IReaction (cdk 2.5 API)

All Superinterfaces:

Cloneable, ICDKObject, IChemObject

All Known Implementing Classes:

DebugReaction, Reaction, Reaction
```
public interface IReaction
extends IChemObject
```
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>

Source code:
master

Belongs to CDK module:
interfaces

Keywords:

reaction

Created on:

2003-02-13

Nested Class Summary

Nested Classes
Modifier and Type Interface and Description

static class IReaction.Direction
Permissible reaction directions.

Nested Classes
Modifier and Type	Interface and Description
`static class`	`IReaction.Direction` Permissible reaction directions.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and 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.
`IAtomContainerSet`	`getAgents()` Returns a IAtomContaineSet containing the agents in this reaction.
`IReaction.Direction`	`getDirection()` Returns the `IReaction.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 IAtomContaineSet 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 IAtomContaineSet 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 products)` Assigns a IAtomContaineSet 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 reactants)` Assigns a IAtomContaineSet to the reactants in this reaction.

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject
addListener, addProperties, clone, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

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

- Method Detail
  - getReactantCount
```
int getReactantCount()
```
    Returns the number of reactants in this reaction.
    
    Returns:
    
    The number of reactants in this reaction
  - getProductCount
```
int getProductCount()
```
    Returns the number of products in this reaction.
    
    Returns:
    
    The number of products in this reaction
  - getReactants
```
IAtomContainerSet getReactants()
```
    Returns a IAtomContaineSet containing the reactants in this reaction.
    
    Returns:
    
    A IAtomContaineSet containing the reactants in this reaction
    
    See Also:
    
    setReactants(org.openscience.cdk.interfaces.IAtomContainerSet)
  - setReactants
```
void setReactants(IAtomContainerSet reactants)
```
    Assigns a IAtomContaineSet to the reactants in this reaction.
    
    Parameters:
    
    reactants - The new set of reactants
    
    See Also:
    
    getReactants()
  - getProducts
```
IAtomContainerSet getProducts()
```
    Returns a IAtomContaineSet containing the products of this reaction.
    
    Returns:
    
    A IAtomContaineSet containing the products in this reaction
    
    See Also:
    
    setProducts(org.openscience.cdk.interfaces.IAtomContainerSet)
  - setProducts
```
void setProducts(IAtomContainerSet products)
```
    Assigns a IAtomContaineSet to the products of this reaction.
    
    Parameters:
    
    products - The new set of products
    
    See Also:
    
    getProducts()
  - getAgents
```
IAtomContainerSet getAgents()
```
    Returns a IAtomContaineSet containing the agents in this reaction.
    
    Returns:
    
    A IAtomContaineSet containing the agents in this reaction
    
    See Also:
    
    addAgent(org.openscience.cdk.interfaces.IAtomContainer)
  - mappings
```
Iterable<IMapping> mappings()
```
    Returns the mappings between the reactant and the product side.
    
    Returns:
    
    An Iterable to the Mappings.
    
    See Also:
    
    addMapping(org.openscience.cdk.interfaces.IMapping)
  - addReactant
```
void addReactant(IAtomContainer reactant)
```
    Adds a reactant to this reaction.
    
    Parameters:
    
    reactant - Molecule added as reactant to this reaction
    
    See Also:
    
    getReactants()
  - addAgent
```
void addAgent(IAtomContainer agent)
```
    Adds an agent to this reaction.
    
    Parameters:
    
    agent - Molecule added as agent to this reaction
    
    See Also:
    
    getAgents()
  - addReactant
```
void addReactant(IAtomContainer reactant,
                 Double coefficient)
```
    Adds a reactant to this reaction with a stoichiometry coefficient.
    
    Parameters:
    
    reactant - Molecule added as reactant to this reaction
    
    coefficient - Stoichiometry coefficient for this molecule
    
    See Also:
    
    getReactants()
  - addProduct
```
void addProduct(IAtomContainer product)
```
    Adds a product to this reaction.
    
    Parameters:
    
    product - Molecule added as product to this reaction
    
    See Also:
    
    getProducts()
  - addProduct
```
void addProduct(IAtomContainer product,
                Double coefficient)
```
    Adds a product to this reaction.
    
    Parameters:
    
    product - Molecule added as product to this reaction
    
    coefficient - Stoichiometry coefficient for this molecule
    
    See Also:
    
    getProducts()
  - getReactantCoefficient
```
Double getReactantCoefficient(IAtomContainer reactant)
```
    Returns the stoichiometry coefficient of the given reactant.
    
    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
```
Double getProductCoefficient(IAtomContainer product)
```
    Returns the stoichiometry coefficient of the given product.
    
    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
```
boolean setReactantCoefficient(IAtomContainer reactant,
                               Double coefficient)
```
    Sets the coefficient of a a reactant to a given value.
    
    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
```
boolean setProductCoefficient(IAtomContainer product,
                              Double coefficient)
```
    Sets the coefficient of a a product to a given value.
    
    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
```
Double[] getReactantCoefficients()
```
    Returns an array of double with the stoichiometric coefficients of the reactants.
    
    Returns:
    
    An array of double's containing the coefficients of the reactants
    
    See Also:
    
    setReactantCoefficients(java.lang.Double[])
  - getProductCoefficients
```
Double[] getProductCoefficients()
```
    Returns an array of double with the stoichiometric coefficients of the products.
    
    Returns:
    
    An array of double's containing the coefficients of the products
    
    See Also:
    
    setProductCoefficients(java.lang.Double[])
  - setReactantCoefficients
```
boolean setReactantCoefficients(Double[] coefficients)
```
    Sets the coefficients of the reactants.
    
    Parameters:
    
    coefficients - An array of double's containing the coefficients of the reactants
    
    Returns:
    
    true if coefficients have been set.
    
    See Also:
    
    getReactantCoefficients()
  - setProductCoefficients
```
boolean setProductCoefficients(Double[] coefficients)
```
    Sets the coefficient of the products.
    
    Parameters:
    
    coefficients - An array of double's containing the coefficients of the products
    
    Returns:
    
    true if coefficients have been set.
    
    See Also:
    
    getProductCoefficients()
  - setDirection
```
void setDirection(IReaction.Direction direction)
```
    Sets the direction of the reaction.
    
    Parameters:
    
    direction - The new reaction direction
    
    See Also:
    
    getDirection()
  - getDirection
```
IReaction.Direction getDirection()
```
    Returns the IReaction.Direction of the reaction.
    
    Returns:
    
    The direction of this reaction (FORWARD, BACKWARD or BIDIRECTIONAL).
    
    See Also:
    
    setDirection(Direction)
  - addMapping
```
void addMapping(IMapping mapping)
```
    Adds a mapping between the reactant and product side to this Reaction.
    
    Parameters:
    
    mapping - Mapping to add.
    
    See Also:
    
    mappings()
  - removeMapping
```
void removeMapping(int pos)
```
    Removes a mapping between the reactant and product side to this Reaction.
    
    Parameters:
    
    pos - Position of the Mapping to remove.
    
    See Also:
    
    mappings()
  - getMapping
```
IMapping getMapping(int pos)
```
    Retrieves a mapping between the reactant and product side to this Reaction.
    
    Parameters:
    
    pos - Position of Mapping to get.
    
    Returns:
    
    the mapping identified by the specified position
  - getMappingCount
```
int getMappingCount()
```
    Get the number of mappings between the reactant and product side to this Reaction.
    
    Returns:
    
    Number of stored Mappings.

Interface IReaction

Nested Class Summary

Method Summary

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

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

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