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

Class 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]
    Source code:
    main
    Belongs to CDK module:
    qsarmolecular
    Keywords:
    TPSA, total polar surface area, descriptor
    Created on:
    2004-11-03

    • Constructor Detail

      • TPSADescriptor

        public TPSADescriptor()
        Constructor for the TPSADescriptor object.

    • Method Detail

      • 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()

      • 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:
        setParameters(java.lang.Object[])

      • 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..

      • 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