Package chemaxon.standardizer.actions

Class AliasToAtomAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.AliasToAtomAction

All Implemented Interfaces:

Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener

@PublicApi
public final class AliasToAtomAction
extends AbstractStandardizerAction

Standardizer action that converts atom aliases to actual atoms. Alias must resolve to an element known by PeriodicTable. If not, no changes are made and the alias is reported by StandardizerLogger.

Since:

5.11

Field Summary

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor	Description
AliasToAtomAction(Map<String,String> params)	Initializes the action

Method Summary

Modifier and Type	Method	Description
protected Changes	standardize1(Molecule molecule)	This method contains the current standardization mechanism.

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener, addPropertyChangeListener, anyBooleanPropertyTrue, clone, cloneItem, getComponents, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize, toString

Methods inherited from class java.lang.Object

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

Constructor Details

AliasToAtomAction

public AliasToAtomAction(Map<String,String> params)

Initializes the action

Parameters:

params - the parameters of the action

Method Details

standardize1

protected Changes standardize1(Molecule molecule)

Description copied from class: AbstractStandardizerAction

This method contains the current standardization mechanism. Descendants needs to implement this method.

Special molecules containing more components (e.g. RgMolecule, RxnMolecule) are decomponented by the method AbstractStandardizerAction.getComponents(Molecule), and AbstractStandardizerAction.standardize1(Molecule) method is called on each component, before applied on the original molecule. If a descendant does not want this to occur, this method must be overridden. Logs of standardization should be generated to a Logger, that can be collected by using StandardizerLogger.getLogger() method.

Specified by:

standardize1 in class AbstractStandardizerAction

Parameters:

molecule - the Molecule instance to be standardized

Returns:

the changes applied on the molecule during the standardization process