Package org.openscience.cdk.qsar.descriptors.molecular

Class ChiPathClusterDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class ChiPathClusterDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    Evaluates chi path cluster descriptors. The code currently evluates the simple and valence chi chain descriptors of orders 3, 4,5 and 6. 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. SPC-4 - Simple path cluster, order 4
    2. SPC-5 - Simple path cluster, order 5
    3. SPC-6 - Simple path cluster, order 6
    4. VPC-4 - Valence path cluster, order 4
    5. VPC-5 - Valence path cluster, order 5
    6. VPC-6 - Valence path cluster, order 6
    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):
    chiPathCluster in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:chiPathCluster]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Keywords:
    chi path cluster index, descriptor
    Created on:
    2006-11-13

    • Constructor Detail

      • ChiPathClusterDescriptor

        public ChiPathClusterDescriptor()

    • 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..

      • 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