Package org.openscience.cdk.debug

Class DebugSubstance

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.AtomContainerSet

org.openscience.cdk.debug.DebugSubstance

All Implemented Interfaces:

Serializable, Cloneable, Iterable<IAtomContainer>, IAtomContainerSet, ICDKObject, IChemObject, IChemObjectListener, ISubstance

public class DebugSubstance
extends AtomContainerSet
implements ISubstance

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Field Summary

Fields inherited from class org.openscience.cdk.AtomContainerSet

atomContainerCount, atomContainers, growArraySize, multipliers

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
DebugSubstance()

Method Summary

Modifier and Type	Method	Description
void	add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	addAtomContainer(IAtomContainer atomContainer)	Adds an atomContainer to this container.
void	addAtomContainer(IAtomContainer atomContainer, double multiplier)	Adds an atomContainer to this container with the given multiplier.
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<IAtomContainer>	atomContainers()	Get an iterator for this AtomContainerSet.
Object	clone()	Clones this AtomContainerSet and its content.
IAtomContainer	getAtomContainer(int number)	Returns the AtomContainer at position number in the container.
int	getAtomContainerCount()	Returns the number of AtomContainers in this Container.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
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.
Double	getMultiplier(int number)	Returns the multiplier for the AtomContainer at position number in the container.
Double	getMultiplier(IAtomContainer container)	Returns the multiplier of the given AtomContainer.
Double[]	getMultipliers()	Returns an array of double with the stoichiometric coefficients of the products.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
boolean	isEmpty()	Returns true if this IAtomContainerSet is empty.
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	removeAllAtomContainers()	Removes all AtomContainer from this container.
void	removeAtomContainer(int pos)	Removes an AtomContainer from this container.
void	removeAtomContainer(IAtomContainer atomContainer)	Removes an AtomContainer from this container.
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	replaceAtomContainer(int position, IAtomContainer container)	Replace the AtomContainer at a specific position (array has to be large enough).
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	setMultiplier(int position, Double multiplier)	Sets the coefficient of a AtomContainer to a given value.
boolean	setMultiplier(IAtomContainer container, Double multiplier)	Sets the coefficient of a AtomContainer to a given value.
boolean	setMultipliers(Double[] newMultipliers)	Sets the multipliers of the AtomContainers.
void	setProperty(Object description, Object property)	Sets a property for a IChemObject.

Methods inherited from class org.openscience.cdk.AtomContainerSet

growAtomContainerArray, sortAtomContainers, stateChanged, toString

Methods inherited from class org.openscience.cdk.ChemObject

clear, compare, 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.IAtomContainerSet

iterator, sortAtomContainers

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

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

DebugSubstance

public DebugSubstance()

Method Details

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 AtomContainerSet and its content.

Specified by:

clone in interface IChemObject

Overrides:

clone in class AtomContainerSet

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

addAtomContainer

public void addAtomContainer(IAtomContainer atomContainer)

Adds an atomContainer to this container.

Specified by:

addAtomContainer in interface IAtomContainerSet

Overrides:

addAtomContainer in class AtomContainerSet

Parameters:

atomContainer - The atomContainer to be added to this container

removeAtomContainer

public void removeAtomContainer(IAtomContainer atomContainer)

Removes an AtomContainer from this container.

Specified by:

removeAtomContainer in interface IAtomContainerSet

Overrides:

removeAtomContainer in class AtomContainerSet

Parameters:

atomContainer - The atomContainer to be removed from this container

removeAllAtomContainers

public void removeAllAtomContainers()

Removes all AtomContainer from this container.

Specified by:

removeAllAtomContainers in interface IAtomContainerSet

Overrides:

removeAllAtomContainers in class AtomContainerSet

removeAtomContainer

public void removeAtomContainer(int pos)

Removes an AtomContainer from this container.

Specified by:

removeAtomContainer in interface IAtomContainerSet

Overrides:

removeAtomContainer in class AtomContainerSet

Parameters:

pos - The position of the AtomContainer to be removed from this container

replaceAtomContainer

public void replaceAtomContainer(int position,
 IAtomContainer container)

Replace the AtomContainer at a specific position (array has to be large enough).

