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

Class WeightedPathDescriptor

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

    • WeightedPathDescriptor

      public WeightedPathDescriptor()

  • Method Details

    • 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

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the WeightedPathDescriptor 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 WeightedPathDescriptor 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..

    • 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