Package org.openscience.cdk.reaction.type

Class RadicalChargeSiteInitiationHReaction

java.lang.Object
org.openscience.cdk.reaction.ReactionEngine
org.openscience.cdk.reaction.type.RadicalChargeSiteInitiationHReaction
All Implemented Interfaces:
IReactionProcess
public class RadicalChargeSiteInitiationHReaction extends ReactionEngine implements IReactionProcess

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

Make sure that the molecule has the correspond 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 RadicalChargeSiteInitiationHReaction();
  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:
Created on:
2006-10-18

  • Constructor Details

    • RadicalChargeSiteInitiationHReaction

      public RadicalChargeSiteInitiationHReaction()
      Constructor of the RadicalChargeSiteInitiationHReaction object

  • Method Details