Class PiBondingMovementReaction
- All Implemented Interfaces:
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.
- Author:
- Miguel Rojas
- Source code:
- main
- Belongs to CDK module:
- reaction
- Created on:
- 2007-02-02
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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 PiBondingMovementReaction object -
Method Summary
Modifier and TypeMethodDescriptionGets the specification attribute of the PiBondingMovementReaction objectinitiate
(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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PiBondingMovementReaction
public PiBondingMovementReaction()Constructor of the PiBondingMovementReaction object
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Method Details
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getSpecification
Gets the specification attribute of the PiBondingMovementReaction 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 reaction.agents
- 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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