r11886 - /1.3/generic_fns/structure/internal.py -- December 17, 2010 - 19:59

Author: bugman
Date: Fri Dec 17 19:59:11 2010
New Revision: 11886

URL: http://svn.gna.org/viewcvs/relax?rev=11886&view=rev
Log:
Fix for bug #17343 (https://gna.org/bugs/?17343).

This bug was reported by Vitaly Vostri <vvostri att gmail dott com>, also in 
the mailing list
message https://mail.gna.org/public/relax-users/2010-12/msg00005.html.

The 'CH2' and 'OT' atoms have been added to the internal PDB reader, for 
those incomplete PDB files
in which the element column is missing.


Modified:
    1.3/generic_fns/structure/internal.py

Modified: 1.3/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=11886&r1=11885&r2=11886&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Fri Dec 17 19:59:11 2010
@@ -1149,10 +1149,10 @@
         element = strip(element, digits)
 
         # Amino acid atom translation table (note, numbers have been 
stripped already!).
-        table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CZ'],
+        table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CH2', 'CZ'],
                  'N': ['ND', 'NE', 'NH', 'NZ'],
                  'H': ['HA', 'HB', 'HG', 'HD', 'HE', 'HH', 'HT', 'HZ'],
-                 'O': ['OG', 'OD', 'OE', 'OH'],
+                 'O': ['OG', 'OD', 'OE', 'OH', 'OT'],
                  'S': ['SD', 'SG']
         }