r27368 - /trunk/lib/sequence.py -- January 29, 2015 - 18:22

Author: bugman
Date: Thu Jan 29 18:22:32 2015
New Revision: 27368

URL: http://svn.gna.org/viewcvs/relax?rev=27368&view=rev
Log:
Reverted r27364 as this was recursive rubbish.

The command used was:
svn merge -r27364:r27363 .

.....
  r27364 | bugman | 2015-01-29 17:38:25 +0100 (Thu, 29 Jan 2015) | 18 lines
  Changed paths:
     M /trunk/lib/sequence.py
  
  Reverted r27291 as this was rubbish.
  
  The command used was:
  svn merge -r27291:r27290 .
  
  .....
    r27291 | bugman | 2015-01-23 15:38:21 +0100 (Fri, 23 Jan 2015) | 7 lines
    Changed paths:
       M /trunk/lib/sequence.py
    
    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=27368&r1=27367&r2=27368&view=diff
==============================================================================
--- trunk/lib/sequence.py       (original)
+++ trunk/lib/sequence.py       Thu Jan 29 18:22:32 2015
@@ -63,12 +63,12 @@
 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
     """
 
@@ -80,7 +80,7 @@
         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):