public class PiBondingMovementReaction extends ReactionEngine implements IReactionProcess
IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings. Only is allowed those movements which produces from neutral to neutral structures and not take account the possible movements influenced from lone pairs, or empty orbitals. This movements are typically from rings without any access or deficiency of charge and have a even number of atoms.
The reaction don't care if the product are the same in symmetry.
IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet(); setOfReactants.addAtomContainer(new AtomContainer()); IReactionProcess type = new PiBondingMovementReaction(); 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 possible reactive center.
mechanism, paramsMap, paramsMap2
Constructor and Description |
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PiBondingMovementReaction()
Constructor of the PiBondingMovementReaction object
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Modifier and Type | Method and Description |
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ReactionSpecification |
getSpecification()
Gets the specification attribute of the PiBondingMovementReaction 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 PiBondingMovementReaction()
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 © 2021. All rights reserved.