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

Class TPSADescriptor

java.lang.Object
org.openscience.cdk.qsar.AbstractMolecularDescriptor
org.openscience.cdk.qsar.descriptors.molecular.TPSADescriptor
All Implemented Interfaces:
IDescriptor, IMolecularDescriptor
public class TPSADescriptor extends AbstractMolecularDescriptor implements IMolecularDescriptor
Calculation of topological polar surface area based on fragment contributions (TPSA) [Ertl, P. et. al.. J. Med. Chem.. 2000. 43].
Parameters for this descriptor:
Name Default Description
checkAromaticity false If true, it will check aromaticity
This descriptor works properly with AtomContainers whose atoms contain either explicit hydrogens or implicit hydrogens. Returns a single value named TopoPSA
Author:
mfe4, ulif
Dictionary pointer(s):
tpsa in the QSAR.sf.net Descriptors Dictionary [qsar-descriptors:tpsa]
Keywords:
TPSA, total polar surface area, descriptor
Created on:
2004-11-03

  • Constructor Details

    • TPSADescriptor

      public TPSADescriptor()
      Constructor for the TPSADescriptor object.

  • Method Details

    • getSpecification

      public DescriptorSpecification getSpecification()
      Gets the specification attribute of the TPSADescriptor 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 TPSADescriptor object. The descriptor takes a Boolean parameter to indicate whether the descriptor routine should check for aromaticity (TRUE) or not (FALSE).
      Specified by:
      setParameters in interface IDescriptor
      Parameters:
      params - The parameter value (TRUE or FALSE)
      Throws:
      CDKException - if the supplied parameter is not of type Boolean
      See Also:

    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the TPSADescriptor object.
      Specified by:
      getParameters in interface IDescriptor
      Returns:
      The parameter value. For this descriptor it returns a Boolean indicating whether aromaticity was to be checked or not
      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 atomContainer)
      Calculates the TPSA for an atom container. Before calling this method, you may want to set the parameter indicating that aromaticity should be checked. If no parameter is specified (or if it is set to FALSE) then it is assumed that aromaticaity has already been checked. Prior to calling this method it is necessary to either add implicit or explicit hydrogens using CDKHydrogenAdder.addImplicitHydrogens(IAtomContainer) or AtomContainerManipulator.convertImplicitToExplicitHydrogens(IAtomContainer).
      Specified by:
      calculate in interface IMolecularDescriptor
      Parameters:
      atomContainer - The AtomContainer whose TPSA is to be calculated
      Returns:
      A double containing the topological surface area

    • 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 TPSADescriptor object.
      Specified by:
      getParameterNames in interface IDescriptor
      Returns:
      The parameterNames value

    • getParameterType

      public Object getParameterType(String name)
      Gets the parameterType attribute of the TPSADescriptor 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