Package org.openscience.cdk.reaction.type

Class HeterolyticCleavageSBReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.HeterolyticCleavageSBReaction

All Implemented Interfaces:

IReactionProcess

public class HeterolyticCleavageSBReaction
extends ReactionEngine
implements IReactionProcess

IReactionProcess which a bond is broken displacing the electron to one of the atoms. The mechanism will produce one atom with excess of charge and the other one deficiency. Depending of the bond order, the bond will be removed or simply the order decreased. As there are two directions for displacing a bond in a polar manner, each case is investigated twice:

A-B => [A+] + |[B-]

A-B => |[A-] + [B+]

It will not be created structures no possible, e.g; C=O => [C-][O+].

Below you have an example how to initiate the mechanism.

It is processed by the HeterolyticCleavageMechanism class

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

HeterolyticCleavageMechanism

Source code:

main

Belongs to CDK module:

reaction

Created on:

2006-06-09

Field Summary

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

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

Constructor	Description
HeterolyticCleavageSBReaction()	Constructor of the HeterolyticCleavageSBReaction object.

Method Summary

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

HeterolyticCleavageSBReaction

public HeterolyticCleavageSBReaction()

Constructor of the HeterolyticCleavageSBReaction object.

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the HeterolyticCleavageSBReaction 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