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

Class PartialTChargeMMFF94Descriptor

    • Constructor Detail

      • PartialTChargeMMFF94Descriptor

        public PartialTChargeMMFF94Descriptor()
        Constructor for the PartialTChargeMMFF94Descriptor object

    • Method Detail

      • getSpecification

        public DescriptorSpecification getSpecification()
        Gets the specification attribute of the PartialTChargeMMFF94Descriptor object
        Returns:
        The specification value

      • setParameters

        public void setParameters​(Object[] params)
                   throws CDKException
        This descriptor does not have any parameter to be set.
        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()

      • getParameters

        public Object[] getParameters()
        Gets the parameters attribute of the PartialTChargeMMFF94Descriptor object
        Returns:
        The parameters value
        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
        Returns:
        An array of descriptor names, equal in length to the number of descriptor calculated..

      • calculate

        public DescriptorValue calculate​(IAtom atom,
                                 IAtomContainer org)
        The method returns partial charges assigned to an heavy atom through MMFF94 method. It is needed to call the addExplicitHydrogensToSatisfyValency method from the class tools.HydrogenAdder.
        Parameters:
        atom - The IAtom for which the DescriptorValue is requested
        org - AtomContainer
        Returns:
        partial charge of parameter atom

      • getParameterNames

        public String[] getParameterNames()
        Gets the parameterNames attribute of the PartialTChargeMMFF94Descriptor object
        Returns:
        The parameterNames value

      • getParameterType

        public Object getParameterType​(String name)
        Gets the parameterType attribute of the PartialTChargeMMFF94Descriptor object
        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