius for this AtomType

See Also:

IAtomType.getCovalentRadius()

getContainer

public IAtomContainer getContainer()

Access the IAtomContainer of which this atom is a member of. Because atoms can be in multiple molecules this method will only work if the atom has been accessed in the context of an IAtomContainer, for example:

 IAtomContainer mol  = new AtomContainer();
 IAtom          atom = new Atom(6);

 atom.getContainer(); // null
 mol.add(atom);
 atom.getContainer(); // still null
 mol.getAtom(0).getContainer(); // not-null, returns 'mol'
 

Specified by:

getContainer in interface IAtom

Returns:

the atom container or null if not accessed in the context of a container

getIndex

public int getIndex()

Acces the index of an atom in the context of an IAtomContainer. If the index is not known, < 0 is returned.

Specified by:

getIndex in interface IAtom

Returns:

atom index or < 0 if the index is not known

getValency

public Integer getValency()

Gets the the exact electron valency of the AtomType object.

Specified by:

getValency in interface IAtomType

Returns:

The valency value

See Also:

IAtomType.setValency(Integer)

setValency

public void setValency(Integer valency)

Sets the the exact electron valency of the AtomType object.

Specified by:

setValency in interface IAtomType

Parameters:

valency - The new valency value

See Also:

IAtomType.getValency()

bonds

public Iterable<IBond> bonds()

Description copied from interface: IAtom

Returns the bonds connected to this atom. If the bonds are not known an exception is thrown. This method will only throw an exception if IAtom.getIndex() returns < 0 or IAtom.getContainer() returns null.

 IAtom atom = ...;

 if (atom.getIndex() >= 0) {
   for (IBond bond : atom.bonds()) {

   }
 }

 if (atom.getContainer() != null) {
   for (IBond bond : atom.bonds()) {

   }
 }

 IAtomContainer mol = ...;
 // guaranteed not throw an exception
 for (IBond bond : mol.getAtom(i).bonds()) {

 }
 

Specified by:

bonds in interface IAtom

Returns:

iterable of bonds

getBondCount

public int getBondCount()

Description copied from interface: IAtom

Get the number of explicit bonds connected to this atom.

Specified by:

getBondCount in interface IAtom

Returns:

the total bond count

getBond

public IBond getBond(IAtom atom)

Returns the bond connecting 'this' atom to the provided atom. If the atoms are not bonded, null is returned.

Specified by:

getBond in interface IAtom

Parameters:

atom - the other atom

Returns:

the bond connecting the atoms

isAromatic

public boolean isAromatic()

Access whether this atom 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 IAtom

Returns:

aromatic status

See Also:

IChemObject.getFlag(int), Aromaticity

setIsAromatic

public void setIsAromatic(boolean arom)

Mark this atom as being aromatic.

Specified by:

setIsAromatic in interface IAtom

Parameters:

arom - aromatic status

See Also:

IChemObject.setFlag(int, boolean)

isInRing

public boolean isInRing()

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

Specified by:

isInRing in interface IAtom

Returns:

ring status

See Also:

IChemObject.getFlag(int), RingSearch

setIsInRing

public void setIsInRing(boolean ring)

Mark this atom as being in a ring.

Specified by:

setIsInRing in interface IAtom

Parameters:

ring - ring status

See Also:

IChemObject.setFlag(int, boolean)

getMapIdx

public int getMapIdx()

Description copied from interface: IAtom

Access the map index for this atom.

Specified by:

getMapIdx in interface IAtom

Returns:

the map index (0 if not set)

setMapIdx

public void setMapIdx(int mapidx)

Description copied from interface: IAtom

Set the map index for this atom.

Specified by:

setMapIdx in interface IAtom

Parameters:

mapidx - the new map index

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

clone

public IAtom clone()
            throws CloneNotSupportedException

Returns a deep clone of this IChemObject.

Specified by:

clone in interface IAtom

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