Class HBParameters


  • @PublicAPI
    public class HBParameters
    extends SDParameters
    Manages parameters for the HDon and HAcc scalar descriptor classes. The native format of the parameter configuration is XML.
    Since:
    JChem 2.2
    • Field Detail

      • DEFAULT_PH

        public static final int DEFAULT_PH
        default values for parameters
        See Also:
        Constant Field Values
    • Constructor Detail

      • HBParameters

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

        public HBParameters​(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
      • HBParameters

        public HBParameters​(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
      • initParameters

        protected void initParameters()
        Description copied from class: SDParameters
        Initializes those data members that depend on the XML configuration but are not directly taken from it.
        Overrides:
        initParameters in class SDParameters
      • generate

        protected float generate​(Molecule m)
                          throws MDGeneratorException
        Calculates the descriptor value for the given molecule.
        Parameters:
        m - input molecule for which the descirptor is calculated
        Returns:
        the value of the descr
        Throws:
        MDGeneratorException
      • readValues

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