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):
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