Author: bugman
Date: Tue Jan 3 17:42:23 2012
New Revision: 15134
URL: http://svn.gna.org/viewcvs/relax?rev=15134&view=rev
Log:
Redesigned the model looping in the atom_loop() and base_vectors() API
methods to fix a bug.
The models are now looped over in numerical order, rather than the order they
were loaded or
created. This reverts to the original behaviour of the main line.
Modified:
branches/frame_order_testing/generic_fns/structure/api_base.py
branches/frame_order_testing/generic_fns/structure/internal.py
branches/frame_order_testing/generic_fns/structure/scientific.py
Modified: branches/frame_order_testing/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/api_base.py?rev=15134&r1=15133&r2=15134&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/api_base.py (original)
+++ branches/frame_order_testing/generic_fns/structure/api_base.py Tue Jan 3
17:42:23 2012
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2011 Edward d'Auvergne
#
+# Copyright (C) 2008-2012 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -1120,6 +1120,15 @@
# Append an empty ModelContainer.
self.append(ModelContainer(model_num))
+ # Store the model indices.
+ if not hasattr(self, 'model_indices'):
+ self.model_indices = {}
+ self.model_indices[model_num] = len(self) - 1
+
+ # The sorted model numbers.
+ self.model_list = self.model_indices.keys()
+ self.model_list.sort()
+
def is_empty(self):
"""Method for testing if this ModelList object is empty.
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=15134&r1=15133&r2=15134&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/internal.py (original)
+++ branches/frame_order_testing/generic_fns/structure/internal.py Tue Jan 3
17:42:23 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.
#
#
#
@@ -745,7 +745,8 @@
continue
# Alias.
- mol2 = self.structural_data[j].mol[mol_index]
+ model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
+ mol2 =
self.structural_data[model_index].mol[mol_index]
# Some sanity checks.
if mol2.atom_num[i] != atom_num:
@@ -769,7 +770,8 @@
continue
# Alias.
- mol2 = self.structural_data[j].mol[mol_index]
+ model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
+ mol2 =
self.structural_data[model_index].mol[mol_index]
# Append the position.
pos.append([mol2.x[i], mol2.y[i], mol2.z[i]])
@@ -835,7 +837,10 @@
model = self.structural_data[0]
# Loop over the molecules.
- for mol in model.mol:
+ for mol_index in range(len(model.mol)):
+ # Alias.
+ mol = model.mol[mol_index]
+
# Skip non-matching molecules.
if mol_name and mol_name != mol.mol_name:
continue
@@ -862,6 +867,10 @@
# A single model.
if model_num != None and self.structural_data[j].num !=
model_num:
continue
+
+ # Alias the molecule.
+ model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
+ mol = self.structural_data[model_index].mol[mol_index]
# 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)
Modified: branches/frame_order_testing/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/structure/scientific.py?rev=15134&r1=15133&r2=15134&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/structure/scientific.py
(original)
+++ branches/frame_order_testing/generic_fns/structure/scientific.py Tue Jan
3 17:42:23 2012
@@ -243,7 +243,8 @@
continue
# Alias.
- mol2 = self.structural_data[j].mol[mol_index]
+ model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
+ mol2 =
self.structural_data[model_index].mol[mol_index]
# The residue.
if mol2.mol_type != 'other':
r15134 - in /branches/frame_order_testing/generic_fns/structure: api_base.py internal.py scientific.py