svn+ssh://bugman@.../svn/relax/1.3
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r7315 | bugman | 2008-09-25 20:33:51 +0200 (Thu, 25 Sep 2008) | 6 lines
Fix for the extraction of unit XH bond vectors.
There was a problem if the loaded sequence had residue names in mixed case when extracting atoms
from a PDB file which has all in upper case.
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r7316 | bugman | 2008-09-25 20:47:56 +0200 (Thu, 25 Sep 2008) | 3 lines
Added a warning if the atom cannot be found in the structure.
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r7317 | bugman | 2008-09-25 20:49:49 +0200 (Thu, 25 Sep 2008) | 3 lines
Improved the warning message.
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r7318 | bugman | 2008-09-25 20:54:23 +0200 (Thu, 25 Sep 2008) | 6 lines
Removed the residue name from the call to generate_spin_id().
This allows point mutations in the loaded structure so that the structure doesn't exactly have to
be that for which the data was collected.
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r7319 | bugman | 2008-09-25 20:55:45 +0200 (Thu, 25 Sep 2008) | 3 lines
Added more comments related to the previous commit.
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r7320 | bugman | 2008-09-25 22:17:12 +0200 (Thu, 25 Sep 2008) | 3 lines
Prevented the sequence data to be printed out during model selection.
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r7321 | bugman | 2008-09-25 22:27:38 +0200 (Thu, 25 Sep 2008) | 3 lines
Blacklisted a few more data pipe objects in the model-free duplicate_data() method.
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r7322 | bugman | 2008-09-26 11:30:48 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote a unit test for the model-free duplicate_data() method.
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r7323 | bugman | 2008-09-26 11:44:08 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote another unit test for testing the model-free duplicate_data() method.
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r7324 | bugman | 2008-09-26 11:59:07 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the model-free duplicate_data() method for when the data pipe is empty.
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r7325 | bugman | 2008-09-26 12:01:11 +0200 (Fri, 26 Sep 2008) | 3 lines
Added a test for the model_index arg in the duplicate_data() method.
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r7326 | bugman | 2008-09-26 12:02:05 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed the model-free duplicate_data() unit tests.
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r7327 | bugman | 2008-09-26 12:04:52 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote another unit test for the model-free duplicate_data() method.
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r7328 | bugman | 2008-09-26 12:08:56 +0200 (Fri, 26 Sep 2008) | 3 lines
Added a few checks to test_duplicate_data3().
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r7329 | bugman | 2008-09-26 12:12:47 +0200 (Fri, 26 Sep 2008) | 5 lines
Added code to duplicate the structural object if it doesn't exist in the new pipe.
This has been added to the model-free duplicate_data() method.
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r7330 | bugman | 2008-09-26 12:20:05 +0200 (Fri, 26 Sep 2008) | 5 lines
Wrote a unit test for catching the failure of the model-free duplicate_data() method.
This happens when the structures are different.
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r7331 | bugman | 2008-09-26 12:25:04 +0200 (Fri, 26 Sep 2008) | 5 lines
Fix for the test_duplicate_data_fail1() unit test.
The attribute modified didn't exist, so the test was failing.
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r7332 | bugman | 2008-09-26 12:25:25 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the structure duplication in duplicate_data().
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r7333 | bugman | 2008-09-26 14:10:30 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote a unit test for the model-free duplicate_data() method for single mf models.
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r7334 | bugman | 2008-09-26 14:12:02 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed the RelaxError printouts in duplicate_data().
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r7335 | bugman | 2008-09-26 14:14:30 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the structure checking in duplicate_data().
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r7336 | bugman | 2008-09-26 14:36:12 +0200 (Fri, 26 Sep 2008) | 3 lines
Skipped the structural object base class methods as well now in duplicate_data().
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r7337 | bugman | 2008-09-26 14:38:50 +0200 (Fri, 26 Sep 2008) | 3 lines
Another fix for the structural object comparison in duplicate_data().
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r7338 | bugman | 2008-09-26 15:31:50 +0200 (Fri, 26 Sep 2008) | 5 lines
Added a script to generate a results file containing a single PDB structure.
The results file has been added too.
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r7339 | bugman | 2008-09-26 15:47:09 +0200 (Fri, 26 Sep 2008) | 3 lines
Added a system test to check the loading of a PDB file using the information in a results file.
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r7340 | bugman | 2008-09-26 15:54:57 +0200 (Fri, 26 Sep 2008) | 3 lines
Added some checks to the test_load_results() system test.
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r7341 | bugman | 2008-09-26 15:59:34 +0200 (Fri, 26 Sep 2008) | 3 lines
Shifted the pipe container xml_create_str_element() method to the to_xml() structural object method.
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r7342 | bugman | 2008-09-26 16:16:13 +0200 (Fri, 26 Sep 2008) | 3 lines
The basic structural object data is now converted to XML in the results file.
