org.openscience.cdk.reaction.type

Class RadicalSiteRrGammaReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.RadicalSiteRrGammaReaction

All Implemented Interfaces:

IReactionProcess

public class RadicalSiteRrGammaReaction
extends ReactionEngine
implements IReactionProcess

This reaction could be represented as [A*]-(C)_4-C5[R] => A([R])-(C_4)-[C5*]. Due to the single electron of atom A the R is moved.

It is processed by the RadicalSiteRearrangementMechanism class

  IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet();
  setOfReactants.addAtomContainer(new AtomContainer());
  IReactionProcess type = new RadicalSiteRrGammaReaction();
  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

See Also:

RadicalSiteRearrangementMechanism

Source code:

master

Belongs to CDK module:

reaction

Created on:

2006-10-20

Field Summary

Fields inherited from class org.openscience.cdk.reaction.ReactionEngine

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

Constructor and Description
RadicalSiteRrGammaReaction() Constructor of the RadicalSiteRrGammaReaction object

Method Summary

Modifier and Type	Method and Description
ReactionSpecification	getSpecification() Gets the specification attribute of the RadicalSiteRrGammaReaction object
IReactionSet	initiate(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

Constructor Detail

RadicalSiteRrGammaReaction

public RadicalSiteRrGammaReaction()

Constructor of the RadicalSiteRrGammaReaction object

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the RadicalSiteRrGammaReaction object

Specified by:

getSpecification in interface IReactionProcess

Returns:

The specification value

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 interface IReactionProcess

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