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Lattice-Automation / seqfold

nucleic acid folding
MIT License
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Incorrect DNA_NN values in dictionary #6

Closed maxhargrea closed 3 years ago

maxhargrea commented 3 years ago

Hi, I think your values are entered wrong.

Below are corrected values based on The Thermodynamics of DNA Structural Motifs Annual Review of Biophysics and Biomolecular Structure

Vol. 33:415-440 (Volume publication date 9 June 2004) https://doi.org/10.1146/annurev.biophys.32.110601.141800 ''' DNA_NN: BpEnergy = { "init": (0.2, -5.7), "init_G/C": (0.0, 0.0), "init_A/T": (2.2, 6.9), "sym": (0, -1.4), "AA/TT": (-7.6, -21.3), "AT/TA": (-7.2, -20.4), "TA/AT": (-7.2, -21.3), "CA/GT": (-8.5, -22.7), "GT/CA": (-8.4, -22.4), "CT/GA": (-7.8, -21.0), "GA/CT": (-8.2, -22.2), "CG/GC": (-10.6, -27.2), "GC/CG": (-9.8, -24.4), "GG/CC": (-8.0, -19.9), } '''

If this is not correct could you explain your values?

Thanks for putting this together! It is a great resource!

jjti commented 3 years ago

Thanks for catching that! I changed the two differing float values and corrected the docstring to the right source https://github.com/Lattice-Automation/seqfold/commit/e400b961943d9e170a0e541d7895917cd54e1064

Should be fixed in 0.7.7

jjti commented 3 years ago

Lmk/re-open if there's still an issue. Also please star the package so I get dopamine