changed 'Conformation.dissimilarity' method to 'Conformation.identity' method

src/projet8.py

@@ -4,6 +4,7 @@ import pandas as pd
 import numpy as np
 import pbxplore as pbx
 import sys
+from scipy.spatial.distance import squareform, pdist, jaccard 
 
 class Conformations:
     """
@@ -18,21 +19,31 @@ class Conformations:
         df : pd.DataFrame object
         Each row of the dataframe is a conformation and each column a position
         of the sequence.
+        dfnum : to compute dissimilarity with the function pdist, elements of
+        the DataFrame must be float
         """
         self.df = pd.DataFrame()
         for chain_name, chain in pbx.chains_from_files([filename]): 
                 dihedrals = chain.get_phi_psi_angles() 
                 pb_seq = pbx.assign(dihedrals) 
-                self.df = self.df.append(pd.Series(list(pb_seq)), ignore_index=True)
-    
-    def dissimilarity(self):
+                self.df = self.df.append(pd.Series(list(pb_seq)),
+                                         ignore_index=True)
+ 
+    def identity(self):
         """
-        computes the dissimilarity matrix of the intance's df
+        Returns a matrix of the distance between all conformations based on
+        wether the PB at each position is identical or not.
+        Returns the matrix as a numpy.ndarray object.
         """
-        matrix = pd.DataFrame(index=np.arange(self.df.shape[0]),
-                              columns=np.arange(self.df.shape[0]))
-        matrix = matrix.fillna(0)
-        return matrix
+        dict_str_to_float = {'Z':0,'a':1,'b':2,'c':3,'d':4,'e':5,'f':6,'g':7,
+                             'h':8,'i':9,'j':10,'k':11,'l':12,'m':13,'n':14,
+                             'o':15,'p':16} # dict to transform PB to int,
+                                            # necessary for the pdsit function
+        dfnum = self.df.replace(dict_str_to_float)
+
+        return squareform(pdist(dfnum, metric ='jaccard'))
+
+
 
 if __name__ == "__main__":
     if len(sys.argv) != 2: