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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

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

Holistic descriptors described by Todeschini et al [Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380]. The descriptors are based on a number of atom weightings. There are 6 different possible weightings:

1. unit weights
2. atomic masses
3. van der Waals volumes
4. Mulliken atomic electronegativites
5. atomic polarizabilities
6. E-state values described by Kier & Hall

Currently weighting schemes 1,2,3,4 & 5 are implemented. The weight values are taken from [Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380] and as a result 19 elements are considered.

For each weighting scheme we can obtain

• 11 directional WHIM descriptors (λ_{1 .. 3}, ν_{1 .. 2}, γ_{1 .. 3}, η_{1 .. 3})
• 6 non-directional WHIM descriptors (T, A, V, K, G, D)

Though [Todeschini, R. and Gramatica, P., New 3D Molecular Descriptors: The WHIM theory and QAR Applications, Persepectives in Drug Discovery and Design, 1998, ?:355-380] mentions that for planar molecules only 8 directional WHIM descriptors are required the current code will return all 11.

The descriptor returns 17 values for a given weighting scheme, named as follows:

1. Wlambda1
2. Wlambda2
3. wlambda3
4. Wnu1
5. Wnu2
6. Wgamma1
7. Wgamma2
8. Wgamma3
9. Weta1
10. Weta2
11. Weta3
12. WT
13. WA
14. WV
15. WK
16. WG
17. WD

Each name will have a suffix of the form .X where X indicates the weighting scheme used. Possible values of X are

• unity
• mass
• volume
• eneg
• polar

This descriptor uses these parameters:

Name	Default	Description
type	unity	Type of weighting as described above

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Keywords:

WHIM, descriptor

Created on:

2004-12-1

Required library to be able to run this class:

Jama-1.0.1.jar

Required library to be able to compile this class:

Jama-1.0.1.jar

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

WHIMDescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculates 11 directional and 6 non-directional WHIM descriptors for.
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 WHIMDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the WHIMDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the WHIMDescriptor object.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	setParameters(Object[] params) Sets the parameters attribute of the WHIMDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

WHIMDescriptor

public WHIMDescriptor()

Method Detail

getSpecification

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

Description copied from interface: IDescriptor

Returns a IImplementationSpecification 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 WHIMDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameter values. The Object array should have a single element which should be a String. The possible values of this String are: unity, mass, volume, eneg, polar

Throws:

CDKException - if the parameters are of the wrong type

See Also:

getParameters()

getParameters

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

Gets the parameters attribute of the WHIMDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

Two element array of Integer representing number of highest and lowest eigenvalues to return respectively

See Also:

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 WHIMDescriptor 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 WHIMDescriptor 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 11 directional and 6 non-directional WHIM descriptors for. the specified weighting scheme

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - Parameter is the atom container.

Returns:

An ArrayList containing the descriptors in the order described above.

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