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added Conformation.dissimilarity method, unfinished

Nicolas Zimmermann 4 years ago
parent
commit
dc6da63651
1 changed files with 13 additions and 1 deletions
  1. 13 1
      src/projet8.py

+ 13 - 1
src/projet8.py View File

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