Package org.openscience.cdk.debug

Class DebugReaction

java.lang.Object

org.openscience.cdk.ChemObject

org.openscience.cdk.Reaction

org.openscience.cdk.debug.DebugReaction

All Implemented Interfaces:

Serializable, Cloneable, Iterable<IAtomContainer>, ICDKObject, IChemObject, IReaction

public class DebugReaction
extends Reaction
implements IReaction

Debugging data class.

Author:

egonw

See Also:

• Serialized Form

Nested Class Summary

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

IReaction.Direction

Field Summary

Fields inherited from class org.openscience.cdk.Reaction

agents, growArraySize, map, mappingCount, products, reactants

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
DebugReaction()

Method Summary

Modifier and Type	Method	Description
void	addAgent(IAtomContainer agent)	Adds an agent to this reaction.
void	addListener(IChemObjectListener col)	Use this to add yourself to this IChemObject as a listener.
void	addProduct(IAtomContainer product)	Adds a product to this reaction.
void	addProduct(IAtomContainer product, Double coefficient)	Adds a product to this reaction.
void	addProperties(Map<Object,Object> properties)	Sets the properties of this object.
void	addReactant(IAtomContainer reactant)	Adds a reactant to this reaction.
void	addReactant(IAtomContainer reactant, Double coefficient)	Adds a reactant to this reaction with a stoichiometry coefficient.
Object	clone()	Clones this Reaction and its content.
int	getAgentCount()	Returns the number of agents in this reaction.
IAtomContainerSet	getAgents()	Returns a MoleculeSet containing the agents in this reaction.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
IReaction.Direction	getDirection()	Returns the direction of the reaction.
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	getProductCoefficient(IAtomContainer product)	Returns the stoichiometry coefficient of the given product.
Double[]	getProductCoefficients()	Returns an array of double with the stoichiometric coefficients of the products.
int	getProductCount()	Returns the number of products in this reaction.
IAtomContainerSet	getProducts()	Returns a MoleculeSet containing the products of this reaction.
Map<Object,Object>	getProperties()	Returns a Map with the IChemObject's properties.
<T> T	getProperty(Object description)	Returns a property for the IChemObject.
Double	getReactantCoefficient(IAtomContainer reactant)	Returns the stoichiometry coefficient of the given reactant.
Double[]	getReactantCoefficients()	Returns an array of double with the stoichiometric coefficients of the reactants.
int	getReactantCount()	Returns the number of reactants in this reaction.
IAtomContainerSet	getReactants()	Returns a MoleculeSet containing the reactants in this reaction.
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	setDirection(IReaction.Direction direction)	Sets the direction of the reaction.
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.
boolean	setProductCoefficient(IAtomContainer product, Double coefficient)	Sets the coefficient of a a product to a given value.
boolean	setProductCoefficients(Double[] coefficients)	Sets the coefficient of the products.
void	setProducts(IAtomContainerSet products)	Assigns a MoleculeSet to the products of this reaction.
void	setProperty(Object description, Object property)	Sets a property for a IChemObject.
boolean	setReactantCoefficient(IAtomContainer reactant, Double coefficient)	Sets the coefficient of a a reactant to a given value.
boolean	setReactantCoefficients(Double[] coefficients)	Sets the coefficients of the reactants.
void	setReactants(IAtomContainerSet reactants)	Assigns a MoleculeSet to the reactants in this reaction.

Methods inherited from class org.openscience.cdk.Reaction

addMapping, getMapping, getMappingCount, mappings, removeMapping, 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.IChemObject

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

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

addMapping, getMapping, getMappingCount, iterator, mappings, removeMapping

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

DebugReaction

public DebugReaction()

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 Reaction and its content.

Specified by:

clone in interface IChemObject

Overrides:

clone in class Reaction

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

getReactantCount

public int getReactantCount()

Returns the number of reactants in this reaction.

