chemaxon.standardizer

Class ConcurrentStandardizerProcessor

java.lang.Object

chemaxon.standardizer.ConcurrentStandardizerProcessor

@PublicAPI
public class ConcurrentStandardizerProcessor
extends java.lang.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:

• User's Guide
• Configuration
• Developer's Guide

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
 csp.setStandardizer(standardizer);
 csp.setMoleculeIterator(importer.getMoleculeIterator());

 Molecule mol;

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

 importer.close();
 exporter.close();
 

Author:

Zsolt Mohacsi

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	ConcurrentStandardizerProcessor.MolTransformer Molecule transformer.

Field Summary

Fields

Modifier and Type	Field and Description
static ConcurrentStandardizerProcessor.MolTransformer	TRANSFORMER_SET_DIM_0 Transformer: sets the molecule dimension to 0.

Constructor Summary

Constructors

Constructor and Description
ConcurrentStandardizerProcessor()

Method Summary

Modifier and Type	Method and Description
java.lang.String[]	getAppliedTaskIDs() Returns the IDs of tasks applied to the last input molecule.
int[]	getAppliedTaskIndexes() Returns the indexes of tasks applied to the last input molecule.
Molecule	getInputMolecule() Returns the input molecule (the molecule before standardization).
double	getProgress() Estimates the progress.
static void	main(java.lang.String[] args) Command line entry point.
void	setMoleculeIterator(MoleculeIterator iterator) Sets the molecule iterator.
void	setPreprocessor(ConcurrentStandardizerProcessor.MolTransformer tr) Sets the preprocessor.
void	setStandardizer(Standardizer standardizer) Sets the standardizer that will be used for performing standardizations.
void	setStoreAppliedTaskData(boolean store) If set, then applied task data is stored and can be retrieved with methods getAppliedTaskIDs(), getAppliedTaskIndexes(), getInputMolecule().
void	setWorkerThreadCount(int workerThreadCount) Sets the number of worker threads.
Molecule	standardize() Performs the standardization of the next input molecule, and returns the standardized molecule.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TRANSFORMER_SET_DIM_0

public static final ConcurrentStandardizerProcessor.MolTransformer TRANSFORMER_SET_DIM_0

Transformer: sets the molecule dimension to 0.

Constructor Detail

ConcurrentStandardizerProcessor

public ConcurrentStandardizerProcessor()

Method Detail

setStandardizer

public void setStandardizer(Standardizer standardizer)

Sets the standardizer that will be used for performing standardizations.

Parameters:

standardizer - the standardizer

setMoleculeIterator

public void setMoleculeIterator(MoleculeIterator iterator)

Sets the molecule iterator. The molecule iterator provides input molecules.

Parameters:

iterator - the molecule iterator

See Also:

MoleculeIteratorFactory

setWorkerThreadCount

public void setWorkerThreadCount(int workerThreadCount)

Sets the number of worker threads.

• 0: worker thread count = number of available CPU cores

(default: 0)

Parameters:

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.

Parameters:

tr - the preprocessor

Since:

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.

Returns:

the input molecule, standardized; null if there are no more input molecules

Throws:

java.lang.IllegalArgumentException - if standardizer or molecule iterator is not set

java.lang.RuntimeException - if an error occurred during standardization and in the case of concurrent processing error

chemaxon.license.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.

Returns:

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.

Parameters:

store - if true then applied task data is stored

See Also:

getAppliedTaskIndexes(), getAppliedTaskIDs(), getInputMolecule()

getInputMolecule

public Molecule getInputMolecule()

Returns the input molecule (the molecule before standardization).

Returns:

the input molecule

Throws:

java.lang.NullPointerException - if setStoreAppliedTaskData(boolean) is not set

See Also:

setStoreAppliedTaskData(boolean)

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.

Returns:

the indexes of tasks applied to the last input molecule

Throws:

java.lang.NullPointerException - if setStoreAppliedTaskData(boolean) is not set

See Also:

setStoreAppliedTaskData(boolean)

getAppliedTaskIDs

public java.lang.String[] getAppliedTaskIDs()

Returns the IDs of tasks applied to the last input molecule. The ID Standardizer.FINAL_CLEAN_ID corresponds to the final clean action.

Returns:

the IDs of tasks applied to the last input molecule

Throws:

java.lang.NullPointerException - if setStoreAppliedTaskData(boolean) is not set

See Also:

setStoreAppliedTaskData(boolean)

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Command line entry point.

Parameters:

args - is the command line argument array

Throws:

java.lang.Exception - on error