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The Lilly MedChem Rules (LMR) \cite{Bruns_2012} apply filters to avoid reactive and promiscuous compounds.  Molpher \cite{Hoksza_2014} generates a virtual chemical library that represents the chemical space between two input molecules as it consists of the path found by morphing one molecule to another.  The Open Molecule Generator (OMG) \cite{Peironcely_2012} enumerates all possible chemical structures given constraints on their composition.  sdf2xyz2sdf \cite{Tosco_2011} converts between SDF and TINKER XYZ files.