Author: bugman
Date: Mon Jan 27 22:06:35 2014
New Revision: 22054
URL: http://svn.gna.org/viewcvs/relax?rev=22054&view=rev
Log:
Merged revisions 22051-22053 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r22051 | bugman | 2014-01-27 19:23:47 +0100 (Mon, 27 Jan 2014) | 6 lines
More speed ups for the internal structural object when huge numbers of
models are present.
Another loop over the structural_data object has been eliminated from the
PDB reading load_pdb()
method.
........
r22052 | bugman | 2014-01-27 20:42:01 +0100 (Mon, 27 Jan 2014) | 6 lines
Another optimisation for the internal structural object for large numbers
of models.
The ModelList.add_item() method no longer loops over all models to check if
a model is already
present, instead using the new current_models list.
........
r22053 | bugman | 2014-01-27 21:49:32 +0100 (Mon, 27 Jan 2014) | 8 lines
Yet more optimisation for handling large quantities of models in the
internal structural model.
Now when adding new models to the object, the model_indices and model_list
objects are no longer
created. This saves much time as the large model_list is now not sorted.
A number of structural
object methods have been updated to handle the change by switching to the
model_loop() method for
looping over the models, rather than using the model_indices and model_list
objects.
........
Modified:
branches/double_rotor/ (props changed)
branches/double_rotor/lib/structure/internal/models.py
branches/double_rotor/lib/structure/internal/object.py
Propchange: branches/double_rotor/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Jan 27 22:06:35 2014
@@ -1,1 +1,1 @@
-/trunk:1-22049
+/trunk:1-22053
Modified: branches/double_rotor/lib/structure/internal/models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/structure/internal/models.py?rev=22054&r1=22053&r2=22054&view=diff
==============================================================================
--- branches/double_rotor/lib/structure/internal/models.py (original)
+++ branches/double_rotor/lib/structure/internal/models.py Mon Jan 27
22:06:35 2014
@@ -75,24 +75,14 @@
# Otherwise append an empty ModelContainer.
else:
# Test if the model number already exists.
- for i in range(len(self)):
- if self[i].num == model_num:
- raise RelaxError("The model '" + repr(model_num) + "'
already exists.")
+ if model_num in self.current_models:
+ raise RelaxError("The model '" + repr(model_num) + "'
already exists.")
# Append an empty ModelContainer.
self.append(ModelContainer(model_num))
# Update the current model list.
self.current_models.append(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 = list(self.model_indices.keys())
- self.model_list.sort()
def is_empty(self):
Modified: branches/double_rotor/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/double_rotor/lib/structure/internal/object.py?rev=22054&r1=22053&r2=22054&view=diff
==============================================================================
--- branches/double_rotor/lib/structure/internal/object.py (original)
+++ branches/double_rotor/lib/structure/internal/object.py Mon Jan 27
22:06:35 2014
@@ -1261,14 +1261,9 @@
pos = zeros(3, float64)
# 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
-
+ for model in self.model_loop(model=model_num):
# Alias.
- model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
- mol2 =
self.structural_data[model_index].mol[mol_index]
+ mol2 = model.mol[mol_index]
# Some sanity checks.
if mol2.atom_num[i] != atom_num:
@@ -1286,14 +1281,9 @@
pos = []
# 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
-
+ for model in self.model_loop(model=model_num):
# Alias.
- model_index =
self.structural_data.model_indices[self.structural_data.model_list[j]]
- mol2 =
self.structural_data[model_index].mol[mol_index]
+ mol2 = model.mol[mol_index]
# Append the position.
pos.append([mol2.x[i], mol2.y[i], mol2.z[i]])
@@ -1389,14 +1379,9 @@
# 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
-
- # 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]
+ for model in self.model_loop(model=model_num):
+ # Alias.
+ mol = model.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)
@@ -1856,9 +1841,8 @@
else:
# Number of structures already present for the model.
num_struct = 0
- for model in self.structural_data:
- if not set_model_num or (model_index <=
len(set_model_num) and set_model_num[model_index] == model.num):
- num_struct = len(model.mol)
+ if self.structural_data != None and
len(self.structural_data) and (not set_model_num or (model_index <=
len(set_model_num) and set_model_num[model_index] ==
self.structural_data[0].num)):
+ num_struct = len(self.structural_data[0].mol)
# Set the name to the file name plus the structure
number.
new_mol_name.append(file_root(file) + '_mol' +
repr(mol_num+num_struct))
r22054 - in /branches/double_rotor: ./ lib/structure/internal/models.py lib/structure/internal/object.py