chemaxon.standardizer.advancedactions

Class RemoveSolventsAction

java.lang.Object

chemaxon.standardizer.AbstractStandardizerAction

chemaxon.standardizer.advancedactions.RemoveSolventsAction

All Implemented Interfaces:

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

@PublicAPI
public class RemoveSolventsAction
extends AbstractStandardizerAction

Remove solvents standardizer action
Additionally solvents can be added in action string:
Example configuration: "removesolvents:benzene='c1ccccc1':water='[#8]'"

Since:

6.4

Author:

Zsolt Mohacsi

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	DEFAULT_SOLVENT_DICTIONARY_PATH Default solvent dictionary file path.
static java.lang.String	SOLVENT_ID_PROPERTY Property key for solvent ID
static java.lang.String	SOLVENT_LIST_KEY Property key for solvent list modification
static java.lang.String	USE_DEFAULT_SOLVENTS_KEY Property key for use default solvent modification

Fields inherited from class chemaxon.standardizer.AbstractStandardizerAction

CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support

Constructor Summary

Constructors

Constructor and Description
RemoveSolventsAction(java.util.Map<java.lang.String,java.lang.String> params) Initializes remove solvents action

Method Summary

Modifier and Type	Method and Description
void	addSolvent(java.lang.String solventID, Molecule molecule) Adds a solvent to the solvent list of the action
RemoveSolventsAction	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	getSolventCount() Gets the count of the solvents of the action
java.lang.String	getSolventID(int index) Gets the solvent ID at the provided index
java.util.List<Molecule>	getSolventList() Gets the custom solvent list of the action
boolean	isUseDefaultSolvents() Gets whether default solvent dictionary should be used
static java.util.List<Molecule>	readSolventDictionary() Reads the default solvent dictionary.
void	removeAllSolvents() Removes all solvents from the solvents list of the action.
void	removeSolvent(int index) Removes a solvent from the solvent list of the action
void	removeSolvents(int... indexes) Removes a solvent from the solvent list of the action
void	setMolecule(int index, Molecule molecule) Sets the molecule of the solvent at the provided index
void	setSolventID(int index, java.lang.String solventID) Sets the name of the solvent at the provided index
void	setUseDefaultSolvents(boolean useDefaultSolvents) Sets whether default solvent 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

SOLVENT_LIST_KEY

public static final java.lang.String SOLVENT_LIST_KEY

Property key for solvent list modification

See Also:

Constant Field Values

USE_DEFAULT_SOLVENTS_KEY

public static final java.lang.String USE_DEFAULT_SOLVENTS_KEY

Property key for use default solvent modification

See Also:

Constant Field Values

DEFAULT_SOLVENT_DICTIONARY_PATH

public static final java.lang.String DEFAULT_SOLVENT_DICTIONARY_PATH

Default solvent dictionary file path.

See Also:

Constant Field Values

SOLVENT_ID_PROPERTY

public static final java.lang.String SOLVENT_ID_PROPERTY

Property key for solvent ID

See Also:

Constant Field Values

Constructor Detail

RemoveSolventsAction

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

Initializes remove solvents action

Parameters:

params - the parameters of the action

Method Detail

isUseDefaultSolvents

public boolean isUseDefaultSolvents()

Gets whether default solvent dictionary should be used

Returns:

whether default solvent dictionary should be used

setUseDefaultSolvents

public void setUseDefaultSolvents(boolean useDefaultSolvents)

Sets whether default solvent dictionary should be used

Parameters:

useDefaultSolvents - whether default solvent dictionary should be used

addSolvent

public void addSolvent(java.lang.String solventID,
                       Molecule molecule)

Adds a solvent to the solvent list of the action

Parameters:

solventID - solvent ID of the solvent

molecule - the molecule of the solvent

setSolventID

public void setSolventID(int index,
                         java.lang.String solventID)

Sets the name of the solvent at the provided index

Parameters:

index - the target index

solventID - the solventID to be set

setMolecule

public void setMolecule(int index,
                        Molecule molecule)

Sets the molecule of the solvent at the provided index

Parameters:

index - the target index

molecule - the molecule to be set

getSolventCount

public int getSolventCount()

Gets the count of the solvents of the action

Returns:

the count of the solvents 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

getSolventID

public java.lang.String getSolventID(int index)

Gets the solvent ID at the provided index

Parameters:

index - the required index

Returns:

the solvent ID at the provided index

removeSolvent

public void removeSolvent(int index)

Removes a solvent from the solvent list of the action

Parameters:

index - index of the solvent to be removed

removeSolvents

public void removeSolvents(int... indexes)

Removes a solvent from the solvent list of the action

Parameters:

indexes - indexes of the solvents to be removed

removeAllSolvents

public void removeAllSolvents()

Removes all solvents from the solvents 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

readSolventDictionary

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

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

Returns:

the default solvent dictionary

getSolventList

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

Gets the custom solvent list of the action

Returns:

the custom solvent list of the action

clone

public RemoveSolventsAction 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