Package chemaxon.sss.search

Class MolSearchOptions

java.lang.Object
chemaxon.sss.search.SearchOptions
chemaxon.sss.search.MolSearchOptions
All Implemented Interfaces:
SearchConstants, Serializable, Cloneable
@PublicApi public class MolSearchOptions extends SearchOptions implements SearchConstants, Cloneable
Class to encapsulate search parameters used by Search implementations(ex: MolSearch).
Since:
5.0
See Also:

  • Constructor Details

  • Method Details

    • 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

      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:

    • 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

      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:

    • getHitIndexType

      public int getHitIndexType()
      Returns the representation on which the hit indexes are given in case of Markush search.
      Returns:
      of which representation the hit indexes are.
      Default value is SearchConstants.MARKUSH_HIT_ORIGINAL.
      See Also:

    • setHitIndexType

      public void setHitIndexType(int value)
      Set the representation to use for hit indexes in case of Markush search.
      Parameters:
      value - specifies the representation on which the hit indexes are given in case of Markush search.
      Default value is SearchConstants.MARKUSH_HIT_ORIGINAL.
      See Also:

    • 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

      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:

    • 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

      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:

    • setSwitchOffAllProtectsForTDF

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setSwitchOffAllProtectsForTDF(boolean value)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
      Sets the switch off all protects for generic tautomer creation. Considered only when tautomer search is on.
      Parameters:
      value - true if all protects should be disabled during generic tautomer creation. Default is false.
      See Also:

    • isSwitchOffAllProtectsForTDF

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public final boolean isSwitchOffAllProtectsForTDF()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Since JChem 5.12, stereo is considered as default in tautomer regions, but SearchOptions.setTautomerSearch(int) with value SearchConstants.TAUTOMER_SEARCH_ON_IGNORE_TAUTOMERSTEREO ignores it.
      Specifies whether all protects are switched off during generic tautomer creation. Considered only when tautomer search is on.
      Returns:
      true if protect features should be disabled during generic tautomer creation
      Default is false.
      See Also:

    • clone

      public Object clone() throws CloneNotSupportedException
      Description copied from class: SearchOptions
      Makes an identical copy of this SearchObject.
      Overrides:
      clone in class SearchOptions
      Throws:
      CloneNotSupportedException

    • 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

    • toList

      public ArrayList<String> toList()
      Description copied from class: SearchOptions
      Returns the text representation of this options object as a list of "optionname:optionvalue" strings. Only those options are listed that have non-default values.
      Overrides:
      toList in class SearchOptions
      Returns:
      a list containing the non-default options as "optionname:optionvalue" pairs

    • getTautomerEqualityMode

      @Beta public TautomerEqualityMode getTautomerEqualityMode()
      Internal use only.

    • setTautomerEqualityMode

      @Beta public void setTautomerEqualityMode(TautomerEqualityMode tautomerEqualityMode)
      Internal use only.

    • getTautomerSubstructureMode

      @Beta public TautomerSubstructureMode getTautomerSubstructureMode()
      Internal use only.

    • setTautomerSubstructureMode

      @Beta public void setTautomerSubstructureMode(TautomerSubstructureMode tautomerSubstructureMode)
      Internal use only.