Package chemaxon.standardizer.advancedactions

Class TransformAction

java.lang.Object
chemaxon.standardizer.AbstractStandardizerAction
chemaxon.standardizer.advancedactions.TransformAction
All Implemented Interfaces:
chemaxon.license.Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener
@PublicApi public final class TransformAction extends AbstractStandardizerAction
Transformation standardizer action
Since:
5.11

  • Field Details

    • EXACT_KEY

      public static final String EXACT_KEY
      Key of exact for parsing and property change
      See Also:

    • SEARCH_OPTIONS_KEY

      public static final String SEARCH_OPTIONS_KEY
      Key of search options for parsing and property change
      See Also:

    • STRUCTURE_KEY

      public static final String STRUCTURE_KEY
      Key of query molecule for parsing and property change
      See Also:

  • Constructor Details

    • TransformAction

      public TransformAction(Map<String,String> params)
      Initializes the action with parameters
      Parameters:
      params - the parameters of the action

  • Method Details

    • setSearchOptions

      public void setSearchOptions(String optionString)
      Sets the search options of the action
      Parameters:
      optionString - the search options of the action

    • getSearchOptions

      public String getSearchOptions()
      Gets the search options of the action
      Returns:
      the search options of the action

    • setEditable

      public void setEditable(boolean editable)
      Sets if this action is editable.
      Parameters:
      editable - the new editable flag

    • isEditable

      public boolean isEditable()
      Returns if this action is editable.
      Returns:
      true if the action is editable

    • setExact

      public void setExact(boolean exact)
      Sets the exact value of the action
      Parameters:
      exact - the exact value of the action

    • isExact

      public boolean isExact()
      Gets the exact value of the action
      Returns:
      the exact value of the action

    • 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.
      use setTransform(RxnMolecule) method instead
      Sets the transformation
      Parameters:
      structure - the molecule defining the transformation

    • setTransform

      public void setTransform(RxnMolecule structure)
      Sets the transformation
      Parameters:
      structure - the molecule defining the transformation

    • getStructure

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public String 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

    • getTransform

      public RxnMolecule getTransform()
      Gets the transformation molecule of the action
      Returns:
      the transformation molecule of the action

    • getType

      public String getType()
      Gets the type of transformation
      Returns:
      the type of the transformation

    • 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 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

    • clone

      public TransformAction clone() throws CloneNotSupportedException
      Overrides:
      clone in class AbstractStandardizerAction
      Throws:
      CloneNotSupportedException

    • toString

      public String toString()
      Overrides:
      toString in class AbstractStandardizerAction