Author: bugman
Date: Mon Jan 12 16:35:59 2009
New Revision: 8421
URL: http://svn.gna.org/viewcvs/relax?rev=8421&view=rev
Log:
Modified the atom_loop() method to handle the new data structure design.
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=8421&r1=8420&r2=8421&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
16:35:59 2009
@@ -409,95 +409,100 @@
# Average properties mode.
if ave:
- # Loop over all atoms.
- for i in xrange(len(self.structural_data[0].atom_name)):
- # Skip non-matching atoms.
- if sel_obj and not
sel_obj.contains_spin(self.structural_data[0].atom_num[i],
self.structural_data[0].atom_name[i], self.structural_data[0].res_num[i],
self.structural_data[0].res_name[i]):
- continue
-
- # Initialise.
- model = None
- mol_name = None
- res_num = self.structural_data[0].res_num[i]
- res_name = self.structural_data[0].res_name[i]
- atom_num = self.structural_data[0].atom_num[i]
- atom_name = self.structural_data[0].atom_name[i]
- element = self.structural_data[0].element[i]
- pos = zeros(3, float64)
-
- # Loop over the structures.
- for struct in self.structural_data:
- # Some sanity checks.
- if struct.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([struct.x[i], struct.y[i],
struct.z[i]], float64)
-
- # Average the position array.
- pos = pos / len(self.structural_data)
-
- # Build the tuple to be yielded.
- atomic_tuple = ()
- if model_num_flag:
- atomic_tuple = atomic_tuple + (model,)
- if mol_name_flag:
- atomic_tuple = atomic_tuple + (mol_name,)
- if res_num_flag:
- atomic_tuple = atomic_tuple + (res_num,)
- if res_name_flag:
- atomic_tuple = atomic_tuple + (res_name,)
- if atom_num_flag:
- atomic_tuple = atomic_tuple + (atom_num,)
- if atom_name_flag:
- atomic_tuple = atomic_tuple + (atom_name,)
- if element_flag:
- atomic_tuple = atomic_tuple + (element,)
- if pos_flag:
- atomic_tuple = atomic_tuple + (pos,)
-
- # Yield the information.
- yield atomic_tuple
+ # 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 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
+
+ # Initialise.
+ res_num = mol.res_num[i]
+ res_name = mol.res_name[i]
+ atom_num = mol.atom_num[i]
+ atom_name = mol.atom_name[i]
+ 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)
+
+ # Build the tuple to be yielded.
+ atomic_tuple = ()
+ if model_num_flag:
+ atomic_tuple = atomic_tuple + (None,)
+ if mol_name_flag:
+ atomic_tuple = atomic_tuple + (mol.mol_name,)
+ if res_num_flag:
+ atomic_tuple = atomic_tuple + (res_num,)
+ if res_name_flag:
+ atomic_tuple = atomic_tuple + (res_name,)
+ if atom_num_flag:
+ atomic_tuple = atomic_tuple + (atom_num,)
+ if atom_name_flag:
+ atomic_tuple = atomic_tuple + (atom_name,)
+ if element_flag:
+ atomic_tuple = atomic_tuple + (element,)
+ if pos_flag:
+ atomic_tuple = atomic_tuple + (pos,)
+
+ # Yield the information.
+ yield atomic_tuple
# Individual structure mode.
else:
# Loop over the models.
- for c in xrange(self.num):
+ for model in self.structural_data:
# Explicit structure identifier.
- if type(str_id) == int:
- if str_id != c:
- continue
-
- # Alias the structural data.
- struct = self.structural_data[c]
-
- # Loop over all atoms.
- for i in xrange(len(struct.atom_name)):
- # Skip non-matching atoms.
- if sel_obj and not
sel_obj.contains_spin(struct.atom_num[i], struct.atom_name[i],
struct.res_num[i], struct.res_name[i]):
- continue
-
- # Build the tuple to be yielded.
- atomic_tuple = ()
- if model_num_flag:
- atomic_tuple = atomic_tuple + (self.model[c],)
- if mol_name_flag:
- atomic_tuple = atomic_tuple + (self.name[c],)
- if res_num_flag:
- atomic_tuple = atomic_tuple + (struct.res_num[i],)
- if res_name_flag:
- atomic_tuple = atomic_tuple + (struct.res_name[i],)
- if atom_num_flag:
- atomic_tuple = atomic_tuple + (struct.atom_num[i],)
- if atom_name_flag:
- atomic_tuple = atomic_tuple + (struct.atom_name[i],)
- if element_flag:
- atomic_tuple = atomic_tuple + (struct.element[i],)
- if pos_flag:
- atomic_tuple = atomic_tuple + (array([struct.x[i],
struct.y[i], struct.z[i]], float64),)
-
- # Yield the information.
- yield atomic_tuple
+ #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
def bond_vectors(self, atom_id=None, attached_atom=None,
struct_index=None, return_name=False, return_warnings=False):
r8421 - /branches/multi_structure/generic_fns/structure/internal.py