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Here is our growing directory of software for chemical/pharmaceutical applications that can integrate with the open-source scripting language Python. If you have suggestions or additions, please contact us at: info@chempython.org

Cheminformatics Toolkits

Cambios Toolkit
Frowns
PyDaylight
Python wrappers for OElib

Molecular Modeling

Molecular Modelling Tool Kit MMTK
Class Library for Advanced Molecular Properties
MDTools for Python

Molecular Visualization

Chimera
PyMol
Python Molecular Viewer PMV
VMD

Bioinformatics

See Biopython.org

Databases

Interfaces to relational databases

GUI Toolkits

PyQT
wxPython
Tcl/Tk

Graphics Toolkits

Visualization Tool Kit (VTK)

Tools drivable from Python via COM

Accelrys Viewer
ChemDraw
Excel
Any other windows application which exposes a COM interface.