org.openscience.cdk.qsar.descriptors.molecular

Class ChiChainDescriptor

java.lang.Object

org.openscience.cdk.qsar.AbstractMolecularDescriptor

org.openscience.cdk.qsar.descriptors.molecular.ChiChainDescriptor

All Implemented Interfaces:

IDescriptor, IMolecularDescriptor

public class ChiChainDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor

Evaluates chi chain descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 3, 4, 5, 6 and 7. It utilizes the graph isomorphism code of the CDK to find fragments matching SMILES strings representing the fragments corresponding to each type of chain. The order of the values returned is

1. SCH-3 - Simple chain, order 3
2. SCH-4 - Simple chain, order 4
3. SCH-5 - Simple chain, order 5
4. SCH-6 - Simple chain, order 6
5. SCH-7 - Simple chain, order 7
6. VCH-3 - Valence chain, order 3
7. VCH-4 - Valence chain, order 4
8. VCH-5 - Valence chain, order 5
9. VCH-6 - Valence chain, order 6
10. VCH-7 - Valence chain, order 7

Note: These descriptors are calculated using graph isomorphism to identify the various fragments. As a result calculations may be slow. In addition, recent versions of Molconn-Z use simplified fragment definitions (i.e., rings without branches etc.) whereas these descriptors use the older more complex fragment definitions.

Author:

Rajarshi Guha

Dictionary pointer(s):

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

Source code:

master

Belongs to CDK module:

qsarmolecular

Keywords:

chi chain index, descriptor

Created on:

2006-11-12

Constructor Summary

Constructors

Constructor and Description
ChiChainDescriptor()

Method Summary

Modifier and Type	Method and Description
DescriptorValue	calculate(IAtomContainer container) Calculates the descriptor value for the given 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() Returns the names of the parameters for this descriptor.
Object[]	getParameters() Returns the current parameter values.
Object	getParameterType(String name) Returns a class matching that of the parameter with the given name.
DescriptorSpecification	getSpecification() Returns a IImplementationSpecification 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 for this descriptor.

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

ChiChainDescriptor

public ChiChainDescriptor()

Method Detail

getSpecification

public DescriptorSpecification getSpecification()

Description copied from interface: IDescriptor

Returns a IImplementationSpecification 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

getParameterNames

public String[] getParameterNames()

Description copied from interface: IDescriptor

Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameterNames in interface IDescriptor

Returns:

An array of String containing the names of the parameters that this descriptor can accept.

getParameterType

public Object getParameterType(String name)

Description copied from interface: IDescriptor

Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.

Specified by:

getParameterType in interface IDescriptor

Parameters:

name - The name of the parameter whose type is requested

Returns:

An Object of the class corresponding to the parameter with the supplied name

setParameters

public void setParameters(Object[] params)
                   throws CDKException

Description copied from interface: IDescriptor

Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.

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

public Object[] getParameters()

Description copied from interface: IDescriptor

Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.

Specified by:

getParameters in interface IDescriptor

Returns:

An array of Object containing the parameter default values

See Also:

IDescriptor.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 container)

Description copied from interface: IMolecularDescriptor

Calculates the descriptor value for the given IAtomContainer.

Specified by:

calculate in interface IMolecularDescriptor

Parameters:

container - An IAtomContainer for which this descriptor should be calculated

Returns:

An object of DescriptorValue that contain the calculated value as well as specification details

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

initialise

public void initialise(IChemObjectBuilder builder)

Default implementation of initialise allows optional override.

Specified by:

initialise in interface IDescriptor

Parameters:

builder - chem object build