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:
Source code:
main
Belongs to CDK module:
reaction
Created on:
2006-05-05
  • Constructor Details

    • RadicalChargeSiteInitiationReaction

      public RadicalChargeSiteInitiationReaction()
      Constructor of the RadicalChargeSiteInitiationReaction object
  • Method Details