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r7343 | bugman | 2008-09-26 16:19:21 +0200 (Fri, 26 Sep 2008) | 5 lines
Shifted the structural data to the end of the XML results file.
This is in preparation for dumping all the structural info into the file.
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r7344 | bugman | 2008-09-26 16:49:16 +0200 (Fri, 26 Sep 2008) | 5 lines
Added the code to from_xml() to load the structural data.
The from_xml() structural object method needs to be implemented.
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r7345 | bugman | 2008-09-26 16:50:24 +0200 (Fri, 26 Sep 2008) | 3 lines
Renamed an incorrectly named variable.
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r7346 | bugman | 2008-09-26 17:04:53 +0200 (Fri, 26 Sep 2008) | 3 lines
Updated the structure results file.
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r7347 | bugman | 2008-09-26 17:15:09 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote the structural object base class method from_xml().
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r7348 | bugman | 2008-09-26 17:20:21 +0200 (Fri, 26 Sep 2008) | 3 lines
Changed the path to the PDB file to not be absolute.
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r7349 | bugman | 2008-09-26 17:21:05 +0200 (Fri, 26 Sep 2008) | 5 lines
Modified the test_load_results() system test to check both the file name and path.
These are not yet implemented in relax.
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r7350 | bugman | 2008-09-26 17:35:58 +0200 (Fri, 26 Sep 2008) | 5 lines
Modified the structural object code to store the file name and path.
This will cause some breakages do to the variable name changes.
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r7351 | bugman | 2008-09-26 17:42:27 +0200 (Fri, 26 Sep 2008) | 5 lines
Fixed the Scientific structural object __init__().
The structural data is no longer initialised (again) and the base class __init__() method is called.
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r7352 | bugman | 2008-09-26 17:43:02 +0200 (Fri, 26 Sep 2008) | 3 lines
Updated the test_load_results() system test for the new file and path variables.
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r7353 | bugman | 2008-09-26 17:43:27 +0200 (Fri, 26 Sep 2008) | 3 lines
Switched to the internal structural object.
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r7354 | bugman | 2008-09-26 17:48:06 +0200 (Fri, 26 Sep 2008) | 3 lines
Added some missing imports.
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r7355 | bugman | 2008-09-26 18:03:25 +0200 (Fri, 26 Sep 2008) | 3 lines
Modified these unit tests to check the new file and path structures.
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r7356 | bugman | 2008-09-26 18:04:05 +0200 (Fri, 26 Sep 2008) | 3 lines
Shifted the setting of the file and path to the specific structural object load_pdb() methods.
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r7357 | bugman | 2008-09-26 18:05:51 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed the test_load_pdb() unit test.
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r7358 | bugman | 2008-09-26 18:06:58 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the test_duplicate_data_fail1() unit test.
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r7359 | bugman | 2008-09-26 18:13:12 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixes for the from_xml() method for the structural object.
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r7360 | bugman | 2008-09-26 18:17:43 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed the loading of the PDB file from from_xml().
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r7361 | bugman | 2008-09-26 18:27:59 +0200 (Fri, 26 Sep 2008) | 5 lines
Updated the from_xml() to check the path and current directory for the structure.
A warning is raised if the file cannot be found.
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r7362 | bugman | 2008-09-26 18:30:19 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the internal structure object load_pdb() method.
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r7363 | bugman | 2008-09-26 18:31:15 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the Scientific structure object load_pdb() method.
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r7364 | bugman | 2008-09-26 18:37:42 +0200 (Fri, 26 Sep 2008) | 3 lines
Added some checks for the PDB files.
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r7365 | bugman | 2008-09-26 18:45:47 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed the test_load_results() system test.
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r7366 | bugman | 2008-09-26 18:51:31 +0200 (Fri, 26 Sep 2008) | 5 lines
Significantly expanded the test_load_results() system test.
All atomic data is now tested.
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r7367 | bugman | 2008-09-26 18:58:49 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the second structure loading attempt.
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r7368 | bugman | 2008-09-26 20:46:46 +0200 (Fri, 26 Sep 2008) | 6 lines
Bug fix for the loading of model-free results files from relax 1.2.
All minimisation statistics were being reset. The generic_fns.value.set() function now has the
reset flag to control this.
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r7369 | bugman | 2008-09-26 21:19:53 +0200 (Fri, 26 Sep 2008) | 3 lines
Wrote the new function find_index() for finding the global or local indices from a spin ID.
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r7370 | bugman | 2008-09-26 21:25:47 +0200 (Fri, 26 Sep 2008) | 3 lines
Added the pipe arg to find_index().
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r7371 | bugman | 2008-09-26 21:28:08 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted the create_mc_data() method to the new design.
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r7372 | bugman | 2008-09-26 21:43:16 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the find_index() function.
