Class ConcurrentStandardizerProcessor


@PublicAPI public class ConcurrentStandardizerProcessor extends Object
Performs standardization of molecules in concurrent mode. It requires a Standardizer object, which is used for performing the standardizations, and a MoleculeIterator, for providing input molecules.

This class can be used from command-line or from the API.
See also the Standardizer documentation:

API usage example:

 MolExporter exporter = new MolExporter(System.out, "sdf");
 MolImporter importer = new MolImporter("mols.sdf");

 // create Standardizer with XML configuration file
 Standardizer standardizer = new Standardizer(new File("config.xml"));

 // create a ConcurrentStandardizerProcessor
 ConcurrentStandardizerProcessor csp = new ConcurrentStandardizerProcessor();

 // set the standardizer and the molecule iterator for ConcurrentStandardizerProcessor

 Molecule mol;

 // standardize the molecules and export the output (standardization is performed in concurrent mode)
 while ((mol = csp.standardize()) != null) {

  • Field Details

  • Constructor Details

    • ConcurrentStandardizerProcessor

      public ConcurrentStandardizerProcessor()
  • Method Details

    • setStandardizer

      public void setStandardizer(Standardizer standardizer)
      Sets the standardizer that will be used for performing standardizations.
      standardizer - the standardizer
    • setMoleculeIterator

      public void setMoleculeIterator(MoleculeIterator iterator)
      Sets the molecule iterator. The molecule iterator provides input molecules.
      iterator - the molecule iterator
      See Also:
    • setWorkerThreadCount

      public void setWorkerThreadCount(int workerThreadCount)
      Sets the number of worker threads.
      • 0: worker thread count = number of available CPU cores
      (default: 0)
      workerThreadCount - number of worker threads
    • setPreprocessor

      public void setPreprocessor(ConcurrentStandardizerProcessor.MolTransformer tr)
      Sets the preprocessor. Preprocessor transforms the input molecule. Preprocessing is performed before standardization. For internal use only.
      tr - the preprocessor
      JChem 5.3
    • standardize

      public Molecule standardize()
      Performs the standardization of the next input molecule, and returns the standardized molecule. The input molecule is transformed and returned, no new molecule object is created. If the input molecule is a reaction then each reactant/product is standardized.
      the input molecule, standardized; null if there are no more input molecules
      IllegalArgumentException - if standardizer or molecule iterator is not set
      RuntimeException - if an error occurred during standardization and in the case of concurrent processing error
      LicenseException - if there is no valid license
    • getProgress

      public double getProgress()
      Estimates the progress. Returns a number between 0 and 1, or returns -1. 0: none of the input molecules are standardized, 1: all of the input molecules are standardized, -1: information about progress can not be provided.
      a number that indicates the progress
    • setStoreAppliedTaskData

      public void setStoreAppliedTaskData(boolean store)
      If set, then applied task data is stored and can be retrieved with methods getAppliedTaskIDs(), getAppliedTaskIndexes(), getInputMolecule(). Otherwise the listed methods throw NullPointerException.
      store - if true then applied task data is stored
      See Also:
    • getInputMolecule

      public Molecule getInputMolecule()
      Returns the input molecule (the molecule before standardization).
      the input molecule
      NullPointerException - if setStoreAppliedTaskData(boolean) is not set
      See Also:
    • getAppliedTaskIndexes

      public int[] getAppliedTaskIndexes()
      Returns the indexes of tasks applied to the last input molecule. Indexing is 0-based, with the largest index which equals to the number of tasks meaning the final clean action.
      the indexes of tasks applied to the last input molecule
      NullPointerException - if setStoreAppliedTaskData(boolean) is not set
      See Also:
    • getAppliedTaskIDs

      public String[] getAppliedTaskIDs()
      Returns the IDs of tasks applied to the last input molecule.
      the IDs of tasks applied to the last input molecule
      NullPointerException - if setStoreAppliedTaskData(boolean) is not set
      See Also:
    • main

      public static void main(String[] args) throws Exception
      Command line entry point.
      args - is the command line argument array
      Exception - on error