org.openscience.cdk.qsar.descriptors.molecular

Class LongestAliphaticChainDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.LongestAliphaticChainDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class LongestAliphaticChainDescriptor
extends AbstractMolecularDescriptor

Counts the number of atoms in the longest aliphatic chain.

Parameters for this descriptor:

Name	Default	Description
checkRingSystem	false	True is the CDKConstant.ISINRING has to be set

Returns a single value named nAtomLAC

Author:

chhoppe from EUROSCREEN, John Mayfield

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Created on:

2006-1-03

Field Summary

Fields

Modifier and Type	Field and Description
static String	CHECK_RING_SYSTEM

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer mol) Calculate the count of atoms of the longest aliphatic 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 LongestAliphaticChainDescriptor object.
Object[]	getParameters() Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
Object	getParameterType(String name) Gets the parameterType attribute of the LongestAliphaticChainDescriptor 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 LongestAliphaticChainDescriptor 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

Field Detail

CHECK_RING_SYSTEM

public static final String CHECK_RING_SYSTEM

See Also:

Constant Field Values

Constructor Detail

LongestAliphaticChainDescriptor

public LongestAliphaticChainDescriptor()

Constructor for the LongestAliphaticChainDescriptor 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

Returns:

An object containing the descriptor specification

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Sets the parameters attribute of the LongestAliphaticChainDescriptor object.

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

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 LongestAliphaticChainDescriptor object.

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

Returns:

An array of descriptor names, equal in length to the number of descriptor calculated..

calculate

public DescriptorValue calculate(IAtomContainer mol)

Calculate the count of atoms of the longest aliphatic chain in the supplied IAtomContainer.

The method require one parameter: if checkRingSyste is true the CDKConstant.ISINRING will be set

Parameters:

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

Returns:

the number of atoms in the longest aliphatic 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.

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 LongestAliphaticChainDescriptor object.

Returns:

The parameterNames value

getParameterType

public Object getParameterType(String name)

Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.

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