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r7373 | bugman | 2008-09-26 21:46:19 +0200 (Fri, 26 Sep 2008) | 3 lines
The min_options list is now passed into minimise_data_setup().
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r7374 | bugman | 2008-09-26 21:47:53 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixed variable references in create_mc_data().
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r7375 | bugman | 2008-09-26 21:52:30 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted the sim_pack_data() method to the new design.
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r7376 | bugman | 2008-09-26 22:01:40 +0200 (Fri, 26 Sep 2008) | 3 lines
Another fix for the find_index() function.
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r7377 | bugman | 2008-09-26 22:31:27 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted the sim_init_values() method to the new design.
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r7378 | bugman | 2008-09-26 22:33:02 +0200 (Fri, 26 Sep 2008) | 3 lines
Shifted 'xh_vect' into the generic data names in data_names().
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r7379 | bugman | 2008-09-26 22:43:10 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted the sim_return_selected() method to the new design.
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r7380 | bugman | 2008-09-26 22:52:18 +0200 (Fri, 26 Sep 2008) | 3 lines
Fixes for the sim_return_selected() method.
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r7381 | bugman | 2008-09-26 23:08:01 +0200 (Fri, 26 Sep 2008) | 3 lines
Decreased the verbosity generating the sequence when reading a 1.2 results file.
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r7382 | bugman | 2008-09-26 23:10:19 +0200 (Fri, 26 Sep 2008) | 3 lines
Decreased the verbosity a little more.
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r7383 | bugman | 2008-09-26 23:18:18 +0200 (Fri, 26 Sep 2008) | 5 lines
Fixes for the Scientific structural object load_pdb() method.
The finding of previously loaded PDBs has been fixed.
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r7384 | bugman | 2008-09-26 23:31:40 +0200 (Fri, 26 Sep 2008) | 3 lines
Changed a cdp.sim_state flag from an int to a bool.
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r7385 | bugman | 2008-09-26 23:32:11 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix an incorrect data pipe reference in the minimise() function.
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r7386 | bugman | 2008-09-26 23:44:40 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the sim_return_selected() method. The wrong argument was assumed.
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r7387 | bugman | 2008-09-26 23:50:24 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted the sim_return_param() method to the new design.
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r7388 | bugman | 2008-09-26 23:52:16 +0200 (Fri, 26 Sep 2008) | 3 lines
Fix for the sim_return_param() method, the model_type variable was missing.
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r7389 | bugman | 2008-09-26 23:54:28 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted sim_return_chi2() to the new design.
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r7390 | bugman | 2008-09-26 23:58:04 +0200 (Fri, 26 Sep 2008) | 3 lines
Converted set_error() to the new design.
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r7391 | bugman | 2008-09-27 00:04:44 +0200 (Sat, 27 Sep 2008) | 3 lines
Print out clean up in load_pdb().
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r7392 | bugman | 2008-09-27 00:48:10 +0200 (Sat, 27 Sep 2008) | 3 lines
Updated the results file.
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r7393 | bugman | 2008-09-27 00:48:35 +0200 (Sat, 27 Sep 2008) | 3 lines
Added a few more checks to the test_load_results() system test.
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r7394 | bugman | 2008-09-27 01:02:10 +0200 (Sat, 27 Sep 2008) | 3 lines
Removed the RelaxNoPDBFileWarning warnings.
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r7395 | bugman | 2008-09-27 01:08:40 +0200 (Sat, 27 Sep 2008) | 3 lines
The load_pdb() method now returns True if the file was loaded or False otherwise.
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r7396 | bugman | 2008-09-27 01:08:56 +0200 (Sat, 27 Sep 2008) | 3 lines
Improvements to the from_xml() method.
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r7397 | bugman | 2008-09-27 01:11:25 +0200 (Sat, 27 Sep 2008) | 3 lines
Moved some files around to let a system test pass.
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r7398 | bugman | 2008-09-27 01:31:51 +0200 (Sat, 27 Sep 2008) | 3 lines
Updates to the test_load_results() system test.
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r7399 | bugman | 2008-09-27 01:45:19 +0200 (Sat, 27 Sep 2008) | 3 lines
Propagation of the results file directory all the way through to the structure reading code.
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r7400 | bugman | 2008-09-27 14:09:32 +0200 (Sat, 27 Sep 2008) | 5 lines
Modified the structural API base class __init__() method.
This is to prepare for the tidying up of the structural object to better handle multiple structures.
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r7401 | bugman | 2008-09-27 14:13:12 +0200 (Sat, 27 Sep 2008) | 3 lines
Modified from_xml() to handle multiple loaded structures.
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r7402 | bugman | 2008-09-27 15:04:05 +0200 (Sat, 27 Sep 2008) | 5 lines
The load_pdb() structural method now accepts the struct_index arg.
This is passed in by from_xml() to place the structure in the correct position.
