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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description ReactionSpecification
getSpecification()
Gets the specification attribute of the PiBondingMovementReaction objectIReactionSet
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
-
-
-
-
Method Detail
-
getSpecification
public ReactionSpecification getSpecification()
Gets the specification attribute of the PiBondingMovementReaction object- Specified by:
getSpecification
in interfaceIReactionProcess
- 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 interfaceIReactionProcess
- 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
-
-