Author: bugman
Date: Wed Jul 2 11:55:35 2014
New Revision: 24401
URL: http://svn.gna.org/viewcvs/relax?rev=24401&view=rev
Log:
Merged revisions 24396,24399 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r24396 | bugman | 2014-07-02 09:50:36 +0200 (Wed, 02 Jul 2014) | 6 lines
Python 3 fixes for the entire codebase using the 2to3 script.
The command used was:
2to3 -j 4 -w -f xrange .
........
r24399 | bugman | 2014-07-02 11:46:40 +0200 (Wed, 02 Jul 2014) | 5 lines
The internal structural object add_molecule() and has_molecule() methods
are now model specific.
This allows for finer control of structural object.
........
Modified:
branches/disp_spin_speed/ (props changed)
branches/disp_spin_speed/lib/structure/internal/object.py
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
Propchange: branches/disp_spin_speed/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jul 2 11:55:35 2014
@@ -1 +1 @@
-/trunk:1-24393
+/trunk:1-24399
Modified: branches/disp_spin_speed/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/structure/internal/object.py?rev=24401&r1=24400&r2=24401&view=diff
==============================================================================
--- branches/disp_spin_speed/lib/structure/internal/object.py (original)
+++ branches/disp_spin_speed/lib/structure/internal/object.py Wed Jul 2
11:55:35 2014
@@ -1140,21 +1140,22 @@
return self.structural_data[-1]
- def add_molecule(self, name=None):
+ def add_molecule(self, model_num=None, name=None):
"""Add a new molecule to the store.
- @keyword name: The molecule identifier string.
- @type name: str
+ @keyword model_num: The optional model to add the molecule to. If
not supplied, the molecule will be added to all models.
+ @type model_num: None or int
+ @keyword name: The molecule identifier string.
+ @type name: str
"""
# Add a model if necessary.
if len(self.structural_data) == 0:
self.add_model()
- # Loop over the models.
- for i in range(len(self.structural_data)):
- # Add the molecule.
- self.structural_data[i].mol.add_item(mol_name=name,
mol_cont=MolContainer())
+ # Add the molecule to each model.
+ for model in self.model_loop(model=model_num):
+ model.mol.add_item(mol_name=name, mol_cont=MolContainer())
def are_bonded(self, atom_id1=None, atom_id2=None):
@@ -1736,13 +1737,15 @@
return mol
- def has_molecule(self, name=None):
+ def has_molecule(self, model_num=None, name=None):
"""Check if the molecule name exists.
- @param name: The molecule name.
- @type name: str
- @return: True if the molecule exists, False otherwise.
- @rtype: bool
+ @keyword model_num: The optional model to check. If not supplied,
the molecule will be searched for across all models.
+ @type model_num: None or int
+ @param name: The molecule name.
+ @type name: str
+ @return: True if the molecule exists, False otherwise.
+ @rtype: bool
"""
# No models.
@@ -1750,7 +1753,7 @@
return False
# Loop over the models.
- for model_cont in self.model_loop():
+ for model_cont in self.model_loop(model=model_num):
# Loop over the molecules.
for mol in model_cont.mol:
# Matching molecule.
Modified:
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py?rev=24401&r1=24400&r2=24401&view=diff
==============================================================================
---
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
(original)
+++
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
Wed Jul 2 11:55:35 2014
@@ -421,7 +421,7 @@
# Loop 100 times for each spin in the clustered analysis (to make the
timing numbers equivalent).
for spin_index in xrange(100):
# Repeat the function call, to simulate minimisation.
- for i in xrange(iter):
+ for i in range(iter):
chi2 = C1.calc(C1.params)
print("chi2 single:", chi2)
@@ -443,7 +443,7 @@
C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9,
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
# Repeat the function call, to simulate minimisation.
- for i in xrange(iter):
+ for i in range(iter):
chi2 = C1.calc(C1.params)
print("chi2 cluster:", chi2)
Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24401&r1=24400&r2=24401&view=diff
==============================================================================
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py Wed
Jul 2 11:55:35 2014
@@ -5342,7 +5342,7 @@
pipe_name = 'base pipe'
pipe_type = 'relax_disp'
pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- select_spin_index = range(0, 1)
+ select_spin_index = list(range(0, 1))
self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
# Generate r20 key.
@@ -5491,7 +5491,7 @@
pipe_name = 'base pipe'
pipe_type = 'relax_disp'
pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- select_spin_index = range(0, 1)
+ select_spin_index = list(range(0, 1))
self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
# Define replicated
@@ -5574,7 +5574,7 @@
pipe_name = 'base pipe'
pipe_type = 'relax_disp'
pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- select_spin_index = range(0, 2)
+ select_spin_index = list(range(0, 2))
self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
# Generate r20 key.
@@ -5742,7 +5742,7 @@
pipe_name = 'base pipe'
pipe_type = 'relax_disp'
pipe_name_r2eff = "%s_R2eff"%(pipe_name)
- select_spin_index = range(0, 2)
+ select_spin_index = list(range(0, 2))
self.setup_sod1wt_t25(pipe_name=pipe_name, pipe_type=pipe_type,
pipe_name_r2eff=pipe_name_r2eff, select_spin_index=select_spin_index)
# Generate r20 key.
r24401 - in /branches/disp_spin_speed: ./ lib/structure/internal/ test_suite/shared_data/dispersion/profiling/ test_suite/sy...