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CurlySMILES \cite{Drefahl_2011} provides parsing functionality for an extension of the SMILES format that supports the description of complex molecular systems.  Fafoom (flexible aalgorithm for optimization of molecules) \cite{Supady_2015} is a Python library for identifying low energy conformers using a genetic algorithm.  fmcsR \cite{Goecks_2010} is an R package that efficiently performs flexible maximum common substructure matching that allows minor mismatches between atoms and bonds in the common substructure.  Frowns is a cheminformatics toolkit mostly written in Python that provides basic support for SMILES and SD files, SMARTS search, fingerprint generation, and property perception.