[BioPython] 3D Structure?

[Harry Mangalam]

not biopython-based, but open source and seems to fit the rest of your 
requirements - why not start here:

http://pymol.sourceforge.net/

On Thursday 16 December 2004 2:51 am, Andreas Klostermann wrote:
> Hi,
>
> I just started browsing around what you can do with Biopython, for
> some educational interest. I'd like to try and implement an Open GL
> Viewer for molecules in Python. In my wild days (before studying
> veterinary medicine) I acquired a solid grasp of Open Gl. In case
> you wonder, if Python is fast enough for this task. It is. Or
> better: it's not, but Open Gl does all the work with hardware
> acceleration, circumventing the speed draw-back of python.
>
> First task would be to obtain the structure of the molecule by
> linking 3D coordinates together. I browsed in the biopython
> documentation, but I did not really get a clue. I suspected the
> neccessary functionality in the PDB module, but could not find a
> way on how to get to 3D coordinates out of a pdb file or whatever
> data object is neccessary for that.
>
> The widget would then be used something like this, in fictional
> code without caring for module importing / referencing.
>
> >>> model = model_from_data(something)
> >>> window = gl_window(model)
> >>> window.show()
>
> A window would popup now, with a slowly rotating molecule in it.
> One tricky part will be to open a window on different platforms,
> but that's pretty simple. At first, pygame will be enough, since it
> runs on Linux, Windows and Mac, but that's a bad dependency (in my
> opinion). The module could check for availability of pyGTK, win32
> or wxPython bindings and use them. The core of the open gl
> representation would not care a bit about the underlying windowing
> API.
>
> Of course that's all future for now. Even more futuristic would be
> to use the same core as a displaying widget in python-driven gui
> programs.
>
> It would be nice to receive some suggestions on this proposal.
>
> best regards,
> Andreas Klostermann
>
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-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hjm at tacgi.com 
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