diff --git a/prymer/thermo.py b/prymer/thermo.py index df9d7fe..df39edc 100644 --- a/prymer/thermo.py +++ b/prymer/thermo.py @@ -11,11 +11,16 @@ class Thermo: """ Class for performing thermodynamic calculations. Available calculations include: - 1. melting temperature (Tm) for short and long sequences ([`tm()`][prymer.thermo.Thermo.tm]) - 2. hairpin / secondary structure Tm for single sequences ([`hairpin_tm`][prymer.thermo.Thermo.hairpin_tm]) - 3. homodimer Tm - the Tm of a duplex formed from two copies of the same sequence ([`homodimer_tm `][prymer.thermo.Thermo. homodimer_tm]) - 4. heterodimer Tm - the Tm of a duplex formed from two different sequences ([`heterodimer_tm `][prymer.thermo.Thermo. heterodimer_tm]) - 5. 3' anchored heterodimer Tm - the heterodimer Tm when annealing of the 3' end is prioritized ([`heterodimer_3p_anchored_tm `][prymer.thermo.Thermo. heterodimer_3p_anchored_tm]) + 1. melting temperature (Tm) for short and long sequences + (see [`tm()`][prymer.thermo.Thermo.tm]) + 2. hairpin / secondary structure Tm for single sequences + (see [`hairpin_tm()`][prymer.thermo.Thermo.hairpin_tm]) + 3. homodimer Tm - the Tm of a duplex formed from two copies of the same sequence + (see [`homodimer_tm()`][prymer.thermo.Thermo.homodimer_tm]) + 4. heterodimer Tm - the Tm of a duplex formed from two different sequences + (see [`heterodimer_tm()`][prymer.thermo.Thermo.heterodimer_tm]) + 5. 3' anchored heterodimer Tm - the heterodimer Tm when annealing of the 3' end is prioritized + (see [`heterodimer_3p_anchored_tm()`][prymer.thermo.Thermo.heterodimer_3p_anchored_tm]) The `tm` method can be used for sequences of any length. For sequences up to `max_nn_length` (default value 60 bases) the nearest neighborhood Tm calculation is used. For sequences above diff --git a/tests/test_thermo.py b/tests/test_thermo.py index 7bfd11c..d59be18 100644 --- a/tests/test_thermo.py +++ b/tests/test_thermo.py @@ -56,8 +56,8 @@ def test_heterodimer_tm() -> None: def test_heterodimer_3p_anchored_tm() -> None: thermo = Thermo() - tm1 = thermo. heterodimer_3p_anchored_tm("AAAAAAAAAA", "CCCCCCCCCC") - tm2 = thermo. heterodimer_3p_anchored_tm("AAAAAAAAAA", "TTTTTTTTTT") + tm1 = thermo.heterodimer_3p_anchored_tm("AAAAAAAAAA", "CCCCCCCCCC") + tm2 = thermo.heterodimer_3p_anchored_tm("AAAAAAAAAA", "TTTTTTTTTT") assert tm1 == 0 assert tm2 > 0