r6826 - /1.3/generic_fns/structure/scientific.py -- July 08, 2008 - 02:18

Author: bugman
Date: Tue Jul  8 02:18:10 2008
New Revision: 6826

URL: http://svn.gna.org/viewcvs/relax?rev=6826&view=rev
Log:
Brought the Scientific PDB structural object into line with the structural 
API.


Modified:
    1.3/generic_fns/structure/scientific.py

Modified: 1.3/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=6826&r1=6825&r2=6826&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Tue Jul  8 02:18:10 2008
@@ -86,13 +86,11 @@
 
         # Problem.
         if num_attached > 1:
-            warn(RelaxWarning('More than one attached atom found: ' + 
`matching_list`))
-            return None, None, None, None
+            return None, None, None, None, None, 'More than one attached 
atom found: ' + `matching_list`
 
         # No attached atoms.
         if num_attached == 0:
-            warn(RelaxWarning('No attached atom found.'))
-            return None, None, None, None
+            return None, None, None, None, None, "No attached atom could be 
found"
 
         # The bonded atom object.
         bonded = res[attached_atom]
@@ -102,15 +100,10 @@
         bonded_name = bonded.name
         element = bonded.properties['element']
         pos = bonded.position.array
-
-        # The bonded atom has been found.
-        bonded_found = True
+        attached_name = matching_list[0]
 
         # Return the information.
-        if bonded_found:
-            return bonded_num, bonded_name, element, pos
-        else:
-            return None, None, None, None
+        return bonded_num, bonded_name, element, pos, attached_name, None
 
 
     def __molecule_loop(self, struct, sel_obj=None):
@@ -444,7 +437,7 @@
             # Found the atom.
             if atom_found:
                 # Find the atom bonded to this 
structure/molecule/residue/atom.
-                bonded_num, bonded_name, element, pos = 
self.__find_bonded_atom(attached_atom, mol_type_match, res_match)
+                bonded_num, bonded_name, element, pos, attached_name, 
warnings = self.__find_bonded_atom(attached_atom, mol_type_match, res_match)
 
                 # No bonded atom.
                 if (bonded_num, bonded_name, element) == (None, None, None):
@@ -456,8 +449,15 @@
                 # Append the vector to the vectors array (converting from a 
Numeric array to a numpy array).
                 vectors.append(array(vector, float64))
 
-        # Return the bond vectors.
-        return vectors
+        # Build the tuple to be yielded.
+        data = (vectors,)
+        if return_name:
+            data = data + (attached_name,)
+        if return_warnings:
+            data = data + (warnings,)
+
+        # Return the data.
+        return data
 
 
     def load_pdb(self, file_path, model=None, verbosity=False):