Class AbbreviatedGroupChecker

java.lang.Object
chemaxon.checkers.AbstractStructureChecker
chemaxon.checkers.AbbreviatedGroupChecker
All Implemented Interfaces:
StructureChecker, chemaxon.license.Licensable, PropertyChangeListener, Cloneable, EventListener

@PublicApi public class AbbreviatedGroupChecker extends AbstractStructureChecker
A descendant of AbstractStructureChecker detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form.
Since:
Marvin 5.3
  • Field Details

    • PROPERTY_KEY_EXPANDED

      public static final String PROPERTY_KEY_EXPANDED
      This public constant String represents the name of the configuration file property which is responsible for searching expanded abbreviated groups
      Since:
      5.4
      See Also:
    • PROPERTY_KEY_CONTRACTED

      public static final String PROPERTY_KEY_CONTRACTED
      This public constant String represents the name of the configuration file property which is responsible for searching contracted abbreviated groups
      Since:
      5.4
      See Also:
    • PROPERTY_KEY_SEARCH_CONTRACTED

      public static final String PROPERTY_KEY_SEARCH_CONTRACTED
      This public constant String represents the name of the property which is responsible for searching contracted abbreviated groups
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_SEARCH_EXPANDED

      public static final String PROPERTY_KEY_SEARCH_EXPANDED
      This public constant String represents the name of the property which is responsible for searching expanded abbreviated groups
      Since:
      5.7
      See Also:
    • PROPERTY_KEY_EXCLUDED

      public static final String PROPERTY_KEY_EXCLUDED
      This public constant String represents the name of the property which is responsible for the list of excluded groups
      Since:
      5.12
      See Also:
    • PROPERTY_KEY_SEARCH_EXCLUDED

      public static final String PROPERTY_KEY_SEARCH_EXCLUDED
      This public constant String represents the name of the property which is responsible for the list of excluded groups
      Since:
      5.12
      See Also:
  • Constructor Details

    • AbbreviatedGroupChecker

      public AbbreviatedGroupChecker()
      Default constructor. Search for both expanded and contracted abbreviated groups.
    • AbbreviatedGroupChecker

      public AbbreviatedGroupChecker(Map<String,String> params)
      Parameterized constructor. If "expanded" parameter given, and its value is "true" expanded abbreviated groups will be detected during the checking mechanism. Otherwise no expanded group will be found. If "contracted" parameter given, and its value is "true" contracted abbreviated groups will be detected during the checking mechanism. Otherwise no contracted group will be found.
      Parameters:
      params - a Map instance which contains String pairs. Key is the name of the parameter.
  • Method Details

    • isSearchContracted

      public boolean isSearchContracted()
      Returns if the checker is searching for contracted SGroups or not
      Returns:
      if the checker is searching for contracted SGroups or not
    • isSearchExpanded

      public boolean isSearchExpanded()
      Returns if the checker is searching for expanded SGroups or not
      Returns:
      if the checker is searching for expanded SGroups or not
    • expandMolecule

      protected Molecule expandMolecule(Molecule molecule, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)
      This implementation does nothing.
      Overrides:
      expandMolecule in class AbstractStructureChecker
      Parameters:
      molecule - the molecule to check
      Returns:
      the molecule
    • convertResult

      protected void convertResult(Molecule originalMolecule, Molecule expandedMolecule, StructureCheckerResult result, Map<MolAtom,MolAtom> atomMap, Map<MolBond,MolBond> bondMap)
      This implementation does nothing.
      Overrides:
      convertResult in class AbstractStructureChecker
      Parameters:
      originalMolecule - the original molecule
      expandedMolecule - the cloned then expanded molecule
      result - the structure checker result on cloned molecule
      atomMap - the mapping of cloned molecule and original molecule atoms
      bondMap - the mapping of cloned molecule and original molecule bonds
    • check1

      protected StructureCheckerResult check1(Molecule molecule)
      Description copied from class: AbstractStructureChecker
      This method contains the current checking mechanism.
      Specified by:
      check1 in class AbstractStructureChecker
      Parameters:
      molecule - the Molecule instance to be checked for problems
      Returns:
      a StructureCheckerResult which represents the problem or null if no problem found
    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class AbstractStructureChecker
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class AbstractStructureChecker
    • setSearchExpanded

      public void setSearchExpanded(boolean searchExpanded)
      Sets the checker should search for expanded abbreviated groups or not
      Parameters:
      searchExpanded - is a boolean property. If true expanded abbreviated groups will be checked during the checking mechanism.
      Since:
      5.4
    • setSearchContracted

      public void setSearchContracted(boolean searchContracted)
      Sets the checker should search for contracted abbreviated groups or not
      Parameters:
      searchContracted - is a boolean property. If true contracted abbreviated groups will be checked during the checking mechanism.
      Since:
      5.4
    • setExcluded

      public void setExcluded(AtomLabels excluded)
      Sets the abbreviations to be excluded
      Parameters:
      excluded - the abbreviations to be excluded
    • isValid

      public boolean isValid()
      Excluded object is initialized. If it is null, the parse was not successful.
      Specified by:
      isValid in interface StructureChecker
      Overrides:
      isValid in class AbstractStructureChecker
      Returns:
      true if the checker's configuration is valid, false otherwise
    • getExcluded

      public AtomLabels getExcluded()
      Gets the excluded abbreviations
      Returns:
      the excluded abbreviations