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

Class WeightedPathDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class WeightedPathDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    Evaluates the weighted path descriptors. These decsriptors were described by Randic ([Randic, M. . Journal of Chemical Information and Computer Science. 1984. 24]) and characterize molecular branching. Five descriptors are calculated, based on the implementation in the ADAPT software package. Note that the descriptor is based on identifying all paths between pairs of atoms and so is NP-hard. This means that it can take some time for large, complex molecules. The class returns a DoubleArrayResult containing the five descriptors in the order described below.
    DMWP
    WTPT1molecular ID
    WTPT2 molecular ID / number of atoms
    WTPT3 sum of path lengths starting from heteroatoms
    WTPT4 sum of path lengths starting from oxygens
    WTPT5 sum of path lengths starting from nitrogens
    Parameters for this descriptor:
    Name Default Description
    no parameters
    Author:
    Rajarshi Guha
    Dictionary pointer(s):
    weightedPath in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:weightedPath]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Created on:
    2006-01-15

    • Constructor Detail

      • WeightedPathDescriptor

        public WeightedPathDescriptor()

    • 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

      • 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..

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the WeightedPathDescriptor object.
        Specified by:
        getParameterNames in interface IDescriptor
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the WeightedPathDescriptor object.
        Specified by:
        getParameterType in interface IDescriptor
        Parameters:
        name - Description of the Parameter
        Returns:
        The parameterType value

      • unique

        public static boolean unique​(List<IAtom> path)

      • calculate

        public DescriptorValue calculate​(IAtomContainer container)
        Calculates the weighted path descriptors.
        Specified by:
        calculate in interface IMolecularDescriptor
        Parameters:
        container - Parameter is the atom container.
        Returns:
        A DoubleArrayResult value representing the weighted path values

      • 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