Package org.openscience.cdk.debug

Class DebugAtomType

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Element

org.openscience.cdk.Isotope

org.openscience.cdk.AtomType

org.openscience.cdk.debug.DebugAtomType

All Implemented Interfaces:

Serializable, Cloneable, IAtomType, ICDKObject, IChemObject, IElement, IIsotope

public class DebugAtomType
extends AtomType
implements IAtomType

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Nested Class Summary

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

IAtomType.Hybridization

Field Summary

Fields inherited from class org.openscience.cdk.AtomType

electronValency, formalCharge, formalNeighbourCount, hybridization

Fields inherited from class org.openscience.cdk.Isotope

exactMass, naturalAbundance

Fields inherited from class org.openscience.cdk.Element

atomicNumber

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

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
DebugAtomType(String elementSymbol)
DebugAtomType(String identifier, String elementSymbol)
DebugAtomType(IElement element)

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.
Object	clone()	Clones this IChemObject.
Integer	getAtomicNumber()	Returns the atomic number of this element.
String	getAtomTypeName()	Gets the id attribute of the AtomType object.
Double	getBondOrderSum()	Gets the bondOrderSum attribute of the AtomType object.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
Double	getCovalentRadius()	Returns the covalent radius for this AtomType.
Double	getExactMass()	Gets the ExactMass attribute of the Isotope object.
boolean	getFlag(int flagType)	Returns the value of a given flag.
boolean[]	getFlags()	Returns the whole set of flags.
Integer	getFormalCharge()	Returns the formal charge of this atom.
Integer	getFormalNeighbourCount()	Returns the formal neighbour count of this atom.
IAtomType.Hybridization	getHybridization()	Returns the hybridization of this atom.
String	getID()	Returns the identifier (ID) of this object.
int	getListenerCount()	Returns the number of ChemObjectListeners registered with this object.
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.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
String	getSymbol()	Returns the element symbol of this element.
Integer	getValency()	Gets the the exact electron valency of the AtomType object.
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	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 flagType, boolean flagValue)	Sets the value of some flag.
void	setFlags(boolean[] flagsNew)	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	setHybridization(IAtomType.Hybridization hybridization)	Sets the hybridization of this atom.
void	setID(String identifier)	Sets the identifier (ID) of this object.
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	setProperty(Object description, Object property)	Sets a property for a IChemObject.
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.

Methods inherited from class org.openscience.cdk.AtomType

compare, 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

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

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

Constructor Details

DebugAtomType

public DebugAtomType(String elementSymbol)

DebugAtomType

public DebugAtomType(String identifier,
 String elementSymbol)

DebugAtomType

public DebugAtomType(IElement element)

Method Details

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

Overrides:

getAtomicNumber in class Element

Returns:

The atomic number of this element

See Also:

• Element.setAtomicNumber(java.lang.Integer)

setAtomicNumber

public void setAtomicNumber(Integer atomicNumber)

Sets the atomic number of this element.

Specified by:

setAtomicNumber in interface IElement

Overrides:

setAtomicNumber in class Element

Parameters:

atomicNumber - The atomic mass to be assigned to this element

See Also:

• Element.getAtomicNumber()

getSymbol

public String getSymbol()

Returns the element symbol of this element.

Specified by:

getSymbol in interface IElement

Overrides:

getSymbol in class Element

Returns:

The element symbol of this element. Null if unset.

See Also:

• Element.setSymbol(java.lang.String)

setSymbol

public void setSymbol(String symbol)

Sets the element symbol of this element.

Specified by:

setSymbol in interface IElement

Overrides:

setSymbol in class Element

Parameters:

symbol - The element symbol to be assigned to this atom

See Also:

• Element.getSymbol()

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 Object clone()
             throws CloneNotSupportedException

Clones this IChemObject. It clones the identifier, flags, properties and pointer vectors. The ChemObjectListeners are not cloned, and neither is the content of the pointer vectors.

Specified by:

clone in interface IChemObject

Overrides:

clone in class AtomType

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

setNaturalAbundance

public void setNaturalAbundance(Double naturalAbundance)

Sets the NaturalAbundance attribute of the Isotope object.

Specified by:

setNaturalAbundance in interface IIsotope

Overrides:

setNaturalAbundance in class Isotope

Parameters:

naturalAbundance - The new NaturalAbundance value

See Also:

• Isotope.getNaturalAbundance()

setExactMass

public void setExactMass(Double exactMass)

Sets the ExactMass attribute of the Isotope object.

Specified by:

setExactMass in interface IIsotope

Overrides:

setExactMass in class Isotope

Parameters:

exactMass - The new ExactMass value

See Also:

• Isotope.getExactMass()

getNaturalAbundance

public Double getNaturalAbundance()

Gets the NaturalAbundance attribute of the Isotope object.

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

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getNaturalAbundance in interface IIsotope

Overrides:

getNaturalAbundance in class Isotope

Returns:

The NaturalAbundance value

See Also:

• Isotope.setNaturalAbundance(java.lang.Double)

getExactMass

public Double getExactMass()

Gets the ExactMass attribute of the Isotope object.

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

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getExactMass in interface IIsotope

Overrides:

getExactMass in class Isotope

Returns:

The ExactMass value

See Also:

• Isotope.setExactMass(java.lang.Double)

getMassNumber

public Integer getMassNumber()

Returns the atomic mass of this element.

