org.openscience.cdk.reaction

Interface IReactionProcess

All Known Implementing Classes:

AdductionProtonLPReaction, AdductionProtonPBReaction, AdductionSodiumLPReaction, CarbonylEliminationReaction, ElectronImpactNBEReaction, ElectronImpactPDBReaction, ElectronImpactSDBReaction, HeterolyticCleavagePBReaction, HeterolyticCleavageSBReaction, HomolyticCleavageReaction, HyperconjugationReaction, PiBondingMovementReaction, RadicalChargeSiteInitiationHReaction, RadicalChargeSiteInitiationReaction, RadicalSiteHrAlphaReaction, RadicalSiteHrBetaReaction, RadicalSiteHrDeltaReaction, RadicalSiteHrGammaReaction, RadicalSiteInitiationHReaction, RadicalSiteInitiationReaction, RadicalSiteRrAlphaReaction, RadicalSiteRrBetaReaction, RadicalSiteRrDeltaReaction, RadicalSiteRrGammaReaction, RearrangementAnionReaction, RearrangementCationReaction, RearrangementLonePairReaction, RearrangementRadicalReaction, SharingAnionReaction, SharingChargeDBReaction, SharingChargeSBReaction, SharingLonePairReaction, TautomerizationReaction

public interface IReactionProcess

Classes that implement this interface are Reactions types.

Author:

Miguel Rojas

Source code:

master

Belongs to CDK module:

reaction

Method Summary

Modifier and Type	Method and Description
IParameterReact	getParameterClass(Class<?> paramClass) Return the IParameterReact if it exists given the class.
List<IParameterReact>	getParameterList() Returns the current parameter values.
ReactionSpecification	getSpecification() Returns a Map which specifies which reaction is implemented by this class.
IReactionSet	initiate(IAtomContainerSet reactants, IAtomContainerSet agents) Initiates the process for the given Reaction.
void	setParameterList(List<IParameterReact> params) Sets the parameters for this reaction.

Method Detail

getSpecification

ReactionSpecification getSpecification()

Returns a Map which specifies which reaction is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary or web page
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Returns:

An object containing the reaction specification

setParameterList

void setParameterList(List<IParameterReact> params)
               throws CDKException

Sets the parameters for this reaction. Must be done before calling calculate as the parameters influence the calculation outcome.

Parameters:

params - A List of Objects containing the parameters for this reaction. The key must be included into the Dictionary reacton-processes

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

getParameterList()

getParameterList

List<IParameterReact> getParameterList()

Returns the current parameter values.

Returns:

A List of Object containing the name and the type of the parameter

See Also:

setParameterList(java.util.List<org.openscience.cdk.reaction.type.parameters.IParameterReact>)

initiate

IReactionSet initiate(IAtomContainerSet reactants,
                      IAtomContainerSet agents)
               throws CDKException

Initiates the process for the given Reaction. Optionally, parameters may be set which can affect the course of the process.

Parameters:

reactants - An IAtomContainerSet for which this process should be initiate.

agents - An IAtomContainerSet for which this process should be initiate.

Returns:

the set of reactions.

Throws:

CDKException - if an error occurs during the reaction process. See documentation for individual reaction processes

getParameterClass

IParameterReact getParameterClass(Class<?> paramClass)

Return the IParameterReact if it exists given the class.

Parameters:

paramClass - The class

Returns:

The IParameterReact