Package chemaxon.standardizer.actions

Class ExpandAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.ExpandAction

All Implemented Interfaces:

chemaxon.license.Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener

@PublicAPI
public final class ExpandAction
extends AbstractStandardizerAction

Expand stoichiometry standardizer action

Since:

5.11

Field Summary

Fields

Modifier and Type	Field	Description
static final String	STOICHIOMETRY_KEY	Key of type for parsing and property changes

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor	Description
ExpandAction(Map<String,String> params)	Initializes the action with parameters

Method Summary

Modifier and Type	Method	Description
ExpandAction	clone()
protected List<Molecule>	getComponents(Molecule molecule)	A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
String	getStoichiometry()	Gets the stoichiometry value of the action
void	setStoichiometry(String stoichiometryData)	Sets the stoichiometry value of the action
protected Changes	standardize1(Molecule molecule)	This method contains the current standardization mechanism.
String	toString()

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

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

Methods inherited from class java.lang.Object

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

Field Details

STOICHIOMETRY_KEY

public static final String STOICHIOMETRY_KEY

Key of type for parsing and property changes

See Also:

• Constant Field Values

Constructor Details

ExpandAction

public ExpandAction(Map<String,String> params)

Initializes the action with parameters

Parameters:

params - the parameters of the action

Method Details

setStoichiometry

public void setStoichiometry(String stoichiometryData)

Sets the stoichiometry value of the action

Parameters:

stoichiometryData - the stoichiometry value of the action

getStoichiometry

public String getStoichiometry()

Gets the stoichiometry value of the action

Returns:

the stoichiometry value of the action

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

getComponents

protected List<Molecule> getComponents(Molecule molecule)

Description copied from class: AbstractStandardizerAction

A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule. Used to collect all. If components must not be standardized, this method should be overridden.

Overrides:

getComponents in class AbstractStandardizerAction

Parameters:

molecule - the target molecule

Returns:

the resulted list of components

clone

public ExpandAction clone()
                   throws CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

CloneNotSupportedException

toString

public String toString()

Overrides:

toString in class AbstractStandardizerAction