The Molecular Modeling Toolkit: a case study of a large scientific application in Python

The Molecular Modeling Toolkit is a library of Python modules and C extension modules that provides an object-oriented description of molecular systems and an implementation of the most common modeling techniques. It is one of the first large scientific applications implemented in Python. This article presents some aspects of its design and implementation that are typical for scientific applications in general. Its aim is to demonstrate by example how scientific computing can benefit from Python, and to show how common problems