Package chemaxon.descriptors

Class ECFPParameters

java.lang.Object
chemaxon.descriptors.MDParameters
chemaxon.descriptors.ECFPParameters
@PublicApi public class ECFPParameters extends MDParameters
Manages ECFP fingerprint parameters. This class reads, stores and provides parameters for ECFP class. These parameters together are called the ECFP fingerprint configuration. The native format of such configuration is XML.
Since:
JChem 5.4

  • Field Details

    • DEFAULT_LENGTH

      public static final int DEFAULT_LENGTH
      default values for parameters
      See Also:

    • DEFAULT_DIAMETER

      public static final int DEFAULT_DIAMETER
      See Also:

  • Constructor Details

    • ECFPParameters

      public ECFPParameters()
      Creates an empty object. Initializes fingerprint parameters to default values.

    • ECFPParameters

      public ECFPParameters(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

    • ECFPParameters

      public ECFPParameters(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

    • 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

    • 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

    • setLength

      public void setLength(int length) throws MDParametersException
      Description copied from class: MDParameters
      Sets the length (number of cells) of the descriptor.
      Overrides:
      setLength in class MDParameters
      Parameters:
      length - the required length (cell count)
      Throws:
      MDParametersException - if argument is not positive

    • setDiameter

      public void setDiameter(int diameter)
      Sets the diameter parameter. It specifies the diameter of the circular neighborhood considered for each atom.

    • getDiameter

      public int getDiameter()
      Gets the preset diameter parameter. It specifies the diameter of the circular neighborhood considered for each atom.
      Returns:
      the diameter parameter

    • setKeepCounts

      public void setKeepCounts(boolean keepCounts)
      Sets the counts (multiplicity) parameter. It controls whether the generated identifiers are stored with occurrence counts or each identifier is kept only once independently of the number of the corresponding substructural features in the input molecule.
      Parameters:
      keepCounts - counts parameter

    • getKeepCounts

      public boolean getKeepCounts()
      Gets the counts (multiplicity) parameter. It controls whether the generated identifiers are stored with occurrence counts or each identifier is kept only once independently of the number of the corresponding substructural features in the input molecule.
      Returns:
      counts parameter

    • initGenerator

      protected void initGenerator() throws MDParametersException
      Initializes the fingerprint generator.
      Throws:
      MDParametersException

    • init

      protected void init()
      This method is called by the constructors before processing the XML configuration. It creates a ECFP object stored in MDParameters.md.

    • initParameters

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

    • generate

      protected String[] generate(Molecule m, MolecularDescriptor ecfp) throws MDGeneratorException
      Calls ECFPGenerator and generates the descriptor for the given molecule.
      Parameters:
      m - a molecular structure
      ecfp - the ECFP descriptor generated for the given molecule, an output parameter
      Returns:
      names of Molecule Property-s (SDfile tags) set by the generator
      Throws:
      MDGeneratorException - when failed to generate descriptor

    • 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

    • getDefaultDocumentFrame

      public String getDefaultDocumentFrame()
      Get the default XML configuration string. This is needed when the optional ECFP XML configuration is not specified.
      Overrides:
      getDefaultDocumentFrame in class MDParameters
      Returns:
      default XML configuration string of the ECFPParameters 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 ECFP includes aromatization.
      Returns:
      standardizer configuration XML string

    • processDocument

      protected void processDocument(boolean all) throws MDParametersException
      Processes pars of the XML configuration specific to ECFP. 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
      Picks parameter 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