org.openscience.cdk.qsar.descriptors.molecular

Class TPSADescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class TPSADescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Calculation of topological polar surface area based on fragment contributions (TPSA) (Ertl, P. et. al.. J. Med. Chem.. 2000. 43).

Parameters for this descriptor:

Name	Default	Description
checkAromaticity	false	If true, it will check aromaticity

This descriptor works properly with AtomContainers whose atoms contain either explicit hydrogens or implicit hydrogens. Returns a single value named TopoPSA

Author:

mfe4, ulif

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

TPSA, total polar surface area, descriptor

Created on:

2004-11-03

Constructor Summary

Constructors

Constructor and Description
TPSADescriptor() Constructor for the TPSADescriptor object.

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer atomContainer) Calculates the TPSA 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 TPSADescriptor object.
Object[]	getParameters() Gets the parameters attribute of the TPSADescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the TPSADescriptor object.
DescriptorSpecification	getSpecification() Gets the specification attribute of the TPSADescriptor object.
void	initialise(IChemObjectBuilder builder) Default implementation of initialise allows optional override.
void	setParameters(Object[] params) Sets the parameters attribute of the TPSADescriptor 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

TPSADescriptor

public TPSADescriptor()

Constructor for the TPSADescriptor object.

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Gets the specification attribute of the TPSADescriptor object.

Specified by:

getSpecification in interface IDescriptor

Returns:

The specification value

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the TPSADescriptor object. The descriptor takes a Boolean parameter to indicate whether the descriptor routine should check for aromaticity (TRUE) or not (FALSE).

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The parameter value (TRUE or FALSE)

Throws:

CDKException - if the supplied parameter is not of type Boolean

See Also:

getParameters()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the TPSADescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameter value. For this descriptor it returns a Boolean indicating whether aromaticity was to be checked or not

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..

calculate

public DescriptorValue calculate(IAtomContainer atomContainer)

Calculates the TPSA for an atom container. Before calling this method, you may want to set the parameter indicating that aromaticity should be checked. If no parameter is specified (or if it is set to FALSE) then it is assumed that aromaticaity has already been checked. Prior to calling this method it is necessary to either add implicit or explicit hydrogens using CDKHydrogenAdder.addImplicitHydrogens(IAtomContainer) or AtomContainerManipulator.convertImplicitToExplicitHydrogens(IAtomContainer).

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

atomContainer - The AtomContainer whose TPSA is to be calculated

Returns:

A double containing the topological surface area

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

getParameterNames

public String[] getParameterNames()

Gets the parameterNames attribute of the TPSADescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the TPSADescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

The parameterType value

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build