chemaxon.standardizer.advancedactions

Class StripSaltsAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.advancedactions.StripSaltsAction

All Implemented Interfaces:

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

@PublicAPI
public class StripSaltsAction
extends AbstractStandardizerAction

Strip salts standardizer action
Additionally salts can be added in action string:
Example configuration: "stripsalts:na='[Na+]':soo='[#8]S([#8])(=O)=O'"

Since:

6.0

Author:

Imre Barna

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_SALT_DICTIONARY_PATH Default salt dictionary file path.
static java.lang.String	DONT_REMOVE_LAST_COMPONENT_KEY Property key for "Don't Remove Last Component" option
static java.lang.String	SALT_ID_PROPERTY Property key for salt ID
static java.lang.String	SALT_LIST_KEY Property key for salt list modification
static java.lang.String	USE_DEFAULT_SALTS_KEY Property key for use default salts modification

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor and Description
StripSaltsAction(java.util.Map<java.lang.String,java.lang.String> params) Initializes strip salts action

Method Summary

Modifier and Type	Method and Description
void	addSalt(java.lang.String saltID, Molecule molecule) Adds a salt to the salt list of the action
StripSaltsAction	clone()
protected java.util.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.
Molecule	getMolecule(int index) Gets the molecule at the provided index
int	getSaltCount() Gets the count of the salts of the action
java.lang.String	getSaltID(int index) Gets the salt ID at the provided index
java.util.List<Molecule>	getSaltList() Gets the custom salt list of the action
boolean	isDontRemoveLastComponent()
boolean	isUseDefaultSalts() Gets whether default salt dictionary should be used
static java.util.List<Molecule>	readSaltDictionary() Reads the default salt dictionary.
void	removeAllSalts() Removes all salts from the salt list of the action.
void	removeSalt(int index) Removes a salt from the salt list of the action
void	removeSalts(int... indexes) Removes a salt from the salt list of the action
void	setDontRemoveLastComponent(boolean dontRemoveLastComponent)
void	setMolecule(int index, Molecule molecule) Sets the molecule of the salt at the provided index
void	setSaltID(int index, java.lang.String saltID) Sets the name of the salt at the provided index
void	setUseDefaultSalts(boolean useDefaultSalts) Sets whether default salt dictionary should be used
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, 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

SALT_LIST_KEY

public static final java.lang.String SALT_LIST_KEY

Property key for salt list modification

See Also:

Constant Field Values

USE_DEFAULT_SALTS_KEY

public static final java.lang.String USE_DEFAULT_SALTS_KEY

Property key for use default salts modification

See Also:

Constant Field Values

DONT_REMOVE_LAST_COMPONENT_KEY

public static final java.lang.String DONT_REMOVE_LAST_COMPONENT_KEY

Property key for "Don't Remove Last Component" option

See Also:

Constant Field Values

DEFAULT_SALT_DICTIONARY_PATH

public static final java.lang.String DEFAULT_SALT_DICTIONARY_PATH

Default salt dictionary file path.

See Also:

Constant Field Values

SALT_ID_PROPERTY

public static final java.lang.String SALT_ID_PROPERTY

Property key for salt ID

See Also:

Constant Field Values

Constructor Detail

StripSaltsAction

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

Initializes strip salts action

Parameters:

params - the parameters of the action

Method Detail

isUseDefaultSalts

public boolean isUseDefaultSalts()

Gets whether default salt dictionary should be used

Returns:

whether default salt dictionary should be used

setUseDefaultSalts

public void setUseDefaultSalts(boolean useDefaultSalts)

Sets whether default salt dictionary should be used

Parameters:

useDefaultSalts - whether default salt dictionary should be used

addSalt

public void addSalt(java.lang.String saltID,
                    Molecule molecule)

Adds a salt to the salt list of the action

Parameters:

saltID - saltID of the salt

molecule - the molecule of the salt

setSaltID

public void setSaltID(int index,
                      java.lang.String saltID)

Sets the name of the salt at the provided index

Parameters:

index - the target index

saltID - the saltID to be set

isDontRemoveLastComponent

public boolean isDontRemoveLastComponent()

setDontRemoveLastComponent

public void setDontRemoveLastComponent(boolean dontRemoveLastComponent)

setMolecule

public void setMolecule(int index,
                        Molecule molecule)

Sets the molecule of the salt at the provided index

Parameters:

index - the target index

molecule - the molecule to be set

getSaltCount

public int getSaltCount()

Gets the count of the salts of the action

Returns:

the count of the salts of the action

getMolecule

public Molecule getMolecule(int index)

Gets the molecule at the provided index

Parameters:

index - the required index

Returns:

the molecule at the provided index

getSaltID

public java.lang.String getSaltID(int index)

Gets the salt ID at the provided index

Parameters:

index - the required index

Returns:

the salt ID at the provided index

removeSalt

public void removeSalt(int index)

Removes a salt from the salt list of the action

Parameters:

index - index of the salt to be removed

removeSalts

public void removeSalts(int... indexes)

Removes a salt from the salt list of the action

Parameters:

indexes - indexes of the salts to be removed

removeAllSalts

public void removeAllSalts()

Removes all salts from the salt list of the 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

readSaltDictionary

public static final java.util.List<Molecule> readSaltDictionary()

Reads the default salt dictionary. The name of the salt will be the name of the molecule

Returns:

the default salt dictionary

getSaltList

public java.util.List<Molecule> getSaltList()

Gets the custom salt list of the action

Returns:

the custom salt list of the action

clone

public StripSaltsAction clone()
                       throws java.lang.CloneNotSupportedException

Overrides:

clone in class AbstractStandardizerAction

Throws:

java.lang.CloneNotSupportedException

toString

public java.lang.String toString()

Overrides:

toString in class AbstractStandardizerAction

getComponents

protected java.util.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