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

Class GravitationalIndexDescriptor

  • All Implemented Interfaces:
    IDescriptor, IMolecularDescriptor
    public class GravitationalIndexDescriptor
extends AbstractMolecularDescriptor
implements IMolecularDescriptor
    IDescriptor characterizing the mass distribution of the molecule. Described by Katritzky et al. [Katritzky, A.R. et. al.. J. Phys. Chem.. 1996. 100]. For modelling purposes the value of the descriptor is calculated both with and without H atoms. Furthermore the square and cube roots of the descriptor are also generated as described by Wessel et al. [Wessel, M.D. et. al.. Journal of Chemical Information and Computer Sciences. 1998. 38]. The descriptor routine generates 9 descriptors:
    • GRAV-1 - gravitational index of heavy atoms
    • GRAV-2 - square root of gravitational index of heavy atoms
    • GRAV-3 - cube root of gravitational index of heavy atoms
    • GRAVH-1 - gravitational index - hydrogens included
    • GRAVH-2 - square root of hydrogen-included gravitational index
    • GRAVH-3 - cube root of hydrogen-included gravitational index
    • GRAV-4 - grav1 for all pairs of atoms (not just bonded pairs)
    • GRAV-5 - grav2 for all pairs of atoms (not just bonded pairs)
    • GRAV-6 - grav3 for all pairs of atoms (not just bonded pairs)
    Parameters for this descriptor:
    Name Default Description
    no parameters
    Author:
    Rajarshi Guha
    Dictionary pointer(s):
    gravitationalIndex in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:gravitationalIndex]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Keywords:
    gravitational index, descriptor
    Created on:
    2004-11-23

    • Constructor Detail

      • GravitationalIndexDescriptor

        public GravitationalIndexDescriptor()

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

      • getParameterType

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

      • calculate

        public DescriptorValue calculate​(IAtomContainer container)
        Calculates the 9 gravitational indices.
        Specified by:
        calculate in interface IMolecularDescriptor
        Parameters:
        container - Parameter is the atom container.
        Returns:
        An ArrayList containing 9 elements in the order described above

      • 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