Package chemaxon.standardizer.actions

Class NeutralizeAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.NeutralizeAction

All Implemented Interfaces:

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

@PublicApi
public final class NeutralizeAction
extends AbstractStandardizerAction

Neutralization standardizer action

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
NeutralizeAction(Map<String,String> params)	Initializes the action

Method Summary

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

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener, addPropertyChangeListener, anyBooleanPropertyTrue, clone, cloneItem, 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

NeutralizeAction

public NeutralizeAction(Map<String,String> params)

Initializes the action

Parameters:

params - the parameters of the action

Method Details

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

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