Package chemaxon.descriptors

Class BCUTParameters

java.lang.Object
chemaxon.descriptors.MDParameters
chemaxon.descriptors.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 Details

    • 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 Details

    • 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