Package com.chemaxon.overlap.io

Class StandardizerWrappers

java.lang.Object

com.chemaxon.overlap.io.StandardizerWrappers

@Beta
@PublicAPI
public final class StandardizerWrappers
extends Object

Provide utility methods for StandardizerWrapper.

Please note that the ThreadLocal based thread safety fix might lead to unexpected memory leaks when worker threads invoking the provided wrappers are pooled. To mitigate this problem make the reference to the wrapper inacessable allowing the garbage collector to free the thread local copies up.

Note that an alternative approach would be to implement a Closeable semantics to allow explicitly freeing up the copies, however this is currently considered not viable.

TODO: investigate the possibility to implement some expiring cache to drop (and if necessary, re-inti) ThreadLocals. TODO: Maybe ExpiringThreadLocal(timeout)? to mitigate this issue?

See Also:

• http://www.javacodegeeks.com/2013/01/how-to-shoot-yourself-in-foot-with-threadlocals.html
• http://stackoverflow.com/questions/817856/when-and-how-should-i-use-a-threadlocal-variable

  Please note that this interface is marked with Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Method Summary

Modifier and Type	Method	Description
static StandardizerWrapper	aromatizeBasic()	Wrap basic aromatization.
static StandardizerWrapper	aromatizeGeneral()	Wrap general aromatization.
static StandardizerWrapper	aromatizeLoose()	Wrap loose aromatization.
static StandardizerWrapper	chainOf(StandardizerWrapper... s)	Create a chained wrapper.
static StandardizerWrapper	fromStandardizer(Standardizer standardizer)	Extract actions from a Standardizer instance.
static StandardizerWrapper	fromStandardizerCfgLocation(String cfglocation)	Deprecated, for removal: This API element is subject to removal in a future version.
static StandardizerWrapper	fromStandardizerConfigXml(String configXml)	Wrap a Standardizer with config XML location.
static StandardizerWrapper	identityStandardizer()	Identity standardization.
static StandardizerWrapper	removeAllExplicitH()	Remove all explicit H atoms.
static StandardizerWrapper	removeSmallFragments()	Remove small fragments (disconnected components).

Methods inherited from class java.lang.Object

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

Method Details

fromStandardizerCfgLocation

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JAN_01_2025)
public static StandardizerWrapper fromStandardizerCfgLocation(String cfglocation)

Deprecated, for removal: This API element is subject to removal in a future version.

Wrap a Standardizer with config file location.

The returned wrapper uses ThreadLocal clones of the supplied Standardizer. For details see fromStandardizer(chemaxon.standardizer.Standardizer)

Parameters:

cfglocation - Config file location

Returns:

Wrapped and initialzied Standardizer

Throws:

IllegalArgumentException - upon initialization proble,

fromStandardizerConfigXml

public static StandardizerWrapper fromStandardizerConfigXml(String configXml)

Wrap a Standardizer with config XML location.

The returned wrapper uses ThreadLocal clones of the supplied Standardizer. For details see fromStandardizer(chemaxon.standardizer.Standardizer)

The returned wrapper is serializable and thread safe. Apart from the ThreadLocal storage state it is immutable.

Parameters:

configXml - Configuration file location

Returns:

Wrapped and initialzied Standardizer

Throws:

IllegalArgumentException - upon initialization proble,

fromStandardizer

public static StandardizerWrapper fromStandardizer(Standardizer standardizer)

Extract actions from a Standardizer instance.

Note that only the following actions are supported:

• AromatizeAction maps to StandardizerWrappers.Aromatize
• RemoveExplicitHydrogensAction maps to StandardizerWrappers.RemoveExplicitH

Parameters:

standardizer - Standardizer to extract enabled actions

Returns:

Wrapper

Throws:

IllegalArgumentException - when non supported action found or a not valid (StandardizerAction.isValid()) action found

identityStandardizer

public static StandardizerWrapper identityStandardizer()

Identity standardization.

Returns:

Wrapper doing nothing

chainOf

public static StandardizerWrapper chainOf(StandardizerWrapper... s)

Create a chained wrapper.

Parameters:

s - Steps

Returns:

Chained wrapper

aromatizeBasic

public static StandardizerWrapper aromatizeBasic()

Wrap basic aromatization.

Returns:

Wrapper

aromatizeGeneral

public static StandardizerWrapper aromatizeGeneral()

Wrap general aromatization.

Returns:

Wrapper

aromatizeLoose

public static StandardizerWrapper aromatizeLoose()

Wrap loose aromatization.

Returns:

Wrapper

removeAllExplicitH

public static StandardizerWrapper removeAllExplicitH()

Remove all explicit H atoms.

Delegates Hydrogenize.convertExplicitHToImplicit(chemaxon.struc.MoleculeGraph, int) with flags value MolAtom.ALL_H to remove all explicit H atoms. This includes lonely, h-bonded, isotope, charged and others, for details see documentation of Hydrogenize.convertExplicitHToImplicit(chemaxon.struc.MoleculeGraph, chemaxon.struc.MolAtom[], int, boolean).

Returns:

Wrapper

removeSmallFragments

public static StandardizerWrapper removeSmallFragments()

Remove small fragments (disconnected components).

Implicit H atoms are also considered. When multiple largest fragments )having the same size) are found the behavior is not specified currently.

Returns:

Wrapper