Author: bugman
Date: Mon Jan 14 17:42:24 2008
New Revision: 4702
URL: http://svn.gna.org/viewcvs/relax?rev=4702&view=rev
Log:
Merged revisions 4618-4701 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
................
r4618 | bugman | 2008-01-10 21:40:40 +0100 (Thu, 10 Jan 2008) | 17 lines
Ported r4617 from the 1.2 line.
The command used was:
svn merge -r4616:4617 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r4617 | bugman | 2008-01-10 21:37:22 +0100 (Thu, 10 Jan 2008) | 6 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py
Modified the full_analysis.py script to be usable when no structure is
available.
This is in response to Sebastien's post at
https://mail.gna.org/public/relax-users/2008-01/msg00006.html.
.....
................
r4621 | semor | 2008-01-11 04:41:34 +0100 (Fri, 11 Jan 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-2505" from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.2
................
r4622 | semor | 2008-01-11 04:43:05 +0100 (Fri, 11 Jan 2008) | 20 lines
Merged revisions 4619-4620 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.2
........
r4619 | semor | 2008-01-10 16:38:09 -0500 (Thu, 10 Jan 2008) | 7 lines
Modified the full_analysis.py script so it can handle cases when no
residues need to be excluded.
This change was proposed in a post at:
https://mail.gna.org/public/relax-users/2008-01/msg00008.html (Message-id:
<47868730.1030205@xxxxxxxxx>)
........
r4620 | semor | 2008-01-10 16:43:29 -0500 (Thu, 10 Jan 2008) | 6 lines
Corrected a mistake.
The inverse of what was wanted was produced concerning the possibility of
not giving a file for
unresolved residues.
........
................
r4623 | bugman | 2008-01-11 09:24:03 +0100 (Fri, 11 Jan 2008) | 9 lines
Reverted r4621, the setting up of svnmerge properties from 1.2 to 1.3.
The following command did not work:
svn merge -r4621:4620 .
So instead the following command was used:
svn propdel svnmerge-integrated
................
r4659 | bugman | 2008-01-11 21:31:18 +0100 (Fri, 11 Jan 2008) | 6 lines
An import change to fix a circular import issue uncovered in the
consistency_tests_1.3 branch.
This was uncovered by Seb. See the thread starting at
https://mail.gna.org/public/relax-devel/2008-01/msg00042.html.
................
r4662 | bugman | 2008-01-13 12:07:18 +0100 (Sun, 13 Jan 2008) | 3 lines
Started to convert the model-free user functions to the new relax design.
................
r4663 | bugman | 2008-01-13 12:09:22 +0100 (Sun, 13 Jan 2008) | 6 lines
Deleted the model_free.copy() user function.
This function was not used anywhere within relax and the model-free
specific copy() method was
complete rubbish anyway (ancient, unused, broken code).
................
r4664 | bugman | 2008-01-13 12:15:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the run argument from all model-free user functions.
................
r4665 | bugman | 2008-01-13 12:16:34 +0100 (Sun, 13 Jan 2008) | 3 lines
Copyright update.
................
r4666 | bugman | 2008-01-13 12:26:29 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted all the res_num args to spin_id in the model-free user functions.
................
r4667 | bugman | 2008-01-13 12:31:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Added the framework for unit tests of the model-free user function args.
................
r4668 | bugman | 2008-01-13 12:41:52 +0100 (Sun, 13 Jan 2008) | 3 lines
Wrote 7 unit tests for all args of the model-free user functions.
................
r4669 | bugman | 2008-01-13 12:43:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.select_model() user function.
................
r4670 | bugman | 2008-01-13 12:44:04 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.create_model() user function.
................
r4671 | bugman | 2008-01-13 12:45:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.remove_tm() user function.
................
r4673 | bugman | 2008-01-13 12:48:43 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the model arg of the model_free.select_model() user function.
The testing of this arg started with and elif statement!!!
................
r4674 | bugman | 2008-01-13 12:53:06 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fixes for the model-free user function arg unit tests.
Some args had to be supplied in the unit tests to prevent RelaxErrors from
reaching the correct arg.
................
r4675 | bugman | 2008-01-13 12:57:32 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the params arg of the model_free.create_model() user function.
This arg is now properly checked.
................
r4676 | bugman | 2008-01-13 13:01:10 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the Model_free_main.__init__() method and converted its docstring
to that of the class.
................
r4677 | bugman | 2008-01-13 17:31:48 +0100 (Sun, 13 Jan 2008) | 5 lines
Renamed all the instantiated classes in specific_fns.__init__.
