Package org.openscience.cdk.tools

Class StructureResonanceGenerator

java.lang.Object

org.openscience.cdk.tools.StructureResonanceGenerator

public class StructureResonanceGenerator
extends Object

This class try to generate resonance structure for a determinate molecule.

Make sure that the molecule has the corresponding lone pair electrons for each atom. You can use the method:

 LonePairElectronChecker 

It is needed to call the addExplicitHydrogensToSatisfyValency from the class tools.HydrogenAdder.

It is based on rearrangements of electrons and charge

The method is based on call by reactions which occur in a resonance.

 StructureResonanceGenerator srG = new StructureReseonanceGenerator(true,true,true,true,false);
 MoleculeSet setOf = srG.getResonances(new Molecule());
 

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 as 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:

IReactionProcess

Source code:

main

Belongs to CDK module:

reaction

Created on:

2006-5-05

Constructor Summary

Constructors

Constructor	Description
StructureResonanceGenerator()	Construct an instance of StructureResonanceGenerator.
StructureResonanceGenerator(boolean lookingSymmetry)	Construct an instance of StructureResonanceGenerator.

Method Summary

Modifier and Type	Method	Description
IAtomContainer	getContainer(IAtomContainer molecule, IAtom atom)	Get the container which the atom is found on resonance from a IAtomContainer.
IAtomContainer	getContainer(IAtomContainer molecule, IBond bond)	Get the container which the bond is found on resonance from a IAtomContainer.
IAtomContainerSet	getContainers(IAtomContainer molecule)	Get the container which is found resonance from a IAtomContainer.
int	getMaximalStructures()	Get the number maximal of resonance structures to be found.
List<IReactionProcess>	getReactions()	Get the reactions that must be presents in the generation of the resonance.
IAtomContainerSet	getStructures(IAtomContainer molecule)	Get the resonance structures from an IAtomContainer.
void	setDefaultReactions()	Set the default reactions that must be presents to generate the resonance.
void	setMaximalStructures(int maxStruct)	Set the number maximal of resonance structures to be found.
void	setReactions(List<IReactionProcess> newReactionsList)	Set the reactions that must be used in the generation of the resonance.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StructureResonanceGenerator

public StructureResonanceGenerator()

Construct an instance of StructureResonanceGenerator. Default restrictions are initiated.

See Also:

setDefaultReactions()

StructureResonanceGenerator

public StructureResonanceGenerator(boolean lookingSymmetry)

Construct an instance of StructureResonanceGenerator. Default restrictions are initiated.

Parameters:

lookingSymmetry - Specify if the resonance generation is based looking at the symmetry

See Also:

setDefaultReactions()

Method Detail

setReactions

public void setReactions(List<IReactionProcess> newReactionsList)

Set the reactions that must be used in the generation of the resonance.

Parameters:

newReactionsList - The IReactionsProcess's to use

See Also:

getReactions(), setReactions(java.util.List), IReactionProcess

getReactions

public List<IReactionProcess> getReactions()

Get the reactions that must be presents in the generation of the resonance.

Returns:

The reactions to be imposed

See Also:

setDefaultReactions()

setMaximalStructures

public void setMaximalStructures(int maxStruct)

Set the number maximal of resonance structures to be found. The algorithm breaks the process when is came to this number.

Parameters:

maxStruct - The maximal number

getMaximalStructures

public int getMaximalStructures()

Get the number maximal of resonance structures to be found.

Returns:

The maximal number

setDefaultReactions

public void setDefaultReactions()

Set the default reactions that must be presents to generate the resonance.

See Also:

getReactions()

getStructures

public IAtomContainerSet getStructures(IAtomContainer molecule)

Get the resonance structures from an IAtomContainer.

Parameters:

molecule - The IAtomContainer to analyze

Returns:

The different resonance structures

getContainers

public IAtomContainerSet getContainers(IAtomContainer molecule)

Get the container which is found resonance from a IAtomContainer. It is based on looking if the order of the bond changes.

Parameters:

molecule - The IAtomContainer to analyze

Returns:

The different containers

getContainer

public IAtomContainer getContainer(IAtomContainer molecule,
                                   IAtom atom)

Get the container which the atom is found on resonance from a IAtomContainer. It is based on looking if the order of the bond changes. Return null is any is found.

Parameters:

molecule - The IAtomContainer to analyze

atom - The IAtom

Returns:

The container with the atom

getContainer

public IAtomContainer getContainer(IAtomContainer molecule,
                                   IBond bond)

Get the container which the bond is found on resonance from a IAtomContainer. It is based on looking if the order of the bond changes. Return null is any is found.

Parameters:

molecule - The IAtomContainer to analyze

bond - The IBond

Returns:

The container with the bond