From dc6da63651a798fd2e3ff32ef26cfeea3293261a Mon Sep 17 00:00:00 2001
From: Nicolas Zimmermann <nicolaszimmermann.snv@gmail.com>
Date: Tue, 17 Sep 2019 01:13:58 +0200
Subject: [PATCH] added Conformation.dissimilarity method, unfinished

---
 src/projet8.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/src/projet8.py b/src/projet8.py
index 17f06e6..b4c6819 100644
--- a/src/projet8.py
+++ b/src/projet8.py
@@ -43,7 +43,19 @@ class Conformations:
 
         return squareform(pdist(dfnum, metric ='jaccard'))
 
-
+    def dissimilarity(self, matrix):
+        """
+        Returns a matrix of the distance between all conformations computed
+        according to a substitution matrix of the protein blocks.
+        If no substitution matrix is specified, use the matrix from the
+        PBxplore package.
+        """
+        dissimilarity = np.ndarray((self.df.shape[0],self.df.shape[0])) 
+        if matrix == None:
+            matrix = pd.read_table("data/PBs_substitution_matrix.dat",
+                                   index_col=False, sep ='\t')
+        matrix.index = matrix.columns
+        
 
 if __name__ == "__main__":
     if len(sys.argv) != 2: