Standardizer (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.standardizer.Standardizer

```
@PublicAPI
public class Standardizer
extends java.lang.Object
```
Performs the standardization determined by the XML configuration file, or simple action string configuration.
See the documentation for details:
API usage examples:
1. A simple example:
```
 Standardizer standardizer = new Standardizer(new File("standardize.xml"));
 standardizer.standardize(molecule);
 
```
2. A more complex example with importing molecules, standardization with a final clean action to arrange changed atoms, storing standardization information in molecule properties and finally exporting the molecules in SDF format:
```
 // create Standardizer based on a XML configuration file
 Standardizer standardizer = new Standardizer(new File("config.xml"));
 try {
     Molecule molecule = null;
     MolExporter exporter = new MolExporter(System.out, "sdf");
     MolImporter importer = new MolImporter("mols.sdf");
     while ((molecule = importer.read()) != null) {

        // standardize molecule
        standardizer.standardize(molecule);

        // get applied task indexes
        int[] appliedTaskIndexes = standardizer.getAppliedTaskIndexes();

        // get applied task IDs
        String[] appliedTaskIdentifiers = standardizer.getAppliedTaskIDs();

        // store applied task indexes and IDs in molecule properties
        StringBuilder indexPropertyValue = new StringBuilder();
        for (int i = 0; i < appliedTaskIndexes.length; ++i) {
            indexPropertyValue.append(appliedTaskIndexes[i]);
            indexPropertyValue.append(" ");
        }
        StringBuilder identifierPropertyValue = new StringBuilder();
        for (int i = 0; i < appliedTaskIdentifiers.length; ++i) {
            identifierPropertyValue.append(appliedTaskIdentifiers[i]);
            identifierPropertyValue.append(" ");
        }
        molecule.setProperty("TASK_INDEXES", indexPropertyValue.toString());
        molecule.setProperty("TASK_IDS", identifierPropertyValue.toString());

        // write output
        exporter.write(molecule);
     }
     importer.close();
     exporter.close();
 } catch (LicenseException e) {
     e.printStackTrace();
 } catch (IOException e) {
     e.printStackTrace();
 }
 
```
Configuration
Defines a sequence of standardizer actions, that should be executed, see StandardizerConfiguration Configuration error
If the provided configuration contains errors, the standardize(Molecule) method throws IllegalArgumentException by default. When the method setIgnoreConfigurationErrors(boolean) is called with true value beforehand, faulty actions are not executed, error message or exception should not occur!
If errors of configuration needs to be checked, use the getConfiguration() method to get the configuration, and check the validity of the configuration by using the function StandardizerConfiguration.isValid().
Standardizer actions
All built-in standardizer actions can be used with the Standardizer. To use external standardizer actions, the XML factory-configuration file userdefinedstandardizers.xml should be placed at the $HOME/chemaxon folder containing the list of user-defined checkers. For more information see StandardizerActionFactory
Built-in standardizer actions
Built in standardizer actions are located in the packages chemaxon.standardizer.actions and chemaxon.standardizer.advancedactions
Concurrent usage
Standardizer works on a single thread. If there are more target molecules, we advise to create more Standardizer instances (by cloning an existing one), and processing the molecules concurrently. For more information see ConcurrentStandardizerProcessor
Logging
Logs are generated to a Logger, that can be collected by using StandardizerLogger.getLogger() method. As for now, only Level.WARNING and Level.SEVERE logs are generated.
Since:

5.11

Author:

Imre Barna

See Also:

ConcurrentStandardizerProcessor

Field Summary

Fields
Modifier and Type Field and Description

static java.lang.String FINAL_CLEAN_ID
Deprecated.

Fields
Modifier and Type	Field and Description
`static java.lang.String`	`FINAL_CLEAN_ID` Deprecated.

Constructor Summary

Constructors
Constructor and Description
`Standardizer(java.io.File file)` Initializes a new standardizer with XML configuration
`Standardizer(java.io.InputStream stream)` Initializes a new standardizer with XML configuration Configurations containing references to molecule files does not work this way! If you may have configurations containing references, use the constructors that provide information on the path ( e.g.
`Standardizer(Standardizer standardizer)` Initializes a new standardizer based on an existing standardizer
`Standardizer(StandardizerConfiguration configuration)` Initializes a new standardizer with XML configuration
`Standardizer(java.lang.String configuration)` Initializes a new standardizer with auto-recognized XML or action string configuration Configurations containing references to molecule files does not work this way! If you have configurations containing references to external files, use the constructors that provide information on the path ( e.g.
`Standardizer(java.lang.String configuration, java.lang.String path)` Initializes a new standardizer with auto-recognized XML or action string configuration

