chemaxon.standardizer.advancedactions

Class Clean2DAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.advancedactions.Clean2DAction

All Implemented Interfaces:

chemaxon.license.Licensable, StandardizerAction, java.beans.PropertyChangeListener, java.lang.Cloneable, java.util.EventListener

@PublicAPI
public class Clean2DAction
extends AbstractStandardizerAction

Clean molecule graph in 2D standardizer action

Since:

6.0

Author:

Imre Barna

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Clean2DAction.Type Type of clean action (partial, full, template based or convert 3D to 2D)

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	PARTIAL_CLEAN_KEY Key for partial clean necessary property change
static java.lang.String	TEMPLATE_FILE_KEY Key of template file for parsing and property change
static java.lang.String	TEMPLATES_KEY Key for templates property change
static java.lang.String	TYPE_KEY Key of type for parsing and property change

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor and Description
Clean2DAction(java.util.Map<java.lang.String,java.lang.String> params) Initializes the action with parameters

Method Summary

Modifier and Type	Method and Description
Clean2DAction	clone()
Molecule[]	getTemplates() Gets the template molecules of the clean action
Clean2DAction.Type	getType() Gets the type of action
void	setTemplates(Molecule[] cleanTemplates) Sets the clean templates of the action
void	setType(Clean2DAction.Type type) Sets the type of action
protected Changes	standardize1(Molecule molecule) This method contains the current standardization mechanism.
java.lang.String	toString()

Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction

addPropertyChangeListener, addPropertyChangeListener, cloneItem, getComponents, 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

TYPE_KEY

public static final java.lang.String TYPE_KEY

Key of type for parsing and property change

See Also:

Constant Field Values

TEMPLATE_FILE_KEY

public static final java.lang.String TEMPLATE_FILE_KEY

Key of template file for parsing and property change

See Also:

Constant Field Values

PARTIAL_CLEAN_KEY

public static final java.lang.String PARTIAL_CLEAN_KEY

Key for partial clean necessary property change

See Also:

Constant Field Values

TEMPLATES_KEY

public static final java.lang.String TEMPLATES_KEY

Key for templates property change

See Also:

Constant Field Values

Constructor Detail

Clean2DAction

public Clean2DAction(java.util.Map<java.lang.String,java.lang.String> params)

Initializes the action with parameters

Parameters:

params - the parameters of the action

Method Detail

setType

public void setType(Clean2DAction.Type type)

Sets the type of action

Parameters:

type - the type of action

getType

public Clean2DAction.Type getType()

Gets the type of action

Returns:

the type of action

standardize1

protected Changes standardize1(Molecule molecule)
                        throws java.lang.IllegalArgumentException

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

Throws:

java.lang.IllegalArgumentException - if the provided molecule or the provided parameters of the action are invalid

clone

public Clean2DAction clone()
                    throws java.lang.CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

java.lang.CloneNotSupportedException

setTemplates

public void setTemplates(Molecule[] cleanTemplates)

Sets the clean templates of the action

Parameters:

cleanTemplates - the clean templates of the action

toString

public java.lang.String toString()

Overrides:

toString in class AbstractStandardizerAction

getTemplates

public Molecule[] getTemplates()

Gets the template molecules of the clean action

Returns:

null if not template based clean, or templates are empty