working version of Conformations.dissimilarity method, SLOW

src/projet8.py

@@ -43,7 +43,7 @@ class Conformations:
 
         return squareform(pdist(dfnum, metric ='jaccard'))
 
-    def dissimilarity(self, matrix):
+    def dissimilarity(self, matrix=None):
         """
         Returns a matrix of the distance between all conformations computed
         according to a substitution matrix of the protein blocks.
@@ -54,13 +54,24 @@ class Conformations:
         if matrix == None:
             matrix = pd.read_table("data/PBs_substitution_matrix.dat",
                                    index_col=False, sep ='\t')
+            matrix = matrix/100 # because in this file weight where multiplied
+                                # by 100.
         matrix.index = matrix.columns
+        ncol = self.df.shape[1]
+        nrow = self.df.shape[0]
+        it1 = self.df.iterrows()
+        for i in range(1,nrow): 
+            for j in range(i): 
+                for k in range(ncol): 
+                    dissimilarity[i][j] += matrix[confs.df.loc[i,k]][confs.df.loc[j,k]]
+        dissimilarity = dissimilarity + dissimilarity.T
+
+        return dissimilarity
 
 
 if __name__ == "__main__":
     if len(sys.argv) != 2:
-        print("Error : usage $ python3 projet8 md.pdb")
-        exit()
+        sys.exit("Error : usage '$ python3 projet8 md.pdb'")
 
     confs = Conformations(sys.argv[1])