biopython/biopython — pull request #192 by MarkusPiotrowski (2013-06-28 22:09:59+00:00)
Title: MeltingTemp completely rewritten and extended

More or less completely rewritten and largely extended.
1. Three different Tm calculations: one 'rule of thumb' (Tm_Wallace), one using approximative formulas basing on GC content (Tm_GC) and one using nearest neighbor calculations (Tm_NN).
2. The new Tm_NN allows the usage of different thermodynamic datasets (8 tables are included for Watson-Crick base-pairing) and includes tables for mismatches (including inosine) and dangling ends. The datasets are Python dictionaries; the user can use his own datasets or change/update existing tables for his needs.
3. Seven different formulas to correct for salt concentration, including correction for Mg2+ ions (method salt_correction).
4. Method chem_correction which allows for Tm correction when using DMSO and formaldehyde.