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TODO LIST
- Add random unfolded code into nast code base.
- Add pdf version of manual for nast, add to MANIFEST.in
- STARTED - Add support for various starting unfolded structures.
- Add support for detection explosions and doing something about it.
    - For now - just detect and trap.
STARTED - (C2A) Make a better .bpseq parser to deal with Sangita's issues
- make sure that the updates for chunxia/intermediates are added
    - test intermedate code?
DONE - uses cutoff of 500 residues to define 'large' - add large molecule fix
STARTED - Pull out C2A from NAST.

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Long helices problem:
- issue is at the ends of helices
- and in the middle of really long helices

- the helices seems to be wound up…
    - Frankly the best solution I see to this is using my old random assembly algorithm…
    - Maybe I should be focusing more on speeding that algorithm up instead of unwinding the helices…
    - I could do some timing tests to show which is worse. Jim's molecule is a good example for this
    - It would be really cool to do this in a high-throughput way and see if the direction of the random adding affects the final product. Also use ease of adding full atomic detail as a metric of comparison.

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Parse BPSEQ
    - Started modifying the script to deal with single-base-pair helices 
    - Still need to make some changes in the code, but comments say what to do.

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Explosion support

- I'm not sure if NAST saves states at the moment
- I think this is what I should work on with Randy on Friday
    - 1. How do I detect an explosion?
        - fast *increase* in energy
    - 2. What do I do if I detect an explosion
        - step back to a previous state
        - if explodes soon after, step back even farther
        - eventually start over again.