Specified by:

getReactantCount in interface IReaction

Overrides:

getReactantCount in class Reaction

Returns:

The number of reactants in this reaction

getProductCount

public int getProductCount()

Returns the number of products in this reaction.

Specified by:

getProductCount in interface IReaction

Overrides:

getProductCount in class Reaction

Returns:

The number of products in this reaction

getAgentCount

public int getAgentCount()

Returns the number of agents in this reaction.

Specified by:

getAgentCount in interface IReaction

Overrides:

getAgentCount in class Reaction

Returns:

The number of agents in this reaction

getReactants

public IAtomContainerSet getReactants()

Returns a MoleculeSet containing the reactants in this reaction.

Specified by:

getReactants in interface IReaction

Overrides:

getReactants in class Reaction

Returns:

A MoleculeSet containing the reactants in this reaction

See Also:

• IReaction.setReactants(org.openscience.cdk.interfaces.IAtomContainerSet)

setReactants

public void setReactants(IAtomContainerSet reactants)

Assigns a MoleculeSet to the reactants in this reaction.

Specified by:

setReactants in interface IReaction

Overrides:

setReactants in class Reaction

Parameters:

reactants - The new set of reactants

See Also:

• Reaction.getReactants()

getProducts

public IAtomContainerSet getProducts()

Returns a MoleculeSet containing the products of this reaction.

Specified by:

getProducts in interface IReaction

Overrides:

getProducts in class Reaction

Returns:

A MoleculeSet containing the products in this reaction

See Also:

• IReaction.setProducts(org.openscience.cdk.interfaces.IAtomContainerSet)

setProducts

public void setProducts(IAtomContainerSet products)

Assigns a MoleculeSet to the products of this reaction.

Specified by:

setProducts in interface IReaction

Overrides:

setProducts in class Reaction

Parameters:

products - The new set of products

See Also:

• Reaction.getProducts()

getAgents

public IAtomContainerSet getAgents()

Returns a MoleculeSet containing the agents in this reaction.

Specified by:

getAgents in interface IReaction

Overrides:

getAgents in class Reaction

Returns:

A MoleculeSet containing the agents in this reaction

See Also:

• Reaction.addAgent(org.openscience.cdk.interfaces.IAtomContainer)

addReactant

public void addReactant(IAtomContainer reactant)

Adds a reactant to this reaction.

Specified by:

addReactant in interface IReaction

Overrides:

addReactant in class Reaction

Parameters:

reactant - Molecule added as reactant to this reaction

See Also:

• Reaction.getReactants()

addAgent

public void addAgent(IAtomContainer agent)

Adds an agent to this reaction.

Specified by:

addAgent in interface IReaction

Overrides:

addAgent in class Reaction

Parameters:

agent - Molecule added as agent to this reaction

See Also:

• Reaction.getAgents()

addReactant

public void addReactant(IAtomContainer reactant,
 Double coefficient)

Adds a reactant to this reaction with a stoichiometry coefficient.

Specified by:

addReactant in interface IReaction

Overrides:

addReactant in class Reaction

Parameters:

reactant - Molecule added as reactant to this reaction

coefficient - Stoichiometry coefficient for this molecule

See Also:

• Reaction.getReactants()

addProduct

public void addProduct(IAtomContainer product)

Adds a product to this reaction.

Specified by:

addProduct in interface IReaction

Overrides:

addProduct in class Reaction

Parameters:

product - Molecule added as product to this reaction

See Also:

• Reaction.getProducts()

addProduct

public void addProduct(IAtomContainer product,
 Double coefficient)

Adds a product to this reaction.

Specified by:

addProduct in interface IReaction

Overrides:

addProduct in class Reaction

Parameters:

product - Molecule added as product to this reaction

coefficient - Stoichiometry coefficient for this molecule

See Also:

• Reaction.getProducts()

getReactantCoefficient

public Double getReactantCoefficient(IAtomContainer reactant)

Returns the stoichiometry coefficient of the given reactant.

