org.openscience.cdk.reaction.type

Class AdductionProtonLPReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.AdductionProtonLPReaction

All Implemented Interfaces:

IReactionProcess

public class AdductionProtonLPReaction
extends ReactionEngine
implements IReactionProcess

IReactionProcess which produces a protonation. As most commonly encountered, this reaction results in the formal migration of a hydrogen atom or proton, accompanied by a switch of a single bond and adjacent double bond

[X-] + [H+] => X -H

|X + [H+]   => [X+]-H

Below you have an example how to initiate the mechanism.

It is processed by the AdductionLPMechanism class

  IAtomContainerSet setOfReactants = DefaultChemObjectBuilder.getInstance().newAtomContainerSet();
  setOfReactants.addAtomContainer(new AtomContainer());
  IReactionProcess type = new AdductionProtonLPReaction();
  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 specify 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 specified then the reaction process will try to find automatically the possible reaction centers.

Author:

Miguel Rojas

See Also:

AdductionLPMechanism

Source code:

master

Belongs to CDK module:

reaction

Created on:

2008-02-11

Field Summary

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

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

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

Method Summary

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

AdductionProtonLPReaction

public AdductionProtonLPReaction()

Constructor of the AdductionProtonLPReaction object.

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the AdductionProtonLPReaction 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