Author: bugman
Date: Tue Dec 1 09:45:39 2009
New Revision: 10036
URL: http://svn.gna.org/viewcvs/relax?rev=10036&view=rev
Log:
Merged revisions 9998-10032 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9998 | bugman | 2009-11-27 16:00:04 +0100 (Fri, 27 Nov 2009) | 3 lines
Added the analysis specific API method is_spin_param() to the frame order
module.
........
r9999 | bugman | 2009-11-27 17:16:08 +0100 (Fri, 27 Nov 2009) | 3 lines
Docstring fixes for the value.set() user function.
........
r10000 | bugman | 2009-11-27 17:39:31 +0100 (Fri, 27 Nov 2009) | 5 lines
Renamed the 'prompt.check' module to the base relax directory module
'arg_check'.
This makes the module more available to other parts of relax that requires
argument type checking.
........
r10001 | bugman | 2009-11-27 17:53:43 +0100 (Fri, 27 Nov 2009) | 3 lines
Removed 'check' from the __all__ list.
........
r10002 | bugman | 2009-11-27 18:03:11 +0100 (Fri, 27 Nov 2009) | 3 lines
Fixed all the calls to the renamed 'arg_check' module.
........
r10003 | bugman | 2009-11-27 18:09:39 +0100 (Fri, 27 Nov 2009) | 5 lines
Specific analysis API clean up.
The get_param_name and get_param_value methods are returned by asking
directly for these names.
........
r10004 | bugman | 2009-11-27 18:29:15 +0100 (Fri, 27 Nov 2009) | 7 lines
Redesigned the specific analysis API for setting parameter values.
Now the set_param_values() method is to be provided. It is for setting
single parameter values.
This will be followed by a complete redesign of the value.set() user
function back end (which is
currently a mess).
........
r10005 | bugman | 2009-11-27 18:31:04 +0100 (Fri, 27 Nov 2009) | 3 lines
Added the set_param_values() method to the base API (matching the changes
of r9986).
........
r10006 | bugman | 2009-11-27 18:32:47 +0100 (Fri, 27 Nov 2009) | 6 lines
Massive simplification of the generic_fns.value.set() function.
This code was previously a mess, spread randomly across the generic code
and specific code. This is
a complete refactorization which will cause breakages for a little while.
........
r10007 | bugman | 2009-11-27 18:34:19 +0100 (Fri, 27 Nov 2009) | 5 lines
Deletion of the set_non_spin_params() method.
This mess is no longer in the base API.
........
r10008 | bugman | 2009-11-27 18:35:09 +0100 (Fri, 27 Nov 2009) | 3 lines
Fixed a typo in the new generic_fns.value.set() function.
........
r10009 | bugman | 2009-11-27 18:47:52 +0100 (Fri, 27 Nov 2009) | 3 lines
Fix for the call to set_param_values().
........
r10010 | bugman | 2009-11-28 20:23:51 +0100 (Sat, 28 Nov 2009) | 7 lines
Added 'HH' and 'HZ' to the amino acid atom names in __det_pdb_element().
This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at
https://mail.gna.org/public/relax-users/2009-11/msg00002.html (Message-id:
<AF0E494FAE984C0BB8D4C8CE521D621D@Mercurio>).
........
r10011 | bugman | 2009-11-29 15:01:19 +0100 (Sun, 29 Nov 2009) | 3 lines
Created a module for storing API methods common to different analysis types.
........
r10012 | bugman | 2009-11-29 15:02:14 +0100 (Sun, 29 Nov 2009) | 3 lines
Added the api_common module to the __all__ list.
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r10013 | bugman | 2009-11-29 15:20:13 +0100 (Sun, 29 Nov 2009) | 5 lines
Created the common API method _set_param_values_spin().
A number of modules are now using this method.
........
r10014 | bugman | 2009-11-29 15:23:13 +0100 (Sun, 29 Nov 2009) | 6 lines
Fix for the generic_fns.value.set() method.
