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 Details

    • DEFAULT_PH

      public static final int DEFAULT_PH
      default values for parameters
      See Also:
  • Constructor Details

    • 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 Details

    • 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