This is to avoid name clashes and the overwriting of the module names.
................
r4678 | bugman | 2008-01-13 17:37:05 +0100 (Sun, 13 Jan 2008) | 3 lines
Imported the specific_fns.model_free_obj object.
................
r4679 | bugman | 2008-01-13 18:19:08 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the create_model() model-free method to the new relax design.
................
r4680 | bugman | 2008-01-13 18:22:22 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the model_setup() model-free method to the new relax design.
................
r4681 | bugman | 2008-01-13 18:25:13 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the data_init() model-free method to the new relax design.
................
r4682 | bugman | 2008-01-13 18:26:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Updated the docstring of the model_setup() model-free method to be in
epydoc format.
................
r4683 | bugman | 2008-01-13 18:28:09 +0100 (Sun, 13 Jan 2008) | 5 lines
Added the missing import of the spin_loop.
The model 'm4' construction system test now passes.
................
r4684 | bugman | 2008-01-13 18:29:44 +0100 (Sun, 13 Jan 2008) | 3 lines
Fixes for all the unit tests of the generic_fns.value.partition_params()
function.
................
r4685 | bugman | 2008-01-13 18:32:16 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the select_model() model-free method to the new relax design.
................
r4686 | bugman | 2008-01-13 18:39:35 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the overfit_deselect() model-free method to the new relax design.
................
r4687 | bugman | 2008-01-13 18:43:26 +0100 (Sun, 13 Jan 2008) | 3 lines
Cleaned up the code of the overfit_deselect() model-free method.
................
r4688 | bugman | 2008-01-13 19:00:31 +0100 (Sun, 13 Jan 2008) | 5 lines
Converted the grid_search() model-free method to the new relax design.
The grid_search_setup() method has been merged into this method.
................
r4689 | bugman | 2008-01-13 19:03:55 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the system test of AIC model selection between two diffusion
tensors.
The diffusion tensor was not been properly set up.
................
r4690 | bugman | 2008-01-13 19:16:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Shifted all of the model-free optimisation related methods into a separate
module.
................
r4691 | bugman | 2008-01-13 19:16:32 +0100 (Sun, 13 Jan 2008) | 3 lines
Renamed the module to avoid a name clash.
................
r4692 | bugman | 2008-01-13 19:50:36 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_names() model-free method to the new relax
design.
................
r4693 | bugman | 2008-01-13 20:02:17 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_vector() model-free method to the new relax
design.
................
r4698 | semor | 2008-01-14 02:26:39 +0100 (Mon, 14 Jan 2008) | 3 lines
Added comments to the imports.
................
r4699 | semor | 2008-01-14 05:25:19 +0100 (Mon, 14 Jan 2008) | 3 lines
Added more comments to the imports.
................
r4700 | semor | 2008-01-14 05:31:50 +0100 (Mon, 14 Jan 2008) | 3 lines
Added somemore comments to the imports.
................
r4701 | semor | 2008-01-14 15:49:41 +0100 (Mon, 14 Jan 2008) | 3 lines
Added some comments to the imports and ordered imports alphabetically.
................
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/pipes.py
branches/N_state_model/maths_fns/chi2.py
branches/N_state_model/maths_fns/correlation_time.py
branches/N_state_model/maths_fns/direction_cosine.py
branches/N_state_model/maths_fns/jw_mapping.py
branches/N_state_model/maths_fns/jw_mf.py
branches/N_state_model/maths_fns/jw_mf_comps.py
branches/N_state_model/maths_fns/mf.py
branches/N_state_model/maths_fns/ri.py
branches/N_state_model/maths_fns/ri_comps.py
branches/N_state_model/maths_fns/weights.py
branches/N_state_model/minimise/bfgs.py
branches/N_state_model/minimise/cauchy_point.py
branches/N_state_model/minimise/constraint_linear.py
branches/N_state_model/minimise/coordinate_descent.py
branches/N_state_model/minimise/dogleg.py
branches/N_state_model/minimise/exact_trust_region.py
branches/N_state_model/minimise/fletcher_reeves_cg.py
branches/N_state_model/minimise/generic.py
branches/N_state_model/minimise/grid.py
branches/N_state_model/minimise/hessian_mods/cholesky.py
branches/N_state_model/minimise/hessian_mods/eigenvalue.py
branches/N_state_model/minimise/hessian_mods/gmw81.py
branches/N_state_model/minimise/hessian_mods/gmw81_old.py
branches/N_state_model/minimise/hessian_mods/se99.py
branches/N_state_model/minimise/hestenes_stiefel_cg.py
branches/N_state_model/minimise/levenberg_marquardt.py
branches/N_state_model/minimise/line_search/backtrack.py
branches/N_state_model/minimise/line_search/grace.py
branches/N_state_model/minimise/line_search/interpolate.py
branches/N_state_model/minimise/line_search/more_thuente.py
branches/N_state_model/minimise/line_search/nocedal_wright_interpol.py
branches/N_state_model/minimise/line_search/nocedal_wright_wolfe.py
branches/N_state_model/minimise/line_search/test_functions.py
branches/N_state_model/minimise/method_of_multipliers.py
branches/N_state_model/minimise/ncg.py
branches/N_state_model/minimise/newton.py
branches/N_state_model/minimise/polak_ribiere_cg.py
branches/N_state_model/minimise/polak_ribiere_plus_cg.py
branches/N_state_model/minimise/simplex.py
branches/N_state_model/minimise/steepest_descent.py
branches/N_state_model/minimise/steihaug_cg.py
branches/N_state_model/prompt/angles.py
branches/N_state_model/prompt/command.py
branches/N_state_model/prompt/dasha.py
branches/N_state_model/prompt/eliminate.py
branches/N_state_model/prompt/fix.py
branches/N_state_model/prompt/grace.py
branches/N_state_model/prompt/help.py
branches/N_state_model/prompt/interpreter.py
branches/N_state_model/prompt/jw_mapping.py
branches/N_state_model/prompt/model_free.py
branches/N_state_model/prompt/model_selection.py
branches/N_state_model/prompt/monte_carlo.py
branches/N_state_model/prompt/noe.py
