r27291 - /trunk/lib/sequence.py -- January 23, 2015 - 15:38

Author: bugman
Date: Fri Jan 23 15:38:21 2015
New Revision: 27291

URL: http://svn.gna.org/viewcvs/relax?rev=27291&view=rev
Log:
Fix for the lib.sequence.aa_codes_three_to_one() function.

Non-standard residues are now converted to the '*' code.  The value of 'X' 
prevents any type of
alignment of a stretch of X residues as X to X in both the BLOSUM62 and 
PAM250 substitution matrices
are set to -1.


Modified:
    trunk/lib/sequence.py

Modified: trunk/lib/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence.py?rev=27291&r1=27290&r2=27291&view=diff
==============================================================================
--- trunk/lib/sequence.py       (original)
+++ trunk/lib/sequence.py       Fri Jan 23 15:38:21 2015
@@ -64,12 +64,12 @@
 def aa_codes_three_to_one(code):
     """Convert the given three letter amino acid code to the corresponding 
one letter code.
 
-    Any non-standard residues will be converted to 'X'.
+    Any non-standard residues will be converted to '*'.
 
 
     @param code:    The three letter amino acid code to convert.
     @type code:     str
-    @return:        The corresponding one letter amino acid code, or 'X'.
+    @return:        The corresponding one letter amino acid code, or '*'.
     @rtype:         str
     """
 
@@ -81,7 +81,7 @@
         return AA_CODES[upper_code]
 
     # No code.
-    return 'X'
+    return '*'
 
 
 def read_spin_data(file=None, dir=None, file_data=None, spin_id_col=None, 
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, 
spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None):