Clean runs the Mengine executable for cleaning small molecules. More specifically, Mengine implements the MMFF94 force field (see J Comp Chem,17, 490-642, 1996 for all the references) and was validated against the published suite of MMFF94 results (see CCL to download validation suite). Basic operation is for PyMOL to generate a complete structure, including hydrogens, and send the structure in SD format on stdin. Extra information about the job - fixed atoms, distances, monitor and so on were encoded in tags (again standard SD format). The current tags used are documented in the source code. Mengine reads the structure, generates the correct atom types, and then optimizes the structure using a first derivative minimization method (BFGS) until the gradient falls below 0.01 and then switches to a second derivative newton-raphson method until the gradient is less than 0.0001. All pretty standard stuff similar to what is in Tinker. Mengine sends the results back on stdout in SD format with added information about energies or charges and more, again using SD tags to encode the information. The MDL SD format is limited to 999 atoms.
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