This is a port of MMTK (Molecular Modeling ToolKit).  In addition to
providing ready-to-use implementations of standard algorithms, MMTK
serves as a code basis that can be easily extended and modified to deal
with standard and non-standard problems in molecular simulations.

MMTK consists of nothing more than a collection of Python modules, most
of which written in Python itself, with only a small time-critical part
(e.g. energy evaluation) written in C. MMTK applications are Python
programs that make use of these modules.

WWW: http://starship.python.net/crew/hinsen/MMTK/index.html