Package chemaxon.standardizer.actions

Class MapReactionAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.actions.MapReactionAction

All Implemented Interfaces:

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

@PublicAPI
public final class MapReactionAction
extends AbstractStandardizerAction

Map reaction standardizer action

Since:

5.11

Field Summary

Fields

Modifier and Type	Field	Description
static String	KEEP_MAPPING	keep mapping property
static String	MAPPING_STYLE	mapping style property
static String	MARK_BONDS	mark bonds property

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected List<Molecule>	getComponents(Molecule target)	A recursive algorithm getting all components (reactants, agents and products of reaction molecules, R-group definitions of Rg-Molecules) of the molecule.
Mapper.MappingStyle	getMappingStyle()	Returns the mapping style of the underlying mapper.
boolean	isKeepMapping()	Returns if underlying mapper keeps existing maps should be kept when mapping.
boolean	isMarkBonds()	Returns if bonds are marked while mapping.
void	setKeepMapping(boolean keepMapping)	Sets keep mapping for the underlying mapper.
void	setMappingStyle(Mapper.MappingStyle mappingStyle)	Sets Mapping Style for the underlying mapper.
void	setMarkBonds(boolean markBonds)	Sets mark bonds for the underlying mapper.
protected Changes	standardize1(Molecule molecule)	This method contains the current standardization mechanism.
String	toString()

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

Methods inherited from class java.lang.Object

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

Field Detail

MAPPING_STYLE

public static final String MAPPING_STYLE

mapping style property

See Also:

Constant Field Values

MARK_BONDS

public static final String MARK_BONDS

mark bonds property

See Also:

Constant Field Values

KEEP_MAPPING

public static final String KEEP_MAPPING

keep mapping property

See Also:

Constant Field Values

Constructor Detail

MapReactionAction

public MapReactionAction(Map<String,String> params)

Initializes the action

Parameters:

params - the parameters of the action

Method Detail

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 target)

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:

target - the target molecule

Returns:

the resulted list of components

setMappingStyle

public void setMappingStyle(Mapper.MappingStyle mappingStyle)

Sets Mapping Style for the underlying mapper.

Parameters:

mappingStyle - the new mapping style

Since:

6.1

setKeepMapping

public void setKeepMapping(boolean keepMapping)

Sets keep mapping for the underlying mapper.

Parameters:

keepMapping - true indicates existing maps should be kept when mapping

Since:

6.1

setMarkBonds

public void setMarkBonds(boolean markBonds)

Sets mark bonds for the underlying mapper.

Parameters:

markBonds - true indicates bond marks should be added when mapping

getMappingStyle

public Mapper.MappingStyle getMappingStyle()

Returns the mapping style of the underlying mapper.

Returns:

the mapping style of the underlying mapper

Since:

6.1

isKeepMapping

public boolean isKeepMapping()

Returns if underlying mapper keeps existing maps should be kept when mapping.

Returns:

true if underlying mapper keeps existing maps should be kept when mapping

Since:

6.1

isMarkBonds

public boolean isMarkBonds()

Returns if bonds are marked while mapping.

Returns:

true when bonds are marked while mapping

Since:

6.1

toString

public String toString()

Overrides:

toString in class AbstractStandardizerAction