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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

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

Evaluates the weighted path descriptors.

These decsriptors were described by Randic ([Randic, M. , On molecular identification numbers , Journal of Chemical Information and Computer Science, 1984, 24:164-175]) and characterize molecular branching. Five descriptors are calculated, based on the implementation in the ADAPT software package. Note that the descriptor is based on identifying all pahs between pairs of atoms and so is NP-hard. This means that it can take some time for large, complex molecules. The class returns a DoubleArrayResult containing the five descriptors in the order described below.

DMWP

WTPT1	molecular ID
WTPT2	molecular ID / number of atoms
WTPT3	sum of path lengths starting from heteroatoms
WTPT4	sum of path lengths starting from oxygens
WTPT5	sum of path lengths starting from nitrogens

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Created on:

2006-01-15

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

HEAD

Constructor Summary

WeightedPathDescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculates the weighted path descriptors.
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 WeightedPathDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the WeightedPathDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the WeightedPathDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(Object[] params) Sets the parameters attribute of the WeightedPathDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

WeightedPathDescriptor

public WeightedPathDescriptor()

Method Detail

getSpecification

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

Description copied from interface: IDescriptor

Returns a Map which specifies which descriptor is implemented by this class. These fields are used in the map:

• Specification-Reference: refers to an entry in a unique dictionary
• Implementation-Title: anything
• Implementation-Identifier: a unique identifier for this version of this class
• Implementation-Vendor: CDK, JOELib, or anything else

Specified by:

getSpecification in interface IDescriptor

Returns:

An object containing the descriptor specification

setParameters

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

Sets the parameters attribute of the WeightedPathDescriptor 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 WeightedPathDescriptor 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..

getParameterNames

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

Gets the parameterNames attribute of the WeightedPathDescriptor 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 WeightedPathDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

calculate

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

Calculates the weighted path descriptors.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - Parameter is the atom container.

Returns:

A DoubleArrayResult value representing the weighted path values

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