Class AdductionProtonPBReaction
- java.lang.Object
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- org.openscience.cdk.reaction.ReactionEngine
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- org.openscience.cdk.reaction.type.AdductionProtonPBReaction
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- All Implemented Interfaces:
IReactionProcess
public class AdductionProtonPBReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which produces a protonation to double bond. 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
A=B + [H+] => [A+]-B-H
Below you have an example how to initiate the mechanism.
It is processed by the AdductionPBMechanism class
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new AdductionProtonLPReaction(); 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:
AdductionPBMechanism
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2008-02-11
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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 AdductionProtonPBReaction()
Constructor of the AdductionProtonPBReaction 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 AdductionProtonPBReaction object.IReactionSet
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 AdductionProtonPBReaction 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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