Package chemaxon.clustering.libmcs.adapter

Interface LegacyLibraryMcsParameters

@PublicApi @Beta public interface LegacyLibraryMcsParameters
Parameters for LibraryMcs clustering implementation.

  • Method Details

    • setAllowedLevelCount

      LegacyLibraryMcsParameters setAllowedLevelCount(int allowedLevelCount)
      Sets the maximum number of hierarchy levels allowed in clustering. Clustering terminates when the hierarchy has this many levels.
      Parameters:
      allowedLevelCount - number of hierarchy levels allowed (tree depth)
      Returns:
      Reference to this instance

    • getAllowedLevelCount

      int getAllowedLevelCount()

    • setAtomCountUpperBound

      LegacyLibraryMcsParameters setAtomCountUpperBound(int atomCountUpperBound)
      Sets the maximum structure size for pairwise mcs search. Structures above this size are not selected for a pair-wise mcs search. This limit has strong effect on the results as well as on the total running time. MCS search for larger structure (e.g. above 40 atoms) can be slow.
      Returns:
      Reference to this instance

    • getAtomCountUpperBound

      int getAtomCountUpperBound()

    • setMCSMode

      LegacyLibraryMcsParameters setMCSMode(SearchMode mode)
      Sets MCS search strategy. Allowed values are NORMAL or FAST (default).
      Parameters:
      mode - mode flag
      Returns:
      Reference to this instance

    • getMCSMode

      SearchMode getMCSMode()

    • setMinimumMCSSize

      LegacyLibraryMcsParameters setMinimumMCSSize(int mcsSize)
      Sets the minimum size of any MCS found. MCSs below this size limit are ignored.
      Parameters:
      mcsSize - minimum required size of any MCS
      Returns:
      Reference to this instance

    • getMinimumMCSSize

      int getMinimumMCSSize()

    • setKeepRings

      LegacyLibraryMcsParameters setKeepRings(boolean keepRings)
      Sets whether rings should be kept or they can be broken.
      Parameters:
      keepRings - false if rings can be broken.
      Returns:
      Reference to this instance

    • getKeepRings

      boolean getKeepRings()

    • setAtomTypeMatch

      LegacyLibraryMcsParameters setAtomTypeMatch(boolean b)
      Sets the matching mode for atom types. Atom types can either be considered (checked) or ignored when two molecules are searched for an MCS.
      Parameters:
      b - flags if atom types are considered (true) or ignored (false)
      Returns:
      Reference to this instance

    • getAtomTypeMatch

      boolean getAtomTypeMatch()

    • setBondTypeMatch

      LegacyLibraryMcsParameters setBondTypeMatch(boolean b)
      Sets the matching mode for bond types. Bond types can either be considered (checked) or ignored when two molecules are searched for an MCS.
      Parameters:
      b - flags if bond types are considered (true) or ignored (false)
      Returns:
      Reference to this instance

    • getBondTypeMatch

      boolean getBondTypeMatch()

    • setChargeMatch

      LegacyLibraryMcsParameters setChargeMatch(boolean b)
      Sets the matching mode for atom formal charges. Charges can either be considered (checked) or ignored when two molecules are searched for an MCS.
      Parameters:
      b - flags if atom charges are considered (true) or ignored (false)
      Returns:
      Reference to this instance

    • getChargeMatch

      boolean getChargeMatch()

    • setRadicalMatch

      LegacyLibraryMcsParameters setRadicalMatch(boolean b)
      Sets the matching mode for radicals on atoms. Radicals can either be considered (checked) or ignored when two molecules are searched for an MCS.
      Parameters:
      b - flags if atom radicals are considered (true) or ignored (false)
      Returns:
      Reference to this instance

    • getRadicalMatch

      boolean getRadicalMatch()

    • setIsotopeMatch

      LegacyLibraryMcsParameters setIsotopeMatch(boolean b)
      Sets the matching mode for isotopes. Isotopes can either be considered (checked) or ignored when two molecules are searched for an MCS.
      Parameters:
      b - flags if atom isotopes are considered (true) or ignored (false)
      Returns:
      Reference to this instance

    • getIsotopeMatch

      boolean getIsotopeMatch()

    • setRequiredClusterCount

      LegacyLibraryMcsParameters setRequiredClusterCount(int requiredClusterCount)
      Sets the minimal number of clusters required on the top level of hierarchy. Search terminates if there is the number of clusters on the highest level of the hierarchy is less than this limit.
      Parameters:
      requiredClusterCount - number of top level clusters
      Returns:
      Reference to this instance

    • getRequiredClusterCount

      int getRequiredClusterCount()