Package org.openscience.cdk.reaction.type

Class PiBondingMovementReaction

java.lang.Object

org.openscience.cdk.reaction.ReactionEngine

org.openscience.cdk.reaction.type.PiBondingMovementReaction

All Implemented Interfaces:

IReactionProcess

public class PiBondingMovementReaction
extends ReactionEngine
implements IReactionProcess

IReactionProcess which tries to reproduce the delocalization of electrons which are unsaturated bonds from conjugated rings. Only is allowed those movements which produces from neutral to neutral structures and not take account the possible movements influenced from lone pairs, or empty orbitals. This movements are typically from rings without any access or deficiency of charge and have a even number of atoms.

The reaction don't care if the product are the same in symmetry.

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

Source code:

main

Belongs to CDK module:

reaction

Created on:

2007-02-02

Field Summary

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

mechanism, paramsMap, paramsMap2

Constructor Summary

Constructors

Constructor	Description
PiBondingMovementReaction()	Constructor of the PiBondingMovementReaction object

Method Summary

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

PiBondingMovementReaction

public PiBondingMovementReaction()

Constructor of the PiBondingMovementReaction object

Method Detail

getSpecification

public ReactionSpecification getSpecification()

Gets the specification attribute of the PiBondingMovementReaction 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