r18889 - in /trunk/generic_fns/structure: main.py scientific.py -- March 19, 2013 - 17:04

Author: bugman
Date: Tue Mar 19 17:04:24 2013
New Revision: 18889

URL: http://svn.gna.org/viewcvs/relax?rev=18889&view=rev
Log:
Lots of fixes for the change to the structural API atom_loop() method.

This method when returning a single item now returns a single item rather 
than a tuple of length 1.


Modified:
    trunk/generic_fns/structure/main.py
    trunk/generic_fns/structure/scientific.py

Modified: trunk/generic_fns/structure/main.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18889&r1=18888&r2=18889&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Tue Mar 19 17:04:24 2013
@@ -198,14 +198,14 @@
         # 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)
 
         # 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)
 
             # 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)
@@ -248,7 +248,7 @@
     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)
         coord[-1] = array(coord[-1])
     coord = array(coord)
 
@@ -655,7 +655,7 @@
     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)
         coord[-1] = array(coord[-1])
 
     # Calculate the RMSD.
@@ -745,7 +745,7 @@
     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)
         coord[-1] = array(coord[-1])
 
     # The different algorithms.

Modified: trunk/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/scientific.py?rev=18889&r1=18888&r2=18889&view=diff
==============================================================================
--- trunk/generic_fns/structure/scientific.py (original)
+++ trunk/generic_fns/structure/scientific.py Tue Mar 19 17:04:24 2013
@@ -168,7 +168,7 @@
         for pos1 in self.atom_loop(atom_id=atom_id1, pos_flag=True):
             for pos2 in self.atom_loop(atom_id=atom_id2, pos_flag=True):
                 # The interatomic distance.
-                dist = linalg.norm(pos2[0]-pos1[0])
+                dist = linalg.norm(pos2-pos1)
 
                 # The atom is within the radius of 2.0 Angstrom.
                 if dist < 2.0: