merged protein_mass calculation.

the integration caused a keyerror issue
adelbke · Mar 19, 2021 · c757dd7 · c757dd7
1 parent 803e1ed
commit c757dd7
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diff --git a/projetsysteme/__pycache__/__init__.cpython-38.pyc b/projetsysteme/__pycache__/__init__.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/acid_mass.cpython-38.pyc b/projetsysteme/__pycache__/acid_mass.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/components.cpython-38.pyc b/projetsysteme/__pycache__/components.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/dna.cpython-38.pyc b/projetsysteme/__pycache__/dna.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/main.cpython-38.pyc b/projetsysteme/__pycache__/main.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/rna_to_acid.cpython-38.pyc b/projetsysteme/__pycache__/rna_to_acid.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/settings.cpython-38.pyc b/projetsysteme/__pycache__/settings.cpython-38.pyc
diff --git a/projetsysteme/__pycache__/views.cpython-38.pyc b/projetsysteme/__pycache__/views.cpython-38.pyc
diff --git a/projetsysteme/acid_mass.py b/projetsysteme/acid_mass.py
@@ -0,0 +1,42 @@
+mass_amino_acid =  {'A': 71.03711,
+                    'C': 103.00919,
+                    'D': 115.02694,
+                    'E': 129.04259,
+                    'F': 147.06841,
+                    'G': 57.02146,
+                    'H': 137.05891,
+                    'I': 113.08406,
+                    'K': 128.09496,
+                    'L': 113.04049,
+                    'M': 131.04049,
+                    'N': 114.04293,
+                    'P': 97.05276,
+                    'Q': 128.05858,
+                    'R': 156.10111,
+                    'S': 87.03203,
+                    'T': 101.04768,
+                    'V': 99.06841,
+                    'W': 186.07931,
+                    'Y': 163.06333,
+                    'Z': 0}
+amino_acid_abr =   {'Ala': 'A',
+                    'Cys': 'C',
+                    'Asp': 'D',
+                    'Glu': 'E',
+                    'Phe': 'F',
+                    'Gly': 'G',
+                    'His': 'H',
+                    'Ile': 'I',
+                    'Lys': 'K',
+                    'Leu': 'L',
+                    'Met': 'M',
+                    'Asn': 'N',
+                    'Pro': 'P',
+                    'Gln': 'Q',
+                    'Arg': 'R',
+                    'Ser': 'S',
+                    'Thr': 'T',
+                    'Val': 'V',
+                    'Trp': 'W',
+                    'Tyr': 'Y',
+                    '---': 'Z'}
diff --git a/projetsysteme/components.py b/projetsysteme/components.py
@@ -55,6 +55,7 @@ def __init__(self, *args, **kwargs):
         self.btn_comp_inv_adn.clicked.connect(self.action_comp_inv_adn)
         self.btn_taux_gc_adn.clicked.connect(self.action_taux_gc_adn)
         self.btn_freq_codons_adn.clicked.connect(self.action_freq_codons_adn)
+        self.btn_masse_proteique.clicked.connect(self.action_masse_proteique)
 
 
     def action_creer_adn(self):
@@ -103,6 +104,11 @@ def action_freq_codons_adn(self):
         DNA.taux_codons()
         MainLayout._instance.output_codon_frequency.setText(str(DNA.codon_frequency))
 
+    def action_masse_proteique(self):
+        DNA.masse()
+        MainLayout._instance.output_protein_mass.setText(str(DNA.protein_mass))
+        pass
+
     def setupButtons(self):
         # setup buttons list
         self.buttons = [
@@ -140,7 +146,8 @@ def __init__(self, *args, **kwargs):
             ('Proteine','protein_chain',chain_width),
             ('Comp Inv','dna_complement',chain_width),
             ('Taux GC','taux_gc',4),
-            ('Fréquence Codons','codon_frequency',4)
+            ('Fréquence Codons','codon_frequency',40),
+            ('Masse Protéique','protein_mass',10)
         ]
         for element in elements:
             label = QLabel(element[0])

diff --git a/projetsysteme/dna.py b/projetsysteme/dna.py
@@ -11,6 +11,7 @@ class DNA():
     dna_complement = ""
     gc_rate = 0
     codon_frequency=0
+    protein_mass = 0
 
 
 
@@ -21,7 +22,6 @@ def generate_dna(cls,length: int):
         for i in range(0,length):
             ADN+='ACGT'[randint(0,3)]
         cls.dna_chain = ADN
-        return cls.dna_chain
 
     @classmethod
     def translate_to_rna(cls):
@@ -76,6 +76,28 @@ def taux_codons(cls):
             if index+3 < len(rna) and RNA_to_acido_dic[rna[index:index+3]] != "---":
                 freq= freq+1
         cls.codon_frequency = freq
+
+    @classmethod
+    def masse(cls):
+        from .acid_mass import amino_acid_abr, mass_amino_acid
+        if (len(cls.protein_chain)>0):
+            index = 0
+            l = []
+            while index <= len(cls.protein_chain)-1:
+                if(len(cls.protein_chain[index:index+3]) == 3):
+                    l.append(amino_acid_abr[cls.protein_chain[index:index+3]])
+
+                index += 3
+            prot_abr = ""
+            for ele in l:  
+                prot_abr += ele
+            mass = 0
+            for x in prot_abr:
+                mass+=mass_amino_acid[x]
+            cls.protein_mass = mass
+            # print(cls.MASSE)
+        # else:
+        #     cls.show_popup("vous devez creer le Proteine")