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

   Isotope isotope = new Isotope("C", 13);
   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
   if.configure(isotope);
 

Specified by:

getMassNumber in interface IIsotope

Overrides:

getMassNumber in class Isotope

Returns:

The atomic mass of this element

See Also:

• Isotope.setMassNumber(Integer)

setMassNumber

public void setMassNumber(Integer massNumber)

Sets the atomic mass of this element.

Specified by:

setMassNumber in interface IIsotope

Overrides:

setMassNumber in class Isotope

Parameters:

massNumber - The atomic mass to be assigned to this element

See Also:

• Isotope.getMassNumber()

setAtomTypeName

public void setAtomTypeName(String identifier)

Sets the if attribute of the AtomType object.

Specified by:

setAtomTypeName in interface IAtomType

Overrides:

setAtomTypeName in class AtomType

Parameters:

identifier - The new AtomTypeID value. Null if unset.

See Also:

• AtomType.getAtomTypeName()

setMaxBondOrder

public void setMaxBondOrder(IBond.Order maxBondOrder)

Sets the MaxBondOrder attribute of the AtomType object.

Specified by:

setMaxBondOrder in interface IAtomType

Overrides:

setMaxBondOrder in class AtomType

Parameters:

maxBondOrder - The new MaxBondOrder value

See Also:

• AtomType.getMaxBondOrder()

setBondOrderSum

public void setBondOrderSum(Double bondOrderSum)

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

Specified by:

setBondOrderSum in interface IAtomType

Overrides:

setBondOrderSum in class AtomType

Parameters:

bondOrderSum - The new bondOrderSum value

See Also:

• AtomType.getBondOrderSum()

getAtomTypeName

public String getAtomTypeName()

Gets the id attribute of the AtomType object.

Specified by:

getAtomTypeName in interface IAtomType

Overrides:

getAtomTypeName in class AtomType

Returns:

The id value

See Also:

• AtomType.setAtomTypeName(java.lang.String)

getMaxBondOrder

public IBond.Order getMaxBondOrder()

Gets the MaxBondOrder attribute of the AtomType object.

Specified by:

getMaxBondOrder in interface IAtomType

Overrides:

getMaxBondOrder in class AtomType

Returns:

The MaxBondOrder value

See Also:

• AtomType.setMaxBondOrder(org.openscience.cdk.interfaces.IBond.Order)

getBondOrderSum

public Double getBondOrderSum()

Gets the bondOrderSum attribute of the AtomType object.

Specified by:

getBondOrderSum in interface IAtomType

Overrides:

getBondOrderSum in class AtomType

Returns:

The bondOrderSum value

See Also:

• AtomType.setBondOrderSum(java.lang.Double)

setFormalCharge

public void setFormalCharge(Integer charge)

Sets the formal charge of this atom.

Specified by:

setFormalCharge in interface IAtomType

Overrides:

setFormalCharge in class AtomType

Parameters:

charge - The formal charge

See Also:

• AtomType.getFormalCharge()

getFormalCharge

public Integer getFormalCharge()

Returns the formal charge of this atom.

Specified by:

getFormalCharge in interface IAtomType

Overrides:

getFormalCharge in class AtomType

Returns:

the formal charge of this atom

See Also:

• AtomType.setFormalCharge(java.lang.Integer)

setFormalNeighbourCount

public void setFormalNeighbourCount(Integer count)

Sets the formal neighbour count of this atom.

Specified by:

setFormalNeighbourCount in interface IAtomType

Overrides:

setFormalNeighbourCount in class AtomType

Parameters:

count - The neighbour count

See Also:

• AtomType.getFormalNeighbourCount()

getFormalNeighbourCount

public Integer getFormalNeighbourCount()

Returns the formal neighbour count of this atom.

Specified by:

getFormalNeighbourCount in interface IAtomType

Overrides:

getFormalNeighbourCount in class AtomType

Returns:

the formal neighbour count of this atom

See Also:

• AtomType.setFormalNeighbourCount(java.lang.Integer)

setHybridization

public void setHybridization(IAtomType.Hybridization hybridization)

Sets the hybridization of this atom.

Specified by:

setHybridization in interface IAtomType

Overrides:

setHybridization in class AtomType

Parameters:

hybridization - The hybridization

See Also:

• AtomType.getHybridization()

getHybridization

public IAtomType.Hybridization getHybridization()

Returns the hybridization of this atom.

Specified by:

getHybridization in interface IAtomType

Overrides:

getHybridization in class AtomType

Returns:

the hybridization of this atom

See Also:

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

setCovalentRadius

public void setCovalentRadius(Double radius)

Sets the covalent radius for this AtomType.

Specified by:

setCovalentRadius in interface IAtomType

Overrides:

setCovalentRadius in class AtomType

Parameters:

radius - The covalent radius for this AtomType

See Also:

• AtomType.getCovalentRadius()

getCovalentRadius

public Double getCovalentRadius()

Returns the covalent radius for this AtomType.

Specified by:

getCovalentRadius in interface IAtomType

Overrides:

getCovalentRadius in class AtomType

Returns:

The covalent radius for this AtomType

See Also:

• AtomType.setCovalentRadius(java.lang.Double)

setValency

public void setValency(Integer valency)

Sets the the exact electron valency of the AtomType object.

Specified by:

setValency in interface IAtomType

Overrides:

setValency in class AtomType

Parameters:

valency - The new valency value

See Also:

• AtomType.getValency()

getValency

public Integer getValency()

Gets the the exact electron valency of the AtomType object.

Specified by:

getValency in interface IAtomType

Overrides:

getValency in class AtomType

Returns:

The valency value

See Also:

• AtomType.setValency(java.lang.Integer)