Author: bugman Date: Thu Oct 2 15:30:41 2008 New Revision: 7496 URL: http://svn.gna.org/viewcvs/relax?rev=7496&view=rev Log: Merged revisions 7443-7492 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/pipe_refs ........ r7443 | bugman | 2008-09-29 23:16:31 +0200 (Mon, 29 Sep 2008) | 3 lines Renamed the current() function to cdp_name() and created cdp() for returning the current data pipe. ........ r7444 | bugman | 2008-09-29 23:20:20 +0200 (Mon, 29 Sep 2008) | 3 lines Renamed cdp() to get_pipe() and allowed it to return any desired data pipe. ........ r7445 | bugman | 2008-09-29 23:27:47 +0200 (Mon, 29 Sep 2008) | 3 lines Removed all references to 'ds.current_pipe' by using the generic_fns.pipes API. ........ r7446 | bugman | 2008-09-29 23:56:26 +0200 (Mon, 29 Sep 2008) | 3 lines Replaced all refs to 'cdp = ds[ds.current_pipe]' with 'cdp = pipes.get_pipe()'. ........ r7447 | bugman | 2008-09-30 00:08:01 +0200 (Tue, 30 Sep 2008) | 3 lines Bug fix for the renamed current() to get_pipe() function. ........ r7448 | bugman | 2008-09-30 00:08:40 +0200 (Tue, 30 Sep 2008) | 3 lines Bug fix for the renaming of current() to cdp_name(). ........ r7449 | bugman | 2008-09-30 00:09:23 +0200 (Tue, 30 Sep 2008) | 3 lines Created the new function get_type() for returning the type of the data pipe. ........ r7450 | bugman | 2008-09-30 00:44:27 +0200 (Tue, 30 Sep 2008) | 3 lines Eliminated all mentions of 'ds[ds.current_pipe]' by using the generic_fns.pipes API. ........ r7451 | bugman | 2008-09-30 01:14:36 +0200 (Tue, 30 Sep 2008) | 3 lines Eliminated all access to 'ds.current_pipe' by using the API of generic_fns.pipes. ........ r7452 | bugman | 2008-09-30 16:32:09 +0200 (Tue, 30 Sep 2008) | 3 lines Removed all references to ds[key] by using the API of generic_fns.pipes. ........ r7453 | bugman | 2008-09-30 16:35:07 +0200 (Tue, 30 Sep 2008) | 3 lines Removed some unused imports of RelaxNoPipeError. ........ r7454 | bugman | 2008-09-30 16:37:24 +0200 (Tue, 30 Sep 2008) | 3 lines Removed a pile of unused and significantly out of date functions. ........ r7455 | bugman | 2008-09-30 16:44:59 +0200 (Tue, 30 Sep 2008) | 3 lines Removed unused RelaxNoPipeError imports and some old code. ........ r7456 | bugman | 2008-09-30 17:02:13 +0200 (Tue, 30 Sep 2008) | 3 lines Removed all unused imports of the relax data store. ........ r7457 | bugman | 2008-09-30 17:06:21 +0200 (Tue, 30 Sep 2008) | 6 lines Removed the columnar formatted results writing code. This is no longer necessary because of the universal XML results file. Found by searching for usage of the relax data store. ........ r7458 | bugman | 2008-09-30 17:16:15 +0200 (Tue, 30 Sep 2008) | 5 lines Converted the relax_curve_diff.py sample script to the new design. This was identified by the unnecessary import of the relax data storage object. ........ r7459 | bugman | 2008-09-30 17:17:52 +0200 (Tue, 30 Sep 2008) | 3 lines Documentation fix in the sample script. ........ r7460 | bugman | 2008-09-30 17:36:29 +0200 (Tue, 30 Sep 2008) | 5 lines Updated the latex_mf_table.py sample script to the new design. The problems were identified with the import of the relax data storage object. ........ r7461 | bugman | 2008-09-30 17:40:37 +0200 (Tue, 30 Sep 2008) | 3 lines Created the has_pipe() function for the pipes API. ........ r7462 | bugman | 2008-09-30 17:41:41 +0200 (Tue, 30 Sep 2008) | 3 lines Removed the dependence on the relax data store by using the pipes API. ........ r7463 | bugman | 2008-09-30 17:53:55 +0200 (Tue, 30 Sep 2008) | 3 lines Shifted the reset() functional code to generic_fns. ........ r7464 | bugman | 2008-09-30 18:01:09 +0200 (Tue, 30 Sep 2008) | 3 lines Converted the back_calc() function to the new relax design. ........ r7465 | bugman | 2008-09-30 18:05:11 +0200 (Tue, 30 Sep 2008) | 3 lines Created the pipes API function pipe_names() to get the list of all data pipes. ........ r7466 | bugman | 2008-09-30 18:09:42 +0200 (Tue, 30 Sep 2008) | 3 lines Removed the dependence on the relax data store. ........ r7467 | bugman | 2008-09-30 18:16:24 +0200 (Tue, 30 Sep 2008) | 7 lines Bug fix for the __set_diff_tensor() method for reading the tensor from a relax 1.2 results file. This was uncovered by searching for the relax data store. This store rather than the current data pipe was being accessed. The additional large bug found is that the diffusion tensor was referred to as 'diff' rather than 'diff_tensor'. ........ r7468 | bugman | 2008-09-30 18:17:30 +0200 (Tue, 30 Sep 2008) | 3 lines Removed the results writing methods. This is now done by the universal XML results file code. ........ r7469 | bugman | 2008-09-30 18:18:00 +0200 (Tue, 30 Sep 2008) | 3 lines Removed the unused relax data store. ........ r7470 | bugman | 2008-09-30 18:21:25 +0200 (Tue, 30 Sep 2008) | 3 lines Alphabetical ordering of the methods. ........ r7471 | bugman | 2008-10-01 13:39:36 +0200 (Wed, 01 Oct 2008) | 5 lines Converted the create_vector_dist() function to the new design. Again the problem was identified by looking at incorrect usage of the relax data store. ........ r7472 | bugman | 2008-10-01 13:40:17 +0200 (Wed, 01 Oct 2008) | 3 lines Removed a reference to 'run' in a comment. ........ r7473 | bugman | 2008-10-01 13:40:36 +0200 (Wed, 01 Oct 2008) | 3 lines Removed the unused import of the relax data store. ........ r7474 | bugman | 2008-10-01 13:44:12 +0200 (Wed, 01 Oct 2008) | 3 lines Created a new pipes API function, the pipe_loop(). ........ r7475 | bugman | 2008-10-01 13:46:39 +0200 (Wed, 01 Oct 2008) | 3 lines The structure objects now use the pipe_loop() in their load_pdb() methods. ........ r7476 | bugman | 2008-10-01 13:49:13 +0200 (Wed, 01 Oct 2008) | 3 lines Updated the delete() method to the new design. ........ r7477 | bugman | 2008-10-01 13:53:28 +0200 (Wed, 01 Oct 2008) | 3 lines Added the switch flag to pipes.create() so that the new pipe doesn't have to be switched to. ........ r7478 | bugman | 2008-10-01 14:05:12 +0200 (Wed, 01 Oct 2008) | 3 lines Clean up of duplicate_data(). ........ r7479 | bugman | 2008-10-01 14:06:45 +0200 (Wed, 01 Oct 2008) | 5 lines Converted the eliminate() method to the new design. Again identified by bad usage of the relax data store. ........ r7480 | bugman | 2008-10-01 14:07:54 +0200 (Wed, 01 Oct 2008) | 3 lines Fix for model_setup(), again bad usage of the relax data store. ........ r7481 | bugman | 2008-10-01 14:17:50 +0200 (Wed, 01 Oct 2008) | 3 lines Converted the deselect() method to the new design. ........ r7482 | bugman | 2008-10-01 14:18:08 +0200 (Wed, 01 Oct 2008) | 3 lines Removed the unused relax data store import. ........ r7483 | bugman | 2008-10-01 14:18:37 +0200 (Wed, 01 Oct 2008) | 3 lines Switched the eliminate function to use the new model_loop(). ........ r7484 | bugman | 2008-10-01 14:20:48 +0200 (Wed, 01 Oct 2008) | 3 lines Missing colon starting a loop. ........ r7485 | bugman | 2008-10-01 14:26:20 +0200 (Wed, 01 Oct 2008) | 3 lines Modified the pipe_loop() generator to return the name of the pipe, if asked for. ........ r7486 | bugman | 2008-10-01 15:52:50 +0200 (Wed, 01 Oct 2008) | 3 lines Fixed a circular import issue. ........ r7487 | bugman | 2008-10-01 16:00:43 +0200 (Wed, 01 Oct 2008) | 3 lines Fixes for the calls to the pipes functions. ........ r7488 | bugman | 2008-10-01 18:36:54 +0200 (Wed, 01 Oct 2008) | 3 lines Bug fix for the add_struct() method. The input structure container was being overwritten. ........ r7489 | bugman | 2008-10-02 13:30:04 +0200 (Thu, 02 Oct 2008) | 3 lines Variable name clash bug fix in load_pdb(). ........ r7490 | bugman | 2008-10-02 13:37:14 +0200 (Thu, 02 Oct 2008) | 3 lines Put back the condition to skip the current data pipe in searching for pre-loaded data in load_pdb(). ........ r7491 | bugman | 2008-10-02 13:42:27 +0200 (Thu, 02 Oct 2008) | 3 lines Bug fix introduced in r7490, '==' should have been used rather than '='. ........ r7492 | bugman | 2008-10-02 13:45:17 +0200 (Thu, 02 Oct 2008) | 5 lines Bug fix for the eliminate() function. 'i' is now called 'model_info' because of the switch to model_loop(). ........ Added: 1.3/generic_fns/reset.py - copied unchanged from r7492, branches/pipe_refs/generic_fns/reset.py Modified: 1.3/ (props changed) 1.3/data/align_tensor.py 1.3/data/mol_res_spin.py 1.3/generic_fns/align_tensor.py 1.3/generic_fns/angles.py 1.3/generic_fns/dasha.py 1.3/generic_fns/diffusion_tensor.py 1.3/generic_fns/eliminate.py 1.3/generic_fns/fix.py 1.3/generic_fns/frq.py 1.3/generic_fns/grace.py 1.3/generic_fns/intensity.py 1.3/generic_fns/minimise.py 1.3/generic_fns/model_selection.py 1.3/generic_fns/mol_res_spin.py 1.3/generic_fns/molmol.py 1.3/generic_fns/monte_carlo.py 1.3/generic_fns/palmer.py 1.3/generic_fns/pcs.py 1.3/generic_fns/pipes.py 1.3/generic_fns/pymol.py 1.3/generic_fns/rdc.py 1.3/generic_fns/relax_data.py 1.3/generic_fns/results.py 1.3/generic_fns/selection.py 1.3/generic_fns/sequence.py 1.3/generic_fns/structure/geometric.py 1.3/generic_fns/structure/internal.py 1.3/generic_fns/structure/main.py 1.3/generic_fns/structure/mass.py 1.3/generic_fns/structure/scientific.py 1.3/generic_fns/temperature.py 1.3/generic_fns/value.py 1.3/generic_fns/vmd.py 1.3/opendx/base_map.py 1.3/opendx/isosurface_3D.py 1.3/opendx/main.py 1.3/prompt/reset.py 1.3/sample_scripts/full_analysis.py 1.3/sample_scripts/generate_ri.py 1.3/sample_scripts/latex_mf_table.py 1.3/sample_scripts/relax_curve_diff.py 1.3/specific_fns/base_class.py 1.3/specific_fns/consistency_tests.py 1.3/specific_fns/hybrid.py 1.3/specific_fns/jw_mapping.py 1.3/specific_fns/model_free/main.py 1.3/specific_fns/model_free/mf_minimise.py 1.3/specific_fns/model_free/molmol.py 