The return_data_name() specific API method should have been used to send
the correct string into
default_value().
........
r10015 | bugman | 2009-11-30 10:16:38 +0100 (Mon, 30 Nov 2009) | 3 lines
Created the arg_check.is_list() function.
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r10016 | bugman | 2009-11-30 10:18:47 +0100 (Mon, 30 Nov 2009) | 3 lines
Added a unit test test_set_n_state_model_rx() for checking value.set() with
the N-state model.
........
r10017 | bugman | 2009-11-30 10:24:41 +0100 (Mon, 30 Nov 2009) | 5 lines
The base analysis API set_param_values() arguments have been changed.
The param and value args now must be lists. Only the docstring has been
modified.
........
r10018 | bugman | 2009-11-30 10:27:24 +0100 (Mon, 30 Nov 2009) | 3 lines
Modified the analysis API common method _set_param_values_spin() to accepts
lists as args.
........
r10019 | bugman | 2009-11-30 10:28:55 +0100 (Mon, 30 Nov 2009) | 6 lines
Analysis API fixes.
The param_names() and param_values() methods are now called
get_param_names() and
get_param_values().
........
r10020 | bugman | 2009-11-30 10:29:47 +0100 (Mon, 30 Nov 2009) | 3 lines
Created the set_param_values() API method for the N-state model.
........
r10021 | bugman | 2009-11-30 10:30:47 +0100 (Mon, 30 Nov 2009) | 3 lines
Created the set_param_values() API method for model-free analysis.
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r10022 | bugman | 2009-11-30 10:32:06 +0100 (Mon, 30 Nov 2009) | 5 lines
Fixes for the value.set() back-end to match the analysis API arg changes.
The param and value args should be lists.
........
r10023 | bugman | 2009-11-30 10:39:02 +0100 (Mon, 30 Nov 2009) | 3 lines
Modified the minimisation set() method to better match that of the analysis
API.
........
r10024 | bugman | 2009-11-30 14:32:58 +0100 (Mon, 30 Nov 2009) | 3 lines
Added a system test for the OpenDX space mapping for Euler angle frame
order parameters.
........
r10025 | bugman | 2009-11-30 14:36:37 +0100 (Mon, 30 Nov 2009) | 5 lines
Set all col args to None so that there are no automatic defaults.
The automatic defaults make it very difficult for users to debug scripts!!!
........
r10026 | bugman | 2009-11-30 14:44:05 +0100 (Mon, 30 Nov 2009) | 3 lines
Created the common method _set_param_values_global() for the analysis API.
........
r10027 | bugman | 2009-11-30 14:46:01 +0100 (Mon, 30 Nov 2009) | 3 lines
Wrote the arg_check.is_none() testing function.
........
r10028 | bugman | 2009-11-30 14:46:32 +0100 (Mon, 30 Nov 2009) | 3 lines
The frame order theory is now using the common _set_param_values_global()
analysis API method.
........
r10029 | bugman | 2009-11-30 15:16:05 +0100 (Mon, 30 Nov 2009) | 3 lines
Shifted the path of the new OpenDX frame order mapping system test.
........
r10030 | bugman | 2009-11-30 22:03:47 +0100 (Mon, 30 Nov 2009) | 3 lines
Significantly decreased the time required for the frame order mapping
system test.
........
r10031 | bugman | 2009-11-30 23:50:43 +0100 (Mon, 30 Nov 2009) | 6 lines
Converted all of the analysis API base methods into prototype methods.
These all now raise RelaxImplementError when called. All the analyses now
alias methods from the
api_common module (which were the original base methods).
........
r10032 | bugman | 2009-12-01 00:12:25 +0100 (Tue, 01 Dec 2009) | 3 lines
Added checks for spin specific, analysis API common methods to see if
model_info is a SpinContainer.
........
