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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class GravitationalIndexDescriptor
extends java.lang.Object
implements IMolecularDescriptor

IDescriptor characterizing the mass distribution of the molecule. Described by Katritzky et al. [Katritzky, A.R. and Mu, L. and Lobanov, V.S. and Karelson, M., Correlation of Boiling Points With Molecular Structure. 1. A Training Set of 298 Diverse Organics and a Test Set of 9 Simple Inorganics, J. Phys. Chem., 1996, 100:10400-10407]. For modelling purposes the value of the descriptor is calculated both with and without H atoms. Furthermore the square and cube roots of the descriptor are also generated as described by Wessel et al. [Wessel, M.D. and Jurs, P.C. and Tolan, J.W. and Muskal, S.M. , Prediction of Human Intestinal Absorption of Drug Compounds From Molecular Structure, Journal of Chemical Information and Computer Sciences, 1998, 38:726-735].

The descriptor routine generates 9 descriptors:

• GRAV-1 - gravitational index of heavy atoms
• GRAV-2 - square root of gravitational index of heavy atoms
• GRAV-3 - cube root of gravitational index of heavy atoms
• GRAVH-1 - gravitational index - hydrogens included
• GRAVH-2 - square root of hydrogen-included gravitational index
• GRAVH-3 - cube root of hydrogen-included gravitational index
• GRAV-4 - grav1 for all pairs of atoms (not just bonded pairs)
• GRAV-5 - grav2 for all pairs of atoms (not just bonded pairs)
• GRAV-6 - grav3 for all pairs of atoms (not just bonded pairs)

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Author:

Rajarshi Guha

Belongs to the set:

qsar-descriptors

Keywords:

gravitational index, descriptor

Created on:

2004-11-23

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

revision 11779

Constructor Summary

GravitationalIndexDescriptor()

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculates the 9 gravitational indices.
java.lang.String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
IDescriptorResult	getDescriptorResultType() Returns the specific type of the DescriptorResult object.
java.lang.String[]	getParameterNames() Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
java.lang.Object[]	getParameters() Gets the parameters attribute of the GravitationalIndexDescriptor object.
java.lang.Object	getParameterType(java.lang.String name) Gets the parameterType attribute of the GravitationalIndexDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(java.lang.Object[] params) Sets the parameters attribute of the GravitationalIndexDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

GravitationalIndexDescriptor

public GravitationalIndexDescriptor()

Method Detail

getSpecification

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

public void setParameters(java.lang.Object[] params)
                   throws CDKException

Sets the parameters attribute of the GravitationalIndexDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - Description of the Exception

See Also:

getParameters()

getParameters

public java.lang.Object[] getParameters()

Gets the parameters attribute of the GravitationalIndexDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

getDescriptorNames

@TestMethod(value="testNamesConsistency")
public java.lang.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

public java.lang.String[] getParameterNames()

Gets the parameterNames attribute of the GravitationalIndexDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public java.lang.Object getParameterType(java.lang.String name)

Gets the parameterType attribute of the GravitationalIndexDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

calculate

public DescriptorValue calculate(IAtomContainer container)

Calculates the 9 gravitational indices.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - Parameter is the atom container.

Returns:

An ArrayList containing 9 elements in the order described above

getDescriptorResultType

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