Class RearrangementCationReaction
- java.lang.Object
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- org.openscience.cdk.reaction.ReactionEngine
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- org.openscience.cdk.reaction.type.RearrangementCationReaction
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- All Implemented Interfaces:
IReactionProcess
public class RearrangementCationReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which participate in movement resonance. This reaction could be represented as [A+]-B=C => A=B-[c+]. Due to deficiency of charge of the atom A, the double bond is desplaced.
Make sure that the molecule has the corresponend lone pair electrons for each atom. You can use the method:
LonePairElectronChecker
It is processed by the RearrangementChargeMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new RearrangementCationReaction(); 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 posible reactive center.
- Author:
- Miguel Rojas
- See Also:
RearrangementChargeMechanism
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2006-05-05
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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 RearrangementCationReaction()
Constructor of the RearrangementCharge2Reaction 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 RearrangementCationReaction 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 RearrangementCationReaction 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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