Author: bugman
Date: Fri Mar 22 12:28:51 2013
New Revision: 18953
URL: http://svn.gna.org/viewcvs/relax?rev=18953&view=rev
Log:
Next block of the manual merger of the frame_order_testing branch.
The commands used were:
svn merge -r15130:15131
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15131:15132
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15132:15133
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15133:15134
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15134:15135
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15135:15136
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15136:15137
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15137:15138
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15138:15139
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
svn merge -r15139:15140
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
The console messages were:
[edau@localhost relax-trunk]$ svn merge -r15130:15131
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'test_suite/system_tests/align_tensor.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15131 into '.':
C test_suite/system_tests/align_tensor.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15131:15132
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r15132 into '.':
U generic_fns/structure/mass.py
[edau@localhost relax-trunk]$ svn merge -r15132:15133
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in
'test_suite/unit_tests/_generic_fns/_structure/test_scientific.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15133 into '.':
C test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15133:15134
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'generic_fns/structure/internal.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15134 into '.':
C generic_fns/structure/internal.py
U generic_fns/structure/scientific.py
Conflict discovered in 'generic_fns/structure/api_base.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
C generic_fns/structure/api_base.py
Summary of conflicts:
Text conflicts: 2
[edau@localhost relax-trunk]$ svn merge -r15134:15135
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'generic_fns/structure/main.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15135 into '.':
C generic_fns/structure/main.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15135:15136
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r15136 into '.':
G generic_fns/structure/main.py
[edau@localhost relax-trunk]$ svn merge -r15136:15137
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'specific_fns/n_state_model.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15137 into '.':
C specific_fns/n_state_model.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15137:15138
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'specific_fns/n_state_model.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15138 into '.':
C specific_fns/n_state_model.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15138:15139
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
Conflict discovered in 'specific_fns/n_state_model.py'.
Select: (p) postpone, (df) diff-full, (e) edit,
(mc) mine-conflict, (tc) theirs-conflict,
(s) show all options: p
--- Merging r15139 into '.':
C specific_fns/n_state_model.py
Summary of conflicts:
Text conflicts: 1
[edau@localhost relax-trunk]$ svn merge -r15139:15140
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_testing .
--- Merging r15140 into '.':
C prompt/align_tensor.py
Summary of conflicts:
Tree conflicts: 1
[edau@localhost relax-trunk]$
Modified:
trunk/generic_fns/structure/api_base.py
trunk/generic_fns/structure/internal.py
trunk/generic_fns/structure/main.py
trunk/generic_fns/structure/mass.py
trunk/generic_fns/structure/scientific.py
trunk/specific_fns/n_state_model.py
trunk/test_suite/system_tests/align_tensor.py
trunk/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
Modified: trunk/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/api_base.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/generic_fns/structure/api_base.py (original)
+++ trunk/generic_fns/structure/api_base.py Fri Mar 22 12:28:51 2013
@@ -1170,6 +1170,15 @@
# 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: trunk/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/internal.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/generic_fns/structure/internal.py (original)
+++ trunk/generic_fns/structure/internal.py Fri Mar 22 12:28:51 2013
@@ -1223,7 +1223,8 @@
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:
@@ -1247,7 +1248,8 @@
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]])
@@ -1315,7 +1317,10 @@
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
@@ -1342,6 +1347,10 @@
# 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: trunk/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/main.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/generic_fns/structure/main.py (original)
+++ trunk/generic_fns/structure/main.py Fri Mar 22 12:28:51 2013
@@ -198,14 +198,14 @@
# Assemble the atomic coordinates.
coord_from = []
for pos in cdp.structure.atom_loop(atom_id=atom_id,
model_num=model_from[i], pos_flag=True):
- coord_from.append(pos)
+ coord_from.append(pos[0])
# Loop over the ending models.
for j in range(len(model_to)):
# Assemble the atomic coordinates.
coord_to = []
for pos in cdp.structure.atom_loop(atom_id=atom_id,
model_num=model_to[j], pos_flag=True):
- coord_to.append(pos)
+ coord_to.append(pos[0])
# Send to the base container for the calculations.
cdp.structure.displacements._calculate(model_from=model_from[i],
model_to=model_to[j], coord_from=array(coord_from), coord_to=array(coord_to),
centroid=centroid)
@@ -248,7 +248,7 @@
for model in models:
coord.append([])
for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
pos_flag=True):
- coord[-1].append(pos)
+ coord[-1].append(pos[0])
coord[-1] = array(coord[-1])
coord = array(coord)
@@ -316,12 +316,7 @@
continue
# Add the position vector to the spin container.
- if ave_pos:
- spin_cont.pos = pos
- else:
- if not hasattr(spin_cont, 'pos'):
- spin_cont.pos = []
- spin_cont.pos.append(pos)
+ spin_cont.pos = pos
# Store the data for a printout at the end.
data.append([id, repr(pos)])
@@ -344,7 +339,7 @@
raise RelaxNoSpinError(atom)
