Package chemaxon.standardizer.actions

Class MapReactionAction

java.lang.Object
chemaxon.standardizer.AbstractStandardizerAction
chemaxon.standardizer.actions.MapReactionAction
All Implemented Interfaces:
chemaxon.license.Licensable, StandardizerAction, PropertyChangeListener, Cloneable, EventListener
@PublicApi public final class MapReactionAction extends AbstractStandardizerAction
Map reaction standardizer action
Since:
5.11

  • Field Details

  • Constructor Details

    • MapReactionAction

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

  • Method Details

    • 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 target)
      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:
      target - the target molecule
      Returns:
      the resulted list of components

    • setMappingStyle

      public void setMappingStyle(Mapper.MappingStyle mappingStyle)
      Sets Mapping Style for the underlying mapper.
      Parameters:
      mappingStyle - the new mapping style
      Since:
      6.1

    • setKeepMapping

      public void setKeepMapping(boolean keepMapping)
      Sets keep mapping for the underlying mapper.
      Parameters:
      keepMapping - true indicates existing maps should be kept when mapping
      Since:
      6.1

    • setMarkBonds

      public void setMarkBonds(boolean markBonds)
      Sets mark bonds for the underlying mapper.
      Parameters:
      markBonds - true indicates bond marks should be added when mapping

    • getMappingStyle

      public Mapper.MappingStyle getMappingStyle()
      Returns the mapping style of the underlying mapper.
      Returns:
      the mapping style of the underlying mapper
      Since:
      6.1

    • isKeepMapping

      public boolean isKeepMapping()
      Returns if underlying mapper keeps existing maps should be kept when mapping.
      Returns:
      true if underlying mapper keeps existing maps should be kept when mapping
      Since:
      6.1

    • isMarkBonds

      public boolean isMarkBonds()
      Returns if bonds are marked while mapping.
      Returns:
      true when bonds are marked while mapping
      Since:
      6.1

    • toString

      public String toString()
      Overrides:
      toString in class AbstractStandardizerAction