Author: bugman
Date: Thu Jan 15 11:42:48 2009
New Revision: 8461
URL: http://svn.gna.org/viewcvs/relax?rev=8461&view=rev
Log:
Simplification of the internal structural object atom_loop() method.
There is now only one block of code for the atom looping for the two options
of the ave argument.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8461&r1=8460&r2=8461&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 15
11:42:48 2009
@@ -407,12 +407,17 @@
# Generate the selection object.
sel_obj = Selection(atom_id)
- # Average properties mode.
- if ave:
- # Loop over the molecules of the first model.
- for mol_index in range(len(self.structural_data[0])):
- # Alias the molecule.
- mol = self.structural_data[0].mol[mol_index]
+ # Loop over the models.
+ for model_index in range(len(self.structural_data)):
+ model = self.structural_data[model_index]
+
+ # Loop over the molecules.
+ for mol_index in range(len(model.mol)):
+ mol = model.mol[mol_index]
+
+ # Skip non-matching molecules.
+ if sel_obj and not sel_obj.contains_mol(mol.name):
+ continue
# Loop over all atoms.
for i in xrange(len(mol.atom_name)):
@@ -428,27 +433,37 @@
element = mol.element[i]
pos = zeros(3, float64)
- # Loop over the models.
- for model_index in range(len(self.structural_data)):
- # Alias.
- mol =
self.structural_data[model_index].mol[mol_index]
-
- # Some sanity checks.
- if mol.atom_num[i] != atom_num:
- raise RelaxError, "The loaded structures do not
contain the same atoms. The average structural properties can not be
calculated."
-
- # Sum the atom positions.
- pos = pos + array([mol.x[i], mol.y[i], mol.z[i]],
float64)
-
- # Average the position array (divide by the number of
models).
- pos = pos / len(self.structural_data)
+ # The atom position.
+ if ave:
+ # Loop over the models.
+ for model_index2 in range(len(self.structural_data)):
+ # Alias.
+ mol =
self.structural_data[model_index2].mol[mol_index]
+
+ # Some sanity checks.
+ if mol.atom_num[i] != atom_num:
+ raise RelaxError, "The loaded structures do
not contain the same atoms. The average structural properties can not be
calculated."
+
+ # Sum the atom positions.
+ pos = pos + array([mol.x[i], mol.y[i],
mol.z[i]], float64)
+
+ # Average the position array (divide by the number
of models).
+ pos = pos / len(self.structural_data)
+ else:
+ pos = array([mol.x[i], mol.y[i], mol.z[i]], float64)
+
+ # The molecule name.
+ mol_name = mol.name
# Build the tuple to be yielded.
atomic_tuple = ()
if model_num_flag:
- atomic_tuple = atomic_tuple + (None,)
+ if ave:
+ atomic_tuple = atomic_tuple + (None,)
+ else:
+ atomic_tuple = atomic_tuple + (model.num,)
if mol_name_flag:
- atomic_tuple = atomic_tuple + (mol.mol_name,)
+ atomic_tuple = atomic_tuple + (mol_name,)
if res_num_flag:
atomic_tuple = atomic_tuple + (res_num,)
if res_name_flag:
@@ -465,44 +480,9 @@
# Yield the information.
yield atomic_tuple
- # Individual structure mode.
- else:
- # Loop over the models.
- for model in self.structural_data:
- # Explicit structure identifier.
- #if type(str_id) == int:
- # if str_id != c:
- # continue
-
- # Loop over the molecules.
- for mol in model.mol:
- # Loop over all atoms.
- for i in xrange(len(mol.atom_name)):
- # Skip non-matching atoms.
- if sel_obj and not
sel_obj.contains_spin(mol.atom_num[i], mol.atom_name[i], mol.res_num[i],
mol.res_name[i]):
- continue
-
- # Build the tuple to be yielded.
- atomic_tuple = ()
- if model_num_flag:
- atomic_tuple = atomic_tuple + (model.num,)
- if mol_name_flag:
- atomic_tuple = atomic_tuple + (mol.mol_name,)
- if res_num_flag:
- atomic_tuple = atomic_tuple + (mol.res_num[i],)
- if res_name_flag:
- atomic_tuple = atomic_tuple + (mol.res_name[i],)
- if atom_num_flag:
- atomic_tuple = atomic_tuple + (mol.atom_num[i],)
- if atom_name_flag:
- atomic_tuple = atomic_tuple + (mol.atom_name[i],)
- if element_flag:
- atomic_tuple = atomic_tuple + (mol.element[i],)
- if pos_flag:
- atomic_tuple = atomic_tuple + (array([mol.x[i],
mol.y[i], mol.z[i]], float64),)
-
- # Yield the information.
- yield atomic_tuple
+ # Break out of the loop if the ave flag is set, as data from
only one model is used.
+ if ave:
+ break
def bond_vectors(self, atom_id=None, attached_atom=None,
struct_index=None, return_name=False, return_warnings=False):
r8461 - /branches/multi_structure/generic_fns/structure/internal.py