Specified by:

getReactantCoefficient in interface IReaction

Overrides:

getReactantCoefficient in class Reaction

Parameters:

reactant - Reactant for which the coefficient is returned.

Returns:

-1, if the given molecule is not a product in this Reaction

See Also:

• Reaction.setReactantCoefficient(org.openscience.cdk.interfaces.IAtomContainer, java.lang.Double)

getProductCoefficient

public Double getProductCoefficient(IAtomContainer product)

Returns the stoichiometry coefficient of the given product.

Specified by:

getProductCoefficient in interface IReaction

Overrides:

getProductCoefficient in class Reaction

Parameters:

product - Product for which the coefficient is returned.

Returns:

-1, if the given molecule is not a product in this Reaction

See Also:

• Reaction.setProductCoefficient(org.openscience.cdk.interfaces.IAtomContainer, java.lang.Double)

setReactantCoefficient

public boolean setReactantCoefficient(IAtomContainer reactant,
 Double coefficient)

Sets the coefficient of a a reactant to a given value.

Specified by:

setReactantCoefficient in interface IReaction

Overrides:

setReactantCoefficient in class Reaction

Parameters:

reactant - Reactant for which the coefficient is set

coefficient - The new coefficient for the given reactant

Returns:

true if Molecule has been found and stoichiometry has been set.

See Also:

• Reaction.getReactantCoefficient(org.openscience.cdk.interfaces.IAtomContainer)

setProductCoefficient

public boolean setProductCoefficient(IAtomContainer product,
 Double coefficient)

Sets the coefficient of a a product to a given value.

Specified by:

setProductCoefficient in interface IReaction

Overrides:

setProductCoefficient in class Reaction

Parameters:

product - Product for which the coefficient is set

coefficient - The new coefficient for the given product

Returns:

true if Molecule has been found and stoichiometry has been set.

See Also:

• Reaction.getProductCoefficient(org.openscience.cdk.interfaces.IAtomContainer)

getReactantCoefficients

public Double[] getReactantCoefficients()

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

Specified by:

getReactantCoefficients in interface IReaction

Overrides:

getReactantCoefficients in class Reaction

Returns:

An array of double's containing the coefficients of the reactants

See Also:

• Reaction.setReactantCoefficients(java.lang.Double[])

getProductCoefficients

public Double[] getProductCoefficients()

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

Specified by:

getProductCoefficients in interface IReaction

Overrides:

getProductCoefficients in class Reaction

Returns:

An array of double's containing the coefficients of the products

See Also:

• Reaction.setProductCoefficients(java.lang.Double[])

setReactantCoefficients

public boolean setReactantCoefficients(Double[] coefficients)

Sets the coefficients of the reactants.

Specified by:

setReactantCoefficients in interface IReaction

Overrides:

setReactantCoefficients in class Reaction

Parameters:

coefficients - An array of double's containing the coefficients of the reactants

Returns:

true if coefficients have been set.

See Also:

• Reaction.getReactantCoefficients()

setProductCoefficients

public boolean setProductCoefficients(Double[] coefficients)

Sets the coefficient of the products.

Specified by:

setProductCoefficients in interface IReaction

Overrides:

setProductCoefficients in class Reaction

Parameters:

coefficients - An array of double's containing the coefficients of the products

Returns:

true if coefficients have been set.

See Also:

• Reaction.getProductCoefficients()

setDirection

public void setDirection(IReaction.Direction direction)

Sets the direction of the reaction.

Specified by:

setDirection in interface IReaction

Overrides:

setDirection in class Reaction

Parameters:

direction - The new reaction direction

See Also:

• Reaction.getDirection()

getDirection

public IReaction.Direction getDirection()

Returns the direction of the reaction.

Specified by:

getDirection in interface IReaction

Overrides:

getDirection in class Reaction

Returns:

The direction of this reaction (FORWARD, BACKWARD or BIDIRECTIONAL).

See Also:

• IReaction.Direction
• Reaction.setDirection(org.openscience.cdk.interfaces.IReaction.Direction)