Class RadicalSiteRrGammaReaction
java.lang.Object
org.openscience.cdk.reaction.ReactionEngine
org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction
- All Implemented Interfaces:
IReactionProcess
This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*]. Due to the single electron of atom A the R is moved.
It is processed by the RadicalSiteRearrangementMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new RadicalSiteRrGammaReaction(); Object[] params = {Boolean.FALSE}; type.setParameters(params); IReactionSet setOfReactions = type.initiate(setOfReactants, null);
We have the possibility to localize the reactive center. Good method if you want to localize the reaction in a fixed point
atoms[0].setFlag(CDKConstants.REACTIVE_CENTER,true);
Moreover you must put the parameter Boolean.TRUE
If the reactive center is not localized then the reaction process will try to find automatically the possible reactive center.
- Author:
- Miguel Rojas
- See Also:
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-10-20
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Field Summary
Fields inherited from class org.openscience.cdk.reaction.ReactionEngine
mechanism, paramsMap, paramsMap2
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Constructor Summary
ConstructorsConstructorDescriptionConstructor of the RadicalSiteRrGammaReaction object -
Method Summary
Modifier and TypeMethodDescriptionGets the specification attribute of the RadicalSiteRrGammaReaction objectinitiate
(IAtomContainerSet reactants, IAtomContainerSet agents) Initiate process.Methods inherited from class org.openscience.cdk.reaction.ReactionEngine
getParameterClass, getParameterList, setParameterList
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.openscience.cdk.reaction.IReactionProcess
getParameterClass, getParameterList, setParameterList
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Constructor Details
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RadicalSiteRrGammaReaction
public RadicalSiteRrGammaReaction()Constructor of the RadicalSiteRrGammaReaction object
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Method Details
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getSpecification
Gets the specification attribute of the RadicalSiteRrGammaReaction object- Specified by:
getSpecification
in interfaceIReactionProcess
- Returns:
- The specification value
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initiate
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class tools.HydrogenAdder.- Specified by:
initiate
in interfaceIReactionProcess
- Parameters:
reactants
- reactants of the reaction.agents
- agents of the reaction (Must be in this case null).- Returns:
- the set of reactions.
- Throws:
CDKException
- Description of the Exception
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