# Test the position.
- if not hasattr(subspin, 'pos') or not subspin.pos:
+ if not hasattr(subspin, 'pos') or subspin.pos == None or not
len(subspin.pos):
raise RelaxError("Positional information is not
available for the atom '%s'." % atom)
# Alias the position.
@@ -707,7 +702,7 @@
for model in models:
coord.append([])
for pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model,
pos_flag=True):
- coord[-1].append(pos)
+ coord[-1].append(pos[0])
coord[-1] = array(coord[-1])
# The different algorithms.
Modified: trunk/generic_fns/structure/mass.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/mass.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/generic_fns/structure/mass.py (original)
+++ trunk/generic_fns/structure/mass.py Fri Mar 22 12:28:51 2013
@@ -58,7 +58,7 @@
M = 0.0
# Loop over all atoms.
- for mol_name, res_num, res_name, atom_num, atom_name, element, pos in
cdp.structure.atom_loop(atom_id=atom_id, model_num=model, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_num_flag=True,
atom_name_flag=True, element_flag=True, pos_flag=True):
+ for mol_name, res_num, res_name, atom_num, atom_name, element, pos in
cdp.structure.atom_loop(atom_id=atom_id, model_num=model, mol_name_flag=True,
res_num_flag=True, res_name_flag=True, atom_num_flag=True,
atom_name_flag=True, element_flag=True, pos_flag=True, ave=True):
# Initialise the spin id string.
id = ''
Modified: trunk/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/structure/scientific.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/generic_fns/structure/scientific.py (original)
+++ trunk/generic_fns/structure/scientific.py Fri Mar 22 12:28:51 2013
@@ -266,7 +266,8 @@
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':
Modified: trunk/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/n_state_model.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/specific_fns/n_state_model.py (original)
+++ trunk/specific_fns/n_state_model.py Fri Mar 22 12:28:51 2013
@@ -855,7 +855,7 @@
interatom.rdc_bc = {}
# Append the back calculated PCS.
- interatom.rdc_bc[align_id] =
model.Dij_theta[align_index, rdc_index]
+ interatom.rdc_bc[align_id] =
model.rdc_theta[align_index, rdc_index]
# Increment the data index if the interatom container
has data.
rdc_index = rdc_index + 1
@@ -1775,17 +1775,17 @@
for id in cdp.align_ids:
# No tensors initialised.
if not hasattr(cdp, 'align_tensors'):
- align_tensor.init(tensor=id, params=[0.0, 0.0, 0.0, 0.0,
0.0])
+ align_tensor.init(tensor=id, align_id=id, params=[0.0,
0.0, 0.0, 0.0, 0.0])
# Find if the tensor corresponding to the id exists.
exists = False
for tensor in cdp.align_tensors:
- if id == tensor.name:
+ if id == tensor.align_id:
exists = True
# Initialise the tensor.
if not exists:
- align_tensor.init(tensor=id, params=[0.0, 0.0, 0.0, 0.0,
0.0])
+ align_tensor.init(tensor=id, align_id=id, params=[0.0,
0.0, 0.0, 0.0, 0.0])
def base_data_loop(self):
Modified: trunk/test_suite/system_tests/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/align_tensor.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/test_suite/system_tests/align_tensor.py (original)
+++ trunk/test_suite/system_tests/align_tensor.py Fri Mar 22 12:28:51 2013
@@ -61,6 +61,10 @@
(0.00014574884684542708, -8.3162940224598374e-05,
7.4927100277784987e-05, 0.00010508245294401461, 3.1156238348722986e-05),
(-0.00011267453337899962, 6.412308037476237e-05,
-5.7897942333203444e-05, -8.1865863377039068e-05, -2.5273427585025123e-05)
]
+
+ # Define the domains.
+ self.interpreter.domain(id='full')
+ self.interpreter.domain(id='red')
# Set up the tensors.
for i in range(5):
Modified:
trunk/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py?rev=18953&r1=18952&r2=18953&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
(original)
+++ trunk/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py
Fri Mar 22 12:28:51 2013
@@ -241,9 +241,10 @@
self.assertEqual(spin_num, 140)
self.assertEqual(spin_name, 'OE1')
self.assertEqual(element, 'O')
- self.assertEqual(pos[0], float('10.055'))
- self.assertEqual(pos[1], float('-2.74'))
- self.assertEqual(pos[2], float('-13.193'))
+ self.assertEqual(len(pos), 1)
+ self.assertEqual(pos[0, 0], float('10.055'))
+ self.assertEqual(pos[0, 1], float('-2.74'))
+ self.assertEqual(pos[0, 2], float('-13.193'))
# Increment the atom count.
atom_count = atom_count + 1
r18953 - in /trunk: generic_fns/structure/ specific_fns/ test_suite/system_tests/ test_suite/unit_tests/_generic_fns/_struct...