Author: bugman
Date: Sat Oct 11 17:34:23 2008
New Revision: 7594
URL: http://svn.gna.org/viewcvs/relax?rev=7594&view=rev
Log:
Merged revisions 7313-7593 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/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@xxxxxxxxxxx/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@xxxxxxxxxxx/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@xxxxxxxxxxx/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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[... 1195 lines stripped ...]
r7594 - in /branches/spectral_errors: ./ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ opendx/ prom...