Class MolSearchOptions

    • Method Detail

      • isQueryAbsoluteStereo

        public boolean isQueryAbsoluteStereo()
        Returns whether the chiral flag is ignored or not for the query molecule.
        Returns:
        true, if chiral centers in the query molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        Default value is true.
        See Also:
        setQueryAbsoluteStereo(boolean)
      • setQueryAbsoluteStereo

        public void setQueryAbsoluteStereo​(boolean value)
        Sets whether the chiral flag should be ignored or not for the query molecule.
        Parameters:
        value - if true, chiral centers in the query molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        Default value is true.
        See Also:
        isQueryAbsoluteStereo()
      • isTargetAbsoluteStereo

        public boolean isTargetAbsoluteStereo()
        Returns whether the chiral flag is ignored or not for the target molecule.
        Returns:
        true, if chiral centers in the target molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        Default value is true
        See Also:
        setTargetAbsoluteStereo(boolean)
      • setTargetAbsoluteStereo

        public void setTargetAbsoluteStereo​(boolean value)
        Sets whether the chiral flag should be ignored or not for the target molecule.
        Parameters:
        value - if true, chiral centers in the target molecule are regarded as absolute stereo, ignoring the chiral flag. If the molecule contains any enhanced stereo labels, this flag has no effect.
        Default value is true.
        See Also:
        isTargetAbsoluteStereo()
      • isMarkushEnabled

        public boolean isMarkushEnabled()
        Specifies whether a target containing Markush features should be treated as a Markush library.
        Returns:
        true, if a target should be treated as a Markush library when it contains Markush features
        Default value is false.
        Since:
        5.0
        See Also:
        setMarkushEnabled(boolean)
      • setMarkushEnabled

        public void setMarkushEnabled​(boolean value)
        Sets whether targets containing Markush features should be treated as Markush libraries
        Parameters:
        value - true, if a target containing Markush features should be treated as Markush library
        Default value is false.
        Since:
        5.0
        See Also:
        isMarkushEnabled()
      • setDistinctFirstAtomMatching

        public void setDistinctFirstAtomMatching​(boolean b)
        Option ensuring that upon the findNext() call the first atom must be stepped as well. Option is considered only in case of searching a recursive SMARTS query.
        The search-internal first atom is ensured to be the original first atom only if the SearchOptions.setKeepQueryOrder(boolean) is set to true. This must be set to true, or the first atom can be arbitrary atom.
        Parameters:
        b - if true the first atom of the query must match on different target atoms in findAll and findNext searches.
        Default value is false.
        See Also:
        isDistinctFirstAtomMatching()
      • isDistinctFirstAtomMatching

        public boolean isDistinctFirstAtomMatching()
        Get option ensuring that upon the findNext() call the first atom must be stepped as well. Option is considered only in case of searching a recursive SMARTS query.
        The search-internal first atom is ensured to be the original first atom only if the SearchOptions.setKeepQueryOrder(boolean) is set to true. This must be set to true, or the first atom can be arbitrary atom.
        Returns:
        true if first atom should be different
        Default value is false.
        See Also:
        setDistinctFirstAtomMatching(boolean)
      • clonecopy

        public void clonecopy​(SearchOptions other)
        Copies parameters to other. It copies
        - all parameters if other is a MolSearchOptions object
        - only the parameters defined in SearchOptions if it is a SearchOptions or JchemSearchOptions object
        Overrides:
        clonecopy in class SearchOptions
        Parameters:
        other - search option to overwrite.
      • clonecopyOptions

        public void clonecopyOptions​(SearchOptions other)
        Description copied from class: SearchOptions
        Copies all search options except search type to other.
        Overrides:
        clonecopyOptions in class SearchOptions
        Parameters:
        other - search option object to overwrite
      • getTautomerEqualityMode

        @Beta
        public chemaxon.sss.search.options.TautomerTransformationMode getTautomerEqualityMode()
      • setTautomerEqualityMode

        @Beta
        public void setTautomerEqualityMode​(chemaxon.sss.search.options.TautomerTransformationMode tautomerEqualityMode)