[BiO BB] FW: finding sequence helix/sheet in pdb

Brad Chapman chapmanb at arches.uga.edu
Tue Apr 17 17:58:00 EDT 2001

[Extracting secondary structure info from pbd files]

>  Thanks kiran.  I know I can do it with RASMOl/MOLMOL but I would like
> to do it an very large scale. 

Andrew Dalke has a PDB format-description in his parser generator, Martel:


Martel uses a high-level regular expression description of the file
format to generate XML output. The internals use python, but if you
just spit out XML then you should be able to easily parse it in your
language of choice.

The comments on the top of the format description (in
formats/PDB_2_1.py if you check it out) say it needs some work, and
I've also never used this format, but it might be worth checking out.


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