Package org.openscience.cdk.interfaces
Interface IReaction
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- 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:
- main
- Belongs to CDK module:
- interfaces
- Keywords:
- reaction
- Created on:
- 2003-02-13
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
IReaction.Direction
Permissible reaction directions.
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Method Summary
All Methods Instance Methods Abstract 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.IAtomContainerSet
getAgents()
Returns a IAtomContaineSet containing the agents in this reaction.IReaction.Direction
getDirection()
Returns theIReaction.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.ICDKObject
getBuilder
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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
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Method Detail
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getReactantCount
int getReactantCount()
Returns the number of reactants in this reaction.- Returns:
- The number of reactants in this reaction
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getProductCount
int getProductCount()
Returns the number of products in this reaction.- Returns:
- The number of products in this reaction
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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)
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setReactants
void setReactants(IAtomContainerSet reactants)
Assigns a IAtomContaineSet to the reactants in this reaction.- Parameters:
reactants
- The new set of reactants- See Also:
getReactants()
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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)
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setProducts
void setProducts(IAtomContainerSet products)
Assigns a IAtomContaineSet to the products of this reaction.- Parameters:
products
- The new set of products- See Also:
getProducts()
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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)
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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)
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addReactant
void addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.- Parameters:
reactant
- Molecule added as reactant to this reaction- See Also:
getReactants()
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addAgent
void addAgent(IAtomContainer agent)
Adds an agent to this reaction.- Parameters:
agent
- Molecule added as agent to this reaction- See Also:
getAgents()
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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 reactioncoefficient
- Stoichiometry coefficient for this molecule- See Also:
getReactants()
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addProduct
void addProduct(IAtomContainer product)
Adds a product to this reaction.- Parameters:
product
- Molecule added as product to this reaction- See Also:
getProducts()
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addProduct
void addProduct(IAtomContainer product, Double coefficient)
Adds a product to this reaction.- Parameters:
product
- Molecule added as product to this reactioncoefficient
- Stoichiometry coefficient for this molecule- See Also:
getProducts()
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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)
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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)
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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 setcoefficient
- 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)
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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 setcoefficient
- 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)
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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[])
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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[])
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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()
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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()
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setDirection
void setDirection(IReaction.Direction direction)
Sets the direction of the reaction.- Parameters:
direction
- The new reaction direction- See Also:
getDirection()
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getDirection
IReaction.Direction getDirection()
Returns theIReaction.Direction
of the reaction.- Returns:
- The direction of this reaction (FORWARD, BACKWARD or BIDIRECTIONAL).
- See Also:
setDirection(Direction)
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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()
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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()
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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
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getMappingCount
int getMappingCount()
Get the number of mappings between the reactant and product side to this Reaction.- Returns:
- Number of stored Mappings.
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