r15119 - /branches/frame_order_testing/generic_fns/structure/internal.py -- January 02, 2012 - 21:43

Author: bugman
Date: Mon Jan  2 21:43:35 2012
New Revision: 15119

URL: http://svn.gna.org/viewcvs/relax?rev=15119&view=rev
Log:
Massive speed (20 times) for the structure.vectors user function for the 
internal structural object.

This is similar to the changes to the structure.load_spins user function 
whereby the model_loop() 
method has been eliminated.


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

Modified: branches/frame_order_testing/generic_fns/structure/internal.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/internal.py?rev=15119&r1=15118&r2=15119&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/internal.py (original)
+++ branches/frame_order_testing/generic_fns/structure/internal.py Mon Jan  2 
21:43:35 2012
@@ -831,31 +831,38 @@
         attached_name = None
         warnings = None
 
-        # Loop over the models.
-        for model in self.model_loop(model_num):
-            # Loop over the molecules.
-            for mol in model.mol:
-                # Skip non-matching molecules.
-                if mol_name and mol_name != mol.mol_name:
+        # Use the first model for the atom matching.
+        model = self.structural_data[0]
+
+        # Loop over the molecules.
+        for mol in model.mol:
+            # Skip non-matching molecules.
+            if mol_name and mol_name != mol.mol_name:
+                continue
+
+            # Find the atomic index of the base atom.
+            index = None
+            for i in range(len(mol.atom_name)):
+                # Residues don't match.
+                if (res_num != None and mol.res_num[i] != res_num) or 
(res_name != None and mol.res_name[i] != res_name):
                     continue
 
-                # Find the atomic index of the base atom.
-                index = None
-                for i in range(len(mol.atom_name)):
-                    # Residues don't match.
-                    if (res_num != None and mol.res_num[i] != res_num) or 
(res_name != None and mol.res_name[i] != res_name):
+                # Atoms don't match.
+                if (spin_num != None and mol.atom_num[i] != spin_num) or 
(spin_name != None and mol.atom_name[i] != spin_name):
+                    continue
+
+                # Update the index and stop searching.
+                index = i
+                break
+
+            # Found the atom.
+            if index != None:
+                # Loop over the models.
+                for j in range(len(self.structural_data)):
+                    # A single model.
+                    if model_num != None and self.structural_data[j].num != 
model_num:
                         continue
 
-                    # Atoms don't match.
-                    if (spin_num != None and mol.atom_num[i] != spin_num) or 
(spin_name != None and mol.atom_name[i] != spin_name):
-                        continue
-
-                    # Update the index and stop searching.
-                    index = i
-                    break
-
-                # Found the atom.
-                if index != None:
                     # Get the atom bonded to this 
model/molecule/residue/atom.
                     bonded_num, bonded_name, element, pos, attached_name, 
warnings = self._bonded_atom(attached_atom, index, mol)
 
@@ -869,9 +876,9 @@
                     # Append the vector to the vectors array.
                     vectors.append(vector)
 
-                # Not found.
-                else:
-                    warnings = "Cannot find the atom in the structure"
+            # Not found.
+            else:
+                warnings = "Cannot find the atom in the structure"
 
         # Build the tuple to be yielded.
         data = (vectors,)