relax SVN archive

Molecular dynamics by NMR data analysis

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SVN archive Commit Log

Commit	Date
[r7322] by bugman Wrote a unit test for the model-free duplicate_data() method.	2008-09-26 09:30:48	Tree
[r7321] by bugman Blacklisted a few more data pipe objects in the model-free duplicate_data() method.	2008-09-25 20:27:38	Tree
[r7320] by bugman Prevented the sequence data to be printed out during model selection.	2008-09-25 20:17:12	Tree
[r7319] by bugman Added more comments related to the previous commit.	2008-09-25 18:55:45	Tree
[r7318] by bugman 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.	2008-09-25 18:54:23	Tree
[r7317] by bugman Improved the warning message.	2008-09-25 18:49:49	Tree
[r7316] by bugman Added a warning if the atom cannot be found in the structure.	2008-09-25 18:47:56	Tree
[r7315] by bugman 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.	2008-09-25 18:33:51	Tree
[r7314] by bugman Merged revisions 7236-7302,7304-7305,7308-7310 via svnmerge from svn+ssh://bugman@.../svn/relax/1.3 ................ 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. ................ r7237 \| bugman \| 2008-09-24 14:49:48 +0200 (Wed, 24 Sep 2008) \| 3 lines Activated the model_loop() generator method. ................ r7238 \| bugman \| 2008-09-24 16:10:56 +0200 (Wed, 24 Sep 2008) \| 3 lines Changed model_loop() to return the spin container. ................ r7239 \| bugman \| 2008-09-24 16:18:13 +0200 (Wed, 24 Sep 2008) \| 3 lines Created the sim_return_chi2() base class method. ................ 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. ................ 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. ................ 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. ................ r7243 \| bugman \| 2008-09-24 16:33:09 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the Grace class methods into module functions. ................ 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. ................ 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. ................ r7246 \| bugman \| 2008-09-24 17:01:41 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the view() function to the new design. ................ r7247 \| bugman \| 2008-09-24 17:23:34 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the 4 write_() functions to the new design. ................ r7248 \| bugman \| 2008-09-24 17:36:02 +0200 (Wed, 24 Sep 2008) \| 3 lines The pipe argument is now optional for RelaxNoSimError. ................ r7249 \| bugman \| 2008-09-24 17:43:04 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the Grace write() function to the new design. ................ 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. ................ r7251 \| bugman \| 2008-09-24 17:56:02 +0200 (Wed, 24 Sep 2008) \| 3 lines A few small fixes for the write() function. ................ r7252 \| bugman \| 2008-09-24 18:00:27 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the grace.write() user function interface. ................ 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. ................ r7254 \| bugman \| 2008-09-24 18:03:32 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the call to get_data(). ................ 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(). ................ 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. ................ r7257 \| bugman \| 2008-09-24 18:33:45 +0200 (Wed, 24 Sep 2008) \| 3 lines Fatal indentation fix. ................ r7258 \| bugman \| 2008-09-24 18:43:16 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the determine_seq_type() function. ................ r7259 \| bugman \| 2008-09-24 18:46:03 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the count_molecules() and count_residues() functions. ................ r7260 \| bugman \| 2008-09-24 18:47:54 +0200 (Wed, 24 Sep 2008) \| 3 lines Merged the count_selected_spins() function into count_spins(). ................ r7261 \| bugman \| 2008-09-24 18:49:04 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed the call to count_selected_spins(). ................ r7262 \| bugman \| 2008-09-24 18:51:20 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the test_count_spins() unit test. ................ r7263 \| bugman \| 2008-09-24 18:52:16 +0200 (Wed, 24 Sep 2008) \| 3 lines Another fix for the test_count_spins() unit test. ................ 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. ................ r7265 \| bugman \| 2008-09-24 19:02:47 +0200 (Wed, 24 Sep 2008) \| 3 lines Propagation of the spin_id variable. ................ 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(). ................ r7267 \| bugman \| 2008-09-24 19:17:29 +0200 (Wed, 24 Sep 2008) \| 3 lines Updated the set_selected_sim() method. ................ r7268 \| bugman \| 2008-09-24 19:18:50 +0200 (Wed, 24 Sep 2008) \| 3 lines Shifted set_selected_sim() to the base class. ................ r7269 \| bugman \| 2008-09-24 19:20:07 +0200 (Wed, 24 Sep 2008) \| 3 lines Docstring and comment fixes for select_all_sims(). ................ r7270 \| bugman \| 2008-09-24 19:28:49 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the model-free model_loop() generator method. ................ r7271 \| bugman \| 2008-09-24 19:32:51 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed some dud arguments to the model_loop() generator. ................ 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. ................ r7273 \| bugman \| 2008-09-24 19:50:08 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed some unused imports of return_spin_from_index(). ................ r7274 \| bugman \| 2008-09-24 19:55:23 +0200 (Wed, 24 Sep 2008) \| 3 lines Fix for the model-free model_loop() generator function. ................ r7275 \| bugman \| 2008-09-24 19:56:41 +0200 (Wed, 24 Sep 2008) \| 3 lines Another fix for the model_loop() generator. ................ 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. ................ r7277 \| bugman \| 2008-09-24 20:18:15 +0200 (Wed, 24 Sep 2008) \| 3 lines Passed the missing 'data' data structure into write_header(). ................ r7278 \| bugman \| 2008-09-24 20:27:38 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the data_names() methods to the new design. ................ r7279 \| bugman \| 2008-09-24 20:36:59 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the call to generate_vector_dist(). ................ 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. ................ r7281 \| bugman \| 2008-09-24 20:55:08 +0200 (Wed, 24 Sep 2008) \| 3 lines The Structure_container no longer needs to be initialised. ................ 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 . ................ 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. ................ 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. ................ 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. ................ 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. ................ r7287 \| bugman \| 2008-09-24 21:57:31 +0200 (Wed, 24 Sep 2008) \| 3 lines Fix for the sim_return_param() method. ................ r7288 \| bugman \| 2008-09-24 21:59:11 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the arg order for set_error(). ................ r7289 \| bugman \| 2008-09-24 23:20:14 +0200 (Wed, 24 Sep 2008) \| 3 lines Created the test_Selection_contains_spin8() unit test. ................ 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! ................ 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 . ................ 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 . ................ 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. ................ r7294 \| bugman \| 2008-09-25 15:57:07 +0200 (Thu, 25 Sep 2008) \| 3 lines Activated the unit vector system test. ................ r7295 \| bugman \| 2008-09-25 16:39:11 +0200 (Thu, 25 Sep 2008) \| 3 lines Fixes for the unit vector system test. ................ 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. ................ 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. ................ r7298 \| bugman \| 2008-09-25 16:50:22 +0200 (Thu, 25 Sep 2008) \| 3 lines Allowed the spin number to be reset to None. ................ 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. ................ 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. ................ r7301 \| bugman \| 2008-09-25 17:01:30 +0200 (Thu, 25 Sep 2008) \| 3 lines Fixed the number arg unit test of spin.number(). ................ 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. ................ r7304 \| bugman \| 2008-09-25 18:04:14 +0200 (Thu, 25 Sep 2008) \| 3 lines Initialized merge tracking via "svnmerge" with revisions "1-6740" from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7305 \| bugman \| 2008-09-25 18:09:31 +0200 (Thu, 25 Sep 2008) \| 3 lines Removed merge tracking for "svnmerge" for svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7308 \| bugman \| 2008-09-25 18:19:56 +0200 (Thu, 25 Sep 2008) \| 3 lines Initialized merge tracking via "svnmerge" with revisions "1-6740" from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7309 \| bugman \| 2008-09-25 18:30:20 +0200 (Thu, 25 Sep 2008) \| 1124 lines Merged revisions 6837,6839,6841-6857,6859-6878,6880,6882-6938,6941-6945,6952,6957-6992,7021,7029,7076-7077,7080-7093,7106-7121,7130-7146,7148-7189,7191-7208,7226-7227,7230-7231,7307 via svnmerge from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ........ r6837 \| bugman \| 2008-07-08 16:23:35 +0200 (Tue, 08 Jul 2008) \| 3 lines Created the framework for a user function class for handling RDCs (by copying the relax_data code). ........ r6839 \| bugman \| 2008-07-08 20:30:14 +0200 (Tue, 08 Jul 2008) \| 3 lines Removed a test for the model setup in the set_non_spin_params() method. ........ r6841 \| bugman \| 2008-07-08 21:02:19 +0200 (Tue, 08 Jul 2008) \| 3 lines Fix for the return_data_name() method when no match occurs and the index flag is True. ........ r6842 \| bugman \| 2008-07-08 21:03:21 +0200 (Tue, 08 Jul 2008) \| 5 lines Added a number of new parameters to the return_data_name() method. This include the bond length, and heteronucleus and proton types. ........ r6843 \| bugman \| 2008-07-08 21:12:31 +0200 (Tue, 08 Jul 2008) \| 3 lines Fix for the return_data_name() method when no match occurs and the index flag is True. ........ r6844 \| bugman \| 2008-07-08 21:17:05 +0200 (Tue, 08 Jul 2008) \| 3 lines Removed some debugging code. ........ r6845 \| bugman \| 2008-07-08 21:24:29 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted the rdc.read() user function from the relax_data.read() code. ........ r6846 \| bugman \| 2008-07-08 21:25:41 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all instances of 'ri_label' to 'id'. ........ r6847 \| bugman \| 2008-07-08 21:26:26 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all instances of 'relax_data' to 'rdc'. ........ r6848 \| bugman \| 2008-07-08 21:36:00 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all of the rdc user functions from the relax_data code. ........ r6849 \| bugman \| 2008-07-08 21:37:46 +0200 (Tue, 08 Jul 2008) \| 3 lines Created a generic_fns rdc module by copying the relax_data module. ........ r6850 \| bugman \| 2008-07-08 21:54:07 +0200 (Tue, 08 Jul 2008) \| 3 lines Created 2 new error classes, RelaxNoRDCError and RelaxRDCError. ........ r6851 \| bugman \| 2008-07-08 22:03:09 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted the read() function from the relax_data code. ........ r6852 \| bugman \| 2008-07-08 22:20:28 +0200 (Tue, 08 Jul 2008) \| 3 lines Made the error column optional in the loading of RDCs. ........ r6853 \| bugman \| 2008-07-08 22:25:44 +0200 (Tue, 08 Jul 2008) \| 3 lines Fixes for the read() function to allow the error column to be missing. ........ r6854 \| bugman \| 2008-07-09 10:59:43 +0200 (Wed, 09 Jul 2008) \| 8 lines Split up the n_state_model.model() user function. The new user functions are: n_state_model.number_of_states() n_state_model.ref_domain() n_state_model.setup_model() ........ r6855 \| bugman \| 2008-07-09 11:02:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the unit tests broken by the split up of n_state_model.model(). ........ r6856 \| bugman \| 2008-07-09 11:04:15 +0200 (Wed, 09 Jul 2008) \| 3 lines Wrote the model arg unit test for the n_state_model.setup_model() user function. ........ r6857 \| bugman \| 2008-07-09 11:06:51 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the N-state model system test. ........ r6859 \| bugman \| 2008-07-09 11:18:53 +0200 (Wed, 09 Jul 2008) \| 3 lines Split up the model_setup() method into number_of_states(), ref_domain(), and setup_model(). ........ r6860 \| bugman \| 2008-07-09 11:20:29 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the new error class RelaxNoModelError. ........ r6861 \| bugman \| 2008-07-09 11:21:18 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the n_state_model.select_model() user function. ........ r6862 \| bugman \| 2008-07-09 11:23:36 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring and print out fixes for the n_state_model.select_model() user function. ........ r6863 \| bugman \| 2008-07-09 11:26:09 +0200 (Wed, 09 Jul 2008) \| 5 lines Renamed the n_state_model.setup_model() user function to n_state_model.select_model(). This is to match the convention of the other analyses. ........ r6864 \| bugman \| 2008-07-09 11:26:58 +0200 (Wed, 09 Jul 2008) \| 3 lines System test fix for the renaming of n_state_model.setup_model(). ........ r6865 \| bugman \| 2008-07-09 11:29:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Added some error checking for the validity of the selected model type. ........ r6866 \| bugman \| 2008-07-09 11:41:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the model checking in the minimise() method. ........ r6867 \| bugman \| 2008-07-09 11:51:05 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the setup_model() method so that the model parameters can be set up by numerous methods. ........ r6868 \| bugman \| 2008-07-09 11:52:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the model arg of the n_state_model.select_model() user function. ........ r6869 \| bugman \| 2008-07-09 13:29:21 +0200 (Wed, 09 Jul 2008) \| 3 lines Spun out some of the minimisation code into the minimise_setup_tensors() method. ........ r6870 \| bugman \| 2008-07-09 13:33:29 +0200 (Wed, 09 Jul 2008) \| 3 lines Renamed setup_model() to the private __update_model() method. ........ r6871 \| bugman \| 2008-07-09 13:34:46 +0200 (Wed, 09 Jul 2008) \| 3 lines Made a call to __update_model() from select_model(). ........ r6872 \| bugman \| 2008-07-09 13:37:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Made the __update_model() method less fatal. ........ r6873 \| bugman \| 2008-07-09 13:38:55 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the call to __update_model() from number_of_states(). ........ r6874 \| bugman \| 2008-07-09 13:39:18 +0200 (Wed, 09 Jul 2008) \| 3 lines Added a call to __update_model() from ref_domain(). ........ r6875 \| bugman \| 2008-07-09 13:40:26 +0200 (Wed, 09 Jul 2008) \| 3 lines Added an alias to the current data pipe in minimise_setup_tensors(). ........ r6876 \| bugman \| 2008-07-09 13:43:57 +0200 (Wed, 09 Jul 2008) \| 3 lines Passed the param_vector into minimise_setup_tensors() and fixed the variable of the returned data. ........ r6877 \| bugman \| 2008-07-09 13:53:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the __update_model() to prevent the model data being overwritten or too many params added. ........ r6878 \| bugman \| 2008-07-09 14:40:41 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the minimise_setup_rdcs() method. ........ r6880 \| bugman \| 2008-07-09 15:05:46 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified minimise_setup_rdcs() to throw a warning if RDCs exist but XH bond vectors are missing. ........ r6882 \| bugman \| 2008-07-09 15:11:47 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for minimise_setup_rdcs(). The spin id is now generated for the warning. ........ r6883 \| bugman \| 2008-07-09 15:18:36 +0200 (Wed, 09 Jul 2008) \| 3 lines The N_state_opt class now accepts the model, rdcs, and xh_vect arguments. ........ r6884 \| bugman \| 2008-07-09 15:35:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified the N_state_opt class to handle both alignment tensor and RDC optimisation. ........ r6885 \| bugman \| 2008-07-09 15:40:54 +0200 (Wed, 09 Jul 2008) \| 6 lines Changed the N_state_opt functions to be model dependent. The func_rdcs() method is now func_population(), and the func_tensors() method is now func_2domain(). ........ r6886 \| bugman \| 2008-07-09 15:42:16 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the N_state_opt class set up for the tensor optimisation. ........ r6887 \| bugman \| 2008-07-09 15:49:39 +0200 (Wed, 09 Jul 2008) \| 3 lines Created an empty module to dump RDC related computational functions into. ........ r6888 \| bugman \| 2008-07-09 16:13:45 +0200 (Wed, 09 Jul 2008) \| 6 lines Created the average_rdc_5D() function. This calculates the average RDC for an ensemble set of XH bond vectors, using the 5D alignment tensor notation. ........ r6889 \| bugman \| 2008-07-09 16:19:13 +0200 (Wed, 09 Jul 2008) \| 6 lines Created the average_rdc_tensor() function. This is equivalent to the average_rdc_5D() function but takes the full tensor in numpy matrix form rather than the elements of the 5D vector. ........ r6890 \| bugman \| 2008-07-09 16:20:01 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring fix for average_rdc_5D(). The XH vectors must be unit vectors! ........ r6891 \| bugman \| 2008-07-09 16:25:57 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the to_tensor() function to convert from 5D vector to 3D matrix. ........ r6892 \| bugman \| 2008-07-09 16:28:49 +0200 (Wed, 09 Jul 2008) \| 3 lines Some fixes for the to_tensor() function. The elements Ayx, Azx, and Azy were being referenced! ........ r6893 \| bugman \| 2008-07-09 16:36:25 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the to_5D() function for converting from matrix form to 5D vector form. ........ r6894 \| bugman \| 2008-07-09 16:39:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified the to_tensor() to be more efficient by working only with numpy arrays. ........ r6895 \| bugman \| 2008-07-09 16:42:14 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the to_tensor() function. The tensor was completely wrong. ........ r6896 \| bugman \| 2008-07-09 16:49:43 +0200 (Wed, 09 Jul 2008) \| 3 lines Created maxA() for finding the maximal alignment or the Azz component in the alignment frame. ........ r6897 \| bugman \| 2008-07-09 16:50:31 +0200 (Wed, 09 Jul 2008) \| 3 lines Imported some of the RDC functions. ........ r6898 \| bugman \| 2008-07-09 16:54:09 +0200 (Wed, 09 Jul 2008) \| 3 lines Renamed the invalid variable name 5D_vector to vector_5D. ........ r6899 \| bugman \| 2008-07-09 17:28:28 +0200 (Wed, 09 Jul 2008) \| 3 lines Implemented the core of the func_population() method. ........ r6900 \| bugman \| 2008-07-09 17:35:01 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the average_rdc_5D() function. The unit XH bond vector indecies were still in Mathematica format. ........ r6901 \| bugman \| 2008-07-09 17:40:12 +0200 (Wed, 09 Jul 2008) \| 6 lines Fix for the func_population() method. The RDC errors are now set to 1.0 if no errors are supplied, converting the chi2 value to a SSE value. ........ r6902 \| bugman \| 2008-07-09 18:03:07 +0200 (Wed, 09 Jul 2008) \| 5 lines Fixes for the __update_model() method. The probabilities and Euler angle parameter arrays are only created for the relevant N-state model. ........ r6903 \| bugman \| 2008-07-09 18:09:14 +0200 (Wed, 09 Jul 2008) \| 3 lines Spun out some of the minimise() code to create the __determine_data_type() method. ........ r6904 \| bugman \| 2008-07-09 18:22:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Updated the assemble_param_vector() method to return the correct parameter vector. ........ r6905 \| bugman \| 2008-07-09 18:23:04 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for a missing cdp alias. ........ r6906 \| bugman \| 2008-07-09 18:26:09 +0200 (Wed, 09 Jul 2008) \| 5 lines Complete change of the __determine_data_type() method. The alignment tensors should be present when RDCs are loaded - they are part of the optimised model! ........ r6907 \| bugman \| 2008-07-09 18:33:20 +0200 (Wed, 09 Jul 2008) \| 5 lines Modified the __update_model() method to create empty alignment tensors as necessary. This is for the RDC based analysis were the tensors are optimised. ........ r6908 \| bugman \| 2008-07-09 18:35:38 +0200 (Wed, 09 Jul 2008) \| 5 lines Fix for the __determine_data_type() method. The flags were not correctly checked. ........ r6909 \| bugman \| 2008-07-09 18:41:40 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the tensor_5D automatically generated object to AlignTensorData. ........ r6910 \| bugman \| 2008-07-09 18:43:34 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the addition of alignment tensor parameters in assemble_param_vector(). ........ r6911 \| bugman \| 2008-07-09 18:55:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the func_population() method. ........ r6912 \| bugman \| 2008-07-09 19:04:20 +0200 (Wed, 09 Jul 2008) \| 6 lines Changed the initialisation of the N_state_opt class. The rdcs, rdc_errors, and xh_vect args are now all expected to be numpy matricies. The rdcs and rdc_errors matricies have also been transposed! ........ r6913 \| bugman \| 2008-07-09 19:13:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Converted the RDC and unit vector lists in minimise_setup_rdcs() to numpy matrices. ........ r6914 \| bugman \| 2008-07-09 19:15:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the incorrect testing for the presence of RDC errors. ........ r6915 \| bugman \| 2008-07-09 19:15:33 +0200 (Wed, 09 Jul 2008) \| 3 lines Missing import. ........ r6916 \| bugman \| 2008-07-09 19:16:32 +0200 (Wed, 09 Jul 2008) \| 3 lines Initialised the back calculated RDC array. ........ r6917 \| bugman \| 2008-07-09 19:18:04 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed all the broken references to self.rdcs_back_calc. ........ r6918 \| bugman \| 2008-07-09 19:21:47 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the calculation of the total number of spins and alignments. ........ r6919 \| bugman \| 2008-07-09 19:23:48 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the setting up of RDC errors when missing. These should be 1.0, not 0.0! ........ r6920 \| bugman \| 2008-07-09 19:35:48 +0200 (Wed, 09 Jul 2008) \| 5 lines Fixed the setting up of self.rdc_errors when no errors are present. Retard, 1.0 times another matrix does not make a matrix of ones! ........ r6921 \| bugman \| 2008-07-09 19:40:11 +0200 (Wed, 09 Jul 2008) \| 3 lines The population weights are now taken into account in the func_population() target function. ........ r6922 \| bugman \| 2008-07-09 19:40:53 +0200 (Wed, 09 Jul 2008) \| 3 lines Added some more comments. ........ r6923 \| bugman \| 2008-07-09 19:41:54 +0200 (Wed, 09 Jul 2008) \| 3 lines The weights are passed into average_rdc_5D() as a keyword to make them optional. ........ r6924 \| bugman \| 2008-07-09 19:44:35 +0200 (Wed, 09 Jul 2008) \| 3 lines Converted average_rdc_5D() to expect a numpy array for the 5D tensor. ........ r6925 \| bugman \| 2008-07-09 19:45:05 +0200 (Wed, 09 Jul 2008) \| 3 lines The 5D tensor is passed directly into average_rdc_5D() from func_population(). ........ r6926 \| bugman \| 2008-07-09 19:52:22 +0200 (Wed, 09 Jul 2008) \| 3 lines Added weights to the average_rdc_5D() function. ........ r6927 \| bugman \| 2008-07-09 19:53:41 +0200 (Wed, 09 Jul 2008) \| 3 lines Added weights to the average_rdc_tensor() function. ........ r6928 \| bugman \| 2008-07-09 19:54:24 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring fixes. ........ r6929 \| bugman \| 2008-07-10 09:43:16 +0200 (Thu, 10 Jul 2008) \| 3 lines Redesigned the disassemble_param_vector() method for the multiple N-state model types. ........ r6930 \| bugman \| 2008-07-10 10:06:29 +0200 (Thu, 10 Jul 2008) \| 3 lines Updated the param_num() method to take the various models into account. ........ r6931 \| bugman \| 2008-07-10 10:54:29 +0200 (Thu, 10 Jul 2008) \| 3 lines Fix for the counting of header lines. The residue or spin number need not be supplied. ........ r6932 \| bugman \| 2008-07-10 13:26:51 +0200 (Thu, 10 Jul 2008) \| 3 lines Wrote the __assemble_scaling_matrix() method for creating a scaling matrix for the N-state model. ........ r6933 \| bugman \| 2008-07-10 13:30:26 +0200 (Thu, 10 Jul 2008) \| 3 lines Made diagonal scaling optional. ........ r6934 \| bugman \| 2008-07-10 13:42:41 +0200 (Thu, 10 Jul 2008) \| 3 lines Made some more use of the scaling matrix. ........ r6935 \| bugman \| 2008-07-10 13:43:36 +0200 (Thu, 10 Jul 2008) \| 3 lines Unscaled the parameter vector after optimisation. ........ r6936 \| bugman \| 2008-07-10 13:44:25 +0200 (Thu, 10 Jul 2008) \| 3 lines Missing import fix. ........ r6937 \| bugman \| 2008-07-10 13:51:21 +0200 (Thu, 10 Jul 2008) \| 3 lines The minimisation code now uses the scaling matrix. ........ r6938 \| bugman \| 2008-07-10 14:46:35 +0200 (Thu, 10 Jul 2008) \| 3 lines Inverted the population scaling factor in __assemble_scaling_matrix(). ........ r6941 \| bugman \| 2008-07-23 11:27:38 +0200 (Wed, 23 Jul 2008) \| 3 lines Started to add the framework for the addition of gradients and Hessians. ........ r6942 \| bugman \| 2008-07-23 11:47:41 +0200 (Wed, 23 Jul 2008) \| 3 lines Split the rdc module in half, shifting the alignment tensor components into their own module. ........ r6943 \| bugman \| 2008-07-23 11:48:36 +0200 (Wed, 23 Jul 2008) \| 3 lines Import fixes. ........ r6944 \| bugman \| 2008-07-23 13:33:22 +0200 (Wed, 23 Jul 2008) \| 3 lines Wrote functions for all the alignment tensor gradients. ........ r6945 \| bugman \| 2008-07-23 13:36:31 +0200 (Wed, 23 Jul 2008) \| 3 lines Fixes for the alignment tensor gradient function code. ........ r6952 \| bugman \| 2008-07-24 14:49:13 +0200 (Thu, 24 Jul 2008) \| 3 lines A lot of modifications to the population N-state model optimisation code. ........ r6957 \| bugman \| 2008-07-24 15:22:13 +0200 (Thu, 24 Jul 2008) \| 3 lines Spelling fix for the word 'indices'. ........ r6958 \| bugman \| 2008-07-24 16:54:46 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed the setting up of optimisation of the population N-state model. ........ r6959 \| bugman \| 2008-07-24 16:55:09 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed the call to to_tensor(). ........ r6960 \| bugman \| 2008-07-24 17:00:43 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixes for the func_population() target function. ........ r6961 \| bugman \| 2008-07-24 17:02:21 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixes for the setup of the N-state model optimisation code. ........ r6962 \| bugman \| 2008-07-24 17:03:06 +0200 (Thu, 24 Jul 2008) \| 3 lines Missing import. ........ r6963 \| bugman \| 2008-07-24 17:07:34 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed a call to the non-existant chi2_element() function (should be to chi2()). ........ r6964 \| bugman \| 2008-07-24 17:07:59 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed some index names. ........ r6965 \| bugman \| 2008-07-24 17:31:20 +0200 (Thu, 24 Jul 2008) \| 3 lines Large expansion of the dfunc_population() docstring. ........ r6966 \| bugman \| 2008-07-25 10:04:15 +0200 (Fri, 25 Jul 2008) \| 3 lines More rewriting of the population N-state model optimisation code. ........ r6967 \| bugman \| 2008-07-25 11:19:15 +0200 (Fri, 25 Jul 2008) \| 5 lines Wrote the average_rdc_tensor_dDij_dAmn() function. This calculates the ensemble averaged RDC gradient element for the Amn partial derivative. ........ r6968 \| bugman \| 2008-07-25 11:21:34 +0200 (Fri, 25 Jul 2008) \| 3 lines Fixed the N-state model code to use the renamed averaged RDC functions. ........ r6969 \| bugman \| 2008-07-25 11:27:44 +0200 (Fri, 25 Jul 2008) \| 3 lines Added a missing import. ........ r6970 \| bugman \| 2008-07-25 11:47:49 +0200 (Fri, 25 Jul 2008) \| 9 lines Wrote the dipolar_constant() function for calculating the dipolar constant. The constant is defined as: mu0 gI.gS.h_bar d = - --- ----------- 4pi r3 ........ r6971 \| bugman \| 2008-07-25 11:49:58 +0200 (Fri, 25 Jul 2008) \| 3 lines Pre-calculated the dipolar constants prior to optimisation. ........ r6972 \| bugman \| 2008-07-25 11:51:42 +0200 (Fri, 25 Jul 2008) \| 3 lines Updated a comment describing why the dipolar constant is multiplied by 3/(2pi). ........ r6973 \| bugman \| 2008-07-25 12:03:53 +0200 (Fri, 25 Jul 2008) \| 3 lines Updated the is_spin_param() method to make a few parameters spin specific. ........ r6974 \| bugman \| 2008-07-25 13:19:18 +0200 (Fri, 25 Jul 2008) \| 3 lines Added a dummy data_init() method to the Common_functions base class. ........ r6975 \| bugman \| 2008-07-25 13:22:27 +0200 (Fri, 25 Jul 2008) \| 3 lines Typo bug fix. ........ r6976 \| bugman \| 2008-07-25 13:24:57 +0200 (Fri, 25 Jul 2008) \| 3 lines Bug fix for the ave_rdc_tensor_dDij_dAmn() function. A numpy array cannot be appended to! ........ r6977 \| bugman \| 2008-07-25 13:53:38 +0200 (Fri, 25 Jul 2008) \| 3 lines Docstring improvements for the ave_rdc_tensor() function. ........ r6978 \| bugman \| 2008-07-25 14:06:08 +0200 (Fri, 25 Jul 2008) \| 3 lines Wrote the function rdc_tensor() to calculate the standard RDC. ........ r6979 \| bugman \| 2008-07-25 14:12:21 +0200 (Fri, 25 Jul 2008) \| 3 lines Created the pc partial derivative part of the RDC gradient. ........ r6980 \| bugman \| 2008-07-25 14:13:27 +0200 (Fri, 25 Jul 2008) \| 3 lines Removed a stray comment. ........ r6981 \| bugman \| 2008-07-25 14:37:41 +0200 (Fri, 25 Jul 2008) \| 3 lines The chi-squared gradient is now calculated. ........ r6982 \| bugman \| 2008-07-25 14:38:40 +0200 (Fri, 25 Jul 2008) \| 3 lines Sent the dipolar constant into the ave_rdc_tensor() function. ........ r6983 \| bugman \| 2008-07-25 14:48:34 +0200 (Fri, 25 Jul 2008) \| 3 lines The dipolar constant is now accepted by the RDC functions. ........ r6984 \| bugman \| 2008-07-25 14:49:29 +0200 (Fri, 25 Jul 2008) \| 3 lines Removed the unused setup_population_eqi() method. ........ r6985 \| bugman \| 2008-07-25 14:57:42 +0200 (Fri, 25 Jul 2008) \| 3 lines No need to multiply by 1.0 to return a copy at the end - the gradient is reset at the start. ........ r6986 \| bugman \| 2008-07-28 14:34:21 +0200 (Mon, 28 Jul 2008) \| 5 lines Changes to the linear_constraints() method. The method is now private and accepts new arguments for the different types of N-state model. ........ r6987 \| bugman \| 2008-07-28 14:37:24 +0200 (Mon, 28 Jul 2008) \| 3 lines Fixed the creation of the A and b constraint matrices. ........ r6988 \| bugman \| 2008-07-28 14:59:26 +0200 (Mon, 28 Jul 2008) \| 3 lines Made the assemble_param_vector() and disassemble_param_vector() methods private. ........ r6989 \| bugman \| 2008-07-28 15:17:00 +0200 (Mon, 28 Jul 2008) \| 3 lines Passed the data_type variable into the __disassemble_param_vector() method. ........ r6990 \| bugman \| 2008-07-28 15:25:01 +0200 (Mon, 28 Jul 2008) \| 3 lines The data_type arg is now accepted by __disassemble_param_vector(). ........ r6991 \| bugman \| 2008-07-28 15:29:53 +0200 (Mon, 28 Jul 2008) \| 6 lines Bug fix for the __disassemble_param_vector() method. The parameter vector with alignment tensor parameters is now properly split into the alignment tensor components and probabilities. ........ r6992 \| bugman \| 2008-07-28 19:18:06 +0200 (Mon, 28 Jul 2008) \| 3 lines Inverted the population parameter scaling factor to 100. ........ r7021 \| bugman \| 2008-07-29 18:56:31 +0200 (Tue, 29 Jul 2008) \| 3 lines Fix in grid_search() for the checking of the set up of the N-state model. ........ r7029 \| bugman \| 2008-07-30 10:02:45 +0200 (Wed, 30 Jul 2008) \| 3 lines Added the ability to handle missing RDCs. ........ r7076 \| bugman \| 2008-08-07 15:11:42 +0200 (Thu, 07 Aug 2008) \| 3 lines Docstring fix for the rdc_tensor() function. ........ r7077 \| bugman \| 2008-08-07 15:28:28 +0200 (Thu, 07 Aug 2008) \| 3 lines Created a module for the calculation of the pseudocontact shift (and its gradient and Hessian). ........ r7080 \| bugman \| 2008-08-07 16:26:06 +0200 (Thu, 07 Aug 2008) \| 5 lines Pseudocontact shifts are supported by the N_state_opt.__init__() method. The target functions still need to be updated. ........ r7081 \| bugman \| 2008-08-07 16:39:06 +0200 (Thu, 07 Aug 2008) \| 3 lines Spelling fix in the docstrings. ........ r7082 \| bugman \| 2008-08-07 16:40:36 +0200 (Thu, 07 Aug 2008) \| 3 lines Modified the func_population() target function to handle both RDCs and PCSs. ........ r7083 \| bugman \| 2008-08-07 16:53:06 +0200 (Thu, 07 Aug 2008) \| 3 lines Modified the dfunc_population() gradient function to handle both RDCs and PCSs. ........ r7084 \| bugman \| 2008-08-07 16:56:29 +0200 (Thu, 07 Aug 2008) \| 3 lines Set up the rdc and pcs flags in the __init__() method. ........ r7085 \| bugman \| 2008-08-07 16:57:37 +0200 (Thu, 07 Aug 2008) \| 3 lines Import fix. ........ r7086 \| bugman \| 2008-08-07 16:58:35 +0200 (Thu, 07 Aug 2008) \| 3 lines Renamed ave_pcs_tensor_ddelta_ij_dAmn() to ave_pcs_tensor_ddeltaij_dAmn() for consistency. ........ r7087 \| bugman \| 2008-08-07 18:04:30 +0200 (Thu, 07 Aug 2008) \| 3 lines Spelling fix in the docstrings. ........ r7088 \| bugman \| 2008-08-07 19:21:09 +0200 (Thu, 07 Aug 2008) \| 3 lines Created the interfaces for the PCS user functions. ........ r7089 \| bugman \| 2008-08-07 19:30:26 +0200 (Thu, 07 Aug 2008) \| 3 lines Renamed the 'RDC identification string' to the 'alignment identification string'. ........ r7090 \| bugman \| 2008-08-07 19:37:08 +0200 (Thu, 07 Aug 2008) \| 3 lines Activated the PCS user functions. ........ r7091 \| bugman \| 2008-08-07 19:51:49 +0200 (Thu, 07 Aug 2008) \| 3 lines Created the generic_fns.pcs module, although nothing will work yet. ........ r7092 \| bugman \| 2008-08-07 19:53:10 +0200 (Thu, 07 Aug 2008) \| 3 lines Removed a useless function. ........ r7093 \| bugman \| 2008-08-07 19:53:50 +0200 (Thu, 07 Aug 2008) \| 3 lines Removed some more useless functions. ........ r7106 \| bugman \| 2008-08-08 10:03:54 +0200 (Fri, 08 Aug 2008) \| 3 lines Changed a lot of references from cdp.rdc_ids to cdp.align_tensors. ........ r7107 \| bugman \| 2008-08-08 10:08:27 +0200 (Fri, 08 Aug 2008) \| 3 lines Converted the read() function to handle PCS rather than RDC data. ........ r7108 \| bugman \| 2008-08-08 10:11:49 +0200 (Fri, 08 Aug 2008) \| 3 lines Created 2 new RelaxErrors for PCSs. ........ r7109 \| bugman \| 2008-08-08 10:20:41 +0200 (Fri, 08 Aug 2008) \| 3 lines Renamed __determine_data_type() to __base_data_type(). ........ r7110 \| bugman \| 2008-08-08 10:27:35 +0200 (Fri, 08 Aug 2008) \| 3 lines Redesigned __base_data_types() to determine all base data types, and return them as a list. ........ r7111 \| bugman \| 2008-08-08 10:33:31 +0200 (Fri, 08 Aug 2008) \| 3 lines Modified the __update_model() to handle both RDCs and PCSs. ........ r7112 \| bugman \| 2008-08-08 10:36:22 +0200 (Fri, 08 Aug 2008) \| 3 lines Fixed __base_data_types() to properly identify tensors as the base data source. ........ r7113 \| bugman \| 2008-08-08 10:46:34 +0200 (Fri, 08 Aug 2008) \| 3 lines Fixed all the calls to __base_data_types() and subsequent use of the returned list. ........ r7114 \| bugman \| 2008-08-08 10:47:39 +0200 (Fri, 08 Aug 2008) \| 3 lines Added a module docstring. ........ r7115 \| bugman \| 2008-08-08 11:17:22 +0200 (Fri, 08 Aug 2008) \| 5 lines Changed the way optimisation of the N-state model is set up. This will allow multiple base data types to be used simultaneously. ........ r7116 \| bugman \| 2008-08-08 11:22:06 +0200 (Fri, 08 Aug 2008) \| 3 lines A call is now made to assemble the PCS data necessary for optimisation. ........ r7117 \| bugman \| 2008-08-08 11:24:54 +0200 (Fri, 08 Aug 2008) \| 5 lines Fix for the __update_model() method. This was only working if both RDC and PCS data are supplied. ........ r7118 \| bugman \| 2008-08-08 11:26:18 +0200 (Fri, 08 Aug 2008) \| 3 lines Shifted the __update_model() method for fixing the alphabetical ordering of methods. ........ r7119 \| bugman \| 2008-08-08 11:27:48 +0200 (Fri, 08 Aug 2008) \| 3 lines Converted minimise_setup_rdcs() and minimise_setup_tensors() into private methods. ........ r7120 \| bugman \| 2008-08-08 11:59:09 +0200 (Fri, 08 Aug 2008) \| 5 lines Modified the N_state_opt class to accept PCS data. The __init__() docstring has been significantly expanded as well. ........ r7121 \| bugman \| 2008-08-08 16:19:24 +0200 (Fri, 08 Aug 2008) \| 3 lines Wrote the __minimise_setup_pcs() method. ........ r7130 \| bugman \| 2008-08-11 11:41:08 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the user function interface for setting the experimental temperature. ........ r7131 \| bugman \| 2008-08-11 11:42:40 +0200 (Mon, 11 Aug 2008) \| 3 lines Activated the temperature user function interface. ........ r7132 \| bugman \| 2008-08-11 11:49:53 +0200 (Mon, 11 Aug 2008) \| 3 lines Added a stub function generic_fns.temperature.set() to fix the missing import problem. ........ r7133 \| bugman \| 2008-08-11 11:51:42 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixed the setting up of the temperature user function. ........ r7134 \| bugman \| 2008-08-11 11:53:42 +0200 (Mon, 11 Aug 2008) \| 3 lines Allowed the temperature to be entered as a integer as well as a float. ........ r7135 \| bugman \| 2008-08-11 11:58:38 +0200 (Mon, 11 Aug 2008) \| 3 lines Completed the generic_fns.temperature.set() function. ........ r7136 \| bugman \| 2008-08-11 13:41:30 +0200 (Mon, 11 Aug 2008) \| 3 lines Made the experimental id string compulsory. ........ r7137 \| bugman \| 2008-08-11 13:47:44 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the user function interface for setting the spectrometer frequency of an experiment. ........ r7138 \| bugman \| 2008-08-11 13:49:13 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the frq and temperature modules to the __all__ list. ........ r7139 \| bugman \| 2008-08-11 13:59:01 +0200 (Mon, 11 Aug 2008) \| 3 lines Wrote the spectrometer frequency setting function generic_fns.frq.set(). ........ r7140 \| bugman \| 2008-08-11 14:00:37 +0200 (Mon, 11 Aug 2008) \| 3 lines Activated the frq.set() user function. ........ r7141 \| bugman \| 2008-08-11 14:02:47 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixes for the frq.set() user function. ........ r7142 \| bugman \| 2008-08-11 14:08:10 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the frq and temperature modules to the __all__ list. ........ r7143 \| bugman \| 2008-08-11 14:21:41 +0200 (Mon, 11 Aug 2008) \| 3 lines Create the interface for the pcs.centre() user function. ........ r7144 \| bugman \| 2008-08-11 14:53:55 +0200 (Mon, 11 Aug 2008) \| 3 lines Implemented the generic_fns.pcs.centre() function. ........ r7145 \| bugman \| 2008-08-11 15:11:40 +0200 (Mon, 11 Aug 2008) \| 3 lines The structure identifier arg is now used by the atom_loop() method. ........ r7146 \| bugman \| 2008-08-11 15:28:34 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixed the atom_loop() call in __minimise_setup_pcs(). ........ r7148 \| bugman \| 2008-08-11 15:37:06 +0200 (Mon, 11 Aug 2008) \| 3 lines Wrote the pcs_constant() function to calculate the pseudocontact shift constant. ........ r7149 \| bugman \| 2008-08-11 15:41:13 +0200 (Mon, 11 Aug 2008) \| 3 lines Added Boltzmann's constant to the physical_constants module. ........ r7150 \| bugman \| 2008-08-11 16:01:02 +0200 (Mon, 11 Aug 2008) \| 8 lines Fixes for the PCS constant, as it is dependent on the indices i, j and c. These are: i, the experiment or alignment index, j, the spin index, c, the state index. ........ r7151 \| bugman \| 2008-08-11 16:48:36 +0200 (Mon, 11 Aug 2008) \| 3 lines Redesigned the __minimise_setup_pcs() method. ........ r7152 \| bugman \| 2008-08-11 18:45:14 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the ave arg to the structure.load_spins() user function. ........ r7153 \| bugman \| 2008-08-11 18:46:21 +0200 (Mon, 11 Aug 2008) \| 3 lines Renamed the ave arg of structure.load_spins() to ave_pos. ........ r7154 \| bugman \| 2008-08-11 18:53:05 +0200 (Mon, 11 Aug 2008) \| 3 lines The load_spins() function is now either loading the average or all atom positions. ........ r7155 \| bugman \| 2008-08-11 19:42:13 +0200 (Mon, 11 Aug 2008) \| 5 lines Fixes for the __minimise_setup_pcs() method. Multi-dimensional arrays were not being properly created or referenced. ........ r7156 \| bugman \| 2008-08-12 09:39:46 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the call to __minimise_setup_pcs(). ........ r7157 \| bugman \| 2008-08-12 09:44:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the initialisation of the variables pcs, pcs_vect, and pcs_dj. ........ r7158 \| bugman \| 2008-08-12 09:52:32 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the N_state_opt.__init__() docstring. ........ r7159 \| bugman \| 2008-08-12 09:53:08 +0200 (Tue, 12 Aug 2008) \| 3 lines Placed the PCS constants into self. ........ r7160 \| bugman \| 2008-08-12 09:58:15 +0200 (Tue, 12 Aug 2008) \| 3 lines Converted the PCS constant data structure into a numpy array in __minimise_setup_pcs(). ........ r7161 \| bugman \| 2008-08-12 09:58:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed a typo bug. ........ r7162 \| bugman \| 2008-08-12 10:00:03 +0200 (Tue, 12 Aug 2008) \| 3 lines Bug fix for the ave_pcs_tensor() function. ........ r7163 \| bugman \| 2008-08-12 10:38:00 +0200 (Tue, 12 Aug 2008) \| 5 lines Modified the setup of the RDC data. Spins missing RDC data but other data now have rows of None appended to the data structures. ........ r7164 \| bugman \| 2008-08-12 10:43:24 +0200 (Tue, 12 Aug 2008) \| 3 lines Converted the RDC constant list into a numpy array. ........ r7165 \| bugman \| 2008-08-12 10:49:16 +0200 (Tue, 12 Aug 2008) \| 6 lines Fixes for the set up of the RDC constant array. None (or NaN after numpy converion) is placed into the list when other data exists but the RDC is missing. ........ r7166 \| bugman \| 2008-08-12 10:50:18 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the __init__() docstring. ........ r7167 \| bugman \| 2008-08-12 10:58:28 +0200 (Tue, 12 Aug 2008) \| 5 lines Bug fix for the target function. The RDC vector and PCS vectors are not the same! ........ r7168 \| bugman \| 2008-08-12 11:45:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Big debugging of the N-state model setup, target, and gradient functions. ........ r7169 \| bugman \| 2008-08-12 11:49:07 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed some of the tests in the __init__() method. ........ r7170 \| bugman \| 2008-08-12 12:10:38 +0200 (Tue, 12 Aug 2008) \| 3 lines Scaled the PCS value from ppm to no units. ........ r7171 \| bugman \| 2008-08-12 12:11:27 +0200 (Tue, 12 Aug 2008) \| 3 lines Removed some commented out and no longer used code. ........ r7172 \| bugman \| 2008-08-12 12:15:06 +0200 (Tue, 12 Aug 2008) \| 3 lines Shrunk the size of the default PCS errors, so the chi-squared value is comparable to the RDC. ........ r7173 \| bugman \| 2008-08-12 12:20:19 +0200 (Tue, 12 Aug 2008) \| 5 lines Fix for the paramagnetic centre to nucleus distances. The distances are now converted from Angstrom to meters. ........ r7174 \| bugman \| 2008-08-12 12:33:19 +0200 (Tue, 12 Aug 2008) \| 3 lines Changed the PCS scaling factor. ........ r7175 \| bugman \| 2008-08-12 14:34:12 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for all the N-state model unit tests. ........ r7176 \| bugman \| 2008-08-12 14:46:48 +0200 (Tue, 12 Aug 2008) \| 3 lines Added a test to see if the model has been selected. ........ r7177 \| bugman \| 2008-08-12 14:47:32 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the test___assemble_param_vector() unit test. ........ r7178 \| bugman \| 2008-08-12 14:53:24 +0200 (Tue, 12 Aug 2008) \| 3 lines Added a test to __disassemble_param_vector() to set if the model has been selected. ........ r7179 \| bugman \| 2008-08-12 14:54:19 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the test___disassemble_param_vector() unit test. ........ r7180 \| bugman \| 2008-08-12 15:05:39 +0200 (Tue, 12 Aug 2008) \| 3 lines Set the 2-domain N-state model gradient and Hessian methods to None. ........ r7181 \| bugman \| 2008-08-12 15:09:22 +0200 (Tue, 12 Aug 2008) \| 3 lines Allowed the align_tensor.display() arg to be None (to display all tensors). ........ r7182 \| bugman \| 2008-08-12 15:15:52 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the display() function to allow all alignment tensors to be displayed. ........ r7183 \| bugman \| 2008-08-12 15:33:09 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the N-state model methods to set the alignment tensor parameter rather Saupe order matrix. ........ r7184 \| bugman \| 2008-08-12 15:34:37 +0200 (Tue, 12 Aug 2008) \| 5 lines Changed the list of modifiable alignment tensor objects. Alignment tensor parameters rather than Saupe order matrix elements can now be changed. ........ r7185 \| bugman \| 2008-08-12 17:04:13 +0200 (Tue, 12 Aug 2008) \| 3 lines Updated the set() function to set the alignment tensor parameters rather than Saupe order matrix. ........ r7186 \| bugman \| 2008-08-12 17:16:06 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the unit tests of the alignment tensor objects to use Axx rather than Sxx, etc. ........ r7187 \| bugman \| 2008-08-12 17:47:57 +0200 (Tue, 12 Aug 2008) \| 6 lines Modified the alignment tensor objects. These are now storing everything as alignment tensor parameters rather than Saupe order matrix components and hence all the updating functions have been modified to match. ........ r7188 \| bugman \| 2008-08-12 17:48:27 +0200 (Tue, 12 Aug 2008) \| 3 lines Loosened some unit tests for the alignment tensor. ........ r7189 \| bugman \| 2008-08-12 17:49:53 +0200 (Tue, 12 Aug 2008) \| 3 lines Fix for the test_display_argfail_tensor() unit test. ........ r7191 \| bugman \| 2008-08-13 11:55:56 +0200 (Wed, 13 Aug 2008) \| 3 lines Added the ability to reload alignment tensors from the XML results file into the relax data store. ........ r7192 \| bugman \| 2008-08-14 11:31:10 +0200 (Thu, 14 Aug 2008) \| 10 lines Bug fixes and expansion of the __linear_constraints() method. The bug fix is that the b array was not being scaled! This is essential when diagonal scaling is active. The added feature is that the pN weight of state N, which is not a parameter of the model, is now constrained to be between 0 and 1. This is because the value is equal to 1 minus the sum of all other probabilities, hence linear constraints can be created. ........ r7193 \| bugman \| 2008-08-14 14:39:24 +0200 (Thu, 14 Aug 2008) \| 3 lines Wrote the model_statistics() method. ........ r7194 \| bugman \| 2008-08-14 14:49:45 +0200 (Thu, 14 Aug 2008) \| 3 lines Wrote the num_data_points() method for determining n. ........ r7195 \| bugman \| 2008-08-14 16:47:29 +0200 (Thu, 14 Aug 2008) \| 3 lines Added the pipe arg to the pcs.centre() user function. ........ r7196 \| bugman \| 2008-08-14 16:52:06 +0200 (Thu, 14 Aug 2008) \| 3 lines The data pipe arg is now accepted by the centre() function. ........ r7197 \| bugman \| 2008-08-14 16:56:46 +0200 (Thu, 14 Aug 2008) \| 3 lines Shifted the calculation of the paramagnetic centre from __minimise_setup_pcs() to centre(). ........ r7198 \| bugman \| 2008-08-14 16:57:58 +0200 (Thu, 14 Aug 2008) \| 3 lines Added a missing import and fixed an incorrect reference to the data pipe container. ........ r7199 \| bugman \| 2008-08-14 17:09:00 +0200 (Thu, 14 Aug 2008) \| 3 lines The calculated paramagnetic centre is now being placed into the current data pipe. ........ r7200 \| bugman \| 2008-08-14 17:09:41 +0200 (Thu, 14 Aug 2008) \| 3 lines Added a print out to the centre() function. ........ r7201 \| bugman \| 2008-08-15 10:09:17 +0200 (Fri, 15 Aug 2008) \| 5 lines Allowed the data column to be None in the rdc.read() user function. This allows a file containing only errors to be read. ........ r7202 \| bugman \| 2008-08-16 14:51:32 +0200 (Sat, 16 Aug 2008) \| 3 lines RDC errors can now be read separately and independently from the data values. ........ r7203 \| bugman \| 2008-08-17 18:25:44 +0200 (Sun, 17 Aug 2008) \| 3 lines Allowed the PCS data column to be None, so that a file with only PCS errors can be read. ........ r7204 \| bugman \| 2008-08-17 19:06:16 +0200 (Sun, 17 Aug 2008) \| 5 lines PCS errors in a file separate from the data can now be read. This matches the changes for the RDC at r7202. ........ r7205 \| bugman \| 2008-08-17 19:08:49 +0200 (Sun, 17 Aug 2008) \| 6 lines Reverted the last revision, r7204, as this included too much. The command used was: svn merge -r7204:7203 . ........ r7206 \| bugman \| 2008-08-17 19:10:17 +0200 (Sun, 17 Aug 2008) \| 5 lines Try 2: PCS errors in a file separate from the data can now be read. This matches the changes for the RDC at r7202, and is what r7204 should have been. ........ r7207 \| bugman \| 2008-08-17 19:12:21 +0200 (Sun, 17 Aug 2008) \| 5 lines The RDC and PCS errors data structures are now created by the __minimise_setup_() methods. These are also passed into the minimisation code. ........ r7208 \| bugman \| 2008-08-17 19:15:29 +0200 (Sun, 17 Aug 2008) \| 3 lines The RDC and PCS error data structures are now properly handled and setup in __init__(). ........ r7226 \| bugman \| 2008-08-23 02:37:51 +0200 (Sat, 23 Aug 2008) \| 3 lines Wrote the __minimise_bc_data() method to extract the back calculated data after minimisation. ........ r7227 \| bugman \| 2008-08-23 03:31:59 +0200 (Sat, 23 Aug 2008) \| 3 lines Wrote a function to calculate the RDC Q-factor. ........ r7230 \| bugman \| 2008-09-24 14:21:18 +0200 (Wed, 24 Sep 2008) \| 3 lines Some bug fixes and added the ability to calculate the Q-factor values. ........ r7231 \| bugman \| 2008-09-24 14:22:11 +0200 (Wed, 24 Sep 2008) \| 3 lines Small bug fix causing insignificant duplication of ID strings. ........ r7307 \| bugman \| 2008-09-25 18:19:41 +0200 (Thu, 25 Sep 2008) \| 5 lines Bug fix for the loading of results files when they contain not alignment tensor data. The bug was in the PipeContainer.from_xml() method. ........ ................ r7310 \| bugman \| 2008-09-25 18:31:04 +0200 (Thu, 25 Sep 2008) \| 3 lines Removed merge tracking for "svnmerge" for svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................	2008-09-25 16:48:48	Tree
