blakesweeney/Dot-Bracket — pull request #2 by AntonPetrov (2012-01-07 04:12:22+00:00)
Title: Add a hairpin test case based on a ty1 structure

Unfortunately the test fails right now. From what I can tell, you identify some very short fragments as hairpins (e.g. [28]). There is a lot of agreement between our results though.

Here is the link to the 2d:
https://www.dropbox.com/s/1kh5owgufsdouwx/2_199.9%28clear%29.pdf
The file is in BGSU_shared/Data_from_Alain/Ty1644structures/-199.9 on Dropbox.

Remember that python string indexes are base 0.

I'll add internal loops later.