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

Class KappaShapeIndicesDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class KappaShapeIndicesDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH : "they are intended to capture different aspects of molecular shape. Note that hydrogens are ignored. In the following description, n denotes the number of atoms in the hydrogen suppressed graph, m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2 and let p3 denote the number of paths of length 3". Returns three values in the order
    1. Kier1 - First kappa shape index
    2. Kier2 - Second kappa shape index
    3. Kier3 - Third kappa (κ) shape index

    This descriptor does not have any parameters.

    Author:
    mfe4
    Dictionary pointer(s):
    kierValues in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:kierValues]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Keywords:
    Kappe shape index, descriptor
    Created on:
    2004-11-03

    • Constructor Detail

      • KappaShapeIndicesDescriptor

        public KappaShapeIndicesDescriptor()
        Constructor for the KappaShapeIndicesDescriptor object

    • Method Detail

      • 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)
        calculates the kier shape indices for an atom container
        Specified by:
        calculate in interface IMolecularDescriptor
        Parameters:
        container - AtomContainer
        Returns:
        kier1, kier2 and kier3 are returned as arrayList of doubles

      • 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 KappaShapeIndicesDescriptor object
        Specified by:
        getParameterNames in interface IDescriptor
        Returns:
        The parameterNames value

      • getParameterType

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

      • initialise

        public void initialise​(IChemObjectBuilder builder)
        Default implementation of initialise allows optional override.
        Specified by:
        initialise in interface IDescriptor
        Parameters:
        builder - chem object build