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r7403 | bugman | 2008-09-27 15:05:09 +0200 (Sat, 27 Sep 2008) | 3 lines
Added the NMR model number to the collection of structural attributes stored as lists.
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r7404 | bugman | 2008-09-27 16:20:16 +0200 (Sat, 27 Sep 2008) | 5 lines
Redesigned the internal and Scientific load_pdb() methods.
An auxiliary method __add_struct() was created for looking after the structure additions.
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r7405 | bugman | 2008-09-27 16:29:54 +0200 (Sat, 27 Sep 2008) | 3 lines
Added the missing struct_index to load_pdb().
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r7406 | bugman | 2008-09-27 16:32:34 +0200 (Sat, 27 Sep 2008) | 3 lines
Fixed some references to os.path.
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r7407 | bugman | 2008-09-27 16:34:34 +0200 (Sat, 27 Sep 2008) | 3 lines
Fix for the test_load_pdb() unit test.
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r7408 | bugman | 2008-09-27 16:39:36 +0200 (Sat, 27 Sep 2008) | 3 lines
Fix for the atom_loop() method needed because of the load_pdb() changes.
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r7409 | bugman | 2008-09-27 16:41:08 +0200 (Sat, 27 Sep 2008) | 3 lines
Fix for the test_atom_loop_spin_selection2() unit test.
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r7410 | bugman | 2008-09-27 16:41:44 +0200 (Sat, 27 Sep 2008) | 3 lines
Try that fix again!
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r7411 | bugman | 2008-09-27 16:43:23 +0200 (Sat, 27 Sep 2008) | 3 lines
Fix for the test_load_pdb() unit test.
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r7412 | bugman | 2008-09-27 16:45:22 +0200 (Sat, 27 Sep 2008) | 3 lines
Fixed the call to load_pdb().
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r7413 | bugman | 2008-09-27 16:46:43 +0200 (Sat, 27 Sep 2008) | 3 lines
Fix for load_pdb(). The structure needs to be loaded before displaying it.
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r7414 | bugman | 2008-09-27 18:12:10 +0200 (Sat, 27 Sep 2008) | 3 lines
Bug fix. The structure for other data pipes was not been added in load_pdb().
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r7415 | bugman | 2008-09-27 18:55:16 +0200 (Sat, 27 Sep 2008) | 3 lines
Updated the from_xml() method to catch RelaxErrors.
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r7416 | bugman | 2008-09-27 18:56:01 +0200 (Sat, 27 Sep 2008) | 3 lines
Results file update.
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r7417 | bugman | 2008-09-27 19:28:07 +0200 (Sat, 27 Sep 2008) | 3 lines
Disabled the path check when reloading a structure.
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r7418 | bugman | 2008-09-27 19:53:15 +0200 (Sat, 27 Sep 2008) | 5 lines
Fix for the __add_struct() method.
The structure was not being added if struct_index was supplied.
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r7419 | bugman | 2008-09-27 19:54:23 +0200 (Sat, 27 Sep 2008) | 3 lines
Fixed all the structure loops.
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r7420 | bugman | 2008-09-27 20:04:20 +0200 (Sat, 27 Sep 2008) | 3 lines
Modified __add_struct() to use Structure_container() if the structural object is not provided.
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r7421 | bugman | 2008-09-27 20:05:03 +0200 (Sat, 27 Sep 2008) | 3 lines
Changed create_diff_tensor_pdb() to call the __add_struct() structural object method.
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r7422 | bugman | 2008-09-27 20:06:24 +0200 (Sat, 27 Sep 2008) | 3 lines
Removed an unused import.
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r7423 | bugman | 2008-09-27 20:07:40 +0200 (Sat, 27 Sep 2008) | 3 lines
Renamed all __add_struct() methods to add_struct().
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r7424 | bugman | 2008-09-27 20:09:41 +0200 (Sat, 27 Sep 2008) | 3 lines
Added the add_struct() stub method to the structural API base class.
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r7427 | bugman | 2008-09-28 22:34:57 +0200 (Sun, 28 Sep 2008) | 14 lines
Ported r7425 from the 1.3.1 tag.
The command used was:
svn merge -r7425:7426 svn+ssh://bugman@.../svn/relax/tags/1.3.1 .
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r7426 | bugman | 2008-09-28 22:32:16 +0200 (Sun, 28 Sep 2008) | 3 lines
Changed paths:
M /tags/1.3.1/docs/CHANGES
Updated the CHANGES for relax version 1.3.1.
.....
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r7428 | bugman | 2008-09-28 22:37:50 +0200 (Sun, 28 Sep 2008) | 12 lines
Ported r3532 from the 1.2.12 tag.
The command used was:
svn merge -r3532:3533 svn+ssh://bugman@.../svn/relax/tags/1.2.12 .