branches/N_state_model/prompt/palmer.py
branches/N_state_model/prompt/relax_fit.py
branches/N_state_model/prompt/results.py
branches/N_state_model/prompt/tab_completion.py
branches/N_state_model/prompt/unselect.py
branches/N_state_model/prompt/view.py
branches/N_state_model/prompt/vmd.py
branches/N_state_model/sample_scripts/full_analysis.py
branches/N_state_model/sample_scripts/remap.py
branches/N_state_model/specific_fns/__init__.py
branches/N_state_model/specific_fns/model_free/__init__.py
branches/N_state_model/specific_fns/model_free/model_free.py
branches/N_state_model/test_suite/system_tests/model_selection.py
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_value.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/pipes.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/chi2.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/chi2.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/correlation_time.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/correlation_time.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/direction_cosine.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/direction_cosine.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mapping.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/jw_mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mf.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/jw_mf_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/jw_mf_comps.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/mf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/mf.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/ri.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/ri_comps.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/ri_comps.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/maths_fns/weights.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/maths_fns/weights.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/bfgs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/bfgs.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/cauchy_point.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/cauchy_point.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/constraint_linear.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/constraint_linear.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/coordinate_descent.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/coordinate_descent.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/dogleg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/dogleg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/exact_trust_region.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/exact_trust_region.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/fletcher_reeves_cg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/fletcher_reeves_cg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/generic.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/generic.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/grid.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/grid.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hessian_mods/cholesky.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hessian_mods/cholesky.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hessian_mods/eigenvalue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hessian_mods/eigenvalue.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hessian_mods/gmw81.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hessian_mods/gmw81.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hessian_mods/gmw81_old.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hessian_mods/gmw81_old.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hessian_mods/se99.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hessian_mods/se99.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/hestenes_stiefel_cg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/hestenes_stiefel_cg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/levenberg_marquardt.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/levenberg_marquardt.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/backtrack.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/backtrack.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/grace.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/interpolate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/interpolate.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/more_thuente.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/more_thuente.py?rev=4702&r1=4701&r2=4702&view=diff
Modified:
branches/N_state_model/minimise/line_search/nocedal_wright_interpol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/nocedal_wright_interpol.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/nocedal_wright_wolfe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/nocedal_wright_wolfe.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/line_search/test_functions.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/line_search/test_functions.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/method_of_multipliers.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/method_of_multipliers.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/ncg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/ncg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/newton.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/newton.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/polak_ribiere_cg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/polak_ribiere_cg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/polak_ribiere_plus_cg.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/polak_ribiere_plus_cg.py?rev=4702&r1=4701&r2=4702&view=diff
Modified: branches/N_state_model/minimise/simplex.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/minimise/simplex.py?rev=4702&r1=4701&r2=4702&view=diff
[... 87 lines stripped ...]
r4702 - in /branches/N_state_model: ./ generic_fns/ maths_fns/ minimise/ minimise/hessian_mods/ minimise/line_search/ prompt...