Feature/melting temp (#19)

* MeltingTemperatureMode enum added

* Melting Temperature basic calculations added to Primer

* add warning message of not-supported methods for melting temperature calculation

* tests for basic melting temperature calculations added

* `CHANGELOG.md` updated

* autopep8.sh applied

* feedback applied

* feedback applied

* feedback applied

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Changed
 ## [0.1] - 2024-06-05
 ### Added
+- MeltingTemperature enum
+- Basic melting temperature calculation
 - `addition` and `multipication` operators overload
 - `len` magic overload
 - `Primer` class

opr/params.py

@@ -24,3 +24,5 @@
 
 PRIMER_ADDITION_ERROR = "You can only add two Primer objects."
 PRIMER_MULTIPICATION_ERROR = "The primer sequence can only be multiplied by an integer."
+
+PRIMER_SUPPORTED_MELTING_TEMPERATURE_CALCULATIONS = "This version currently supports only the Basic calculation for Melting Temperature."

opr/primer.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """OPR primer."""
+from enum import Enum
 from warnings import warn
 from .errors import OPRBaseError
 from .params import VALID_BASES
@@ -9,6 +10,15 @@
 from .params import A_WEIGHT, T_WEIGHT, C_WEIGHT, G_WEIGHT, ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
 from .params import DNA_COMPLEMENT_MAP
 from .params import PRIMER_ADDITION_ERROR, PRIMER_MULTIPICATION_ERROR
+from .params import PRIMER_SUPPORTED_MELTING_TEMPERATURE_CALCULATIONS
+
+
+class MeltingTemperature(Enum):
+    """Mode used to calculate the Melting Temperature of the Primer accordingly."""
+
+    BASIC = 1
+    SALT_ADJUSTED = 2
+    NEAREST_NEIGHBOR = 3
 
 
 class Primer:
@@ -30,6 +40,11 @@ def __init__(self, primer_sequence):
         self._sequence = Primer.validate_primer(primer_sequence)
         self._molecular_weight = None
         self._gc_content = None
+        self._melting_temperature = {
+            MeltingTemperature.BASIC: None,
+            MeltingTemperature.SALT_ADJUSTED: None,
+            MeltingTemperature.NEAREST_NEIGHBOR: None,
+        }
 
     def __len__(self):
         """
@@ -144,8 +159,8 @@ def molecular_weight(self):
         c_count = self._sequence.count('C')
         g_count = self._sequence.count('G')
         # Anhydrous Molecular Weight = (An x 313.21) + (Tn x 304.2) + (Cn x 289.18) + (Gn x 329.21) - 61.96
-        self._molecular_weight = (a_count * A_WEIGHT) + (t_count * T_WEIGHT) + (c_count * \
-                                  C_WEIGHT) + (g_count * G_WEIGHT) - ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
+        self._molecular_weight = (a_count * A_WEIGHT) + (t_count * T_WEIGHT) + (c_count *
+                                                                                C_WEIGHT) + (g_count * G_WEIGHT) - ANHYDROUS_MOLECULAR_WEIGHT_CONSTANT
         return self._molecular_weight
 
     @molecular_weight.setter
@@ -177,3 +192,38 @@ def gc_content(self, _):
     @gc_content.deleter
     def gc_content(self, _):
         raise OPRBaseError(PRIMER_NOT_REMOVABLE_ATTRIBUTE_ERROR)
+
+    def melting_temperature(self, method=MeltingTemperature.BASIC):
+        """
+        Calculate(if needed) the melting temperature.
+
+        :param method: requested calculation mode for melting temperature
+        :type method: MeltingTemperature
+        :return: approximated melting temperature
+        """
+        if self._melting_temperature[method] != None:
+            return self._melting_temperature[method]
+        a_count = self._sequence.count('A')
+        t_count = self._sequence.count('T')
+        c_count = self._sequence.count('C')
+        g_count = self._sequence.count('G')
+        if method == MeltingTemperature.BASIC:
+            if len(self) <= 13:
+                # Tm= (wA+xT) * 2 + (yG+zC) * 4
+                # where w,x,y,z are the number of the bases A,T,G,C in the sequence,
+                # respectively (from Marmur,J., and Doty,P. (1962) J Mol Biol 5:109-118
+                # [PubMed]).
+                self._melting_temperature[MeltingTemperature.BASIC] = (
+                    a_count + t_count) * 2 + (g_count + c_count) * 4
+            else:
+                # Tm= 64.9 +41 * (yG+zC-16.4)/(wA+xT+yG+zC)
+                # See Wallace,R.B., Shaffer,J., Murphy,R.F., Bonner,J., Hirose,T., and
+                # Itakura,K. (1979) Nucleic Acids Res 6:3543-3557 (Abstract) and
+                # Sambrook,J., and Russell,D.W. (2001) Molecular Cloning: A Laboratory
+                # Manual. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, NY.
+                # (CHSL Press)
+                self._melting_temperature[MeltingTemperature.BASIC] = 64.9 + 41 * \
+                    ((g_count + c_count - 16.4) / (a_count + t_count + g_count + c_count))
+        else:
+            raise(NotImplementedError(PRIMER_SUPPORTED_MELTING_TEMPERATURE_CALCULATIONS))
+        return self._melting_temperature[method]

tests/test_calculations.py

@@ -1,21 +1,30 @@
 from opr import Primer
+from opr.primer import MeltingTemperature
 
 TEST_CASE_NAME = "Calculations tests"
 
 def test_mwc():
     oprimer = Primer("ATCGATCGATCGATCGAT")
     assert round(oprimer.molecular_weight, 1) == 5498.7
 
-
 def test_gc_content_1(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATCG")
     assert oprimer.gc_content == 0.5
 
-
 def test_gc_content_2(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATTCG")
     assert oprimer.gc_content == 0.4
 
 def test_gc_content_3(): #Reference: https://jamiemcgowan.ie/bioinf/gc_content.html
     oprimer = Primer("ATTTTTT")
     assert oprimer.gc_content == 0
+
+def test_melt_temp_1(): #Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("ATCGATCGATCGATCGATCG")
+    basic_melt_temp = oprimer.melting_temperature(MeltingTemperature.BASIC)
+    assert round(basic_melt_temp,1) == 51.8
+
+def test_melt_temp_2(): #Reference: http://biotools.nubic.northwestern.edu/OligoCalc.html
+    oprimer = Primer("ATCG")
+    basic_melt_temp = oprimer.melting_temperature(method=MeltingTemperature.BASIC)
+    assert round(basic_melt_temp,1) == 12