org.openscience.cdk.qsar.descriptors.molecular

Class LargestChainDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.LargestChainDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class LargestChainDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Class that returns the number of atoms in the largest chain.

Parameters for this descriptor:

Name	Default	Description
checkAromaticity (deprecated)	false	Old parameter is now ignored
checkRingSystem	false	True is the CDKConstant.ISINRING has to be set

Returns a single value named nAtomLAC. Note that a chain exists if there are two or more atoms. Thus single atom molecules will return 0

Author:

chhoppe from EUROSCREEN

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Created on:

2006-1-03

Constructor Summary

Constructors

Constructor and Description
LargestChainDescriptor() Constructor for the LargestChain object.

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer atomContainer) Calculate the count of atoms of the largest chain in the supplied 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 LargestPiSystemDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the LargestChainDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the LargestChainDescriptor object.
DescriptorSpecification	getSpecification() Returns a Map 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 LargestChain 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

LargestChainDescriptor

public LargestChainDescriptor()

Constructor for the LargestChain object.

Method Detail

getSpecification

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

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the LargestChain object. This descriptor takes two parameters, which should be Booleans to indicate whether aromaticity and ring member ship needs been checked (TRUE) or not (FALSE). The first parameter (aromaticity) is deprecated and ignored.

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

public Object[] getParameters()

Gets the parameters attribute of the LargestChainDescriptor object.

Specified by:

getParameters in interface IDescriptor

Returns:

The parameters value

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)

Calculate the count of atoms of the largest chain in the supplied IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

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

Returns:

the number of atoms in the largest chain of this AtomContainer

See Also:

setParameters(java.lang.Object[])

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 LargestPiSystemDescriptor object.

Specified by:

getParameterNames in interface IDescriptor

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the LargestChainDescriptor 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

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build