org.openscience.cdk.qsar.descriptors.molecular

Class BCUTDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.BCUTDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class BCUTDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Eigenvalue based descriptor noted for its utility in chemical diversity. Described by Pearlman et al. (Pearlman, R.S. and Smith, K.M.. J. Chem. Inf. Comput. Sci.. 1999. 39).

The descriptor is based on a weighted version of the Burden matrix (Burden, F.R.. J. Chem. Inf. Comput. Sci.. 1989. 29, Burden, F.R.. Quant. Struct .-Act. Relat.. 1997. 16) which takes into account both the connectivity as well as atomic properties of a molecule. The weights are a variety of atom properties placed along the diagonal of the Burden matrix. Currently three weighting schemes are employed

• atomic weight
• partial charge (Gasteiger Marsilli)
• polarizability (Kang, Y.K. and Jhon, M.S.. Theoretica Chimica Acta. 1982. 61)

By default, the descriptor will return the highest and lowest eigenvalues for the three classes of descriptor in a single ArrayList (in the order shown above). However it is also possible to supply a parameter list indicating how many of the highest and lowest eigenvalues (for each class of descriptor) are required. The descriptor works with the hydrogen depleted molecule. A side effect of specifying the number of highest and lowest eigenvalues is that it is possible to get two copies of all the eigenvalues. That is, if a molecule has 5 heavy atoms, then specifying the 5 highest eigenvalues returns all of them, and specifying the 5 lowest eigenvalues returns all of them, resulting in two copies of all the eigenvalues.

Note that it is possible to specify an arbitrarily large number of eigenvalues to be returned. However if the number (i.e., nhigh or nlow) is larger than the number of heavy atoms, the remaining eignevalues will be NaN. Given the above description, if the aim is to gt all the eigenvalues for a molecule, you should set nlow to 0 and specify the number of heavy atoms (or some large number) for nhigh (or vice versa).

Parameters for this descriptor:

Name	Default	Description
nhigh	1	The number of highest eigenvalue
nlow	1	The number of lowest eigenvalue
checkAromaticity	true	Whether aromaticity should be checked

Returns an array of values in the following order

1. BCUTw-1l, BCUTw-2l ... - nhigh lowest atom weighted BCUTS
2. BCUTw-1h, BCUTw-2h ... - nlow highest atom weighted BCUTS
3. BCUTc-1l, BCUTc-2l ... - nhigh lowest partial charge weighted BCUTS
4. BCUTc-1h, BCUTc-2h ... - nlow highest partial charge weighted BCUTS
5. BCUTp-1l, BCUTp-2l ... - nhigh lowest polarizability weighted BCUTS
6. BCUTp-1h, BCUTp-2h ... - nlow highest polarizability weighted BCUTS

Author:

Rajarshi Guha

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

BCUT, descriptor

Created on:

2004-11-30

Constructor Summary

Constructors

Constructor and Description
BCUTDescriptor()

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer container) Calculates the three classes of BCUT 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 BCUTDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the BCUTDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the BCUTDescriptor object.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification which specifies which descriptor is implemented by this class.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the BCUTDescriptor object.

Methods inherited from class org.openscience.cdk.qsar.AbstractMolecularDescriptor

clone

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

BCUTDescriptor

public BCUTDescriptor()

Method Detail

getSpecification

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

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the BCUTDescriptor object.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameter values. This descriptor takes 3 parameters: number of highest eigenvalues and number of lowest eigenvalues. If 0 is specified for either (the default) then all calculated eigenvalues are returned. The third parameter checkAromaticity is a boolean. If checkAromaticity is true, the method check the aromaticity, if false, means that the aromaticity has already been checked.

Throws:

CDKException - if the parameters are of the wrong type

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the BCUTDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

Three element array of Integer and one boolean representing number of highest and lowest eigenvalues and the checkAromaticity flag to return respectively

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..

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the BCUTDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the BCUTDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter (can be either 'nhigh' or 'nlow' or checkAromaticity)

Returns:

The parameterType value

calculate

public DescriptorValue calculate(IAtomContainer container)

Calculates the three classes of BCUT descriptors.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - Parameter is the atom container.

Returns:

An ArrayList containing the descriptors. The default is to return all calculated eigenvalues of the Burden matrices in the order described above. If a parameter list was supplied, then only the specified number of highest and lowest eigenvalues (for each class of BCUT) will be returned.

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

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build