The Biopython Project - Freely available Python tools for computational molecular biology. - http://www.biopython.org/
Pmv, ADT and ViPEr - Python software from the Molecular Graphics Lab (MGL) of the Scripps Research institute. [Free for non-commercial use] - http://www.scripps.edu/~sanner/python/
PyDaylight - Turns the Daylight toolkit into a rapid application development system for chemical information by providing a full Python interface. [Open Source, LGPL] - http://sourceforge.net/projects/pydaylight/
pyCGNS - Python interface for CGNS (data standard for computational fluid dynamics). [Open Source, GPL] - http://elsa.onera.fr/CGNS/releases/