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r3533 | bugman | 2007-11-17 12:25:43 +0100 (Sat, 17 Nov 2007) | 3 lines
Updated the CHANGES file for relax 1.2.12.
.....
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r7429 | bugman | 2008-09-28 22:39:43 +0200 (Sun, 28 Sep 2008) | 12 lines
Ported r5815 from the 1.2.13 tag.
The command used was:
svn merge -r5815:5816 svn+ssh://bugman@.../svn/relax/tags/1.2.13 .
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r5816 | bugman | 2008-04-19 13:04:23 +0200 (Sat, 19 Apr 2008) | 3 lines
Updated the CHANGES file for relax version 1.2.13.
.....
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r7430 | bugman | 2008-09-29 00:04:43 +0200 (Mon, 29 Sep 2008) | 12 lines
Ported r7122 from the 1.2.14 tag.
The command used was:
svn merge -r7122:7123 svn+ssh://bugman@.../svn/relax/tags/1.2.14 .
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r7123 | bugman | 2008-08-09 15:57:33 +0200 (Sat, 09 Aug 2008) | 3 lines
Updated the CHANGES file for the new version.
.....
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r7435 | bugman | 2008-09-29 01:01:59 +0200 (Mon, 29 Sep 2008) | 3 lines
Improvements to the release checklist.
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r7440 | bugman | 2008-09-29 23:01:06 +0200 (Mon, 29 Sep 2008) | 3 lines
Bug fix for the creation of the cone geometric object for the N-state model analysis.
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r7442 | bugman | 2008-09-29 23:13:08 +0200 (Mon, 29 Sep 2008) | 14 lines
Merged r7434 from the 1.3.1 tag, the updates to the distribution file creation.
The command used was:
svn merge -r7433:7434 svn+ssh://bugman@.../svn/relax/tags/1.3.1 .
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r7434 | bugman | 2008-09-29 00:41:59 +0200 (Mon, 29 Sep 2008) | 5 lines
Redesigned the packaging of the distribution files.
The GPG key name is now passed into scons and the user manual is no longer compiled.
.....
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r7495 | bugman | 2008-10-02 15:28:47 +0200 (Thu, 02 Oct 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-7441" from
svn+ssh://bugman@.../svn/relax/branches/pipe_refs
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r7496 | bugman | 2008-10-02 15:30:41 +0200 (Thu, 02 Oct 2008) | 222 lines
Merged revisions 7443-7492 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/pipe_refs
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r7443 | bugman | 2008-09-29 23:16:31 +0200 (Mon, 29 Sep 2008) | 3 lines
Renamed the current() function to cdp_name() and created cdp() for returning the current data pipe.
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r7444 | bugman | 2008-09-29 23:20:20 +0200 (Mon, 29 Sep 2008) | 3 lines
Renamed cdp() to get_pipe() and allowed it to return any desired data pipe.
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r7445 | bugman | 2008-09-29 23:27:47 +0200 (Mon, 29 Sep 2008) | 3 lines
Removed all references to 'ds.current_pipe' by using the generic_fns.pipes API.
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r7446 | bugman | 2008-09-29 23:56:26 +0200 (Mon, 29 Sep 2008) | 3 lines
Replaced all refs to 'cdp = ds[ds.current_pipe]' with 'cdp = pipes.get_pipe()'.
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r7447 | bugman | 2008-09-30 00:08:01 +0200 (Tue, 30 Sep 2008) | 3 lines
Bug fix for the renamed current() to get_pipe() function.
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r7448 | bugman | 2008-09-30 00:08:40 +0200 (Tue, 30 Sep 2008) | 3 lines
Bug fix for the renaming of current() to cdp_name().
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r7449 | bugman | 2008-09-30 00:09:23 +0200 (Tue, 30 Sep 2008) | 3 lines
Created the new function get_type() for returning the type of the data pipe.
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r7450 | bugman | 2008-09-30 00:44:27 +0200 (Tue, 30 Sep 2008) | 3 lines
Eliminated all mentions of 'ds[ds.current_pipe]' by using the generic_fns.pipes API.
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r7451 | bugman | 2008-09-30 01:14:36 +0200 (Tue, 30 Sep 2008) | 3 lines
Eliminated all access to 'ds.current_pipe' by using the API of generic_fns.pipes.
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r7452 | bugman | 2008-09-30 16:32:09 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed all references to ds[key] by using the API of generic_fns.pipes.
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r7453 | bugman | 2008-09-30 16:35:07 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed some unused imports of RelaxNoPipeError.
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r7454 | bugman | 2008-09-30 16:37:24 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed a pile of unused and significantly out of date functions.
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r7455 | bugman | 2008-09-30 16:44:59 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed unused RelaxNoPipeError imports and some old code.
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r7456 | bugman | 2008-09-30 17:02:13 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed all unused imports of the relax data store.
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r7457 | bugman | 2008-09-30 17:06:21 +0200 (Tue, 30 Sep 2008) | 6 lines
Removed the columnar formatted results writing code.
This is no longer necessary because of the universal XML results file. Found by searching for
usage of the relax data store.
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r7458 | bugman | 2008-09-30 17:16:15 +0200 (Tue, 30 Sep 2008) | 5 lines
Converted the relax_curve_diff.py sample script to the new design.
This was identified by the unnecessary import of the relax data storage object.
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r7459 | bugman | 2008-09-30 17:17:52 +0200 (Tue, 30 Sep 2008) | 3 lines
Documentation fix in the sample script.
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r7460 | bugman | 2008-09-30 17:36:29 +0200 (Tue, 30 Sep 2008) | 5 lines
Updated the latex_mf_table.py sample script to the new design.
The problems were identified with the import of the relax data storage object.
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r7461 | bugman | 2008-09-30 17:40:37 +0200 (Tue, 30 Sep 2008) | 3 lines
Created the has_pipe() function for the pipes API.
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r7462 | bugman | 2008-09-30 17:41:41 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed the dependence on the relax data store by using the pipes API.
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r7463 | bugman | 2008-09-30 17:53:55 +0200 (Tue, 30 Sep 2008) | 3 lines
Shifted the reset() functional code to generic_fns.
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r7464 | bugman | 2008-09-30 18:01:09 +0200 (Tue, 30 Sep 2008) | 3 lines
Converted the back_calc() function to the new relax design.
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r7465 | bugman | 2008-09-30 18:05:11 +0200 (Tue, 30 Sep 2008) | 3 lines
Created the pipes API function pipe_names() to get the list of all data pipes.
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r7466 | bugman | 2008-09-30 18:09:42 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed the dependence on the relax data store.
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r7467 | bugman | 2008-09-30 18:16:24 +0200 (Tue, 30 Sep 2008) | 7 lines
Bug fix for the __set_diff_tensor() method for reading the tensor from a relax 1.2 results file.
This was uncovered by searching for the relax data store. This store rather than the current data
pipe was being accessed. The additional large bug found is that the diffusion tensor was referred
to as 'diff' rather than 'diff_tensor'.
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r7468 | bugman | 2008-09-30 18:17:30 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed the results writing methods. This is now done by the universal XML results file code.
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r7469 | bugman | 2008-09-30 18:18:00 +0200 (Tue, 30 Sep 2008) | 3 lines
Removed the unused relax data store.
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r7470 | bugman | 2008-09-30 18:21:25 +0200 (Tue, 30 Sep 2008) | 3 lines
Alphabetical ordering of the methods.
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r7471 | bugman | 2008-10-01 13:39:36 +0200 (Wed, 01 Oct 2008) | 5 lines
Converted the create_vector_dist() function to the new design.
Again the problem was identified by looking at incorrect usage of the relax data store.
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r7472 | bugman | 2008-10-01 13:40:17 +0200 (Wed, 01 Oct 2008) | 3 lines
Removed a reference to 'run' in a comment.
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r7473 | bugman | 2008-10-01 13:40:36 +0200 (Wed, 01 Oct 2008) | 3 lines
Removed the unused import of the relax data store.
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r7474 | bugman | 2008-10-01 13:44:12 +0200 (Wed, 01 Oct 2008) | 3 lines
Created a new pipes API function, the pipe_loop().
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r7475 | bugman | 2008-10-01 13:46:39 +0200 (Wed, 01 Oct 2008) | 3 lines
The structure objects now use the pipe_loop() in their load_pdb() methods.
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r7476 | bugman | 2008-10-01 13:49:13 +0200 (Wed, 01 Oct 2008) | 3 lines
Updated the delete() method to the new design.
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r7477 | bugman | 2008-10-01 13:53:28 +0200 (Wed, 01 Oct 2008) | 3 lines
Added the switch flag to pipes.create() so that the new pipe doesn't have to be switched to.
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r7478 | bugman | 2008-10-01 14:05:12 +0200 (Wed, 01 Oct 2008) | 3 lines
Clean up of duplicate_data().
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r7479 | bugman | 2008-10-01 14:06:45 +0200 (Wed, 01 Oct 2008) | 5 lines
Converted the eliminate() method to the new design.
Again identified by bad usage of the relax data store.
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r7480 | bugman | 2008-10-01 14:07:54 +0200 (Wed, 01 Oct 2008) | 3 lines
Fix for model_setup(), again bad usage of the relax data store.
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r7481 | bugman | 2008-10-01 14:17:50 +0200 (Wed, 01 Oct 2008) | 3 lines
Converted the deselect() method to the new design.
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r7482 | bugman | 2008-10-01 14:18:08 +0200 (Wed, 01 Oct 2008) | 3 lines
Removed the unused relax data store import.
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r7483 | bugman | 2008-10-01 14:18:37 +0200 (Wed, 01 Oct 2008) | 3 lines
Switched the eliminate function to use the new model_loop().
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r7484 | bugman | 2008-10-01 14:20:48 +0200 (Wed, 01 Oct 2008) | 3 lines
Missing colon starting a loop.
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r7485 | bugman | 2008-10-01 14:26:20 +0200 (Wed, 01 Oct 2008) | 3 lines
Modified the pipe_loop() generator to return the name of the pipe, if asked for.
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r7486 | bugman | 2008-10-01 15:52:50 +0200 (Wed, 01 Oct 2008) | 3 lines
Fixed a circular import issue.
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r7487 | bugman | 2008-10-01 16:00:43 +0200 (Wed, 01 Oct 2008) | 3 lines
Fixes for the calls to the pipes functions.
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r7488 | bugman | 2008-10-01 18:36:54 +0200 (Wed, 01 Oct 2008) | 3 lines
Bug fix for the add_struct() method. The input structure container was being overwritten.
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r7489 | bugman | 2008-10-02 13:30:04 +0200 (Thu, 02 Oct 2008) | 3 lines
Variable name clash bug fix in load_pdb().
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r7490 | bugman | 2008-10-02 13:37:14 +0200 (Thu, 02 Oct 2008) | 3 lines
Put back the condition to skip the current data pipe in searching for pre-loaded data in load_pdb().
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r7491 | bugman | 2008-10-02 13:42:27 +0200 (Thu, 02 Oct 2008) | 3 lines
Bug fix introduced in r7490, '==' should have been used rather than '='.
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r7492 | bugman | 2008-10-02 13:45:17 +0200 (Thu, 02 Oct 2008) | 5 lines
Bug fix for the eliminate() function.
'i' is now called 'model_info' because of the switch to model_loop().
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r7497 | bugman | 2008-10-02 15:30:59 +0200 (Thu, 02 Oct 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/pipe_refs
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r7499 | bugman | 2008-10-05 10:49:03 +0200 (Sun, 05 Oct 2008) | 3 lines
Created a system test for model elimination of a model-free model.
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r7500 | bugman | 2008-10-05 11:10:28 +0200 (Sun, 05 Oct 2008) | 5 lines
Fix for the system test of the model elimination module.
The setUp() method has been added and it creates a data pipe to store the data.
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r7501 | bugman | 2008-10-05 11:12:34 +0200 (Sun, 05 Oct 2008) | 6 lines
Fix for bug #12406 (https://gna.org/bugs/?12406).
The issue was that the force flag should have had a default value of True so that value.set() can
overwrite existing parameters.
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r7502 | bugman | 2008-10-05 11:31:08 +0200 (Sun, 05 Oct 2008) | 3 lines
Missing import fix for the model elimination system test.
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r7503 | bugman | 2008-10-05 11:32:45 +0200 (Sun, 05 Oct 2008) | 6 lines
Partial fix for bug #12407 (https://gna.org/bugs/index.php?12407).
The model-free assemble_param_names() method was not returning the parameter names. This could
affect much more than model elimination!
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r7504 | bugman | 2008-10-05 11:42:12 +0200 (Sun, 05 Oct 2008) | 6 lines
Completed the fix for bug #12407 (https://gna.org/bugs/index.php?12407).
This latest problem was caused by the use of the wrong Boolean operator in the model-free
eliminate() method. The method has also been converted to return the Booleans True or False.
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r7505 | bugman | 2008-10-05 12:03:59 +0200 (Sun, 05 Oct 2008) | 3 lines
Created a system test for model-free model elimination when local tm > 50 ns.
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r7506 | bugman | 2008-10-05 12:17:27 +0200 (Sun, 05 Oct 2008) | 7 lines
Conversion to bools in determine_model_type() and a fix for bug #12408 (https://gna.org/bugs/?12408).
All internal flags in the method have been converted to Booleans. This commit also contains a bit
of a fix for bug #12408. The bug was a false alarm and now determine_model_type() raises a more
relevant RelaxError.
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r7507 | bugman | 2008-10-05 12:19:51 +0200 (Sun, 05 Oct 2008) | 5 lines
Fix for the test_tm_51ns() system test.
The model 'tm4' is set rather than 'm4'.
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r7508 | bugman | 2008-10-05 12:40:53 +0200 (Sun, 05 Oct 2008) | 7 lines
Partial fix for bug #12407 (https://gna.org/bugs/index.php?12407).
This catches the "TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'" error. If
the local or global tm is missing for some reason, the eliminate function returns False indicating
that the model has not been eliminated.
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r7509 | bugman | 2008-10-05 12:55:16 +0200 (Sun, 05 Oct 2008) | 3 lines
Made the structure reading from a results file system test specific to the internal structure object.
