Class AdductionSodiumLPReaction
java.lang.Object
org.openscience.cdk.reaction.ReactionEngine
org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
- All Implemented Interfaces:
IReactionProcess
IReactionProcess which produces an adduction of the Sodium. As most commonly encountered, this reaction results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond
[X-] + [Na+] => X -Na
|X + [Na+] => [X+]-Na
Below you have an example how to initiate the mechanism.
It is processed by the AdductionLPMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new AdductionSodiumLPReaction(); 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 specify 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 specified then the reaction process will try to find automatically the possible reaction centers.
- Author:
- Miguel Rojas
- See Also:
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2008-02-11
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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 AdductionSodiumLPReaction object. -
Method Summary
Modifier and TypeMethodDescriptionGets the specification attribute of the AdductionSodiumLPReaction object.initiate
(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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AdductionSodiumLPReaction
public AdductionSodiumLPReaction()Constructor of the AdductionSodiumLPReaction object.
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Method Details
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getSpecification
Gets the specification attribute of the AdductionSodiumLPReaction 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 reactionagents
- 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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