Package org.openscience.cdk.qsar.descriptors.atomic

Class ProtonAffinityHOSEDescriptor

    • Constructor Detail

      • ProtonAffinityHOSEDescriptor

        public ProtonAffinityHOSEDescriptor()
        Constructor for the ProtonAffinityDescriptor object.

    • Method Detail

      • getSpecification

        public DescriptorSpecification getSpecification()
        Gets the specification attribute of the ProtonAffinityDescriptor object
        Returns:
        The specification value

      • setParameters

        public void setParameters​(Object[] params)
                   throws CDKException
        This descriptor does have any parameter.
        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:
        IDescriptor.getParameters()

      • 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
        Returns:
        An array of descriptor names, equal in length to the number of descriptor calculated..

      • calculate

        public DescriptorValue calculate​(IAtom atom,
                                 IAtomContainer container)
        This method calculates the protonation affinity of an atom.
        Parameters:
        atom - The IAtom to protonate
        container - Parameter is the IAtomContainer.
        Returns:
        The protonation affinity. Not possible the ionization.

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the ProtonAffinityDescriptor object.
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the ProtonAffinityDescriptor object.
        Parameters:
        name - Description of the Parameter
        Returns:
        An Object of class equal to that of the parameter being requested

      • initialise

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