[Chimera-users] NumPy in Chimera

Tom Goddard goddard at cgl.ucsf.edu
Tue Feb 6 16:56:19 PST 2007

Hi Chimera Extension Writers,

  If you have written Chimera extensions that use Numeric Python you 
will need to convert them to instead use NumPy to work with future 
versions of Chimera.  NumPy provides almost all the same routines as 
Numeric but some function and module names have changed.

  We are switching Chimera over from Numeric Python to NumPy and will 
have a Chimera snapshot out in one to three weeks that uses NumPy.  We 
envision having a Chimera production release that uses NumPy in perhaps 
3 months.  The change was necessary because Numeric is no longer maintained.

  Numeric will no longer be included with Chimera because dynamic 
library name space collisions with NumPy occur on the Mac because of 
certain Chimera compilation options.

  The conversion of Chimera code was not much trouble, but we had to 
also convert third party packages that are included with Chimera 
(PyOpenGL, MMTK, Scientific (for netcdf file reading), MSMS molecular 
surfaces) and that took some work.

  Thanks for your patience.



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