Author: bugman Date: Mon Oct 6 14:43:37 2008 New Revision: 7529 URL: http://svn.gna.org/viewcvs/relax?rev=7529&view=rev Log: Merged revisions 7315-7424,7427-7430,7435,7440,7442,7495-7497,7499-7527 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ 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. ................ 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. ................ r7317 | bugman | 2008-09-25 20:49:49 +0200 (Thu, 25 Sep 2008) | 3 lines Improved the warning message. ................ 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. ................ r7319 | bugman | 2008-09-25 20:55:45 +0200 (Thu, 25 Sep 2008) | 3 lines Added more comments related to the previous commit. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ r7326 | bugman | 2008-09-26 12:02:05 +0200 (Fri, 26 Sep 2008) | 3 lines Fixed the model-free duplicate_data() unit tests. ................ 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. ................ r7328 | bugman | 2008-09-26 12:08:56 +0200 (Fri, 26 Sep 2008) | 3 lines Added a few checks to test_duplicate_data3(). ................ 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. ................ 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. ................ 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. ................ r7332 | bugman | 2008-09-26 12:25:25 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the structure duplication in duplicate_data(). ................ 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. ................ r7334 | bugman | 2008-09-26 14:12:02 +0200 (Fri, 26 Sep 2008) | 3 lines Fixed the RelaxError printouts in duplicate_data(). ................ r7335 | bugman | 2008-09-26 14:14:30 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the structure checking in duplicate_data(). ................ 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(). ................ 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(). ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ r7345 | bugman | 2008-09-26 16:50:24 +0200 (Fri, 26 Sep 2008) | 3 lines Renamed an incorrectly named variable. ................ r7346 | bugman | 2008-09-26 17:04:53 +0200 (Fri, 26 Sep 2008) | 3 lines Updated the structure results file. ................ r7347 | bugman | 2008-09-26 17:15:09 +0200 (Fri, 26 Sep 2008) | 3 lines Wrote the structural object base class method from_xml(). ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ r7353 | bugman | 2008-09-26 17:43:27 +0200 (Fri, 26 Sep 2008) | 3 lines Switched to the internal structural object. ................ r7354 | bugman | 2008-09-26 17:48:06 +0200 (Fri, 26 Sep 2008) | 3 lines Added some missing imports. ................ 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. ................ 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. ................ r7357 | bugman | 2008-09-26 18:05:51 +0200 (Fri, 26 Sep 2008) | 3 lines Fixed the test_load_pdb() unit test. ................ r7358 | bugman | 2008-09-26 18:06:58 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the test_duplicate_data_fail1() unit test. ................ 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. ................ 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(). ................ 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. ................ r7362 | bugman | 2008-09-26 18:30:19 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the internal structure object load_pdb() method. ................ r7363 | bugman | 2008-09-26 18:31:15 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the Scientific structure object load_pdb() method. ................ r7364 | bugman | 2008-09-26 18:37:42 +0200 (Fri, 26 Sep 2008) | 3 lines Added some checks for the PDB files. ................ r7365 | bugman | 2008-09-26 18:45:47 +0200 (Fri, 26 Sep 2008) | 3 lines Fixed the test_load_results() system test. ................ 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. ................ r7367 | bugman | 2008-09-26 18:58:49 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the second structure loading attempt. ................ 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. ................ 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. ................ r7370 | bugman | 2008-09-26 21:25:47 +0200 (Fri, 26 Sep 2008) | 3 lines Added the pipe arg to find_index(). ................ 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. ................ r7372 | bugman | 2008-09-26 21:43:16 +0200 (Fri, 26 Sep 2008) | 3 lines Fix for the find_index() function. ................ 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(). ................ r7374 | bugman | 2008-09-26 21:47:53 +0200 (Fri, 26 Sep 2008) | 3 lines Fixed variable references in create_mc_data(). ................ 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. ................ r7376 | bugman | 2008-09-26 22:01:40 +0200 (Fri, 26 Sep 2008) | 3 lines Another fix for the find_index() function. ................ 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. ................ 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(). ................ 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. ................ r7380 | bugman | 2008-09-26 22:52:18 +0200 (Fri, 26 Sep 2008) | 3 lines Fixes for the sim_return_selected() method. ................ 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. ................ r7382 | bugman | 2008-09-26 23:10:19 +0200 (Fri, 26 Sep 2008) | 3 lines Decreased the verbosity a little more. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ r7389 | bugman | 2008-09-26 23:54:28 +0200 (Fri, 26 Sep 2008) | 3 lines Converted sim_return_chi2() to the new design. ................ r7390 | bugman | 2008-09-26 23:58:04 +0200 (Fri, 26 Sep 2008) | 3 lines Converted set_error() to the new design. ................ r7391 | bugman | 2008-09-27 00:04:44 +0200 (Sat, 27 Sep 2008) | 3 lines Print out clean up in load_pdb(). ................ r7392 | bugman | 2008-09-27 00:48:10 +0200 (Sat, 27 Sep 2008) | 3 lines Updated the results file. ................ 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. ................ r7394 | bugman | 2008-09-27 01:02:10 +0200 (Sat, 27 Sep 2008) | 3 lines Removed the RelaxNoPDBFileWarning warnings. ................ 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. ................ r7396 | bugman | 2008-09-27 01:08:56 +0200 (Sat, 27 Sep 2008) | 3 lines Improvements to the from_xml() method. ................ 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. ................ r7398 | bugman | 2008-09-27 01:31:51 +0200 (Sat, 27 Sep 2008) | 3 lines Updates to the test_load_results() system test. ................ 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. ................ 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. ................ r7401 | bugman | 2008-09-27 14:13:12 +0200 (Sat, 27 Sep 2008) | 3 lines Modified from_xml() to handle multiple loaded structures. ................ 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. ................ 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. ................ 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. ................ r7405 | bugman | 2008-09-27 16:29:54 +0200 (Sat, 27 Sep 2008) | 3 lines Added the missing struct_index to load_pdb(). ................ r7406 | bugman | 2008-09-27 16:32:34 +0200 (Sat, 27 Sep 2008) | 3 lines Fixed some references to os.path. ................ r7407 | bugman | 2008-09-27 16:34:34 +0200 (Sat, 27 Sep 2008) | 3 lines Fix for the test_load_pdb() unit test. ................ 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. ................ 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. ................ r7410 | bugman | 2008-09-27 16:41:44 +0200 (Sat, 27 Sep 2008) | 3 lines Try that fix again! ................ r7411 | bugman | 2008-09-27 16:43:23 +0200 (Sat, 27 Sep 2008) | 3 lines Fix for the test_load_pdb() unit test. ................ r7412 | bugman | 2008-09-27 16:45:22 +0200 (Sat, 27 Sep 2008) | 3 lines Fixed the call to load_pdb(). ................ 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. ................ 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(). ................ r7415 | bugman | 2008-09-27 18:55:16 +0200 (Sat, 27 Sep 2008) | 3 lines Updated the from_xml() method to catch RelaxErrors. ................ r7416 | bugman | 2008-09-27 18:56:01 +0200 (Sat, 27 Sep 2008) | 3 lines Results file update. ................ r7417 | bugman | 2008-09-27 19:28:07 +0200 (Sat, 27 Sep 2008) | 3 lines Disabled the path check when reloading a structure. ................ 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. ................ r7419 | bugman | 2008-09-27 19:54:23 +0200 (Sat, 27 Sep 2008) | 3 lines Fixed all the structure loops. ................ 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. ................ 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. ................ r7422 | bugman | 2008-09-27 20:06:24 +0200 (Sat, 27 Sep 2008) | 3 lines Removed an unused import. ................ r7423 | bugman | 2008-09-27 20:07:40 +0200 (Sat, 27 Sep 2008) | 3 lines Renamed all __add_struct() methods to add_struct(). ................ 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. ................ 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 . ..... 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. ..... ................ 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 . ..... r3533 | bugman | 2007-11-17 12:25:43 +0100 (Sat, 17 Nov 2007) | 3 lines Updated the CHANGES file for relax 1.2.12. ..... ................ 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 . ..... 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. ..... [... 827 lines stripped ...]