org.openscience.cdk.qsar.descriptors.atomic

Class InductiveAtomicSoftnessDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractAtomicDescriptor

org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

public class InductiveAtomicSoftnessDescriptor
extends AbstractAtomicDescriptor
implements IAtomicDescriptor

Inductive atomic softness of an atom in a polyatomic system can be defined as charge delocalizing ability. Only works with 3D coordinates, which must be calculated beforehand.

Table 1 - Parameters for this descriptor

Name	Default	Description
		no parameters

Author:

mfe4

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsaratomic

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor and Description
InductiveAtomicSoftnessDescriptor() Constructor for the InductiveAtomicSoftnessDescriptor object

Method Summary

Methods

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtom atom, IAtomContainer ac) It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) This descriptor does have any parameter.

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

InductiveAtomicSoftnessDescriptor

public InductiveAtomicSoftnessDescriptor()
                                  throws IOException,
                                         ClassNotFoundException

Constructor for the InductiveAtomicSoftnessDescriptor object

Throws:

IOException - Description of the Exception

ClassNotFoundException - Description of the Exception

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the InductiveAtomicSoftnessDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

This descriptor does have any parameter.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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)

It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder, and 3D coordinates.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

atom - The IAtom for which the DescriptorValue is requested

ac - AtomContainer

Returns:

a double with polarizability of the heavy atom

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor 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