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

Class KappaShapeIndicesDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.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 Details

    • KappaShapeIndicesDescriptor

      public KappaShapeIndicesDescriptor()
      Constructor for the KappaShapeIndicesDescriptor object

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the KappaShapeIndicesDescriptor object
      Specified by:
      getSpecification in interface IDescriptor
      Returns:
      The specification value

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the KappaShapeIndicesDescriptor object
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - Description of the Exception
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the KappaShapeIndicesDescriptor object
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      The parameters value
      See Also:

    • 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