Class TransformAction
java.lang.Object
chemaxon.standardizer.AbstractStandardizerAction
chemaxon.standardizer.advancedactions.TransformAction
- All Implemented Interfaces:
chemaxon.license.Licensable
,StandardizerAction
,PropertyChangeListener
,Cloneable
,EventListener
Transformation standardizer action
- Since:
- 5.11
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Field Summary
Modifier and TypeFieldDescriptionstatic final String
Key of exact for parsing and property changestatic final String
Key of search options for parsing and property changestatic final String
Key of query molecule for parsing and property changeFields inherited from class chemaxon.standardizer.AbstractStandardizerAction
CONFIG_PATH_KEY, FORMAT_KEY, ID_KEY, support
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Constructor Summary
ConstructorDescriptionTransformAction
(Map<String, String> params) Initializes the action with parameters -
Method Summary
Modifier and TypeMethodDescriptionclone()
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.Gets the search options of the actionDeprecated, for removal: This API element is subject to removal in a future version.Gets the transformation molecule of the actiongetType()
Gets the type of transformationboolean
Returns if this action is editable.boolean
isExact()
Gets the exact value of the actionvoid
setEditable
(boolean editable) Sets if this action is editable.void
setExact
(boolean exact) Sets the exact value of the actionvoid
setSearchOptions
(String optionString) Sets the search options of the actionvoid
setStructure
(String structure) Deprecated, for removal: This API element is subject to removal in a future version.void
setTransform
(RxnMolecule structure) Sets the transformationprotected Changes
standardize1
(Molecule molecule) This method contains the current standardization mechanism.toString()
Methods inherited from class chemaxon.standardizer.AbstractStandardizerAction
addPropertyChangeListener, addPropertyChangeListener, anyBooleanPropertyTrue, cloneItem, getDescriptor, getID, isActive, isAvailable, isLicensed, isValid, propertyChange, removePropertyChangeListener, removePropertyChangeListener, setActive, setID, setLicenseEnvironment, setValid, standardize
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Field Details
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EXACT_KEY
Key of exact for parsing and property change- See Also:
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SEARCH_OPTIONS_KEY
Key of search options for parsing and property change- See Also:
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STRUCTURE_KEY
Key of query molecule for parsing and property change- See Also:
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Constructor Details
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TransformAction
Initializes the action with parameters- Parameters:
params
- the parameters of the action
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Method Details
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setSearchOptions
Sets the search options of the action- Parameters:
optionString
- the search options of the action
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getSearchOptions
Gets the search options of the action- Returns:
- the search options of the action
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setEditable
public void setEditable(boolean editable) Sets if this action is editable.- Parameters:
editable
- the new editable flag
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isEditable
public boolean isEditable()Returns if this action is editable.- Returns:
true
if the action is editable
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setExact
public void setExact(boolean exact) Sets the exact value of the action- Parameters:
exact
- the exact value of the action
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isExact
public boolean isExact()Gets the exact value of the action- Returns:
- the exact value of the action
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setStructure
@Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setStructure(String structure) Deprecated, for removal: This API element is subject to removal in a future version.usesetTransform(RxnMolecule)
method insteadSets the transformation- Parameters:
structure
- the molecule defining the transformation
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setTransform
Sets the transformation- Parameters:
structure
- the molecule defining the transformation
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getStructure
Deprecated, for removal: This API element is subject to removal in a future version.Gets the transformation- Returns:
- the string representation of the molecule defining the transformation
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getTransform
Gets the transformation molecule of the action- Returns:
- the transformation molecule of the action
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getType
Gets the type of transformation- Returns:
- the type of the transformation
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standardize1
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 methodAbstractStandardizerAction.getComponents(Molecule)
, andAbstractStandardizerAction.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 aLogger
, that can be collected by usingStandardizerLogger.getLogger()
method.- Specified by:
standardize1
in classAbstractStandardizerAction
- Parameters:
molecule
- theMolecule
instance to be standardized- Returns:
- the changes applied on the molecule during the standardization process
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getComponents
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 classAbstractStandardizerAction
- Parameters:
molecule
- the target molecule- Returns:
- the resulted list of components
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clone
- Overrides:
clone
in classAbstractStandardizerAction
- Throws:
CloneNotSupportedException
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toString
- Overrides:
toString
in classAbstractStandardizerAction
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setTransform(RxnMolecule)
method instead