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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

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

Sum of the atomic polarizabilities (including implicit hydrogens). Polarizabilities are taken from http://www.sunysccc.edu/academic/mst/ptable/p-table2.htm.

This class need explicit hydrogens.

This descriptor uses these parameters:

Name	Default	Description
		no parameters

Returns a single value with name apol.

Author:

mfe4

Belongs to the set:

qsar-descriptors

Keywords:

polarizability, atomic

Created on:

2004-11-13

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

HEAD

Constructor Summary

APolDescriptor()
Constructor for the APolDescriptor object.

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculate the sum of atomic polarizabilities in an IAtomContainer.
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 APolDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the APolDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the APolDescriptor 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 APolDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

APolDescriptor

public APolDescriptor()

Constructor for the APolDescriptor object.

Method Detail

getSpecification

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

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 APolDescriptor object. This descriptor does not take any parameters

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - no exception is thrown

See Also:

getParameters()

getParameters

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

Gets the parameters attribute of the APolDescriptor object. This method does not return any parameters

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

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..

calculate

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

Calculate the sum of atomic polarizabilities in an IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - The IAtomContainer for which the descriptor is to be calculated

Returns:

The sum of atomic polarizabilities IsotopeFactory

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

getParameterNames

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

Gets the parameterNames attribute of the APolDescriptor 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 APolDescriptor object.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - Description of the Parameter

Returns:

An Object of class equal to that of the parameter being requested