r15135 - /branches/frame_order_testing/generic_fns/structure/main.py -- January 03, 2012 - 18:26

Author: bugman
Date: Tue Jan  3 18:26:54 2012
New Revision: 15135

URL: http://svn.gna.org/viewcvs/relax?rev=15135&view=rev
Log:
Fixes for the structure.superimpose and structure.displacement user functions.

This is needed for the new atom_loop() API design.


Modified:
    branches/frame_order_testing/generic_fns/structure/main.py

Modified: branches/frame_order_testing/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/main.py?rev=15135&r1=15134&r2=15135&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/main.py (original)
+++ branches/frame_order_testing/generic_fns/structure/main.py Tue Jan  3 
18:26:54 2012
@@ -1,6 +1,6 @@
 
###############################################################################
 #                                                                            
 #
-# Copyright (C) 2003-2011 Edward d'Auvergne                                  
 #
+# Copyright (C) 2003-2012 Edward d'Auvergne                                  
 #
 #                                                                            
 #
 # This file is part of the program relax.                                    
 #
 #                                                                            
 #
@@ -158,14 +158,14 @@
         # Assemble the atomic coordinates.
         coord_from = []
         for pos in cdp.structure.atom_loop(atom_id=atom_id, 
model_num=model_from[i], pos_flag=True):
-            coord_from.append(pos[0])
+            coord_from.append(pos[0][0])
 
         # Loop over the ending models.
         for j in range(len(model_to)):
             # Assemble the atomic coordinates.
             coord_to = []
             for pos in cdp.structure.atom_loop(atom_id=atom_id, 
model_num=model_to[j], pos_flag=True):
-                coord_to.append(pos[0])
+                coord_to.append(pos[0][0])
 
             # Send to the base container for the calculations.
             cdp.structure.displacements._calculate(model_from=model_from[i], 
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to), 
centroid=centroid)
@@ -201,7 +201,7 @@
     for model in models:
         coord.append([])
         for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, 
pos_flag=True):
-            coord[-1].append(pos[0])
+            coord[-1].append(pos[0][0])
         coord[-1] = array(coord[-1])
     coord = array(coord)
 
@@ -594,7 +594,7 @@
     for model in models:
         coord.append([])
         for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, 
pos_flag=True):
-            coord[-1].append(pos[0])
+            coord[-1].append(pos[0][0])
         coord[-1] = array(coord[-1])
 
     # The different algorithms.