Author: bugman
Date: Thu Sep 25 17:54:36 2008
New Revision: 7303
URL: http://svn.gna.org/viewcvs/relax?rev=7303&view=rev
Log:
Merged revisions 7236-7302 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r7236 | bugman | 2008-09-24 14:47:48 +0200 (Wed, 24 Sep 2008) | 5 lines
Created the specific base class method model_loop().
This defaults to one model per spin system, and can be used by most
analysis types.
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r7237 | bugman | 2008-09-24 14:49:48 +0200 (Wed, 24 Sep 2008) | 3 lines
Activated the model_loop() generator method.
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r7238 | bugman | 2008-09-24 16:10:56 +0200 (Wed, 24 Sep 2008) | 3 lines
Changed model_loop() to return the spin container.
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r7239 | bugman | 2008-09-24 16:18:13 +0200 (Wed, 24 Sep 2008) | 3 lines
Created the sim_return_chi2() base class method.
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r7240 | bugman | 2008-09-24 16:19:59 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the sim_return_selected() base class method to accept the spin
container.
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r7241 | bugman | 2008-09-24 16:22:23 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the sim_return_param() base class method to accept the spin
container.
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r7242 | bugman | 2008-09-24 16:26:40 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the set_error() base class method to accept the spin container.
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r7243 | bugman | 2008-09-24 16:33:09 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the Grace class methods into module functions.
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r7244 | bugman | 2008-09-24 16:41:32 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the determine_graph_type() function to the new relax design.
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r7245 | bugman | 2008-09-24 16:59:13 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the get_data() function to the new relax design.
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r7246 | bugman | 2008-09-24 17:01:41 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the view() function to the new design.
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r7247 | bugman | 2008-09-24 17:23:34 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the 4 write_*() functions to the new design.
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r7248 | bugman | 2008-09-24 17:36:02 +0200 (Wed, 24 Sep 2008) | 3 lines
The pipe argument is now optional for RelaxNoSimError.
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r7249 | bugman | 2008-09-24 17:43:04 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the Grace write() function to the new design.
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r7250 | bugman | 2008-09-24 17:54:52 +0200 (Wed, 24 Sep 2008) | 3 lines
Updated the grace.write() user function interface to the new design.
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r7251 | bugman | 2008-09-24 17:56:02 +0200 (Wed, 24 Sep 2008) | 3 lines
A few small fixes for the write() function.
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r7252 | bugman | 2008-09-24 18:00:27 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the grace.write() user function interface.
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r7253 | bugman | 2008-09-24 18:02:10 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed a remaining instance of 'self' from the write() function.
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r7254 | bugman | 2008-09-24 18:03:32 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the call to get_data().
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r7255 | bugman | 2008-09-24 18:06:31 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the calls to x_return_value() and y_return_value().
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r7256 | bugman | 2008-09-24 18:33:07 +0200 (Wed, 24 Sep 2008) | 3 lines
Shifted the focus of the Grace module from residues to spins.
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r7257 | bugman | 2008-09-24 18:33:45 +0200 (Wed, 24 Sep 2008) | 3 lines
Fatal indentation fix.
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r7258 | bugman | 2008-09-24 18:43:16 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the determine_seq_type() function.
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r7259 | bugman | 2008-09-24 18:46:03 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the count_molecules() and count_residues() functions.
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r7260 | bugman | 2008-09-24 18:47:54 +0200 (Wed, 24 Sep 2008) | 3 lines
Merged the count_selected_spins() function into count_spins().
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r7261 | bugman | 2008-09-24 18:49:04 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed the call to count_selected_spins().
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r7262 | bugman | 2008-09-24 18:51:20 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the test_count_spins() unit test.
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r7263 | bugman | 2008-09-24 18:52:16 +0200 (Wed, 24 Sep 2008) | 3 lines
Another fix for the test_count_spins() unit test.
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r7264 | bugman | 2008-09-24 19:00:08 +0200 (Wed, 24 Sep 2008) | 3 lines
An important fix for the model-free minimisation code for the merged
count_spins() function.
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r7265 | bugman | 2008-09-24 19:02:47 +0200 (Wed, 24 Sep 2008) | 3 lines
Propagation of the spin_id variable.
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r7266 | bugman | 2008-09-24 19:15:52 +0200 (Wed, 24 Sep 2008) | 3 lines
Modified the select_all_sims() function to use the model_loop().
