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

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

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

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

Class that returns the number of atoms in the largest pi system.

This descriptor uses these parameters:

Name	Default	Description
checkAromaticity	false	True is the aromaticity has to be checked

Returns a single value named nAtomPi

Author:

chhoppe from EUROSCREEN

Belongs to the set:

qsar-descriptors

Created on:

2006-1-03

Belongs to CDK module:

qsarmolecular

Dictionary pointer(s):

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

Source code:

cdk-1.4.x

Constructor Summary

LargestPiSystemDescriptor()
Constructor for the LargestPiSystemDescriptor object.

Method Summary

DescriptorValue	calculate(IAtomContainer container) Calculate the count of atoms of the largest pi system in the supplied AtomContainer.
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 LargestPiSystemDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the LargestPiSystemDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the LargestPiSystemDescriptor 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 LargestPiSystemDescriptor object.

Methods inherited from class java.lang.Object

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

Constructor Detail

LargestPiSystemDescriptor

public LargestPiSystemDescriptor()

Constructor for the LargestPiSystemDescriptor 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 LargestPiSystemDescriptor object.

This descriptor takes one parameter, which should be Boolean to indicate whether aromaticity has been checked (TRUE) or not (FALSE).

Specified by:

setParameters in interface IDescriptor

Parameters:

params - The new parameters value

Throws:

CDKException - if more than one parameter or a non-Boolean parameter is specified

See Also:

getParameters()

getParameters

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

Gets the parameters attribute of the LargestPiSystemDescriptor 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(IAtomContainer container)

Calculate the count of atoms of the largest pi system in the supplied AtomContainer.

The method require one parameter:

1. if checkAromaticity is true, the method check the aromaticity,
2. if false, means that the aromaticity has already been checked

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

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

Returns:

the number of atoms in the largest pi system of this AtomContainer

See Also:

setParameters(java.lang.Object[])

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 LargestPiSystemDescriptor 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 LargestPiSystemDescriptor 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