r11152 - /1.3/generic_fns/structure/internal.py -- April 27, 2010 - 17:45

Author: bugman
Date: Tue Apr 27 17:45:01 2010
New Revision: 11152

URL: http://svn.gna.org/viewcvs/relax?rev=11152&view=rev
Log:
Bug fix for the __det_pdb_element() method.

RNA PDB files with missing element information is now handled properly.  The 
stripping of the "'"
was being ignored.


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=11152&r1=11151&r2=11152&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Tue Apr 27 17:45:01 2010
@@ -513,9 +513,7 @@
 
         @keyword attached_atom:     The name of the bonded atom.
         @type attached_atom:        str
-        @keyword model_num:         The model of which to return the vectors 
from.  If not supplied
-                                    and multiple models exist, then vectors 
from all models will be
-                                    returned.
+        @keyword model_num:         The model of which to return the vectors 
from.  If not supplied and multiple models exist, then vectors from all 
models will be returned.
         @type model_num:            None or int
         @keyword mol_name:          The name of the molecule that 
attached_atom belongs to.
         @type mol_name:             str
@@ -527,14 +525,12 @@
         @type spin_num:             str
         @keyword spin_name:         The name of the spin that attached_atom 
is attached to.
         @type spin_name:            str
-        @keyword return_name:       A flag which if True will cause the name 
of the attached atom to
-                                    be returned together with the bond 
vectors.
+        @keyword return_name:       A flag which if True will cause the name 
of the attached atom to be returned together with the bond vectors.
         @type return_name:          bool
         @keyword return_warnings:   A flag which if True will cause warning 
messages to be returned.
         @type return_warnings:      bool
         @return:                    The list of bond vectors for each model.
-        @rtype:                     list of numpy arrays (or a tuple if 
return_name or
-                                    return_warnings are set)
+        @rtype:                     list of numpy arrays (or a tuple if 
return_name or return_warnings are set)
         """
 
         # Initialise some objects.
@@ -565,12 +561,9 @@
                     if (spin_num != None and mol.atom_num[i] != spin_num) or 
(spin_name != None and mol.atom_name[i] != spin_name):
                         continue
 
-                    # More than one matching atom!
-                    if index != None:
-                        raise RelaxError("The atom_id argument " + 
repr(atom_id) + " must correspond to a single atom.")
-
-                    # Update the index.
+                    # Update the index and stop searching.
                     index = i
+                    break
 
                 # Found the atom.
                 if index != None:
@@ -1147,7 +1140,7 @@
         element = strip(atom_name, "'")
 
         # Strip away atom numbering, from the front and end.
-        element = strip(atom_name, digits)
+        element = strip(element, digits)
 
         # Amino acid atom translation table (note, numbers have been 
stripped already!).
         table = {'C': ['CA', 'CB', 'CG', 'CD', 'CE', 'CZ'],