Class ShapeParameters

java.lang.Object
chemaxon.descriptors.MDParameters
chemaxon.descriptors.ShapeParameters

@PublicApi @Beta public class ShapeParameters extends MDParameters
  • Constructor Details

  • Method Details

    • fromString

      public void fromString(String parameterString) throws MDParametersException
      Description copied from class: MDParameters
      Sets parameters from a string representation. This method assumes that parameters are described in XML format.
      Overrides:
      fromString in class MDParameters
      Parameters:
      parameterString - configuration parameters in string
      Throws:
      MDParametersException - when the parameter string is not well-formed
    • setFlexible

      public void setFlexible(boolean flexible)
    • initGenerator

      protected final void initGenerator() throws MDParametersException
      Throws:
      MDParametersException
    • fromFile

      public void fromFile(File parameterFile) throws MDParametersException
      Sets parameters from an XML file. Derived classes may overload this and define their own format (even other than XML).
      Overrides:
      fromFile in class MDParameters
      Parameters:
      parameterFile - initialized parameter file
      Throws:
      MDParametersException - failed to process parameter file
    • initEmbeddedMD

      protected final void initEmbeddedMD()
      This method is called by the constructors before processing the XML configuration. It creates a ShapeDescriptor object stored in MDParameters.md.
    • getDefaultDocumentFrame

      public String getDefaultDocumentFrame()
      Get the default XML configuration string. This is needed when the optional Shape XML configuration is not specified.
      Overrides:
      getDefaultDocumentFrame in class MDParameters
      Returns:
      default XML configuration string of the ShapeParameters class
    • getDefaultStandardizerConfiguration

      public static String getDefaultStandardizerConfiguration()
      Gets the default configuration of the standardizer. This method is called if no standardizer configuration is set in the parameters configuration. The default standardization for Shape includes aromatization.
      Returns:
      standardizer configuration XML string
    • processDocument

      protected void processDocument(boolean all) throws MDParametersException
      Processes pars of the XML configuration specific to Shape. Find the node in the DOM tree and leaves the rest of the work to the parent class.
      Overrides:
      processDocument in class MDParameters
      Parameters:
      all - indicates if the entire document has to be processed in which case the existing configuration is overwritten
      Throws:
      MDParametersException
    • readValues

      protected void readValues(boolean all) throws MDParametersException
      Description copied from class: MDParameters
      Picks attribute values from the document tree that are relevant to the actual MDParameters sub-class.
      Overrides:
      readValues in class MDParameters
      Parameters:
      all - process the complete document or only the ScreeningConfiguration tag
      Throws:
      MDParametersException