org.openscience.cdk.qsar.descriptors.molecular
Class KappaShapeIndicesDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptorTest")
public class KappaShapeIndicesDescriptor
extends Object
implements IMolecularDescriptor

Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape. Note that hydrogens are ignored. In the following description, n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3".

Returns three values in the order

1. Kier1 - First kappa shape index
2. Kier2 - Second kappa shape index
3. Kier3 - Third kappa (κ) shape index

This descriptor does not have any parameters.

Author:

mfe4

Belongs to the set:

qsar-descriptors

Keywords:

Kappe shape index, descriptor

Created on:

2004-11-03

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

KappaShapeIndicesDescriptor()
Constructor for the KappaShapeIndicesDescriptor object

Method Summary

DescriptorValue	calculate(IAtomContainer container) calculates the kier shape indices for an atom container
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
String[]	getParameterNames() Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object
Object[]	getParameters() Gets the parameters attribute of the KappaShapeIndicesDescriptor object
Object	getParameterType(String name) Gets the parameterType attribute of the KappaShapeIndicesDescriptor object
DescriptorSpecification	getSpecification() Gets the specification attribute of the KappaShapeIndicesDescriptor object
void	setParameters(Object[] params) Sets the parameters attribute of the KappaShapeIndicesDescriptor object

Methods inherited from class java.lang.Object

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

Constructor Detail

KappaShapeIndicesDescriptor

public KappaShapeIndicesDescriptor()

Constructor for the KappaShapeIndicesDescriptor object

Method Detail

getSpecification

@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification()

Gets the specification attribute of the KappaShapeIndicesDescriptor object

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the KappaShapeIndicesDescriptor object

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

IDescriptor.getParameters()

getParameters

@TestMethod(value="testGetParameters")
public Object[] getParameters()

Gets the parameters attribute of the KappaShapeIndicesDescriptor object

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

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

getDescriptorNames

@TestMethod(value="testNamesConsistency")
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 decsriptor (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

@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container)

calculates the kier shape indices for an atom container

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - AtomContainer

Returns:

kier1, kier2 and kier3 are returned as arrayList of doubles

Throws:

CDKException - Possible Exceptions

getDescriptorResultType

@TestMethod(value="testGetDescriptorResultType")
public IDescriptorResult getDescriptorResultType()

Returns the specific type of the DescriptorResult object.

The return value from this method really indicates what type of result will be obtained from the DescriptorValue object. Note that the same result can be achieved by interrogating the DescriptorValue object; this method allows you to do the same thing, without actually calculating the descriptor.

Specified by:

getDescriptorResultType in interface IMolecularDescriptor

Returns:

an object that implements the IDescriptorResult interface indicating the actual type of values returned by the descriptor in the DescriptorValue object

getParameterNames

@TestMethod(value="testGetParameterNames")
public String[] getParameterNames()

Gets the parameterNames attribute of the KappaShapeIndicesDescriptor object

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name)

Gets the parameterType attribute of the KappaShapeIndicesDescriptor object

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value