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r7267 | bugman | 2008-09-24 19:17:29 +0200 (Wed, 24 Sep 2008) | 3 lines
Updated the set_selected_sim() method.
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r7268 | bugman | 2008-09-24 19:18:50 +0200 (Wed, 24 Sep 2008) | 3 lines
Shifted set_selected_sim() to the base class.
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r7269 | bugman | 2008-09-24 19:20:07 +0200 (Wed, 24 Sep 2008) | 3 lines
Docstring and comment fixes for select_all_sims().
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r7270 | bugman | 2008-09-24 19:28:49 +0200 (Wed, 24 Sep 2008) | 3 lines
Wrote the model-free model_loop() generator method.
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r7271 | bugman | 2008-09-24 19:32:51 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed some dud arguments to the model_loop() generator.
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r7272 | bugman | 2008-09-24 19:49:02 +0200 (Wed, 24 Sep 2008) | 3 lines
Deleted the set_selected_sim() methods, as the base class method is
sufficient.
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r7273 | bugman | 2008-09-24 19:50:08 +0200 (Wed, 24 Sep 2008) | 3 lines
Removed some unused imports of return_spin_from_index().
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r7274 | bugman | 2008-09-24 19:55:23 +0200 (Wed, 24 Sep 2008) | 3 lines
Fix for the model-free model_loop() generator function.
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r7275 | bugman | 2008-09-24 19:56:41 +0200 (Wed, 24 Sep 2008) | 3 lines
Another fix for the model_loop() generator.
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r7276 | bugman | 2008-09-24 20:16:55 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the identification of multiple data sets in the write() function.
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r7277 | bugman | 2008-09-24 20:18:15 +0200 (Wed, 24 Sep 2008) | 3 lines
Passed the missing 'data' data structure into write_header().
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r7278 | bugman | 2008-09-24 20:27:38 +0200 (Wed, 24 Sep 2008) | 3 lines
Converted the data_names() methods to the new design.
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r7279 | bugman | 2008-09-24 20:36:59 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the call to generate_vector_dist().
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r7280 | bugman | 2008-09-24 20:54:46 +0200 (Wed, 24 Sep 2008) | 3 lines
The structural object is now initialised with an empty Structure_container
appended.
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r7281 | bugman | 2008-09-24 20:55:08 +0200 (Wed, 24 Sep 2008) | 3 lines
The Structure_container no longer needs to be initialised.
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r7282 | bugman | 2008-09-24 21:07:12 +0200 (Wed, 24 Sep 2008) | 7 lines
Reverted r7280 and r7281 as this fix was flawed.
The command used was:
svn merge -r7281:7279 .
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r7283 | bugman | 2008-09-24 21:20:07 +0200 (Wed, 24 Sep 2008) | 3 lines
The Structure_container is appended in the create_diff_tensor_pdb()
function.
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r7284 | bugman | 2008-09-24 21:22:03 +0200 (Wed, 24 Sep 2008) | 3 lines
The centre of mass atom is now set to the first.
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r7285 | bugman | 2008-09-24 21:45:20 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the setting of j_min in generate_vector_dist() when the maximum angle
is not given.
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r7286 | bugman | 2008-09-24 21:54:17 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixes for the generate_vector_residues() function when the neg flag is True.
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r7287 | bugman | 2008-09-24 21:57:31 +0200 (Wed, 24 Sep 2008) | 3 lines
Fix for the sim_return_param() method.
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r7288 | bugman | 2008-09-24 21:59:11 +0200 (Wed, 24 Sep 2008) | 3 lines
Fixed the arg order for set_error().
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r7289 | bugman | 2008-09-24 23:20:14 +0200 (Wed, 24 Sep 2008) | 3 lines
Created the test_Selection_contains_spin8() unit test.
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r7290 | bugman | 2008-09-24 23:24:02 +0200 (Wed, 24 Sep 2008) | 5 lines
Fix for the contains_spin() class method.
This is a hack which might cause failures!
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r7291 | bugman | 2008-09-24 23:31:34 +0200 (Wed, 24 Sep 2008) | 6 lines
Reverted the hack of r7290.
The command used was:
svn merge -r7290:7289 .
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r7292 | bugman | 2008-09-25 15:32:17 +0200 (Thu, 25 Sep 2008) | 6 lines
Reverted r7289 as this unit test was bad.
