org.openscience.cdk.qsar.descriptors.atomic

Class SigmaElectronegativityDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.SigmaElectronegativityDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class SigmaElectronegativityDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor

Atomic descriptor that reflects that Gasteiger-Marsili sigma electronegativity. The used approach is given by

X = a + bq + c(q*q)

where a, b, and c are the Gasteiger-Marsili parameters and q is the sigma charge. For the actual calculation it uses the Electronegativity class.

Parameters for this descriptor:

Name	Default	Description
maxIterations	0	Number of maximum iterations

Author:

mfe4

See Also:

Electronegativity

Dictionary pointer(s):

sigmaElectronegativity in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:sigmaElectronegativity]

Source code:

master

Belongs to CDK module:

qsaratomic

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor and Description
SigmaElectronegativityDescriptor() Constructor for the SigmaElectronegativityDescriptor object

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer ac) The method calculates the sigma electronegativity 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 SigmaElectronegativityDescriptor object
Object[]	getParameters() Gets the parameters attribute of the SigmaElectronegativityDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the SigmaElectronegativityDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the SigmaElectronegativityDescriptor object
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the SigmaElectronegativityDescriptor 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

SigmaElectronegativityDescriptor

public SigmaElectronegativityDescriptor()

Constructor for the SigmaElectronegativityDescriptor object

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the SigmaElectronegativityDescriptor 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 SigmaElectronegativityDescriptor 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 SigmaElectronegativityDescriptor 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 ac)

The method calculates the sigma electronegativity 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

ac - AtomContainer

Returns:

return the sigma electronegativity

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the SigmaElectronegativityDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the SigmaElectronegativityDescriptor 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