org.openscience.cdk.reaction.type

Class RadicalChargeSiteInitiationReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationReaction

All Implemented Interfaces:

IReactionProcess

public class RadicalChargeSiteInitiationReaction
extends ReactionEngine
implements IReactionProcess

IReactionProcess which participate mass spectrum process. Homolitic dissocitation. This reaction could be represented as A-B-[c*+] => [A*] + B=[C+].

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 RadicalSiteIonizationMechanism class

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

RadicalSiteIonizationMechanism

Source code:

master

Belongs to CDK module:

reaction

Created on:

2006-05-05

Field Summary

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

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

Constructor and Description
RadicalChargeSiteInitiationReaction() Constructor of the RadicalChargeSiteInitiationReaction object

Method Summary

Modifier and Type	Method and Description
ReactionSpecification	getSpecification() Gets the specification attribute of the RadicalChargeSiteInitiationReaction 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

RadicalChargeSiteInitiationReaction

public RadicalChargeSiteInitiationReaction()

Constructor of the RadicalChargeSiteInitiationReaction object

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the RadicalChargeSiteInitiationReaction object

Specified by:

getSpecification in interface IReactionProcess

Returns:

The specification value

initiate

public IReactionSet initiate(IAtomContainerSet reactants,
                             IAtomContainerSet agents)
                      throws CDKException

Initiate process.

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