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`java.lang.String[]`	`getActiveGroups()` Deprecated. use `ConfigurationUtility.filterGroups(StandardizerConfiguration, String[])` on the configuration returned by the method `getConfiguration()`
`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.
`StandardizerConfiguration`	`getConfiguration()` Gets the configuration of the standardizer.
`java.lang.String`	`getLicenseEnvironment()` Gets the license environment of the standardizer
`int[]`	`getNewToOld()` Returns the new -> old atom index mapping.
`int[]`	`getOldToNew()` Returns the old -> new atom index mapping.
`boolean`	`isLicensed()` Gets whether the standardizer is licensed
`boolean`	`isStereoFix()` Gets whether last stereo fix should be applied
`void`	`setActiveGroups(java.lang.String[] groups)` Deprecated. use `ConfigurationUtility.filterGroups(StandardizerConfiguration, String[])` on the configuration returned by the method `getConfiguration()`
`void`	`setFinalClean()` Deprecated. use `ConfigurationUtility.setFinalClean(StandardizerConfiguration)` on the configuration returned by the method `getConfiguration()`
`void`	`setFinalClean(int dim)` Deprecated. use `ConfigurationUtility.setFinalClean(StandardizerConfiguration, int)` on the configuration returned by the method `getConfiguration()`
`void`	`setFinalClean(int dim, boolean partial)` Deprecated. use `ConfigurationUtility.setFinalClean(StandardizerConfiguration, int, boolean)` on the configuration returned by the method `getConfiguration()`
`void`	`setFinalStereoFix(boolean clean)` Sets to perform final stereo fixes.
`void`	`setIgnoreConfigurationErrors(boolean ignore)` Sets whether the configuration errors should be ignored by the standardization process. When configuration errors are ignored, invalid standardizer actions in the configuration are not executed, however all valid actions are to be executed. When configuration errors are not ignored, `IllegalArgumentException` thrown when `standardize(Molecule)` method is called on an invalid configuration.
`void`	`setLicenseEnvironment(java.lang.String env)` Sets the license environment.
`java.util.List<Changes>`	`standardize(Molecule mol)` Standardization for one input molecule: performs the standardization actions according to the XML configuration.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - FINAL_CLEAN_ID
```
public static final java.lang.String FINAL_CLEAN_ID
```
    Deprecated.
    
    Final clean task ID.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Standardizer
```
public Standardizer(java.lang.String configuration)
             throws java.lang.IllegalArgumentException
```
    Initializes a new standardizer with auto-recognized XML or action string configuration Configurations containing references to molecule files does not work this way! If you have configurations containing references to external files, use the constructors that provide information on the path ( e.g. Standardizer(File) or Standardizer(String, String)
    
    Parameters:
    
    configuration - the configuration defined by action string or XML
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
  - Standardizer
```
public Standardizer(java.lang.String configuration,
                    java.lang.String path)
             throws java.lang.IllegalArgumentException
```
    Initializes a new standardizer with auto-recognized XML or action string configuration
    
    Parameters:
    
    configuration - the configuration defined by action string or XML
    
    path - the root path of referenced contents in the configuration
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
  - Standardizer
```
public Standardizer(java.io.File file)
             throws java.lang.IllegalArgumentException
```
    Initializes a new standardizer with XML configuration
    
    Parameters:
    
    file - the configuration XML input file
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
  - Standardizer
```
public Standardizer(java.io.InputStream stream)
             throws java.lang.IllegalArgumentException
```
    Initializes a new standardizer with XML configuration Configurations containing references to molecule files does not work this way! If you may have configurations containing references, use the constructors that provide information on the path ( e.g. Standardizer(File) or Standardizer(String, String)
    
    Parameters:
    
    stream - the configuration XML input stream
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
  - Standardizer
```
public Standardizer(StandardizerConfiguration configuration)
             throws java.lang.IllegalArgumentException
```
    Initializes a new standardizer with XML configuration
    
    Parameters:
    
    configuration - the configuration of the standardizer
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
  - Standardizer
```
public Standardizer(Standardizer standardizer)
```
    Initializes a new standardizer based on an existing standardizer
    
    Parameters:
    
    standardizer - an initialized standardizer instance as a base
    
    Throws:
    
    java.lang.IllegalArgumentException - on invalid configuration
- Method Detail
  - isLicensed
```
public boolean isLicensed()
```
    Gets whether the standardizer is licensed
    
    Returns:
    
    whether the standardizer is licensed
  - setLicenseEnvironment
```
public void setLicenseEnvironment(java.lang.String env)
```
    Sets the license environment. For internal usage only.
    
    Parameters:
    
    env - the license environment
  - getOldToNew
```
public int[] getOldToNew()
```
    Returns the old -> new atom index mapping.
    oldToNew[i]==j means that the i-th atom of the old molecule corresponds to the j-th atom of the new molecule.
    
    Returns:
    
    the old -> new atom index mapping
  - getNewToOld
```
public int[] getNewToOld()
```
    Returns the new -> old atom index mapping.
    newToOld[i]==j means that the i-th atom of the new molecule corresponds to the j-th atom of the old molecule.
    
