org.openscience.cdk.reaction.type

Class ElectronImpactPDBReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.ElectronImpactPDBReaction

All Implemented Interfaces:

IReactionProcess

public class ElectronImpactPDBReaction
extends ReactionEngine
implements IReactionProcess

IReactionProcess which make an electron impact for pi-Bond Dissociation.

This reaction type is a representation of the processes which occurs in the mass spectrometer.

It is processed by the RemovingSEofPBMechanism class

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

RemovingSEofBMechanism

Source code:

master

Belongs to CDK module:

reaction

Created on:

2006-04-01

Field Summary

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

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

Constructor and Description
ElectronImpactPDBReaction() Constructor of the ElectronImpactPDBReaction object.

Method Summary

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

ElectronImpactPDBReaction

public ElectronImpactPDBReaction()

Constructor of the ElectronImpactPDBReaction object.

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the ElectronImpactPDBReaction 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