r27287 - /trunk/lib/sequence.py -- January 23, 2015 - 11:02

Author: bugman
Date: Fri Jan 23 11:02:05 2015
New Revision: 27287

URL: http://svn.gna.org/viewcvs/relax?rev=27287&view=rev
Log:
Created the lib.sequence.aa_codes_three_to_one() function.

The lib.sequence module now contains the AA_CODES dictionary which is a 
translation table for the 3
letter amino acid codes to the one letter codes.  The new 
aa_codes_three_to_one() function performs
the conversion.


Modified:
    trunk/lib/sequence.py

Modified: trunk/lib/sequence.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence.py?rev=27287&r1=27286&r2=27287&view=diff
==============================================================================
--- trunk/lib/sequence.py       (original)
+++ trunk/lib/sequence.py       Fri Jan 23 11:02:05 2015
@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 
###############################################################################
 #                                                                            
 #
-# Copyright (C) 2003-2014 Edward d'Auvergne                                  
 #
+# Copyright (C) 2003-2015 Edward d'Auvergne                                  
 #
 #                                                                            
 #
 # This file is part of the program relax (http://www.nmr-relax.com).         
 #
 #                                                                            
 #
@@ -24,6 +24,7 @@
 """Module for handling the molecule, residue, and spin sequence data."""
 
 # Python module imports.
+from string import upper
 import sys
 from warnings import warn
 
@@ -33,6 +34,54 @@
 from lib.io import extract_data, open_write_file, strip, write_data
 from lib.selection import spin_id_to_data_list
 from lib.warnings import RelaxWarning, RelaxFileEmptyWarning
+
+
+# The 3 letter to 1 letter amino acid code table.
+AA_CODES = {
+    "ALA": "A",
+    "ARG": "R",
+    "ASN": "N",
+    "ASP": "D",
+    "CYS": "C",
+    "GLU": "E",
+    "GLN": "Q",
+    "GLY": "G",
+    "HIS": "H",
+    "ILE": "I",
+    "LEU": "L",
+    "LYS": "K",
+    "MET": "M",
+    "PHE": "F",
+    "PRO": "P",
+    "SER": "S",
+    "THR": "T",
+    "TRP": "W",
+    "TYR": "Y",
+    "VAL": "V",
+}
+
+
+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'.
+
+
+    @param code:    The three letter amino acid code to convert.
+    @type code:     str
+    @return:        The corresponding one letter amino acid code, or 'X'.
+    @rtype:         str
+    """
+
+    # Convert to uppercase.
+    upper_code = upper(code)
+
+    # The code exists.
+    if upper_code in AA_CODES:
+        return AA_CODES[upper_code]
+
+    # No code.
+    return 'X'
 
 
 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):