changed aa_prop_water to 3 categ according to KD, updated ref dict

scripts/mut_electrostatic_changes.py

@@ -5,13 +5,15 @@ Created on Tue Aug  6 12:56:03 2019
 
 @author: tanu
 '''
-
 # FIXME: import dirs.py to get the basic dir paths available
 #=======================================================================
 # TASK: calculate how many mutations result in 
 # electrostatic changes wrt wt
 
-# Input: merged_df3
+# Input: mCSM-normalised file or any file containing one-letter aa code 
+# of wt and mut
+# Note: this can be easily modified into 3-letter code
+# TODO: turn to a function
 
 # Output: mut_elec_changes_results.txt 
 #=======================================================================

scripts/reference_dict.py

@@ -132,9 +132,11 @@ qualities_taylor = { ('R', 'H', 'K'): 'Basic'
              , ('C', 'G', 'P'): 'Special'
 }
 
-# binary classification: hydrophilic or hydrophobic
-qualities_water = { ('D', 'E', 'N', 'P', 'Q', 'R', 'S'): 'hydrophilic'
-                   , ('A', 'C', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'T', 'V', 'W', 'X', 'Y'): 'hydrophobic'
+# ternary classification: hydrophobic --> neutral --> hydrophilic (KD scale)
+#http://www.imgt.org/IMGTeducation/Aide-memoire/_UK/aminoacids/IMGTclasses.html
+qualities_water = { ('I','V','L','F','C','M','A','W'): 'hydrophobic'
+                   , ('G','T','S','Y','P','H'): 'neutral'
+                   , ('N','D','Q','E','K','R'): 'hydrophilic'
 }
 
 # polarity: no overlap