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r7510 | bugman | 2008-10-05 13:04:19 +0200 (Sun, 05 Oct 2008) | 7 lines
Created the new test_load_scientific_results() system test.
This test checks the loading of a PDB file using the Scientific python PDB internal object when
reading a results file. The test_load_results() system test has been renamed to
test_load_internal_results().
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r7511 | bugman | 2008-10-05 13:30:09 +0200 (Sun, 05 Oct 2008) | 5 lines
Partial fix for bug #12409 (https://gna.org/bugs/index.php?12409).
Updated the add_struct() method to match that of the internal structural object.
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r7512 | bugman | 2008-10-05 13:45:13 +0200 (Sun, 05 Oct 2008) | 3 lines
Fix for the checks in the test_load_scientific_results() system test.
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r7513 | bugman | 2008-10-05 14:37:31 +0200 (Sun, 05 Oct 2008) | 7 lines
Added a fix for the aliasing of a PDB file for when no structural data exists in the data pipe.
This is related to bug #12409 (https://gna.org/bugs/index.php?12409), so that rather than an
unrelated RelaxError, the structure is not aliased is the structural data could not be loaded in
another data pipe.
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r7514 | bugman | 2008-10-05 14:54:33 +0200 (Sun, 05 Oct 2008) | 6 lines
Fix for bug #12409 (https://gna.org/bugs/index.php?12409).
This bug is the failure of the final stage of the 'full_analysis.py' script. If no models exist in
the PDB file, a model number is no longer passed into add_struct().
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r7515 | bugman | 2008-10-05 14:58:48 +0200 (Sun, 05 Oct 2008) | 5 lines
Bug fix for model elimination in 'full_analysis.py'.
Added a check to the 'full_analysis.py' script to avoid model elimination of the global model.
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r7516 | bugman | 2008-10-05 16:51:58 +0200 (Sun, 05 Oct 2008) | 5 lines
Extended the system test of a minimal model-free analysis using the OMP relaxation data.
This now includes the basics of the 'final' stage of the 'full_analysis.py' script.
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r7517 | bugman | 2008-10-05 17:05:38 +0200 (Sun, 05 Oct 2008) | 5 lines
Bug fix for the fix() function.
The fix flag for the spins was not being set when the 'all' element was sent into the function.
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r7518 | bugman | 2008-10-05 17:36:49 +0200 (Sun, 05 Oct 2008) | 6 lines
Bug fix for the duplication of sequence data during model selection.
The sequence.copy() function was not preserving the selection flag so that new option is sent into
the copy() and generate() functions, originating from the duplicate_data() model-free method.
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r7519 | bugman | 2008-10-05 19:51:23 +0200 (Sun, 05 Oct 2008) | 7 lines
Fix for bug #12411 (https://gna.org/bugs/?12411).
The problem was with the duplicate_data() skipping the duplication of the spin specific data if the
new data pipe (which should start off as empty) contained no sequence data. Hence the data was not
being copied.
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r7520 | bugman | 2008-10-05 19:56:49 +0200 (Sun, 05 Oct 2008) | 3 lines
Model elimination is no longer performed on the global model in the omp_model_free system test.
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r7521 | bugman | 2008-10-05 20:35:18 +0200 (Sun, 05 Oct 2008) | 3 lines
Renamed a number of the data pipes to better reflect what they are.
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r7522 | bugman | 2008-10-05 20:38:31 +0200 (Sun, 05 Oct 2008) | 3 lines
Fix for the final model selection, the data pipes 'local_tm' and 'sphere' should be used.
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r7523 | bugman | 2008-10-05 20:51:19 +0200 (Sun, 05 Oct 2008) | 6 lines
Fix for bug #12412 (https://gna.org/bugs/index.php?12412).
Caught the situation of when the global chi-squared value is missing when performing global model
model selection. This now throws a RelaxError explaining the situation.
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r7524 | bugman | 2008-10-05 21:09:56 +0200 (Sun, 05 Oct 2008) | 3 lines
Restructured the introductory docstring and added the references for all techniques in the script.
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r7525 | bugman | 2008-10-05 21:24:06 +0200 (Sun, 05 Oct 2008) | 5 lines
Added a final 10 step optimisation of the 'sphere' global model.
This completes the system test.
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r7526 | bugman | 2008-10-06 00:02:26 +0200 (Mon, 06 Oct 2008) | 5 lines
Fixes for the print out of eliminated Monte Carlo simulations.
The previous print out was saying that the spin system is eliminated, which is incorrect.
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r7527 | bugman | 2008-10-06 11:17:19 +0200 (Mon, 06 Oct 2008) | 8 lines
Fix for a bug introduced at r7519.
The problem was being picked up by the unit tests. The duplicate_data() model-free method was
failing when sequence data was missing from the source data pipe. This was supposed to be caught
in the code before r7519 but the wrong data pipe was being checked and the code was removed at that
revision.
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