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.
RearrangementChargeMechanism
mechanism, paramsMap, paramsMap2
Constructor and Description |
---|
RearrangementCationReaction()
Constructor of the RearrangementCharge2Reaction object
|
Modifier and Type | Method and Description |
---|---|
ReactionSpecification |
getSpecification()
Gets the specification attribute of the RearrangementCationReaction object
|
IReactionSet |
initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
getParameterClass, getParameterList, setParameterList
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getParameterClass, getParameterList, setParameterList
public RearrangementCationReaction()
public ReactionSpecification getSpecification()
getSpecification
in interface IReactionProcess
public IReactionSet initiate(IAtomContainerSet reactants, IAtomContainerSet agents) throws CDKException
initiate
in interface IReactionProcess
reactants
- reactants of the reaction.agents
- agents of the reaction (Must be in this case null).CDKException
- Description of the ExceptionCopyright © 2018. All Rights Reserved.