    Returns:
    
    the new -> old atom index mapping
  - setFinalClean
```
@Deprecated
public void setFinalClean()
                               throws java.lang.IllegalArgumentException
```
    Deprecated. use ConfigurationUtility.setFinalClean(StandardizerConfiguration) on the configuration returned by the method getConfiguration()
    
    Sets final clean task: original molecule dimension, partial, optional.
    
    Throws:
    
    java.lang.IllegalArgumentException
  - setFinalClean
```
@Deprecated
public void setFinalClean(int dim)
                               throws java.lang.IllegalArgumentException
```
    Deprecated. use ConfigurationUtility.setFinalClean(StandardizerConfiguration, int) on the configuration returned by the method getConfiguration()
    
    Sets final clean task: partial, target-only.
    
    Parameters:
    
    dim - is the clean dimension, set -1 for the original molecule dimension
    
    Throws:
    
    java.lang.IllegalArgumentException
  - setFinalClean
```
@Deprecated
public void setFinalClean(int dim,
                                      boolean partial)
                               throws java.lang.IllegalArgumentException
```
    Deprecated. use ConfigurationUtility.setFinalClean(StandardizerConfiguration, int, boolean) on the configuration returned by the method getConfiguration()
    
    Sets final clean task: target-only.
    
    Parameters:
    
    dim - is the clean dimension, currently partial clean only works in 2D - if set to 3 then full clean is performed
    
    partial - is true if only the changing atoms should be cleaned, false if full clean is needed - if the clean dimension is different from the molecule dimension then always full clean is performed
    
    Throws:
    
    java.lang.IllegalArgumentException
  - standardize
```
public java.util.List<Changes> standardize(Molecule mol)
                                    throws chemaxon.license.LicenseException,
                                           java.lang.IllegalArgumentException
```
    Standardization for one input molecule: performs the standardization actions according to the XML configuration. 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.
    
    Parameters:
    
    mol - is the input molecule to be standardized
    
    Returns:
    
    the list of changes applied by the standardizer (each entry of the list is a change set of a standardizer action execution)
    
    Throws:
    
    chemaxon.license.LicenseException - if there is no valid license
    
    java.lang.IllegalArgumentException - if the parameter molecule, or the set configuration is not valid
  - 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
  - getAppliedTaskIDs
```
public java.lang.String[] getAppliedTaskIDs()
```
    Returns the IDs of tasks applied to the last input molecule. The ID FINAL_CLEAN_ID corresponds to the final clean action.
    
    Returns:
    
    the IDs of tasks applied to the last input molecule
  - setFinalStereoFix
```
public void setFinalStereoFix(boolean clean)
```
    Sets to perform final stereo fixes.
    
    Parameters:
    
    clean - if true then final stereo fix is performed
  - setActiveGroups
```
@Deprecated
public void setActiveGroups(java.lang.String[] groups)
```
    Deprecated. use ConfigurationUtility.filterGroups(StandardizerConfiguration, String[]) on the configuration returned by the method getConfiguration()
    
    Sets the active groups of the runners
    
    Parameters:
    
    groups - the list of names of active groups
  - getActiveGroups
```
@Deprecated
public java.lang.String[] getActiveGroups()
```
    Deprecated. use ConfigurationUtility.filterGroups(StandardizerConfiguration, String[]) on the configuration returned by the method getConfiguration()
    
    Gets the active groups of the runners
    
    Returns:
    
    the list of names of active groups
  - getConfiguration
```
public StandardizerConfiguration getConfiguration()
```
    Gets the configuration of the standardizer. Note that modifications on the configuration is not applied to the standardizer.
    
    Returns:
    
    the configuration of the standardizer
  - getLicenseEnvironment
```
public java.lang.String getLicenseEnvironment()
```
    Gets the license environment of the standardizer
    
    Returns:
    
    the license environment of the standardizer
  - isStereoFix
```
public boolean isStereoFix()
```
    Gets whether last stereo fix should be applied
    
    Returns:
    
    whether last stereo fix should be applied
  - setIgnoreConfigurationErrors
```
public void setIgnoreConfigurationErrors(boolean ignore)
```
    Sets whether the configuration errors should be ignored by the standardization process.
    When configuration errors are ignored, invalid standardizer actions in the configuration are not executed, however all valid actions are to be executed.
    When configuration errors are not ignored, IllegalArgumentException thrown when standardize(Molecule) method is called on an invalid configuration.
    
    Parameters:
    
    ignore - true if configuration errors should be ignored

Class Standardizer

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

FINAL_CLEAN_ID

Constructor Detail

Standardizer

Standardizer

Standardizer

Standardizer

Standardizer

Standardizer

Method Detail

isLicensed

setLicenseEnvironment

getOldToNew

getNewToOld

setFinalClean

setFinalClean

setFinalClean

standardize

getAppliedTaskIndexes

getAppliedTaskIDs

setFinalStereoFix

setActiveGroups

getActiveGroups

getConfiguration

getLicenseEnvironment

isStereoFix

setIgnoreConfigurationErrors