org.openscience.cdk.qsar.descriptors.atomic
Class VdWRadiusDescriptor

java.lang.Object
  org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptor

All Implemented Interfaces:

IAtomicDescriptor, IDescriptor

@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.VdWRadiusDescriptorTest")
public class VdWRadiusDescriptor
extends Object
implements IAtomicDescriptor

This class return the VdW radius of a given atom.

This descriptor uses these parameters:

Name	Default	Description

Author:

mfe4

Belongs to the set:

qsar-descriptors

Created on:

2004-11-13

Belongs to CDK module:

qsaratomic

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

VdWRadiusDescriptor()
Constructor for the VdWRadiusDescriptor object.

Method Summary

DescriptorValue	calculate(IAtom atom, IAtomContainer container) This method calculate the Van der Waals radius of an atom.
String[]	getDescriptorNames() Returns an array of names for each descriptor value calculated.
String[]	getParameterNames() Gets the parameterNames attribute of the VdWRadiusDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the VdWRadiusDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the VdWRadiusDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map which specifies which descriptor is implemented by this class.
void	setParameters(Object[] params) This descriptor does have any parameter.

Methods inherited from class java.lang.Object

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

Constructor Detail

VdWRadiusDescriptor

public VdWRadiusDescriptor()
                    throws IOException,
                           ClassNotFoundException

Constructor for the VdWRadiusDescriptor object.

Throws:

IOException - if an error ocurrs when reading atom type information

ClassNotFoundException - if an error occurs during tom typing

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

This descriptor does have any parameter.

Specified by:

setParameters in interface IDescriptor

Parameters:

params - An array of Object containing the parameters for this descriptor

Throws:

CDKException - if invalid number of type of parameters are passed to it

See Also:

IDescriptor.getParameters()

getParameters

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

Gets the parameters attribute of the VdWRadiusDescriptor object.

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")
public DescriptorValue calculate(IAtom atom,
                                                 IAtomContainer container)

This method calculate the Van der Waals radius of an atom.

Specified by:

calculate in interface IAtomicDescriptor

Parameters:

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

atom - An IAtom for which this descriptor should be calculated

Returns:

The Van der Waals radius of the atom

getParameterNames

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

Gets the parameterNames attribute of the VdWRadiusDescriptor 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 VdWRadiusDescriptor 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