Package org.openscience.cdk.silent

Class Reaction

java.lang.Object

org.openscience.cdk.silent.ChemObject

org.openscience.cdk.silent.Reaction

All Implemented Interfaces:

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

public class Reaction
extends ChemObject
implements Serializable, IReaction, Cloneable

Represents the idea of a chemical reaction. The reaction consists of a set of reactants and a set of products.

The class mostly represents abstract reactions, such as 2D diagrams, and is not intended to represent reaction trajectories. Such can better be represented with a ChemSequence.

Author:

Egon Willighagen <elw38@cam.ac.uk>

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

silent

Keywords:

reaction

Created on:

2003-02-13

Nested Class Summary

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

IReaction.Direction

Field Summary

Fields

Modifier and Type	Field	Description
protected IAtomContainerSet	agents	These are the used solvent, catalysts etc that normally appear above the reaction arrow
protected int	growArraySize
protected IMapping[]	map
protected int	mappingCount
protected IAtomContainerSet	products
protected IAtomContainerSet	reactants

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

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

Constructor Summary

Constructors

Constructor	Description
Reaction()	Constructs an empty, forward reaction.

Method Summary

Modifier and Type	Method	Description
void	addAgent(IAtomContainer agent)	Adds an agent to this reaction.
void	addMapping(IMapping mapping)	Adds a mapping between the reactant and product side to this Reaction.
void	addProduct(IAtomContainer product)	Adds a product to this reaction.
void	addProduct(IAtomContainer product, Double coefficient)	Adds a product to this reaction.
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.
IReaction.Direction	getDirection()	Returns the direction of the reaction.
IMapping	getMapping(int pos)	Retrieves a mapping between the reactant and product side to this Reaction.
int	getMappingCount()	Get the number of mappings between the reactant and product side to this Reaction.
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.
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.
Iterable<IMapping>	mappings()	Returns the mappings between the reactant and the product side.
void	removeMapping(int pos)	Removes a mapping between the reactant and product side to this Reaction.
void	setDirection(IReaction.Direction direction)	Sets the direction of the reaction.
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 setOfMolecules)	Assigns a MoleculeSet to the products of this reaction.
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 setOfMolecules)	Assigns a MoleculeSet to the reactants in this reaction.
String	toString()	Returns a one line string representation of this Atom.

Methods inherited from class org.openscience.cdk.silent.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, 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.ICDKObject

getBuilder

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

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

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

iterator

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

growArraySize

protected final int growArraySize

See Also:

Constant Field Values

reactants

protected IAtomContainerSet reactants

products

protected IAtomContainerSet products

agents

protected IAtomContainerSet agents

These are the used solvent, catalysts etc that normally appear above the reaction arrow

map

protected IMapping[] map

mappingCount

protected int mappingCount

Constructor Detail

Reaction

public Reaction()

Constructs an empty, forward reaction.

Method Detail

getReactantCount

public int getReactantCount()

Returns the number of reactants in this reaction.

Specified by:

getReactantCount in interface IReaction

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

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

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

Returns:

A MoleculeSet containing the reactants in this reaction

See Also:

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

setReactants

public void setReactants(IAtomContainerSet setOfMolecules)

Assigns a MoleculeSet to the reactants in this reaction.

Specified by:

setReactants in interface IReaction

Parameters:

setOfMolecules - The new set of reactants

See Also:

getReactants()

getProducts

public IAtomContainerSet getProducts()

Returns a MoleculeSet containing the products of this reaction.

Specified by:

getProducts in interface IReaction

Returns:

A MoleculeSet containing the products in this reaction

See Also:

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

setProducts

public void setProducts(IAtomContainerSet setOfMolecules)

Assigns a MoleculeSet to the products of this reaction.

Specified by:

setProducts in interface IReaction

Parameters:

setOfMolecules - The new set of products

See Also:

getProducts()

getAgents

public IAtomContainerSet getAgents()

Returns a MoleculeSet containing the agents in this reaction.

Specified by:

getAgents in interface IReaction

Returns:

A MoleculeSet containing the agents in this reaction

See Also:

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

mappings

public Iterable<IMapping> mappings()

Returns the mappings between the reactant and the product side.

