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Python Tool To Assign Secondary Structure Elements To A 3D/Pdb Structure
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5.5 years ago
dimkal • 730
United States

Does anybody know if there's an a python alternative to STRIDE or DSSP for assigning secondary structure elements to protein structures?

Thanks,

Dima

pdb python • 3.4k views
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Why Python? There are lots of protein secondary structure tools available. Performance-wise, lots of them are pretty similar. STRIDE/DSSP are both well-established, widely-used, easy to parse and easy to call from other languages, including Python.

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there are a bunch of reasons why python can be preferred over c/fortran -- easier to redistribute, easier to read, modify, extend, no need to deal with compilers.

-d

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Yes, but do those reasons justify writing code when perfectly reasonable solutions already exist? What do you care about more: language aesthetics or getting the job done?

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at the moment i care about the code's readability and ease of use. python, is preferred language. Perhaps the answer to my question is that no alternatives exist since the original codes works so well. That's perfectly acceptable. I'm having hard time to believe that nobody implemented any of the two methods in python.

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