Author: bugman Date: Wed Jan 7 14:40:39 2009 New Revision: 8284 URL: http://svn.gna.org/viewcvs/relax?rev=8284&view=rev Log: Merged revisions 8198-8212,8224,8226-8227,8230,8234,8237-8240,8245,8249-8282 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r8198 | bugman | 2008-12-12 00:06:08 +0100 (Fri, 12 Dec 2008) | 3 lines Fixed a typo bug in the centre() function. ........ r8199 | bugman | 2008-12-12 00:12:20 +0100 (Fri, 12 Dec 2008) | 3 lines Reverted r8198 and added the real fix for the centre() function. ........ r8200 | bugman | 2008-12-12 10:28:59 +0100 (Fri, 12 Dec 2008) | 3 lines Created a directory for putting a number of lactose structures into. ........ r8201 | bugman | 2008-12-12 10:29:31 +0100 (Fri, 12 Dec 2008) | 3 lines Shifted the lactose structure into the lactose directory. ........ r8202 | bugman | 2008-12-12 10:31:12 +0100 (Fri, 12 Dec 2008) | 3 lines Added 3 more lactose structures. ........ r8203 | bugman | 2008-12-12 10:44:12 +0100 (Fri, 12 Dec 2008) | 3 lines Created a directory for storing alignment data such as RDCs and PCSs. ........ r8204 | bugman | 2008-12-12 10:47:28 +0100 (Fri, 12 Dec 2008) | 3 lines Added some lactose RDC and PCS data. Note this is randomised and truncated for protection!!! ........ r8205 | bugman | 2008-12-12 10:56:09 +0100 (Fri, 12 Dec 2008) | 3 lines Added 10 tag PDB files for the lactose system test. ........ r8206 | bugman | 2008-12-12 10:57:13 +0100 (Fri, 12 Dec 2008) | 3 lines Added a system test script for the lactose N-state analysis using RDCs and PCSs. ........ r8207 | bugman | 2008-12-12 11:02:35 +0100 (Fri, 12 Dec 2008) | 3 lines Activated the lactose N-state model system test. ........ r8208 | bugman | 2008-12-12 11:05:28 +0100 (Fri, 12 Dec 2008) | 3 lines Fixes for the lactose PDB file reading system tests. The path to the files has changed! ........ r8209 | bugman | 2008-12-12 11:24:10 +0100 (Fri, 12 Dec 2008) | 6 lines Partial bug fix for the lactose N-state model system test. The bond vector returning function for the internal PDB reader was converting the atom_id to uppercase. This meant that molecule name corresponding to the file name was not matching! ........ r8210 | bugman | 2008-12-12 11:31:06 +0100 (Fri, 12 Dec 2008) | 7 lines Another bug fix for the load_pdb() internal structure object method. This was found by the lactose N-state model system test. The __fill_object_from_pdb() method was not being called properly and when loading multiple PDB files containing model information, the first would contain the atomic information of all files! ........ r8211 | bugman | 2008-12-12 16:07:07 +0100 (Fri, 12 Dec 2008) | 6 lines Created a new arg 'combine_models' to the structure.load_spins() user function. This will allow spins to be extracted separately for each model in an ensemble or for only one set of spins for all structures. ........ r8212 | bugman | 2008-12-12 16:31:37 +0100 (Fri, 12 Dec 2008) | 3 lines The combine_models flag is now effective in the load_spins() function. ........ r8224 | semor | 2008-12-23 17:04:48 +0100 (Tue, 23 Dec 2008) | 6 lines Many corrections of formatting. These were found using the relax 'code_validator' script (E. d'Auvergne) and mainly include trailing whitespaces and missing empty lines before functions. ........ r8226 | semor | 2009-01-06 19:30:55 +0100 (Tue, 06 Jan 2009) | 3 lines Corrected a small typo in the development chapter of the manual. ........ r8227 | semor | 2009-01-06 19:50:20 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8230 | semor | 2009-01-06 21:13:44 +0100 (Tue, 06 Jan 2009) | 3 lines Removed some unused imports. ........ r8234 | semor | 2009-01-06 21:38:49 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8237 | semor | 2009-01-06 21:54:22 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8238 | semor | 2009-01-06 21:58:29 +0100 (Tue, 06 Jan 2009) | 3 lines Removed unused imports. ........ r8239 | semor | 2009-01-06 22:02:54 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8240 | semor | 2009-01-06 22:07:04 +0100 (Tue, 06 Jan 2009) | 3 lines Removed another unused import... ........ r8245 | semor | 2009-01-06 22:27:39 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8249 | semor | 2009-01-06 23:32:30 +0100 (Tue, 06 Jan 2009) | 3 lines Removed unused imports. ........ r8250 | semor | 2009-01-06 23:36:25 +0100 (Tue, 06 Jan 2009) | 3 lines Removed an unused import. ........ r8251 | semor | 2009-01-06 23:39:45 +0100 (Tue, 06 Jan 2009) | 3 lines Removed more unused imports. ........ r8252 | semor | 2009-01-06 23:43:31 +0100 (Tue, 06 Jan 2009) | 3 lines Removed other unused imports. ........ r8253 | semor | 2009-01-06 23:55:48 +0100 (Tue, 06 Jan 2009) | 3 lines Removed unused imports. ........ r8254 | semor | 2009-01-06 23:59:48 +0100 (Tue, 06 Jan 2009) | 3 lines Removed more unused imports. ........ r8255 | semor | 2009-01-07 00:03:21 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8256 | semor | 2009-01-07 00:07:24 +0100 (Wed, 07 Jan 2009) | 3 lines Removed another unused import. ........ r8257 | semor | 2009-01-07 00:11:03 +0100 (Wed, 07 Jan 2009) | 3 lines Removed more unused imports. ........ r8258 | semor | 2009-01-07 00:18:05 +0100 (Wed, 07 Jan 2009) | 3 lines Removed another unused import. ........ r8259 | semor | 2009-01-07 00:21:37 +0100 (Wed, 07 Jan 2009) | 3 lines More unused imports removed. ........ r8260 | semor | 2009-01-07 00:24:55 +0100 (Wed, 07 Jan 2009) | 3 lines One more unused import removed. ........ r8261 | semor | 2009-01-07 00:31:07 +0100 (Wed, 07 Jan 2009) | 3 lines A few more unused imports removed. ........ r8262 | semor | 2009-01-07 00:34:29 +0100 (Wed, 07 Jan 2009) | 3 lines A few more unused imports removed. ........ r8263 | semor | 2009-01-07 00:37:39 +0100 (Wed, 07 Jan 2009) | 3 lines Removed one more unused import. ........ r8264 | semor | 2009-01-07 00:41:35 +0100 (Wed, 07 Jan 2009) | 3 lines Removed other unused imports. ........ r8265 | semor | 2009-01-07 00:47:44 +0100 (Wed, 07 Jan 2009) | 3 lines Again an unused import. ........ r8266 | semor | 2009-01-07 00:53:32 +0100 (Wed, 07 Jan 2009) | 3 lines Again, an unused import. ........ r8267 | semor | 2009-01-07 01:08:55 +0100 (Wed, 07 Jan 2009) | 3 lines A few more unused imports removed. ........ r8268 | semor | 2009-01-07 01:14:09 +0100 (Wed, 07 Jan 2009) | 3 lines Added a missing import and removed a few unused ones. ........ r8269 | semor | 2009-01-07 02:32:01 +0100 (Wed, 07 Jan 2009) | 3 lines Added a missing import. ........ r8270 | semor | 2009-01-07 02:56:38 +0100 (Wed, 07 Jan 2009) | 3 lines Added two missing imports. ........ r8271 | semor | 2009-01-07 03:01:43 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8272 | semor | 2009-01-07 03:04:29 +0100 (Wed, 07 Jan 2009) | 3 lines Removed more unused imports. ........ r8273 | semor | 2009-01-07 03:09:15 +0100 (Wed, 07 Jan 2009) | 3 lines Removed more unused imports. ........ r8274 | semor | 2009-01-07 03:12:22 +0100 (Wed, 07 Jan 2009) | 3 lines Removed another unused import. ........ r8275 | semor | 2009-01-07 03:25:00 +0100 (Wed, 07 Jan 2009) | 3 lines Added a missing import and removed an unused one. ........ r8276 | semor | 2009-01-07 03:34:14 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8277 | semor | 2009-01-07 03:37:13 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8278 | semor | 2009-01-07 03:40:15 +0100 (Wed, 07 Jan 2009) | 3 lines Removed another unused import. ........ r8279 | semor | 2009-01-07 03:43:14 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8280 | semor | 2009-01-07 03:53:52 +0100 (Wed, 07 Jan 2009) | 3 lines Removed more unused imports. ........ r8281 | semor | 2009-01-07 04:01:31 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ r8282 | semor | 2009-01-07 04:07:25 +0100 (Wed, 07 Jan 2009) | 3 lines Removed an unused import. ........ Added: branches/bmrb/test_suite/shared_data/align_data/ - copied from r8282, 1.3/test_suite/shared_data/align_data/ branches/bmrb/test_suite/shared_data/structures/lactose/ - copied from r8282, 1.3/test_suite/shared_data/structures/lactose/ branches/bmrb/test_suite/system_tests/scripts/lactose_n_state.py - copied unchanged from r8282, 1.3/test_suite/system_tests/scripts/lactose_n_state.py Removed: branches/bmrb/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb Modified: branches/bmrb/ (props changed) branches/bmrb/data/diff_tensor.py branches/bmrb/data/mol_res_spin.py branches/bmrb/data/pipe_container.py branches/bmrb/docs/latex/develop.tex branches/bmrb/generic_fns/align_tensor.py branches/bmrb/generic_fns/dasha.py branches/bmrb/generic_fns/eliminate.py branches/bmrb/generic_fns/fix.py branches/bmrb/generic_fns/grace.py branches/bmrb/generic_fns/model_selection.py branches/bmrb/generic_fns/mol_res_spin.py branches/bmrb/generic_fns/monte_carlo.py 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branches/bmrb/prompt/vmd.py branches/bmrb/relax_io.py branches/bmrb/sample_scripts/latex_mf_table.py branches/bmrb/specific_fns/base_class.py branches/bmrb/specific_fns/consistency_tests.py branches/bmrb/specific_fns/jw_mapping.py branches/bmrb/specific_fns/model_free/main.py branches/bmrb/specific_fns/n_state_model.py branches/bmrb/specific_fns/noe.py branches/bmrb/specific_fns/relax_fit.py branches/bmrb/test_suite/shared_data/structures/generate_str_internal_results.py branches/bmrb/test_suite/shared_data/structures/generate_str_scientific_results.py branches/bmrb/test_suite/system_tests/angles.py branches/bmrb/test_suite/system_tests/diffusion_tensor.py branches/bmrb/test_suite/system_tests/n_state_model.py branches/bmrb/test_suite/system_tests/peak_lists.py branches/bmrb/test_suite/system_tests/relax_fit.py branches/bmrb/test_suite/system_tests/scripts/5_state_xz.py branches/bmrb/test_suite/system_tests/structure.py branches/bmrb/test_suite/system_tests/unit_vectors.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/bmrb/data/diff_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/data/diff_tensor.py?rev=8284&r1=8283&r2=8284&view=diff Modified: branches/bmrb/data/mol_res_spin.py URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/data/mol_res_spin.py?rev=8284&r1=8283&r2=8284&view=diff Modified: branches/bmrb/data/pipe_container.py URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/data/pipe_container.py?rev=8284&r1=8283&r2=8284&view=diff Modified: branches/bmrb/docs/latex/develop.tex URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/latex/develop.tex?rev=8284&r1=8283&r2=8284&view=diff Modified: branches/bmrb/generic_fns/align_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/align_tensor.py?rev=8284&r1=8283&r2=8284&view=diff Modified: branches/bmrb/generic_fns/dasha.py URL: http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/dasha.py?rev=8284&r1=8283&r2=8284&view=diff 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