Class RadicalSiteHrGammaReaction
- java.lang.Object
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- org.openscience.cdk.reaction.ReactionEngine
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- org.openscience.cdk.reaction.type.RadicalSiteHrGammaReaction
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- All Implemented Interfaces:
IReactionProcess
public class RadicalSiteHrGammaReaction extends ReactionEngine implements IReactionProcess
This reaction could be represented as [A*]-C1-C2-C3[H] => A([H])-C1-C2-[C3*]. Due to the single electron of atom A the proton is moved.
It is processed by the RadicalSiteRearrangementMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new RadicalSiteHrGammaReaction(); 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.
The rearrangements are not possible with the atomtype is inside of a ring
- Author:
- Miguel Rojas
- See Also:
RadicalSiteRearrangementMechanism
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-10-20
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Field Summary
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Fields inherited from class org.openscience.cdk.reaction.ReactionEngine
mechanism, paramsMap, paramsMap2
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Constructor Summary
Constructors Constructor Description RadicalSiteHrGammaReaction()
Constructor of the RadicalSiteHrGammaReaction object
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ReactionSpecification
getSpecification()
Gets the specification attribute of the RadicalSiteHrGammaReaction objectIReactionSet
initiate(IAtomContainerSet reactants, IAtomContainerSet agents)
Initiate process.-
Methods inherited from class org.openscience.cdk.reaction.ReactionEngine
getParameterClass, getParameterList, setParameterList
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.reaction.IReactionProcess
getParameterClass, getParameterList, setParameterList
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Method Detail
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getSpecification
public ReactionSpecification getSpecification()
Gets the specification attribute of the RadicalSiteHrGammaReaction 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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