1.3/specific_fns/model_free/results.py 1.3/specific_fns/n_state_model.py 1.3/specific_fns/noe.py 1.3/specific_fns/relax_fit.py 1.3/test_suite/system_tests/angles.py 1.3/test_suite/system_tests/generic.py 1.3/test_suite/system_tests/load_spins.py 1.3/test_suite/system_tests/model_free.py 1.3/test_suite/system_tests/model_selection.py 1.3/test_suite/system_tests/n_state_model.py 1.3/test_suite/system_tests/nmrview.py 1.3/test_suite/system_tests/relax_fit.py 1.3/test_suite/system_tests/sequence.py 1.3/test_suite/system_tests/structure.py 1.3/test_suite/system_tests/unit_vectors.py 1.3/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py 1.3/test_suite/unit_tests/_generic_fns/test_pipes.py 1.3/test_suite/unit_tests/_generic_fns/test_selection.py 1.3/test_suite/unit_tests/_generic_fns/test_value.py 1.3/test_suite/unit_tests/_prompt/test_value.py 1.3/test_suite/unit_tests/_specific_fns/_model_free/test_main.py 1.3/test_suite/unit_tests/_specific_fns/test_n_state_model.py 1.3/test_suite/unit_tests/align_tensor_testing_base.py 1.3/test_suite/unit_tests/diffusion_tensor_testing_base.py 1.3/test_suite/unit_tests/molecule_testing_base.py 1.3/test_suite/unit_tests/relax_data_testing_base.py 1.3/test_suite/unit_tests/residue_testing_base.py 1.3/test_suite/unit_tests/sequence_testing_base.py 1.3/test_suite/unit_tests/spin_testing_base.py 1.3/test_suite/unit_tests/state_testing_base.py 1.3/test_suite/unit_tests/value_testing_base.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: 1.3/data/align_tensor.py URL: http://svn.gna.org/viewcvs/relax/1.3/data/align_tensor.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/data/mol_res_spin.py URL: http://svn.gna.org/viewcvs/relax/1.3/data/mol_res_spin.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/align_tensor.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/align_tensor.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/angles.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/angles.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/dasha.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/dasha.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/diffusion_tensor.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/diffusion_tensor.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/eliminate.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/eliminate.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/fix.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/fix.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/frq.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/frq.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/grace.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/grace.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/intensity.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/intensity.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/minimise.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/minimise.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/model_selection.py URL: 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http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pymol.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/rdc.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/relax_data.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/relax_data.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/results.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/results.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/selection.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/selection.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/sequence.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/structure/geometric.py URL: http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/generic_fns/structure/internal.py URL: 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1.3/sample_scripts/relax_curve_diff.py URL: http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/relax_curve_diff.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/base_class.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/base_class.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/consistency_tests.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/consistency_tests.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/hybrid.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/hybrid.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/jw_mapping.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/jw_mapping.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/model_free/main.py URL: http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=7496&r1=7495&r2=7496&view=diff Modified: 1.3/specific_fns/model_free/mf_minimise.py URL: 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