[r7313] by bugman Merged revisions 7236-7302,7304-7305,7308-7310 via svnmerge from svn+ssh://bugman@.../svn/relax/1.3 ................ 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. ................ r7237 \| bugman \| 2008-09-24 14:49:48 +0200 (Wed, 24 Sep 2008) \| 3 lines Activated the model_loop() generator method. ................ r7238 \| bugman \| 2008-09-24 16:10:56 +0200 (Wed, 24 Sep 2008) \| 3 lines Changed model_loop() to return the spin container. ................ r7239 \| bugman \| 2008-09-24 16:18:13 +0200 (Wed, 24 Sep 2008) \| 3 lines Created the sim_return_chi2() base class method. ................ 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. ................ 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. ................ 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. ................ r7243 \| bugman \| 2008-09-24 16:33:09 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the Grace class methods into module functions. ................ 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. ................ 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. ................ r7246 \| bugman \| 2008-09-24 17:01:41 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the view() function to the new design. ................ r7247 \| bugman \| 2008-09-24 17:23:34 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the 4 write_() functions to the new design. ................ r7248 \| bugman \| 2008-09-24 17:36:02 +0200 (Wed, 24 Sep 2008) \| 3 lines The pipe argument is now optional for RelaxNoSimError. ................ r7249 \| bugman \| 2008-09-24 17:43:04 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the Grace write() function to the new design. ................ 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. ................ r7251 \| bugman \| 2008-09-24 17:56:02 +0200 (Wed, 24 Sep 2008) \| 3 lines A few small fixes for the write() function. ................ r7252 \| bugman \| 2008-09-24 18:00:27 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the grace.write() user function interface. ................ 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. ................ r7254 \| bugman \| 2008-09-24 18:03:32 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the call to get_data(). ................ 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(). ................ 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. ................ r7257 \| bugman \| 2008-09-24 18:33:45 +0200 (Wed, 24 Sep 2008) \| 3 lines Fatal indentation fix. ................ r7258 \| bugman \| 2008-09-24 18:43:16 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the determine_seq_type() function. ................ r7259 \| bugman \| 2008-09-24 18:46:03 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the count_molecules() and count_residues() functions. ................ r7260 \| bugman \| 2008-09-24 18:47:54 +0200 (Wed, 24 Sep 2008) \| 3 lines Merged the count_selected_spins() function into count_spins(). ................ r7261 \| bugman \| 2008-09-24 18:49:04 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed the call to count_selected_spins(). ................ r7262 \| bugman \| 2008-09-24 18:51:20 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the test_count_spins() unit test. ................ r7263 \| bugman \| 2008-09-24 18:52:16 +0200 (Wed, 24 Sep 2008) \| 3 lines Another fix for the test_count_spins() unit test. ................ 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. ................ r7265 \| bugman \| 2008-09-24 19:02:47 +0200 (Wed, 24 Sep 2008) \| 3 lines Propagation of the spin_id variable. ................ 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(). ................ r7267 \| bugman \| 2008-09-24 19:17:29 +0200 (Wed, 24 Sep 2008) \| 3 lines Updated the set_selected_sim() method. ................ r7268 \| bugman \| 2008-09-24 19:18:50 +0200 (Wed, 24 Sep 2008) \| 3 lines Shifted set_selected_sim() to the base class. ................ r7269 \| bugman \| 2008-09-24 19:20:07 +0200 (Wed, 24 Sep 2008) \| 3 lines Docstring and comment fixes for select_all_sims(). ................ r7270 \| bugman \| 2008-09-24 19:28:49 +0200 (Wed, 24 Sep 2008) \| 3 lines Wrote the model-free model_loop() generator method. ................ r7271 \| bugman \| 2008-09-24 19:32:51 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed some dud arguments to the model_loop() generator. ................ 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. ................ r7273 \| bugman \| 2008-09-24 19:50:08 +0200 (Wed, 24 Sep 2008) \| 3 lines Removed some unused imports of return_spin_from_index(). ................ r7274 \| bugman \| 2008-09-24 19:55:23 +0200 (Wed, 24 Sep 2008) \| 3 lines Fix for the model-free model_loop() generator function. ................ r7275 \| bugman \| 2008-09-24 19:56:41 +0200 (Wed, 24 Sep 2008) \| 3 lines Another fix for the model_loop() generator. ................ 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. ................ r7277 \| bugman \| 2008-09-24 20:18:15 +0200 (Wed, 24 Sep 2008) \| 3 lines Passed the missing 'data' data structure into write_header(). ................ r7278 \| bugman \| 2008-09-24 20:27:38 +0200 (Wed, 24 Sep 2008) \| 3 lines Converted the data_names() methods to the new design. ................ r7279 \| bugman \| 2008-09-24 20:36:59 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the call to generate_vector_dist(). ................ 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. ................ r7281 \| bugman \| 2008-09-24 20:55:08 +0200 (Wed, 24 Sep 2008) \| 3 lines The Structure_container no longer needs to be initialised. ................ 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 . ................ 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. ................ 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. ................ 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. ................ 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. ................ r7287 \| bugman \| 2008-09-24 21:57:31 +0200 (Wed, 24 Sep 2008) \| 3 lines Fix for the sim_return_param() method. ................ r7288 \| bugman \| 2008-09-24 21:59:11 +0200 (Wed, 24 Sep 2008) \| 3 lines Fixed the arg order for set_error(). ................ r7289 \| bugman \| 2008-09-24 23:20:14 +0200 (Wed, 24 Sep 2008) \| 3 lines Created the test_Selection_contains_spin8() unit test. ................ 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! ................ 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 . ................ 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 . ................ 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. ................ r7294 \| bugman \| 2008-09-25 15:57:07 +0200 (Thu, 25 Sep 2008) \| 3 lines Activated the unit vector system test. ................ r7295 \| bugman \| 2008-09-25 16:39:11 +0200 (Thu, 25 Sep 2008) \| 3 lines Fixes for the unit vector system test. ................ 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. ................ 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. ................ r7298 \| bugman \| 2008-09-25 16:50:22 +0200 (Thu, 25 Sep 2008) \| 3 lines Allowed the spin number to be reset to None. ................ 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. ................ 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. ................ r7301 \| bugman \| 2008-09-25 17:01:30 +0200 (Thu, 25 Sep 2008) \| 3 lines Fixed the number arg unit test of spin.number(). ................ 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. ................ r7304 \| bugman \| 2008-09-25 18:04:14 +0200 (Thu, 25 Sep 2008) \| 3 lines Initialized merge tracking via "svnmerge" with revisions "1-6740" from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7305 \| bugman \| 2008-09-25 18:09:31 +0200 (Thu, 25 Sep 2008) \| 3 lines Removed merge tracking for "svnmerge" for svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7308 \| bugman \| 2008-09-25 18:19:56 +0200 (Thu, 25 Sep 2008) \| 3 lines Initialized merge tracking via "svnmerge" with revisions "1-6740" from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................ r7309 \| bugman \| 2008-09-25 18:30:20 +0200 (Thu, 25 Sep 2008) \| 1124 lines Merged revisions 6837,6839,6841-6857,6859-6878,6880,6882-6938,6941-6945,6952,6957-6992,7021,7029,7076-7077,7080-7093,7106-7121,7130-7146,7148-7189,7191-7208,7226-7227,7230-7231,7307 via svnmerge from svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ........ r6837 \| bugman \| 2008-07-08 16:23:35 +0200 (Tue, 08 Jul 2008) \| 3 lines Created the framework for a user function class for handling RDCs (by copying the relax_data code). ........ r6839 \| bugman \| 2008-07-08 20:30:14 +0200 (Tue, 08 Jul 2008) \| 3 lines Removed a test for the model setup in the set_non_spin_params() method. ........ r6841 \| bugman \| 2008-07-08 21:02:19 +0200 (Tue, 08 Jul 2008) \| 3 lines Fix for the return_data_name() method when no match occurs and the index flag is True. ........ r6842 \| bugman \| 2008-07-08 21:03:21 +0200 (Tue, 08 Jul 2008) \| 5 lines Added a number of new parameters to the return_data_name() method. This include the bond length, and heteronucleus and proton types. ........ r6843 \| bugman \| 2008-07-08 21:12:31 +0200 (Tue, 08 Jul 2008) \| 3 lines Fix for the return_data_name() method when no match occurs and the index flag is True. ........ r6844 \| bugman \| 2008-07-08 21:17:05 +0200 (Tue, 08 Jul 2008) \| 3 lines Removed some debugging code. ........ r6845 \| bugman \| 2008-07-08 21:24:29 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted the rdc.read() user function from the relax_data.read() code. ........ r6846 \| bugman \| 2008-07-08 21:25:41 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all instances of 'ri_label' to 'id'. ........ r6847 \| bugman \| 2008-07-08 21:26:26 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all instances of 'relax_data' to 'rdc'. ........ r6848 \| bugman \| 2008-07-08 21:36:00 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted all of the rdc user functions from the relax_data code. ........ r6849 \| bugman \| 2008-07-08 21:37:46 +0200 (Tue, 08 Jul 2008) \| 3 lines Created a generic_fns rdc module by copying the relax_data module. ........ r6850 \| bugman \| 2008-07-08 21:54:07 +0200 (Tue, 08 Jul 2008) \| 3 lines Created 2 new error classes, RelaxNoRDCError and RelaxRDCError. ........ r6851 \| bugman \| 2008-07-08 22:03:09 +0200 (Tue, 08 Jul 2008) \| 3 lines Converted the read() function from the relax_data code. ........ r6852 \| bugman \| 2008-07-08 22:20:28 +0200 (Tue, 08 Jul 2008) \| 3 lines Made the error column optional in the loading of RDCs. ........ r6853 \| bugman \| 2008-07-08 22:25:44 +0200 (Tue, 08 Jul 2008) \| 3 lines Fixes for the read() function to allow the error column to be missing. ........ r6854 \| bugman \| 2008-07-09 10:59:43 +0200 (Wed, 09 Jul 2008) \| 8 lines Split up the n_state_model.model() user function. The new user functions are: n_state_model.number_of_states() n_state_model.ref_domain() n_state_model.setup_model() ........ r6855 \| bugman \| 2008-07-09 11:02:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the unit tests broken by the split up of n_state_model.model(). ........ r6856 \| bugman \| 2008-07-09 11:04:15 +0200 (Wed, 09 Jul 2008) \| 3 lines Wrote the model arg unit test for the n_state_model.setup_model() user function. ........ r6857 \| bugman \| 2008-07-09 11:06:51 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the N-state model system test. ........ r6859 \| bugman \| 2008-07-09 11:18:53 +0200 (Wed, 09 Jul 2008) \| 3 lines Split up the model_setup() method into number_of_states(), ref_domain(), and setup_model(). ........ r6860 \| bugman \| 2008-07-09 11:20:29 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the new error class RelaxNoModelError. ........ r6861 \| bugman \| 2008-07-09 11:21:18 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the n_state_model.select_model() user function. ........ r6862 \| bugman \| 2008-07-09 11:23:36 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring and print out fixes for the n_state_model.select_model() user function. ........ r6863 \| bugman \| 2008-07-09 11:26:09 +0200 (Wed, 09 Jul 2008) \| 5 lines Renamed the n_state_model.setup_model() user function to n_state_model.select_model(). This is to match the convention of the other analyses. ........ r6864 \| bugman \| 2008-07-09 11:26:58 +0200 (Wed, 09 Jul 2008) \| 3 lines System test fix for the renaming of n_state_model.setup_model(). ........ r6865 \| bugman \| 2008-07-09 11:29:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Added some error checking for the validity of the selected model type. ........ r6866 \| bugman \| 2008-07-09 11:41:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the model checking in the minimise() method. ........ r6867 \| bugman \| 2008-07-09 11:51:05 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the setup_model() method so that the model parameters can be set up by numerous methods. ........ r6868 \| bugman \| 2008-07-09 11:52:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the model arg of the n_state_model.select_model() user function. ........ r6869 \| bugman \| 2008-07-09 13:29:21 +0200 (Wed, 09 Jul 2008) \| 3 lines Spun out some of the minimisation code into the minimise_setup_tensors() method. ........ r6870 \| bugman \| 2008-07-09 13:33:29 +0200 (Wed, 09 Jul 2008) \| 3 lines Renamed setup_model() to the private __update_model() method. ........ r6871 \| bugman \| 2008-07-09 13:34:46 +0200 (Wed, 09 Jul 2008) \| 3 lines Made a call to __update_model() from select_model(). ........ r6872 \| bugman \| 2008-07-09 13:37:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Made the __update_model() method less fatal. ........ r6873 \| bugman \| 2008-07-09 13:38:55 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the call to __update_model() from number_of_states(). ........ r6874 \| bugman \| 2008-07-09 13:39:18 +0200 (Wed, 09 Jul 2008) \| 3 lines Added a call to __update_model() from ref_domain(). ........ r6875 \| bugman \| 2008-07-09 13:40:26 +0200 (Wed, 09 Jul 2008) \| 3 lines Added an alias to the current data pipe in minimise_setup_tensors(). ........ r6876 \| bugman \| 2008-07-09 13:43:57 +0200 (Wed, 09 Jul 2008) \| 3 lines Passed the param_vector into minimise_setup_tensors() and fixed the variable of the returned data. ........ r6877 \| bugman \| 2008-07-09 13:53:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the __update_model() to prevent the model data being overwritten or too many params added. ........ r6878 \| bugman \| 2008-07-09 14:40:41 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the minimise_setup_rdcs() method. ........ r6880 \| bugman \| 2008-07-09 15:05:46 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified minimise_setup_rdcs() to throw a warning if RDCs exist but XH bond vectors are missing. ........ r6882 \| bugman \| 2008-07-09 15:11:47 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for minimise_setup_rdcs(). The spin id is now generated for the warning. ........ r6883 \| bugman \| 2008-07-09 15:18:36 +0200 (Wed, 09 Jul 2008) \| 3 lines The N_state_opt class now accepts the model, rdcs, and xh_vect arguments. ........ r6884 \| bugman \| 2008-07-09 15:35:23 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified the N_state_opt class to handle both alignment tensor and RDC optimisation. ........ r6885 \| bugman \| 2008-07-09 15:40:54 +0200 (Wed, 09 Jul 2008) \| 6 lines Changed the N_state_opt functions to be model dependent. The func_rdcs() method is now func_population(), and the func_tensors() method is now func_2domain(). ........ r6886 \| bugman \| 2008-07-09 15:42:16 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the N_state_opt class set up for the tensor optimisation. ........ r6887 \| bugman \| 2008-07-09 15:49:39 +0200 (Wed, 09 Jul 2008) \| 3 lines Created an empty module to dump RDC related computational functions into. ........ r6888 \| bugman \| 2008-07-09 16:13:45 +0200 (Wed, 09 Jul 2008) \| 6 lines Created the average_rdc_5D() function. This calculates the average RDC for an ensemble set of XH bond vectors, using the 5D alignment tensor notation. ........ r6889 \| bugman \| 2008-07-09 16:19:13 +0200 (Wed, 09 Jul 2008) \| 6 lines Created the average_rdc_tensor() function. This is equivalent to the average_rdc_5D() function but takes the full tensor in numpy matrix form rather than the elements of the 5D vector. ........ r6890 \| bugman \| 2008-07-09 16:20:01 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring fix for average_rdc_5D(). The XH vectors must be unit vectors! ........ r6891 \| bugman \| 2008-07-09 16:25:57 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the to_tensor() function to convert from 5D vector to 3D matrix. ........ r6892 \| bugman \| 2008-07-09 16:28:49 +0200 (Wed, 09 Jul 2008) \| 3 lines Some fixes for the to_tensor() function. The elements Ayx, Azx, and Azy were being referenced! ........ r6893 \| bugman \| 2008-07-09 16:36:25 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the to_5D() function for converting from matrix form to 5D vector form. ........ r6894 \| bugman \| 2008-07-09 16:39:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Modified the to_tensor() to be more efficient by working only with numpy arrays. ........ r6895 \| bugman \| 2008-07-09 16:42:14 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the to_tensor() function. The tensor was completely wrong. ........ r6896 \| bugman \| 2008-07-09 16:49:43 +0200 (Wed, 09 Jul 2008) \| 3 lines Created maxA() for finding the maximal alignment or the Azz component in the alignment frame. ........ r6897 \| bugman \| 2008-07-09 16:50:31 +0200 (Wed, 09 Jul 2008) \| 3 lines Imported some of the RDC functions. ........ r6898 \| bugman \| 2008-07-09 16:54:09 +0200 (Wed, 09 Jul 2008) \| 3 lines Renamed the invalid variable name 5D_vector to vector_5D. ........ r6899 \| bugman \| 2008-07-09 17:28:28 +0200 (Wed, 09 Jul 2008) \| 3 lines Implemented the core of the func_population() method. ........ r6900 \| bugman \| 2008-07-09 17:35:01 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the average_rdc_5D() function. The unit XH bond vector indecies were still in Mathematica format. ........ r6901 \| bugman \| 2008-07-09 17:40:12 +0200 (Wed, 09 Jul 2008) \| 6 lines Fix for the func_population() method. The RDC errors are now set to 1.0 if no errors are supplied, converting the chi2 value to a SSE value. ........ r6902 \| bugman \| 2008-07-09 18:03:07 +0200 (Wed, 09 Jul 2008) \| 5 lines Fixes for the __update_model() method. The probabilities and Euler angle parameter arrays are only created for the relevant N-state model. ........ r6903 \| bugman \| 2008-07-09 18:09:14 +0200 (Wed, 09 Jul 2008) \| 3 lines Spun out some of the minimise() code to create the __determine_data_type() method. ........ r6904 \| bugman \| 2008-07-09 18:22:10 +0200 (Wed, 09 Jul 2008) \| 3 lines Updated the assemble_param_vector() method to return the correct parameter vector. ........ r6905 \| bugman \| 2008-07-09 18:23:04 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for a missing cdp alias. ........ r6906 \| bugman \| 2008-07-09 18:26:09 +0200 (Wed, 09 Jul 2008) \| 5 lines Complete change of the __determine_data_type() method. The alignment tensors should be present when RDCs are loaded - they are part of the optimised model! ........ r6907 \| bugman \| 2008-07-09 18:33:20 +0200 (Wed, 09 Jul 2008) \| 5 lines Modified the __update_model() method to create empty alignment tensors as necessary. This is for the RDC based analysis were the tensors are optimised. ........ r6908 \| bugman \| 2008-07-09 18:35:38 +0200 (Wed, 09 Jul 2008) \| 5 lines Fix for the __determine_data_type() method. The flags were not correctly checked. ........ r6909 \| bugman \| 2008-07-09 18:41:40 +0200 (Wed, 09 Jul 2008) \| 3 lines Created the tensor_5D automatically generated object to AlignTensorData. ........ r6910 \| bugman \| 2008-07-09 18:43:34 +0200 (Wed, 09 Jul 2008) \| 3 lines Fix for the addition of alignment tensor parameters in assemble_param_vector(). ........ r6911 \| bugman \| 2008-07-09 18:55:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixes for the func_population() method. ........ r6912 \| bugman \| 2008-07-09 19:04:20 +0200 (Wed, 09 Jul 2008) \| 6 lines Changed the initialisation of the N_state_opt class. The rdcs, rdc_errors, and xh_vect args are now all expected to be numpy matricies. The rdcs and rdc_errors matricies have also been transposed! ........ r6913 \| bugman \| 2008-07-09 19:13:45 +0200 (Wed, 09 Jul 2008) \| 3 lines Converted the RDC and unit vector lists in minimise_setup_rdcs() to numpy matrices. ........ r6914 \| bugman \| 2008-07-09 19:15:11 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the incorrect testing for the presence of RDC errors. ........ r6915 \| bugman \| 2008-07-09 19:15:33 +0200 (Wed, 09 Jul 2008) \| 3 lines Missing import. ........ r6916 \| bugman \| 2008-07-09 19:16:32 +0200 (Wed, 09 Jul 2008) \| 3 lines Initialised the back calculated RDC array. ........ r6917 \| bugman \| 2008-07-09 19:18:04 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed all the broken references to self.rdcs_back_calc. ........ r6918 \| bugman \| 2008-07-09 19:21:47 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the calculation of the total number of spins and alignments. ........ r6919 \| bugman \| 2008-07-09 19:23:48 +0200 (Wed, 09 Jul 2008) \| 3 lines Fixed the setting up of RDC errors when missing. These should be 1.0, not 0.0! ........ r6920 \| bugman \| 2008-07-09 19:35:48 +0200 (Wed, 09 Jul 2008) \| 5 lines Fixed the setting up of self.rdc_errors when no errors are present. Retard, 1.0 times another matrix does not make a matrix of ones! ........ r6921 \| bugman \| 2008-07-09 19:40:11 +0200 (Wed, 09 Jul 2008) \| 3 lines The population weights are now taken into account in the func_population() target function. ........ r6922 \| bugman \| 2008-07-09 19:40:53 +0200 (Wed, 09 Jul 2008) \| 3 lines Added some more comments. ........ r6923 \| bugman \| 2008-07-09 19:41:54 +0200 (Wed, 09 Jul 2008) \| 3 lines The weights are passed into average_rdc_5D() as a keyword to make them optional. ........ r6924 \| bugman \| 2008-07-09 19:44:35 +0200 (Wed, 09 Jul 2008) \| 3 lines Converted average_rdc_5D() to expect a numpy array for the 5D tensor. ........ r6925 \| bugman \| 2008-07-09 19:45:05 +0200 (Wed, 09 Jul 2008) \| 3 lines The 5D tensor is passed directly into average_rdc_5D() from func_population(). ........ r6926 \| bugman \| 2008-07-09 19:52:22 +0200 (Wed, 09 Jul 2008) \| 3 lines Added weights to the average_rdc_5D() function. ........ r6927 \| bugman \| 2008-07-09 19:53:41 +0200 (Wed, 09 Jul 2008) \| 3 lines Added weights to the average_rdc_tensor() function. ........ r6928 \| bugman \| 2008-07-09 19:54:24 +0200 (Wed, 09 Jul 2008) \| 3 lines Docstring fixes. ........ r6929 \| bugman \| 2008-07-10 09:43:16 +0200 (Thu, 10 Jul 2008) \| 3 lines Redesigned the disassemble_param_vector() method for the multiple N-state model types. ........ r6930 \| bugman \| 2008-07-10 10:06:29 +0200 (Thu, 10 Jul 2008) \| 3 lines Updated the param_num() method to take the various models into account. ........ r6931 \| bugman \| 2008-07-10 10:54:29 +0200 (Thu, 10 Jul 2008) \| 3 lines Fix for the counting of header lines. The residue or spin number need not be supplied. ........ r6932 \| bugman \| 2008-07-10 13:26:51 +0200 (Thu, 10 Jul 2008) \| 3 lines Wrote the __assemble_scaling_matrix() method for creating a scaling matrix for the N-state model. ........ r6933 \| bugman \| 2008-07-10 13:30:26 +0200 (Thu, 10 Jul 2008) \| 3 lines Made diagonal scaling optional. ........ r6934 \| bugman \| 2008-07-10 13:42:41 +0200 (Thu, 10 Jul 2008) \| 3 lines Made some more use of the scaling matrix. ........ r6935 \| bugman \| 2008-07-10 13:43:36 +0200 (Thu, 10 Jul 2008) \| 3 lines Unscaled the parameter vector after optimisation. ........ r6936 \| bugman \| 2008-07-10 13:44:25 +0200 (Thu, 10 Jul 2008) \| 3 lines Missing import fix. ........ r6937 \| bugman \| 2008-07-10 13:51:21 +0200 (Thu, 10 Jul 2008) \| 3 lines The minimisation code now uses the scaling matrix. ........ r6938 \| bugman \| 2008-07-10 14:46:35 +0200 (Thu, 10 Jul 2008) \| 3 lines Inverted the population scaling factor in __assemble_scaling_matrix(). ........ r6941 \| bugman \| 2008-07-23 11:27:38 +0200 (Wed, 23 Jul 2008) \| 3 lines Started to add the framework for the addition of gradients and Hessians. ........ r6942 \| bugman \| 2008-07-23 11:47:41 +0200 (Wed, 23 Jul 2008) \| 3 lines Split the rdc module in half, shifting the alignment tensor components into their own module. ........ r6943 \| bugman \| 2008-07-23 11:48:36 +0200 (Wed, 23 Jul 2008) \| 3 lines Import fixes. ........ r6944 \| bugman \| 2008-07-23 13:33:22 +0200 (Wed, 23 Jul 2008) \| 3 lines Wrote functions for all the alignment tensor gradients. ........ r6945 \| bugman \| 2008-07-23 13:36:31 +0200 (Wed, 23 Jul 2008) \| 3 lines Fixes for the alignment tensor gradient function code. ........ r6952 \| bugman \| 2008-07-24 14:49:13 +0200 (Thu, 24 Jul 2008) \| 3 lines A lot of modifications to the population N-state model optimisation code. ........ r6957 \| bugman \| 2008-07-24 15:22:13 +0200 (Thu, 24 Jul 2008) \| 3 lines Spelling fix for the word 'indices'. ........ r6958 \| bugman \| 2008-07-24 16:54:46 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed the setting up of optimisation of the population N-state model. ........ r6959 \| bugman \| 2008-07-24 16:55:09 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed the call to to_tensor(). ........ r6960 \| bugman \| 2008-07-24 17:00:43 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixes for the func_population() target function. ........ r6961 \| bugman \| 2008-07-24 17:02:21 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixes for the setup of the N-state model optimisation code. ........ r6962 \| bugman \| 2008-07-24 17:03:06 +0200 (Thu, 24 Jul 2008) \| 3 lines Missing import. ........ r6963 \| bugman \| 2008-07-24 17:07:34 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed a call to the non-existant chi2_element() function (should be to chi2()). ........ r6964 \| bugman \| 2008-07-24 17:07:59 +0200 (Thu, 24 Jul 2008) \| 3 lines Fixed some index names. ........ r6965 \| bugman \| 2008-07-24 17:31:20 +0200 (Thu, 24 Jul 2008) \| 3 lines Large expansion of the dfunc_population() docstring. ........ r6966 \| bugman \| 2008-07-25 10:04:15 +0200 (Fri, 25 Jul 2008) \| 3 lines More rewriting of the population N-state model optimisation code. ........ r6967 \| bugman \| 2008-07-25 11:19:15 +0200 (Fri, 25 Jul 2008) \| 5 lines Wrote the average_rdc_tensor_dDij_dAmn() function. This calculates the ensemble averaged RDC gradient element for the Amn partial derivative. ........ r6968 \| bugman \| 2008-07-25 11:21:34 +0200 (Fri, 25 Jul 2008) \| 3 lines Fixed the N-state model code to use the renamed averaged RDC functions. ........ r6969 \| bugman \| 2008-07-25 11:27:44 +0200 (Fri, 25 Jul 2008) \| 3 lines Added a missing import. ........ r6970 \| bugman \| 2008-07-25 11:47:49 +0200 (Fri, 25 Jul 2008) \| 9 lines Wrote the dipolar_constant() function for calculating the dipolar constant. The constant is defined as: mu0 gI.gS.h_bar d = - --- ----------- 4pi r3 ........ r6971 \| bugman \| 2008-07-25 11:49:58 +0200 (Fri, 25 Jul 2008) \| 3 lines Pre-calculated the dipolar constants prior to optimisation. ........ r6972 \| bugman \| 2008-07-25 11:51:42 +0200 (Fri, 25 Jul 2008) \| 3 lines Updated a comment describing why the dipolar constant is multiplied by 3/(2pi). ........ r6973 \| bugman \| 2008-07-25 12:03:53 +0200 (Fri, 25 Jul 2008) \| 3 lines Updated the is_spin_param() method to make a few parameters spin specific. ........ r6974 \| bugman \| 2008-07-25 13:19:18 +0200 (Fri, 25 Jul 2008) \| 3 lines Added a dummy data_init() method to the Common_functions base class. ........ r6975 \| bugman \| 2008-07-25 13:22:27 +0200 (Fri, 25 Jul 2008) \| 3 lines Typo bug fix. ........ r6976 \| bugman \| 2008-07-25 13:24:57 +0200 (Fri, 25 Jul 2008) \| 3 lines Bug fix for the ave_rdc_tensor_dDij_dAmn() function. A numpy array cannot be appended to! ........ r6977 \| bugman \| 2008-07-25 13:53:38 +0200 (Fri, 25 Jul 2008) \| 3 lines Docstring improvements for the ave_rdc_tensor() function. ........ r6978 \| bugman \| 2008-07-25 14:06:08 +0200 (Fri, 25 Jul 2008) \| 3 lines Wrote the function rdc_tensor() to calculate the standard RDC. ........ r6979 \| bugman \| 2008-07-25 14:12:21 +0200 (Fri, 25 Jul 2008) \| 3 lines Created the pc partial derivative part of the RDC gradient. ........ r6980 \| bugman \| 2008-07-25 14:13:27 +0200 (Fri, 25 Jul 2008) \| 3 lines Removed a stray comment. ........ r6981 \| bugman \| 2008-07-25 14:37:41 +0200 (Fri, 25 Jul 2008) \| 3 lines The chi-squared gradient is now calculated. ........ r6982 \| bugman \| 2008-07-25 14:38:40 +0200 (Fri, 25 Jul 2008) \| 3 lines Sent the dipolar constant into the ave_rdc_tensor() function. ........ r6983 \| bugman \| 2008-07-25 14:48:34 +0200 (Fri, 25 Jul 2008) \| 3 lines The dipolar constant is now accepted by the RDC functions. ........ r6984 \| bugman \| 2008-07-25 14:49:29 +0200 (Fri, 25 Jul 2008) \| 3 lines Removed the unused setup_population_eqi() method. ........ r6985 \| bugman \| 2008-07-25 14:57:42 +0200 (Fri, 25 Jul 2008) \| 3 lines No need to multiply by 1.0 to return a copy at the end - the gradient is reset at the start. ........ r6986 \| bugman \| 2008-07-28 14:34:21 +0200 (Mon, 28 Jul 2008) \| 5 lines Changes to the linear_constraints() method. The method is now private and accepts new arguments for the different types of N-state model. ........ r6987 \| bugman \| 2008-07-28 14:37:24 +0200 (Mon, 28 Jul 2008) \| 3 lines Fixed the creation of the A and b constraint matrices. ........ r6988 \| bugman \| 2008-07-28 14:59:26 +0200 (Mon, 28 Jul 2008) \| 3 lines Made the assemble_param_vector() and disassemble_param_vector() methods private. ........ r6989 \| bugman \| 2008-07-28 15:17:00 +0200 (Mon, 28 Jul 2008) \| 3 lines Passed the data_type variable into the __disassemble_param_vector() method. ........ r6990 \| bugman \| 2008-07-28 15:25:01 +0200 (Mon, 28 Jul 2008) \| 3 lines The data_type arg is now accepted by __disassemble_param_vector(). ........ r6991 \| bugman \| 2008-07-28 15:29:53 +0200 (Mon, 28 Jul 2008) \| 6 lines Bug fix for the __disassemble_param_vector() method. The parameter vector with alignment tensor parameters is now properly split into the alignment tensor components and probabilities. ........ r6992 \| bugman \| 2008-07-28 19:18:06 +0200 (Mon, 28 Jul 2008) \| 3 lines Inverted the population parameter scaling factor to 100. ........ r7021 \| bugman \| 2008-07-29 18:56:31 +0200 (Tue, 29 Jul 2008) \| 3 lines Fix in grid_search() for the checking of the set up of the N-state model. ........ r7029 \| bugman \| 2008-07-30 10:02:45 +0200 (Wed, 30 Jul 2008) \| 3 lines Added the ability to handle missing RDCs. ........ r7076 \| bugman \| 2008-08-07 15:11:42 +0200 (Thu, 07 Aug 2008) \| 3 lines Docstring fix for the rdc_tensor() function. ........ r7077 \| bugman \| 2008-08-07 15:28:28 +0200 (Thu, 07 Aug 2008) \| 3 lines Created a module for the calculation of the pseudocontact shift (and its gradient and Hessian). ........ r7080 \| bugman \| 2008-08-07 16:26:06 +0200 (Thu, 07 Aug 2008) \| 5 lines Pseudocontact shifts are supported by the N_state_opt.__init__() method. The target functions still need to be updated. ........ r7081 \| bugman \| 2008-08-07 16:39:06 +0200 (Thu, 07 Aug 2008) \| 3 lines Spelling fix in the docstrings. ........ r7082 \| bugman \| 2008-08-07 16:40:36 +0200 (Thu, 07 Aug 2008) \| 3 lines Modified the func_population() target function to handle both RDCs and PCSs. ........ r7083 \| bugman \| 2008-08-07 16:53:06 +0200 (Thu, 07 Aug 2008) \| 3 lines Modified the dfunc_population() gradient function to handle both RDCs and PCSs. ........ r7084 \| bugman \| 2008-08-07 16:56:29 +0200 (Thu, 07 Aug 2008) \| 3 lines Set up the rdc and pcs flags in the __init__() method. ........ r7085 \| bugman \| 2008-08-07 16:57:37 +0200 (Thu, 07 Aug 2008) \| 3 lines Import fix. ........ r7086 \| bugman \| 2008-08-07 16:58:35 +0200 (Thu, 07 Aug 2008) \| 3 lines Renamed ave_pcs_tensor_ddelta_ij_dAmn() to ave_pcs_tensor_ddeltaij_dAmn() for consistency. ........ r7087 \| bugman \| 2008-08-07 18:04:30 +0200 (Thu, 07 Aug 2008) \| 3 lines Spelling fix in the docstrings. ........ r7088 \| bugman \| 2008-08-07 19:21:09 +0200 (Thu, 07 Aug 2008) \| 3 lines Created the interfaces for the PCS user functions. ........ r7089 \| bugman \| 2008-08-07 19:30:26 +0200 (Thu, 07 Aug 2008) \| 3 lines Renamed the 'RDC identification string' to the 'alignment identification string'. ........ r7090 \| bugman \| 2008-08-07 19:37:08 +0200 (Thu, 07 Aug 2008) \| 3 lines Activated the PCS user functions. ........ r7091 \| bugman \| 2008-08-07 19:51:49 +0200 (Thu, 07 Aug 2008) \| 3 lines Created the generic_fns.pcs module, although nothing will work yet. ........ r7092 \| bugman \| 2008-08-07 19:53:10 +0200 (Thu, 07 Aug 2008) \| 3 lines Removed a useless function. ........ r7093 \| bugman \| 2008-08-07 19:53:50 +0200 (Thu, 07 Aug 2008) \| 3 lines Removed some more useless functions. ........ r7106 \| bugman \| 2008-08-08 10:03:54 +0200 (Fri, 08 Aug 2008) \| 3 lines Changed a lot of references from cdp.rdc_ids to cdp.align_tensors. ........ r7107 \| bugman \| 2008-08-08 10:08:27 +0200 (Fri, 08 Aug 2008) \| 3 lines Converted the read() function to handle PCS rather than RDC data. ........ r7108 \| bugman \| 2008-08-08 10:11:49 +0200 (Fri, 08 Aug 2008) \| 3 lines Created 2 new RelaxErrors for PCSs. ........ r7109 \| bugman \| 2008-08-08 10:20:41 +0200 (Fri, 08 Aug 2008) \| 3 lines Renamed __determine_data_type() to __base_data_type(). ........ r7110 \| bugman \| 2008-08-08 10:27:35 +0200 (Fri, 08 Aug 2008) \| 3 lines Redesigned __base_data_types() to determine all base data types, and return them as a list. ........ r7111 \| bugman \| 2008-08-08 10:33:31 +0200 (Fri, 08 Aug 2008) \| 3 lines Modified the __update_model() to handle both RDCs and PCSs. ........ r7112 \| bugman \| 2008-08-08 10:36:22 +0200 (Fri, 08 Aug 2008) \| 3 lines Fixed __base_data_types() to properly identify tensors as the base data source. ........ r7113 \| bugman \| 2008-08-08 10:46:34 +0200 (Fri, 08 Aug 2008) \| 3 lines Fixed all the calls to __base_data_types() and subsequent use of the returned list. ........ r7114 \| bugman \| 2008-08-08 10:47:39 +0200 (Fri, 08 Aug 2008) \| 3 lines Added a module docstring. ........ r7115 \| bugman \| 2008-08-08 11:17:22 +0200 (Fri, 08 Aug 2008) \| 5 lines Changed the way optimisation of the N-state model is set up. This will allow multiple base data types to be used simultaneously. ........ r7116 \| bugman \| 2008-08-08 11:22:06 +0200 (Fri, 08 Aug 2008) \| 3 lines A call is now made to assemble the PCS data necessary for optimisation. ........ r7117 \| bugman \| 2008-08-08 11:24:54 +0200 (Fri, 08 Aug 2008) \| 5 lines Fix for the __update_model() method. This was only working if both RDC and PCS data are supplied. ........ r7118 \| bugman \| 2008-08-08 11:26:18 +0200 (Fri, 08 Aug 2008) \| 3 lines Shifted the __update_model() method for fixing the alphabetical ordering of methods. ........ r7119 \| bugman \| 2008-08-08 11:27:48 +0200 (Fri, 08 Aug 2008) \| 3 lines Converted minimise_setup_rdcs() and minimise_setup_tensors() into private methods. ........ r7120 \| bugman \| 2008-08-08 11:59:09 +0200 (Fri, 08 Aug 2008) \| 5 lines Modified the N_state_opt class to accept PCS data. The __init__() docstring has been significantly expanded as well. ........ r7121 \| bugman \| 2008-08-08 16:19:24 +0200 (Fri, 08 Aug 2008) \| 3 lines Wrote the __minimise_setup_pcs() method. ........ r7130 \| bugman \| 2008-08-11 11:41:08 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the user function interface for setting the experimental temperature. ........ r7131 \| bugman \| 2008-08-11 11:42:40 +0200 (Mon, 11 Aug 2008) \| 3 lines Activated the temperature user function interface. ........ r7132 \| bugman \| 2008-08-11 11:49:53 +0200 (Mon, 11 Aug 2008) \| 3 lines Added a stub function generic_fns.temperature.set() to fix the missing import problem. ........ r7133 \| bugman \| 2008-08-11 11:51:42 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixed the setting up of the temperature user function. ........ r7134 \| bugman \| 2008-08-11 11:53:42 +0200 (Mon, 11 Aug 2008) \| 3 lines Allowed the temperature to be entered as a integer as well as a float. ........ r7135 \| bugman \| 2008-08-11 11:58:38 +0200 (Mon, 11 Aug 2008) \| 3 lines Completed the generic_fns.temperature.set() function. ........ r7136 \| bugman \| 2008-08-11 13:41:30 +0200 (Mon, 11 Aug 2008) \| 3 lines Made the experimental id string compulsory. ........ r7137 \| bugman \| 2008-08-11 13:47:44 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the user function interface for setting the spectrometer frequency of an experiment. ........ r7138 \| bugman \| 2008-08-11 13:49:13 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the frq and temperature modules to the __all__ list. ........ r7139 \| bugman \| 2008-08-11 13:59:01 +0200 (Mon, 11 Aug 2008) \| 3 lines Wrote the spectrometer frequency setting function generic_fns.frq.set(). ........ r7140 \| bugman \| 2008-08-11 14:00:37 +0200 (Mon, 11 Aug 2008) \| 3 lines Activated the frq.set() user function. ........ r7141 \| bugman \| 2008-08-11 14:02:47 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixes for the frq.set() user function. ........ r7142 \| bugman \| 2008-08-11 14:08:10 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the frq and temperature modules to the __all__ list. ........ r7143 \| bugman \| 2008-08-11 14:21:41 +0200 (Mon, 11 Aug 2008) \| 3 lines Create the interface for the pcs.centre() user function. ........ r7144 \| bugman \| 2008-08-11 14:53:55 +0200 (Mon, 11 Aug 2008) \| 3 lines Implemented the generic_fns.pcs.centre() function. ........ r7145 \| bugman \| 2008-08-11 15:11:40 +0200 (Mon, 11 Aug 2008) \| 3 lines The structure identifier arg is now used by the atom_loop() method. ........ r7146 \| bugman \| 2008-08-11 15:28:34 +0200 (Mon, 11 Aug 2008) \| 3 lines Fixed the atom_loop() call in __minimise_setup_pcs(). ........ r7148 \| bugman \| 2008-08-11 15:37:06 +0200 (Mon, 11 Aug 2008) \| 3 lines Wrote the pcs_constant() function to calculate the pseudocontact shift constant. ........ r7149 \| bugman \| 2008-08-11 15:41:13 +0200 (Mon, 11 Aug 2008) \| 3 lines Added Boltzmann's constant to the physical_constants module. ........ r7150 \| bugman \| 2008-08-11 16:01:02 +0200 (Mon, 11 Aug 2008) \| 8 lines Fixes for the PCS constant, as it is dependent on the indices i, j and c. These are: i, the experiment or alignment index, j, the spin index, c, the state index. ........ r7151 \| bugman \| 2008-08-11 16:48:36 +0200 (Mon, 11 Aug 2008) \| 3 lines Redesigned the __minimise_setup_pcs() method. ........ r7152 \| bugman \| 2008-08-11 18:45:14 +0200 (Mon, 11 Aug 2008) \| 3 lines Added the ave arg to the structure.load_spins() user function. ........ r7153 \| bugman \| 2008-08-11 18:46:21 +0200 (Mon, 11 Aug 2008) \| 3 lines Renamed the ave arg of structure.load_spins() to ave_pos. ........ r7154 \| bugman \| 2008-08-11 18:53:05 +0200 (Mon, 11 Aug 2008) \| 3 lines The load_spins() function is now either loading the average or all atom positions. ........ r7155 \| bugman \| 2008-08-11 19:42:13 +0200 (Mon, 11 Aug 2008) \| 5 lines Fixes for the __minimise_setup_pcs() method. Multi-dimensional arrays were not being properly created or referenced. ........ r7156 \| bugman \| 2008-08-12 09:39:46 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the call to __minimise_setup_pcs(). ........ r7157 \| bugman \| 2008-08-12 09:44:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the initialisation of the variables pcs, pcs_vect, and pcs_dj. ........ r7158 \| bugman \| 2008-08-12 09:52:32 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the N_state_opt.__init__() docstring. ........ r7159 \| bugman \| 2008-08-12 09:53:08 +0200 (Tue, 12 Aug 2008) \| 3 lines Placed the PCS constants into self. ........ r7160 \| bugman \| 2008-08-12 09:58:15 +0200 (Tue, 12 Aug 2008) \| 3 lines Converted the PCS constant data structure into a numpy array in __minimise_setup_pcs(). ........ r7161 \| bugman \| 2008-08-12 09:58:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed a typo bug. ........ r7162 \| bugman \| 2008-08-12 10:00:03 +0200 (Tue, 12 Aug 2008) \| 3 lines Bug fix for the ave_pcs_tensor() function. ........ r7163 \| bugman \| 2008-08-12 10:38:00 +0200 (Tue, 12 Aug 2008) \| 5 lines Modified the setup of the RDC data. Spins missing RDC data but other data now have rows of None appended to the data structures. ........ r7164 \| bugman \| 2008-08-12 10:43:24 +0200 (Tue, 12 Aug 2008) \| 3 lines Converted the RDC constant list into a numpy array. ........ r7165 \| bugman \| 2008-08-12 10:49:16 +0200 (Tue, 12 Aug 2008) \| 6 lines Fixes for the set up of the RDC constant array. None (or NaN after numpy converion) is placed into the list when other data exists but the RDC is missing. ........ r7166 \| bugman \| 2008-08-12 10:50:18 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the __init__() docstring. ........ r7167 \| bugman \| 2008-08-12 10:58:28 +0200 (Tue, 12 Aug 2008) \| 5 lines Bug fix for the target function. The RDC vector and PCS vectors are not the same! ........ r7168 \| bugman \| 2008-08-12 11:45:44 +0200 (Tue, 12 Aug 2008) \| 3 lines Big debugging of the N-state model setup, target, and gradient functions. ........ r7169 \| bugman \| 2008-08-12 11:49:07 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed some of the tests in the __init__() method. ........ r7170 \| bugman \| 2008-08-12 12:10:38 +0200 (Tue, 12 Aug 2008) \| 3 lines Scaled the PCS value from ppm to no units. ........ r7171 \| bugman \| 2008-08-12 12:11:27 +0200 (Tue, 12 Aug 2008) \| 3 lines Removed some commented out and no longer used code. ........ r7172 \| bugman \| 2008-08-12 12:15:06 +0200 (Tue, 12 Aug 2008) \| 3 lines Shrunk the size of the default PCS errors, so the chi-squared value is comparable to the RDC. ........ r7173 \| bugman \| 2008-08-12 12:20:19 +0200 (Tue, 12 Aug 2008) \| 5 lines Fix for the paramagnetic centre to nucleus distances. The distances are now converted from Angstrom to meters. ........ r7174 \| bugman \| 2008-08-12 12:33:19 +0200 (Tue, 12 Aug 2008) \| 3 lines Changed the PCS scaling factor. ........ r7175 \| bugman \| 2008-08-12 14:34:12 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for all the N-state model unit tests. ........ r7176 \| bugman \| 2008-08-12 14:46:48 +0200 (Tue, 12 Aug 2008) \| 3 lines Added a test to see if the model has been selected. ........ r7177 \| bugman \| 2008-08-12 14:47:32 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixed the test___assemble_param_vector() unit test. ........ r7178 \| bugman \| 2008-08-12 14:53:24 +0200 (Tue, 12 Aug 2008) \| 3 lines Added a test to __disassemble_param_vector() to set if the model has been selected. ........ r7179 \| bugman \| 2008-08-12 14:54:19 +0200 (Tue, 12 Aug 2008) \| 3 lines Fixes for the test___disassemble_param_vector() unit test. ........ r7180 \| bugman \| 2008-08-12 15:05:39 +0200 (Tue, 12 Aug 2008) \| 3 lines Set the 2-domain N-state model gradient and Hessian methods to None. ........ r7181 \| bugman \| 2008-08-12 15:09:22 +0200 (Tue, 12 Aug 2008) \| 3 lines Allowed the align_tensor.display() arg to be None (to display all tensors). ........ r7182 \| bugman \| 2008-08-12 15:15:52 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the display() function to allow all alignment tensors to be displayed. ........ r7183 \| bugman \| 2008-08-12 15:33:09 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the N-state model methods to set the alignment tensor parameter rather Saupe order matrix. ........ r7184 \| bugman \| 2008-08-12 15:34:37 +0200 (Tue, 12 Aug 2008) \| 5 lines Changed the list of modifiable alignment tensor objects. Alignment tensor parameters rather than Saupe order matrix elements can now be changed. ........ r7185 \| bugman \| 2008-08-12 17:04:13 +0200 (Tue, 12 Aug 2008) \| 3 lines Updated the set() function to set the alignment tensor parameters rather than Saupe order matrix. ........ r7186 \| bugman \| 2008-08-12 17:16:06 +0200 (Tue, 12 Aug 2008) \| 3 lines Modified the unit tests of the alignment tensor objects to use Axx rather than Sxx, etc. ........ r7187 \| bugman \| 2008-08-12 17:47:57 +0200 (Tue, 12 Aug 2008) \| 6 lines Modified the alignment tensor objects. These are now storing everything as alignment tensor parameters rather than Saupe order matrix components and hence all the updating functions have been modified to match. ........ r7188 \| bugman \| 2008-08-12 17:48:27 +0200 (Tue, 12 Aug 2008) \| 3 lines Loosened some unit tests for the alignment tensor. ........ r7189 \| bugman \| 2008-08-12 17:49:53 +0200 (Tue, 12 Aug 2008) \| 3 lines Fix for the test_display_argfail_tensor() unit test. ........ r7191 \| bugman \| 2008-08-13 11:55:56 +0200 (Wed, 13 Aug 2008) \| 3 lines Added the ability to reload alignment tensors from the XML results file into the relax data store. ........ r7192 \| bugman \| 2008-08-14 11:31:10 +0200 (Thu, 14 Aug 2008) \| 10 lines Bug fixes and expansion of the __linear_constraints() method. The bug fix is that the b array was not being scaled! This is essential when diagonal scaling is active. The added feature is that the pN weight of state N, which is not a parameter of the model, is now constrained to be between 0 and 1. This is because the value is equal to 1 minus the sum of all other probabilities, hence linear constraints can be created. ........ r7193 \| bugman \| 2008-08-14 14:39:24 +0200 (Thu, 14 Aug 2008) \| 3 lines Wrote the model_statistics() method. ........ r7194 \| bugman \| 2008-08-14 14:49:45 +0200 (Thu, 14 Aug 2008) \| 3 lines Wrote the num_data_points() method for determining n. ........ r7195 \| bugman \| 2008-08-14 16:47:29 +0200 (Thu, 14 Aug 2008) \| 3 lines Added the pipe arg to the pcs.centre() user function. ........ r7196 \| bugman \| 2008-08-14 16:52:06 +0200 (Thu, 14 Aug 2008) \| 3 lines The data pipe arg is now accepted by the centre() function. ........ r7197 \| bugman \| 2008-08-14 16:56:46 +0200 (Thu, 14 Aug 2008) \| 3 lines Shifted the calculation of the paramagnetic centre from __minimise_setup_pcs() to centre(). ........ r7198 \| bugman \| 2008-08-14 16:57:58 +0200 (Thu, 14 Aug 2008) \| 3 lines Added a missing import and fixed an incorrect reference to the data pipe container. ........ r7199 \| bugman \| 2008-08-14 17:09:00 +0200 (Thu, 14 Aug 2008) \| 3 lines The calculated paramagnetic centre is now being placed into the current data pipe. ........ r7200 \| bugman \| 2008-08-14 17:09:41 +0200 (Thu, 14 Aug 2008) \| 3 lines Added a print out to the centre() function. ........ r7201 \| bugman \| 2008-08-15 10:09:17 +0200 (Fri, 15 Aug 2008) \| 5 lines Allowed the data column to be None in the rdc.read() user function. This allows a file containing only errors to be read. ........ r7202 \| bugman \| 2008-08-16 14:51:32 +0200 (Sat, 16 Aug 2008) \| 3 lines RDC errors can now be read separately and independently from the data values. ........ r7203 \| bugman \| 2008-08-17 18:25:44 +0200 (Sun, 17 Aug 2008) \| 3 lines Allowed the PCS data column to be None, so that a file with only PCS errors can be read. ........ r7204 \| bugman \| 2008-08-17 19:06:16 +0200 (Sun, 17 Aug 2008) \| 5 lines PCS errors in a file separate from the data can now be read. This matches the changes for the RDC at r7202. ........ r7205 \| bugman \| 2008-08-17 19:08:49 +0200 (Sun, 17 Aug 2008) \| 6 lines Reverted the last revision, r7204, as this included too much. The command used was: svn merge -r7204:7203 . ........ r7206 \| bugman \| 2008-08-17 19:10:17 +0200 (Sun, 17 Aug 2008) \| 5 lines Try 2: PCS errors in a file separate from the data can now be read. This matches the changes for the RDC at r7202, and is what r7204 should have been. ........ r7207 \| bugman \| 2008-08-17 19:12:21 +0200 (Sun, 17 Aug 2008) \| 5 lines The RDC and PCS errors data structures are now created by the __minimise_setup_() methods. These are also passed into the minimisation code. ........ r7208 \| bugman \| 2008-08-17 19:15:29 +0200 (Sun, 17 Aug 2008) \| 3 lines The RDC and PCS error data structures are now properly handled and setup in __init__(). ........ r7226 \| bugman \| 2008-08-23 02:37:51 +0200 (Sat, 23 Aug 2008) \| 3 lines Wrote the __minimise_bc_data() method to extract the back calculated data after minimisation. ........ r7227 \| bugman \| 2008-08-23 03:31:59 +0200 (Sat, 23 Aug 2008) \| 3 lines Wrote a function to calculate the RDC Q-factor. ........ r7230 \| bugman \| 2008-09-24 14:21:18 +0200 (Wed, 24 Sep 2008) \| 3 lines Some bug fixes and added the ability to calculate the Q-factor values. ........ r7231 \| bugman \| 2008-09-24 14:22:11 +0200 (Wed, 24 Sep 2008) \| 3 lines Small bug fix causing insignificant duplication of ID strings. ........ r7307 \| bugman \| 2008-09-25 18:19:41 +0200 (Thu, 25 Sep 2008) \| 5 lines Bug fix for the loading of results files when they contain not alignment tensor data. The bug was in the PipeContainer.from_xml() method. ........ ................ r7310 \| bugman \| 2008-09-25 18:31:04 +0200 (Thu, 25 Sep 2008) \| 3 lines Removed merge tracking for "svnmerge" for svn+ssh://bugman@.../svn/relax/branches/rdc_analysis ................	2008-09-25 16:45:20	Tree

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