The command used was:
svn merge -r7289:7288 .
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r7293 | bugman | 2008-09-25 15:48:24 +0200 (Thu, 25 Sep 2008) | 3 lines
Added a simple system test for the calculation of unit XH bond vectors.
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r7294 | bugman | 2008-09-25 15:57:07 +0200 (Thu, 25 Sep 2008) | 3 lines
Activated the unit vector system test.
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r7295 | bugman | 2008-09-25 16:39:11 +0200 (Thu, 25 Sep 2008) | 3 lines
Fixes for the unit vector system test.
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r7296 | bugman | 2008-09-25 16:42:37 +0200 (Thu, 25 Sep 2008) | 3 lines
Added another system test for the calculation of unit XH vectors, but with
spin numbers removed.
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r7297 | bugman | 2008-09-25 16:45:26 +0200 (Thu, 25 Sep 2008) | 3 lines
Allowed the number arg in the spin.number() user function to be None.
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r7298 | bugman | 2008-09-25 16:50:22 +0200 (Thu, 25 Sep 2008) | 3 lines
Allowed the spin number to be reset to None.
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r7299 | bugman | 2008-09-25 16:55:03 +0200 (Thu, 25 Sep 2008) | 3 lines
Added some more checks in the unit vector system tests.
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r7300 | bugman | 2008-09-25 16:59:26 +0200 (Thu, 25 Sep 2008) | 3 lines
Added 2 more unit vector system tests, this time using the internal PDB
reader.
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r7301 | bugman | 2008-09-25 17:01:30 +0200 (Thu, 25 Sep 2008) | 3 lines
Fixed the number arg unit test of spin.number().
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r7302 | bugman | 2008-09-25 17:52:15 +0200 (Thu, 25 Sep 2008) | 7 lines
Added support to the internal PDB structural object for determining
connected atoms.
This is for when no CONECT records exist. The method __find_bonded_atom()
has been renamed to
__bonded_atom(), and the new method __find_bonded_atoms() has been written.
This new method
connects all atoms located a certain distance from each other.
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Added:
branches/rdc_analysis/test_suite/system_tests/unit_vectors.py
- copied unchanged from r7302,
1.3/test_suite/system_tests/unit_vectors.py
Modified:
branches/rdc_analysis/ (props changed)
branches/rdc_analysis/generic_fns/grace.py
branches/rdc_analysis/generic_fns/mol_res_spin.py
branches/rdc_analysis/generic_fns/monte_carlo.py
branches/rdc_analysis/generic_fns/structure/geometric.py
branches/rdc_analysis/generic_fns/structure/internal.py
branches/rdc_analysis/prompt/grace.py
branches/rdc_analysis/prompt/spin.py
branches/rdc_analysis/relax_errors.py
branches/rdc_analysis/specific_fns/base_class.py
branches/rdc_analysis/specific_fns/consistency_tests.py
branches/rdc_analysis/specific_fns/jw_mapping.py
branches/rdc_analysis/specific_fns/model_free/main.py
branches/rdc_analysis/specific_fns/model_free/mf_minimise.py
branches/rdc_analysis/specific_fns/relax_fit.py
branches/rdc_analysis/specific_fns/setup.py
branches/rdc_analysis/test_suite/system_tests/__init__.py
branches/rdc_analysis/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
branches/rdc_analysis/test_suite/unit_tests/_prompt/test_spin.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/rdc_analysis/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/grace.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/mol_res_spin.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/generic_fns/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/monte_carlo.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/geometric.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/internal.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/prompt/grace.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/prompt/spin.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/relax_errors.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/base_class.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/consistency_tests.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/jw_mapping.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/model_free/main.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/model_free/mf_minimise.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/relax_fit.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/setup.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/test_suite/system_tests/__init__.py?rev=7303&r1=7302&r2=7303&view=diff
Modified:
branches/rdc_analysis/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py?rev=7303&r1=7302&r2=7303&view=diff
Modified: branches/rdc_analysis/test_suite/unit_tests/_prompt/test_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/test_suite/unit_tests/_prompt/test_spin.py?rev=7303&r1=7302&r2=7303&view=diff
r7303 - in /branches/rdc_analysis: ./ generic_fns/ generic_fns/structure/ prompt/ specific_fns/ specific_fns/model_free/ tes...