Merge branch 'dev' into add/internal_cache_flag

CHANGELOG.md

@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+### Added
+- Salt-adjusted melting temperature calculation
+### Changed
 ## [0.3] - 2025-02-06
 ### Added
 - `_computed` internal cache flag attribute

README.md

@@ -64,8 +64,8 @@
 
 ### Load
 ```pycon
->>> from opr import Primer
->>> primer1 = Primer(sequence="CTGGAGGACGGAAGAGGAAGTAA")
+>>> from opr import Primer, MeltingTemperature
+>>> primer1 = Primer(sequence="CTGGAGGACGGAAGAGGAAGTAA", salt=50)
 >>> primer1.sequence
 'CTGGAGGACGGAAGAGGAAGTAA'
 ```
@@ -107,9 +107,17 @@
 1
 ```
 #### Melting temperature
+##### Basic
 ```pycon
 >>> primer1.melting_temperature()
 57.056521739130446
+>>> primer1.melting_temperature(MeltingTemperature.BASIC)
+57.056521739130446
+```
+##### Salt-adjusted
+```pycon
+>>> primer1.melting_temperature(MeltingTemperature.SALT_ADJUSTED)
+64.64203250676053
 ```
 ### Operations
 

opr/functions.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """OPR functions."""
+import math
 from .params import A_WEIGHT, T_WEIGHT, C_WEIGHT, G_WEIGHT, ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
 
 
@@ -38,6 +39,33 @@ def basic_melting_temperature_calc(sequence):
     return melting_temperature
 
 
+def salt_adjusted_melting_temperature_calc(sequence, salt):
+    """
+    Calculate the salt-adjusted melting temperature (Tm) of a primer sequence.
+
+    :param sequence: Primer nucleotides sequence
+    :type sequence: str
+    :param salt: Sodium ion concentration in moles (unit mM)
+    :type salt: float
+    :return: Salt-adjusted melting temperature as float
+    """
+    a_count = sequence.count('A')
+    t_count = sequence.count('T')
+    c_count = sequence.count('C')
+    g_count = sequence.count('G')
+    seq_length = len(sequence)
+    if seq_length <= 13:
+        salt_adjustment = 16.6 * (math.log10(salt)-3) - 16.6 * math.log10(0.050)
+        tm = (a_count + t_count) * 2 + (g_count + c_count) * 4 + salt_adjustment
+    else:
+        tm = (
+            100.5 + (41 * (g_count + c_count) / seq_length) 
+            - (820 / seq_length) 
+            + 16.6 * (math.log10(salt)-3)
+        )
+    return tm
+
+
 def gc_clamp_calc(sequence):
     """
     Calculate GC clamp.

opr/primer.py

@@ -11,8 +11,9 @@
 from .params import DNA_COMPLEMENT_MAP
 from .params import PRIMER_ADDITION_ERROR, PRIMER_MULTIPLICATION_ERROR
 from .params import PRIMER_MELTING_TEMPERATURE_NOT_IMPLEMENTED_ERROR
+
 from .params import PRIMER_ATTRIBUTE_NOT_COMPUTABLE_ERROR
-from .functions import molecular_weight_calc, basic_melting_temperature_calc, gc_clamp_calc
+from .functions import molecular_weight_calc, basic_melting_temperature_calc, salt_adjusted_melting_temperature_calc, gc_clamp_calc
 
 
 class MeltingTemperature(Enum):
@@ -31,14 +32,16 @@ class Primer:
     >>> oprimer.molecular_weight
     """
 
-    def __init__(self, sequence, name=DEFAULT_PRIMER_NAME):
+    def __init__(self, sequence, name=DEFAULT_PRIMER_NAME, salt=50):
         """
         Initialize the Primer instance.
 
         :param sequence: primer nucleotides sequence
         :type sequence: str
         :param name: primer name
         :type name: str
+        :param salt: Sodium ion concentration in moles (unit mM)
+        :type salt: float
         :return: an instance of the Primer class
         """
         self._sequence = Primer.validate_primer(sequence)
@@ -48,6 +51,7 @@ def __init__(self, sequence, name=DEFAULT_PRIMER_NAME):
         self._gc_clamp = None
         self._single_runs = None
         self._double_runs = None
+        self._salt_level = salt
         self._melting_temperature = {
             MeltingTemperature.BASIC: None,
             MeltingTemperature.SALT_ADJUSTED: None,
@@ -311,6 +315,8 @@ def melting_temperature(self, method=MeltingTemperature.BASIC):
             return self._melting_temperature[method]
         if method == MeltingTemperature.BASIC:
             self._melting_temperature[MeltingTemperature.BASIC] = basic_melting_temperature_calc(self._sequence)
+        elif method == MeltingTemperature.SALT_ADJUSTED:
+            self._melting_temperature[MeltingTemperature.SALT_ADJUSTED] = salt_adjusted_melting_temperature_calc(self._sequence, self._salt_level)
         else:
             raise NotImplementedError(PRIMER_MELTING_TEMPERATURE_NOT_IMPLEMENTED_ERROR)
         self._computed["melting_temperature"][method] = True

tests/test_calculations.py

@@ -50,6 +50,30 @@ def test_melt_temp_2():  # Reference: http://biotools.nubic.northwestern.edu/Oli
     assert round(basic_melt_temp, 1) == 12
 
 
+def test_melt_temp_3():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("CTGGAGGACGGAAGAGGAAGTAA")
+    salt_adjusted_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.SALT_ADJUSTED)
+    assert round(salt_adjusted_melt_temp, 0) == 65.0
+
+
+def test_melt_temp_4():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("CTGGAGGACGGAAGAGGAAGTAAA", salt=65)
+    salt_adjusted_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.SALT_ADJUSTED)
+    assert round(salt_adjusted_melt_temp, 0) == 67.0
+
+
+def test_melt_temp_5():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("CTGGAGG")
+    salt_adjusted_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.SALT_ADJUSTED)
+    assert round(salt_adjusted_melt_temp, 0) == 24.0
+
+
+def test_melt_temp_6():  # Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("CTGGAGG", salt=65)
+    salt_adjusted_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.SALT_ADJUSTED)
+    assert round(salt_adjusted_melt_temp, 0) == 26.0
+
+
 def test_single_runs_1():  # Reference: https://www.oligoevaluator.com/OligoCalcServlet
     oprimer = Primer("ATCGATCG")
     runs = oprimer.single_runs