org.openscience.cdk.qsar.descriptors.atomic

Class StabilizationPlusChargeDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.StabilizationPlusChargeDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class StabilizationPlusChargeDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor

The stabilization of the positive charge (e.g.) obtained in the polar breaking of a bond is calculated from the sigma- and lone pair-electronegativity values of the atoms that are in conjugation to the atoms obtaining the charges. The method is based following (Saller, H., Quantitative Emperische Modelle fur Elektronische Effekte in Pi-Systemen und fur die Chemische Reaktivitat, 1985, ?Institute?). The value is calculated looking for resonance structures which can stabilize the charge.

Parameters for this descriptor:

Name	Default	Description
maxIterations	0	Number of maximum iterations

Author:

Miguel Rojas Cherto

See Also:

StabilizationCharges

Source code:

master

Belongs to CDK module:

qsaratomic

Created on:

2008-104-31

Constructor Summary

Constructors

Constructor and Description
StabilizationPlusChargeDescriptor() Constructor for the StabilizationPlusChargeDescriptor object

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer container) The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor object
Object[]	getParameters() Gets the parameters attribute of the StabilizationPlusChargeDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the StabilizationPlusChargeDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the StabilizationPlusChargeDescriptor object
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the StabilizationPlusChargeDescriptor object

Methods inherited from class org.openscience.cdk.qsar.AbstractAtomicDescriptor

cacheDescriptorValue, getCachedDescriptorValue, isCachedAtomContainer

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.qsar.IDescriptor

initialise

Constructor Detail

StabilizationPlusChargeDescriptor

public StabilizationPlusChargeDescriptor()

Constructor for the StabilizationPlusChargeDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the StabilizationPlusChargeDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the StabilizationPlusChargeDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - 1: max iterations (optional, defaults to 20)

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the StabilizationPlusChargeDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

IDescriptor.setParameters(java.lang.Object[])

getDescriptorNames

public String[] getDescriptorNames()

Description copied from interface: IDescriptor

Returns an array of names for each descriptor value calculated. Many descriptors return multiple values. In general it is useful for the descriptor to indicate the names for each value. In many cases, these names can be as simple as X1, X2, ..., XN where X is a prefix and 1, 2, ..., N are the indices. On the other hand it is also possible to return other arbitrary names, which should be documented in the Javadocs for the descriptor (e.g., the CPSA descriptor). Note that by default if a descriptor returns a single value (such as ALOGPDescriptor the return array will have a single element

Specified by:

getDescriptorNames in interface IDescriptor

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

public DescriptorValue calculate(IAtom atom,
                                 IAtomContainer container)

The method calculates the stabilization of charge of a given atom It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

container - AtomContainer

Returns:

return the stabilization value

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the StabilizationPlusChargeDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the StabilizationPlusChargeDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build