Class BCUTParameters


  • @PublicAPI
    public class BCUTParameters
    extends MDParameters
    Manages parameters for the BCUT descriptor class. The native format of the parameter configuration is XML.
    Since:
    JChem 2.3
    • Constructor Detail

      • BCUTParameters

        public BCUTParameters()
        Creates an empty object. Initializes parameters to default values.
      • BCUTParameters

        public BCUTParameters​(File configFile)
                       throws MDParametersException
        Creates a new object based on a given configuration file.
        Parameters:
        configFile - XML configuration file
        Throws:
        MDParametersException - missing or bad XML configuration
      • BCUTParameters

        public BCUTParameters​(String XMLconfig)
                       throws MDParametersException
        Creates a new object based on a given configuration string.
        Parameters:
        XMLconfig - XML configuration string
        Throws:
        MDParametersException - missing or bad XML configuration
    • Method Detail

      • toString

        public String toString()
        Returns the XML configuration in a string.
        Overrides:
        toString in class MDParameters
        Returns:
        configuration string in XML format
      • fromString

        public void fromString​(String parameterString)
                        throws MDParametersException
        Sets parameters from a string representation. This method processes an XML format, but derived classes may overload this and define their own format.
        Overrides:
        fromString in class MDParameters
        Parameters:
        parameterString - parameters in string
        Throws:
        MDParametersException - when the parameter string is not well-formed
      • getLowestEigenvaluesCount

        public int getLowestEigenvaluesCount​(int idx)
        Gets the number of lowest eigenvalues calculated.
        Parameters:
        idx - the index of descriptor
        Returns:
        number of lowest eigenvalues
      • getHighestEigenvaluesCount

        public int getHighestEigenvaluesCount​(int idx)
        Gets the number of highest eigenvalues calculated.
        Parameters:
        idx - the index of descriptor
        Returns:
        number of highest eigenvalues
      • getType

        public String getType​(int idx)
        Gets the type of the BCUT descriptor. Valid types are: Burden, Charge, Polarizability, HBond.
        Parameters:
        idx - the index of descriptor
        Returns:
        type of the BCUT descriptor
      • getTypeCount

        public int getTypeCount()
        Gets the count of descriptor types.
        Returns:
        the count of descriptor types
      • getDefaultDocumentFrame

        public String getDefaultDocumentFrame()
        Gets the default XML configuration string. This is needed when the XML configuration is not specified.
        Overrides:
        getDefaultDocumentFrame in class MDParameters
        Returns:
        default XML configuration string of the BCUTParameters class
        Since:
        JChem 2.3
      • initParameters

        protected void initParameters()
        Description copied from class: MDParameters
        Initializes object after configuration parameters are loaded.
        Overrides:
        initParameters in class MDParameters
      • generate

        protected String[] generate​(Molecule m,
                                    MolecularDescriptor bc)
                             throws MDGeneratorException
        Calls the descriptor generator for the molecule provided and stores result (the descriptor) in the MolecularDescriptor object.
        Parameters:
        m - the Molecule for which the descriptor is generated
        bc - the BCUT descriptor will be stored here (out parameter)
        Returns:
        always null
        Throws:
        MDGeneratorException
      • getNumberOfWeights

        protected int getNumberOfWeights​(int parametrizedMetricIndex)
                                  throws IllegalArgumentException
        Gets the number of weight factors used by the specified metric. This method can be applied to the dissimilarity metrics provided by the MolecularDescriptor class or its derived classes, but not to parametrized metric.
        Overrides:
        getNumberOfWeights in class MDParameters
        Parameters:
        parametrizedMetricIndex - parametrized metric index
        Returns:
        number of weights the metric uses
        Throws:
        IllegalArgumentException - if the given parameter is not a valid metric index
      • readValues

        protected void readValues​(boolean all)
                           throws MDParametersException
        Retrieves relavant parameters values from the DOM tree.
        Overrides:
        readValues in class MDParameters
        Parameters:
        all - indicates if the entire document has to be processed in which case the existing configuration is overwritten
        Throws:
        MDParametersException