ScientificPython is a collection of Python modules that are useful for scientific applications. Most of them need the NumPy package (

This is release 2.9 of ScientificPython. The odd minor release number indicates a development release.

All the documentation is in Doc. To browse the reference manual for all the modules, point your browser at Doc/Reference/index.html.

If you find bugs, please tell me, and if you improve something, please send me the modified version. I don't promise anything, but since I use these modules a lot for my own work, I have an interest in keeping them bug-free and usable.

For updates, check

from time to time.

Konrad Hinsen Centre de Biophysique Mol��culaire (CNRS) et Synchrotron Soleil E-Mail:


Required: Python 2.5 or higher. Most modules also require NumPy 1.6 to 1.8. ScientificPython is NOT compatible with NumPy 1.9 or later, because it relies on a submodule of NumPy that was removed in version 1.9. If you want to use the netCDF interface module, you also need the netCDF library, version 3.0 or higher.

  1. Unix-like systems, including Linux and MacOS X

Installation is as simple as

python build python install

(the second command requires root privileges on many installations). This will build the netCDF module if it can find a netCDF installation in either /usr/local or in /usr. If your netCDF installation is elsewhere, set the environment variable "NETCDF_PREFIX" to the directory in which "include/netcdf.h" and "lib/" are located.

  1. Windows

To build the netCDF interface module, you must have a binary version of netCDF. You can either compile it yourself, or download the precompiled netcdf.dll from the netCDF Web site. You also need the file netcdf.h, which you can find in the netCDF source code distribution. PLEASE MAKE SURE THAT NETCDF.DLL AND NETCDF.H ARE FOR THE SAME NETCDF RELEASE!

Installation is as simple as

python build --netcdf_prefix=dir_h --netcdf_dll=dir_dll python install --netcdf_prefix=dir_h --netcdf_dll=dir_dll

where "dir_h" is the directory in which netcdf.h is located and "dir_dll" is the the directory in which netcdf.dll is located.

Alternatively, you can create a binary installer using

python bdist_wininst --netcdf_prefix=dir_h --netcdf_dll=dir_dll


The directory Examples provides a few simple example applications, including a C extension module that uses the netCDF C-API.

Using Scientific.Visualization.VMD under Windows

If VMD is installed in its default location, everything should work fine automatically. Otherwise, an error message will be printed. The default location is

c:Program FilesUniversity of IllinoisVMDvmd.exe

or its equivalent on non-English Windows versions ("Program Files" changes its name).