Class ALOGPDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.ALOGPDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor

public class ALOGPDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
This class calculates ALOGP (Ghose-Crippen LogKow) and the Ghose-Crippen molar refractivity [Ghose, A.K. and Crippen, G.M. . Journal of Computational Chemistry. 1986. 7, Ghose, A.K. and Crippen, G.M. . Journal of Chemical Information and Computer Science. 1987. 27]. Note The code assumes that aromaticity has been detected before evaluating this descriptor. The code also expects that the molecule will have hydrogens explicitly set. For SD files, this is usually not a problem since hydrogens are explicit. But for the case of molecules obtained from SMILES, hydrogens must be made explicit.

TODO: what should sub return if have missing fragment? Just report sum for other fragments? Or report as -9999 and then do not use descriptor if have this value for any chemicals in cluster?

Parameters for this descriptor:
Name Default Description
no parameters
Returns three values
  1. ALogP - Ghose-Crippen LogKow
  2. ALogP2
  3. amr - molar refractivity
Author:
Todd Martin
See Also:
Source code:
main
Belongs to CDK module:
qsarmolecular
Keywords:
logP, lipophilicity, refractivity
  • Field Details

    • frags

      public final int[] frags
    • alogpfrag

      public int[] alogpfrag
  • Constructor Details

  • Method Details

    • calculate

      public DescriptorValue calculate(IAtomContainer container)
      The AlogP descriptor. TODO Ideally we should explicit H addition should be cached
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      container - the molecule to calculate on
      Returns:
      the result of the calculation
    • 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
    • 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
    • getParameterNames

      public String[] getParameterNames()
      Description copied from interface: IDescriptor
      Returns the names of the parameters for this descriptor. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      An array of String containing the names of the parameters that this descriptor can accept.
    • getParameterType

      public Object getParameterType(String name)
      Description copied from interface: IDescriptor
      Returns a class matching that of the parameter with the given name. May only return null for when 'name' does not match any parameters returned by the getParameters() method.
      Specified by:
      getParameterType in interface IDescriptor
      Parameters:
      name - The name of the parameter whose type is requested
      Returns:
      An Object of the class corresponding to the parameter with the supplied name
    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Description copied from interface: IDescriptor
      Sets the parameters for this descriptor. Must be done before calling calculate as the parameters influence the calculation outcome.
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - An array of Object containing the parameters for this descriptor
      Throws:
      CDKException - if invalid number of type of parameters are passed to it
      See Also:
    • getParameters

      public Object[] getParameters()
      Description copied from interface: IDescriptor
      Returns the current parameter values. If not parameters have been set, it must return the default parameters. The method returns null or a zero-length Object[] array if the descriptor does not have any parameters.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      An array of Object containing the parameter default values
      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..
    • initialise

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