Specified by:

mappings in interface IReaction

Returns:

An Iterator to the Mappings.

See Also:

addMapping(org.openscience.cdk.interfaces.IMapping)

addReactant

public void addReactant(IAtomContainer reactant)

Adds a reactant to this reaction.

Specified by:

addReactant in interface IReaction

Parameters:

reactant - Molecule added as reactant to this reaction

See Also:

getReactants()

addAgent

public void addAgent(IAtomContainer agent)

Adds an agent to this reaction.

Specified by:

addAgent in interface IReaction

Parameters:

agent - Molecule added as agent to this reaction

See Also:

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

Parameters:

reactant - Molecule added as reactant to this reaction

coefficient - Stoichiometry coefficient for this molecule

See Also:

getReactants()

addProduct

public void addProduct(IAtomContainer product)

Adds a product to this reaction.

Specified by:

addProduct in interface IReaction

Parameters:

product - Molecule added as product to this reaction

See Also:

getProducts()

addProduct

public void addProduct(IAtomContainer product,
                       Double coefficient)

Adds a product to this reaction.

Specified by:

addProduct in interface IReaction

Parameters:

product - Molecule added as product to this reaction

coefficient - Stoichiometry coefficient for this molecule

See Also:

getProducts()

getReactantCoefficient

public Double getReactantCoefficient(IAtomContainer reactant)

Returns the stoichiometry coefficient of the given reactant.

Specified by:

getReactantCoefficient in interface IReaction

Parameters:

reactant - Reactant for which the coefficient is returned.

Returns:

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

See Also:

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

Parameters:

product - Product for which the coefficient is returned.

Returns:

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

See Also:

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

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:

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

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:

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

Returns:

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

See Also:

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

Returns:

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

See Also:

setProductCoefficients(java.lang.Double[])

setReactantCoefficients

public boolean setReactantCoefficients(Double[] coefficients)

Sets the coefficients of the reactants.

Specified by:

setReactantCoefficients in interface IReaction

Parameters:

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

Returns:

true if coefficients have been set.

See Also:

getReactantCoefficients()

setProductCoefficients

public boolean setProductCoefficients(Double[] coefficients)

Sets the coefficient of the products.

Specified by:

setProductCoefficients in interface IReaction

Parameters:

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

Returns:

true if coefficients have been set.

See Also:

getProductCoefficients()

setDirection

public void setDirection(IReaction.Direction direction)

Sets the direction of the reaction.

Specified by:

setDirection in interface IReaction

Parameters:

direction - The new reaction direction

See Also:

getDirection()

getDirection

public IReaction.Direction getDirection()

Returns the direction of the reaction.

Specified by:

getDirection in interface IReaction

Returns:

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

See Also:

IReaction.Direction, setDirection(org.openscience.cdk.interfaces.IReaction.Direction)

addMapping

public void addMapping(IMapping mapping)

Adds a mapping between the reactant and product side to this Reaction.

Specified by:

addMapping in interface IReaction

Parameters:

mapping - Mapping to add.

See Also:

mappings()

removeMapping

public void removeMapping(int pos)

Removes a mapping between the reactant and product side to this Reaction.

Specified by:

removeMapping in interface IReaction

Parameters:

pos - Position of the Mapping to remove.

See Also:

mappings()

getMapping

public IMapping getMapping(int pos)

Retrieves a mapping between the reactant and product side to this Reaction.

Specified by:

getMapping in interface IReaction

Parameters:

pos - Position of Mapping to get.

Returns:

the mapping identified by the specified position

getMappingCount

public int getMappingCount()

Get the number of mappings between the reactant and product side to this Reaction.

Specified by:

getMappingCount in interface IReaction

Returns:

Number of stored Mappings.

toString

public String toString()

Returns a one line string representation of this Atom. Methods is conform RFC #9.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

The string representation of this Atom

clone

public Object clone()
             throws CloneNotSupportedException

Clones this Reaction and its content.

Specified by:

clone in interface IChemObject

Overrides:

clone in class ChemObject

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned