public class AdductionProtonLPReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which produces a protonation. 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-] + [H+] => X -H
|X + [H+] => [X+]-H
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 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.
AdductionLPMechanism
mechanism, paramsMap, paramsMap2
Constructor and Description |
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AdductionProtonLPReaction()
Constructor of the AdductionProtonLPReaction object.
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Modifier and Type | Method and Description |
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ReactionSpecification |
getSpecification()
Gets the specification attribute of the AdductionProtonLPReaction object.
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IReactionSet |
initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
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getParameterClass, getParameterList, setParameterList
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getParameterClass, getParameterList, setParameterList
public AdductionProtonLPReaction()
public ReactionSpecification getSpecification()
getSpecification
in interface IReactionProcess
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException
initiate
in interface IReactionProcess
reactants
- reactants of the reactionagents
- agents of the reaction (Must be in this case null)CDKException
- Description of the ExceptionCopyright © 2017. All Rights Reserved.