python-fmcs

Find Maximum Common Substructure
  https://bitbucket.org/dalke/fmcs/overview
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Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string.

More specifically, the MCS found is a common edge subgraph, and not a common induced subgraph. Only connected MCSes are found.