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

Class FMFDescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.FMFDescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class FMFDescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
An implementation of the FMF descriptor characterizing complexity of a molecule. The descriptor is described in [Yang, Y. et. al.. J. Med. Chem.. 2010. ASAP] and is an approach to characterizing molecular complexity based on the Murcko framework present in the molecule. The descriptor is the ratio of heavy atoms in the framework to the total number of heavy atoms in the molecule. By definition, acyclic molecules which have no frameworks, will have a value of 0. Note that the authors consider an isolated ring system to be a framework (even though there is no linker). This descriptor returns a single double value, labeled as "FMF"
Author:
Rajarshi Guha
See Also:
Dictionary pointer(s):
FMF in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:FMF]
Source code:
main
Belongs to CDK module:
qsarmolecular

  • Constructor Details

    • FMFDescriptor

      public FMFDescriptor()

  • Method Details

    • calculate

      public DescriptorValue calculate(IAtomContainer container)
      Calculates the FMF descriptor value for the given IAtomContainer.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      container - An IAtomContainer for which this descriptor should be calculated
      Returns:
      An object of DescriptorValue that contains the calculated FMF descriptor value as well as specification details

    • getDescriptorResultType

      public IDescriptorResult getDescriptorResultType()
      Returns the specific type of the FMF descriptor value. The FMF descriptor is a single, double value. 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.

      Additionally, the length indicated by the result type must match the actual length of a descriptor calculated with the current parameters. Typically, the length of array result types vary with the values of the parameters. See IDescriptor for more details.

      Specified by:
      getDescriptorResultType in interface IMolecularDescriptor
      Returns:
      an instance of the DoubleResultType

    • getSpecification

      public DescriptorSpecification getSpecification()
      Returns a Map 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()
      Returns the names of the parameters for this descriptor. Since this descriptor takes no parameters, null is returned
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      null, since there are no parameters

    • getParameterType

      public Object getParameterType(String name)
      Returns a class matching that of the parameter with the given name. Since this descriptor has no parameters, null is always returned
      Specified by:
      getParameterType in interface IDescriptor
      Parameters:
      name - The name of the parameter whose type is requested
      Returns:
      null, since this descriptor has no parameters

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters for this descriptor. This method does nothing, since the descriptor has no parameters
      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()
      Returns the current parameter values. null is returned since the descriptor has no parameters
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      null, since there are no parameters
      See Also:

    • getDescriptorNames

      public String[] getDescriptorNames()
      Returns an array of names for each descriptor value calculated. Since this descriptor returns a single value, the array has a single element, viz., "FMF"
      Specified by:
      getDescriptorNames in interface IDescriptor
      Returns:
      A 1-element string array, with the value "FMF"

    • initialise

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