Class AbbreviatedGroupChecker

    • Field Detail

      • 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:
        Constant Field Values
      • 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:
        Constant Field Values
      • 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:
        Constant Field Values
      • 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:
        Constant Field Values
      • 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:
        Constant Field Values
      • 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:
        Constant Field Values
    • Constructor Detail

      • 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 Detail

      • 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
      • 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
      • 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​(chemaxon.checkers.util.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 chemaxon.checkers.util.AtomLabels getExcluded()
        Gets the excluded abbreviations
        Returns:
        the excluded abbreviations