Specified by:

replaceAtomContainer in interface IAtomContainerSet

Overrides:

replaceAtomContainer in class AtomContainerSet

Parameters:

position - position in array for AtomContainer

container - the replacement AtomContainer

setMultiplier

public boolean setMultiplier(IAtomContainer container,
 Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

Specified by:

setMultiplier in interface IAtomContainerSet

Overrides:

setMultiplier in class AtomContainerSet

Parameters:

container - The AtomContainer for which the multiplier is set

multiplier - The new multiplier for the AtomContatiner

Returns:

true if multiplier has been set

See Also:

• AtomContainerSet.getMultiplier(IAtomContainer)

setMultiplier

public void setMultiplier(int position,
 Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

Specified by:

setMultiplier in interface IAtomContainerSet

Overrides:

setMultiplier in class AtomContainerSet

Parameters:

position - The position of the AtomContainer for which the multiplier is set in [0,..]

multiplier - The new multiplier for the AtomContatiner at position

See Also:

• AtomContainerSet.getMultiplier(int)

getMultipliers

public Double[] getMultipliers()

Returns an array of double with the stoichiometric coefficients of the products.

Specified by:

getMultipliers in interface IAtomContainerSet

Overrides:

getMultipliers in class AtomContainerSet

Returns:

The multipliers for the AtomContainer's in this set

See Also:

• AtomContainerSet.setMultipliers(java.lang.Double[])

setMultipliers

public boolean setMultipliers(Double[] newMultipliers)

Sets the multipliers of the AtomContainers.

Specified by:

setMultipliers in interface IAtomContainerSet

Overrides:

setMultipliers in class AtomContainerSet

Parameters:

newMultipliers - The new multipliers for the AtomContainers in this set

Returns:

true if multipliers have been set.

See Also:

• AtomContainerSet.getMultipliers()

addAtomContainer

public void addAtomContainer(IAtomContainer atomContainer,
 double multiplier)

Adds an atomContainer to this container with the given multiplier.

Specified by:

addAtomContainer in interface IAtomContainerSet

Overrides:

addAtomContainer in class AtomContainerSet

Parameters:

atomContainer - The atomContainer to be added to this container

multiplier - The multiplier of this atomContainer

add

public void add(IAtomContainerSet atomContainerSet)

Adds all atomContainers in the AtomContainerSet to this container.

Specified by:

add in interface IAtomContainerSet

Overrides:

add in class AtomContainerSet

Parameters:

atomContainerSet - The AtomContainerSet

atomContainers

public Iterable<IAtomContainer> atomContainers()

Get an iterator for this AtomContainerSet.

Specified by:

atomContainers in interface IAtomContainerSet

Overrides:

atomContainers in class AtomContainerSet

Returns:

A new Iterator for this AtomContainerSet.

getAtomContainer

public IAtomContainer getAtomContainer(int number)

Returns the AtomContainer at position number in the container.

Specified by:

getAtomContainer in interface IAtomContainerSet

Overrides:

getAtomContainer in class AtomContainerSet

Parameters:

number - The position of the AtomContainer to be returned.

Returns:

The AtomContainer at position number .

getMultiplier

public Double getMultiplier(int number)

Returns the multiplier for the AtomContainer at position number in the container.

Specified by:

getMultiplier in interface IAtomContainerSet

Overrides:

getMultiplier in class AtomContainerSet

Parameters:

number - The position of the multiplier of the AtomContainer to be returned.

Returns:

The multiplier for the AtomContainer at position number .

See Also:

• AtomContainerSet.setMultiplier(int, Double)

getMultiplier

public Double getMultiplier(IAtomContainer container)

Returns the multiplier of the given AtomContainer.

Specified by:

getMultiplier in interface IAtomContainerSet

Overrides:

getMultiplier in class AtomContainerSet

Parameters:

container - The AtomContainer for which the multiplier is given

Returns:

-1, if the given molecule is not a container in this set

See Also:

• AtomContainerSet.setMultiplier(IAtomContainer, Double)

getAtomContainerCount

public int getAtomContainerCount()

Returns the number of AtomContainers in this Container.

Specified by:

getAtomContainerCount in interface IAtomContainerSet

Overrides:

getAtomContainerCount in class AtomContainerSet

Returns:

The number of AtomContainers in this Container

isEmpty

public boolean isEmpty()

Returns true if this IAtomContainerSet is empty.

Specified by:

isEmpty in interface IAtomContainerSet

Overrides:

isEmpty in class AtomContainerSet

Returns:

a boolean indicating if this ring set no atom containers