Class FractionalCSP3Descriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.FractionalCSP3Descriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor

public class FractionalCSP3Descriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
An implementation of the Fractional CSP3 descriptor described in [Lovering, Frank et. al.. J. Med. Chem.. 2009. 52]. This descriptor is characterizing non-flatness of a molecule. This descriptor returns a single double value, labeled as "Fsp3"
Author:
Kazuya Ujihara
Dictionary pointer(s):
Fsp3 in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:Fsp3]
Belongs to CDK module:
qsarmolecular
  • Constructor Details

    • FractionalCSP3Descriptor

      public FractionalCSP3Descriptor()
  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      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()
      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)
      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
      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()
      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:
    • calculate

      public DescriptorValue calculate(IAtomContainer mol)
      Calculates the Fsp3 descriptor value for the given IAtomContainer.
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      mol - An IAtomContainer for which this descriptor should be calculated
      Returns:
      An object of DescriptorValue that contains the calculated Fsp3 descriptor value
    • getDescriptorResultType

      public IDescriptorResult getDescriptorResultType()
      Returns the specific type of the Fsp3 descriptor value. The Fsp3 descriptor is a single, double value.
      Specified by:
      getDescriptorResultType in interface IMolecularDescriptor
      Returns:
      an instance of the DoubleResultType
    • 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