Author: bugman
Date: Mon May 3 00:52:26 2010
New Revision: 11172
URL: http://svn.gna.org/viewcvs/relax?rev=11172&view=rev
Log:
Bug fix for when structural models are loaded out of order.
Now the API generator method model_loop() is being used by the scientific
python and internal
structural objects. The bond vectors and atomic positions are now loaded
into the spin containers
in correct numerical model order.
Modified:
1.3/generic_fns/structure/api_base.py
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/scientific.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=11172&r1=11171&r2=11172&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Mon May 3 00:52:26 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2009 Edward d'Auvergne
#
+# Copyright (C) 2008-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -276,6 +276,46 @@
raise RelaxImplementError
+ def model_loop(self, model=None):
+ """Generator method for looping over the models in numerical order.
+
+ @keyword model: Limit the loop to a single number.
+ @type model: int
+ @return: The model structural object.
+ @rtype: ModelContainer container
+ """
+
+ # A single model.
+ if model:
+ for i in range(len(self.structural_data)):
+ if self.structural_data[i].num == model:
+ yield self.structural_data[i]
+
+ # All models.
+ else:
+ # The models.
+ model_nums = []
+ for i in range(len(self.structural_data)):
+ if self.structural_data[i].num != None:
+ model_nums.append(self.structural_data[i].num)
+
+ # Sort.
+ if model_nums:
+ model_nums.sort()
+
+ # Loop over the models in order.
+ for model_num in model_nums:
+ # Find the model.
+ for i in range(len(self.structural_data)):
+ # Yield the model.
+ if self.structural_data[i].num == model_num:
+ yield self.structural_data[i]
+
+ # No models, so just yield the single container.
+ if not model_nums:
+ yield self.structural_data[0]
+
+
def num_models(self):
"""Method for returning the number of models.
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=11172&r1=11171&r2=11172&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Mon May 3 00:52:26 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -430,10 +430,8 @@
# Generate the selection object.
sel_obj = Selection(atom_id)
- # Loop over the models.
- for model_index in range(len(self.structural_data)):
- model = self.structural_data[model_index]
-
+ # Model loop.
+ for model in self.model_loop():
# Loop over the molecules.
for mol_index in range(len(model.mol)):
mol = model.mol[mol_index]
@@ -459,9 +457,9 @@
# The atom position.
if ave:
# Loop over the models.
- for model_index2 in range(len(self.structural_data)):
+ for model in self.model_loop():
# Alias.
- mol =
self.structural_data[model_index2].mol[mol_index]
+ mol = model.mol[mol_index]
# Some sanity checks.
if mol.atom_num[i] != atom_num:
@@ -539,11 +537,7 @@
warnings = None
# Loop over the models.
- for model in self.structural_data:
- # Single model.
- if model_num and model_num != model.num:
- continue
-
+ for model in self.model_loop(model_num):
# Loop over the molecules.
for mol in model.mol:
# Skip non-matching molecules.
@@ -760,7 +754,7 @@
# Determine if model records will be created.
model_records = False
- for model in self.structural_data:
+ for model in self.model_loop():
if hasattr(model, 'num') and model.num != None:
model_records = True
@@ -912,11 +906,7 @@
######################
# Loop over the models.
- for model in self.structural_data:
- # Single model.
- if model_num and model_num != model.num:
- continue
-
+ for model in self.model_loop(model_num):
# MODEL record, for multiple models.
####################################
Modified: 1.3/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=11172&r1=11171&r2=11172&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Mon May 3 00:52:26 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -198,10 +198,8 @@
# Generate the selection object.
sel_obj = Selection(atom_id)
- # Loop over the models.
- for model_index in range(len(self.structural_data)):
- model = self.structural_data[model_index]
-
+ # Model loop.
+ for model in self.model_loop():
# Loop over the molecules.
for mol_index in range(len(model.mol)):
mol = model.mol[mol_index]
@@ -304,13 +302,9 @@
pos_array = []
# Loop over the models.
- for model in self.structural_data:
+ for model in self.model_loop(model):
# Init.
atom_found = False
-
- # Skip non-matching models.
- if model != None and model != model.num:
- continue
# Loop over each individual molecule.
for mol in model.mol:
@@ -364,7 +358,7 @@
pos = zeros(3, float64)
# Loop over the models.
- for model in self.structural_data:
+ for model in self.model_loop():
# The exact molecule.
mol = model.mol[mol_index]
@@ -424,11 +418,7 @@
warnings = None
# Loop over the models.
- for model in self.structural_data:
- # Single model.
- if model_num and model_num != model.num:
- continue
-
+ for model in self.model_loop(model_num):
# Init.
atom_found = False
r11172 - in /1.3/generic_fns/structure: api_base.py internal.py scientific.py