java.lang.Object
- org.openscience.cdk.silent.ChemObject
- - org.openscience.cdk.silent.Reaction

All Implemented Interfaces:

Serializable, Cloneable, 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`

Constructor Summary

Constructors
Constructor Description

Reaction()
Constructs an empty, forward reaction.

Method Summary

All Methods Instance Methods Concrete Methods
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.
`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, compare, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, 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, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty

- 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
  - 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

Class Reaction

Nested Class Summary

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

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

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

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

Field Detail

growArraySize

reactants

products

agents

map

mappingCount

Constructor Detail

Reaction

Method Detail

getReactantCount

getProductCount

getReactants

setReactants

getProducts

setProducts

getAgents

mappings

addReactant

addAgent

addReactant

addProduct

addProduct

getReactantCoefficient

getProductCoefficient

setReactantCoefficient

setProductCoefficient

getReactantCoefficients

getProductCoefficients

setReactantCoefficients

setProductCoefficients

setDirection

getDirection

addMapping

removeMapping

getMapping

getMappingCount

toString

clone