Added:
branches/multi_processor_merge/arg_check.py
- copied unchanged from r10032, 1.3/arg_check.py
branches/multi_processor_merge/specific_fns/api_common.py
- copied unchanged from r10032, 1.3/specific_fns/api_common.py
branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py
- copied unchanged from r10032,
1.3/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py
Removed:
branches/multi_processor_merge/prompt/check.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/generic_fns/eliminate.py
branches/multi_processor_merge/generic_fns/minimise.py
branches/multi_processor_merge/generic_fns/structure/internal.py
branches/multi_processor_merge/generic_fns/value.py
branches/multi_processor_merge/prompt/__init__.py
branches/multi_processor_merge/prompt/align_tensor.py
branches/multi_processor_merge/prompt/command.py
branches/multi_processor_merge/prompt/consistency_tests.py
branches/multi_processor_merge/prompt/dasha.py
branches/multi_processor_merge/prompt/deselect.py
branches/multi_processor_merge/prompt/diffusion_tensor.py
branches/multi_processor_merge/prompt/dx.py
branches/multi_processor_merge/prompt/eliminate.py
branches/multi_processor_merge/prompt/fix.py
branches/multi_processor_merge/prompt/frame_order.py
branches/multi_processor_merge/prompt/frq.py
branches/multi_processor_merge/prompt/grace.py
branches/multi_processor_merge/prompt/jw_mapping.py
branches/multi_processor_merge/prompt/minimisation.py
branches/multi_processor_merge/prompt/model_free.py
branches/multi_processor_merge/prompt/model_selection.py
branches/multi_processor_merge/prompt/molecule.py
branches/multi_processor_merge/prompt/molmol.py
branches/multi_processor_merge/prompt/monte_carlo.py
branches/multi_processor_merge/prompt/n_state_model.py
branches/multi_processor_merge/prompt/noe.py
branches/multi_processor_merge/prompt/palmer.py
branches/multi_processor_merge/prompt/pcs.py
branches/multi_processor_merge/prompt/pipe.py
branches/multi_processor_merge/prompt/pymol.py
branches/multi_processor_merge/prompt/rdc.py
branches/multi_processor_merge/prompt/relax_data.py
branches/multi_processor_merge/prompt/relax_fit.py
branches/multi_processor_merge/prompt/residue.py
branches/multi_processor_merge/prompt/results.py
branches/multi_processor_merge/prompt/select.py
branches/multi_processor_merge/prompt/sequence.py
branches/multi_processor_merge/prompt/spectrum.py
branches/multi_processor_merge/prompt/spin.py
branches/multi_processor_merge/prompt/state.py
branches/multi_processor_merge/prompt/structure.py
branches/multi_processor_merge/prompt/temperature.py
branches/multi_processor_merge/prompt/value.py
branches/multi_processor_merge/prompt/vmd.py
branches/multi_processor_merge/specific_fns/__init__.py
branches/multi_processor_merge/specific_fns/api_base.py
branches/multi_processor_merge/specific_fns/consistency_tests.py
branches/multi_processor_merge/specific_fns/frame_order.py
branches/multi_processor_merge/specific_fns/jw_mapping.py
branches/multi_processor_merge/specific_fns/model_free/__init__.py
branches/multi_processor_merge/specific_fns/model_free/main.py
branches/multi_processor_merge/specific_fns/n_state_model.py
branches/multi_processor_merge/specific_fns/noe.py
branches/multi_processor_merge/specific_fns/relax_fit.py
branches/multi_processor_merge/specific_fns/setup.py
branches/multi_processor_merge/test_suite/system_tests/frame_order.py
branches/multi_processor_merge/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/generic_fns/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/eliminate.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/minimise.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/internal.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/value.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/__init__.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/align_tensor.py?rev=10036&r1=10035&r2=10036&view=diff
Removed: branches/multi_processor_merge/prompt/check.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/check.py?rev=10035&view=auto
Modified: branches/multi_processor_merge/prompt/command.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/command.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/consistency_tests.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/dasha.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/deselect.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/deselect.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/diffusion_tensor.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/dx.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/eliminate.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/eliminate.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/fix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/fix.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/frame_order.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/frq.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/frq.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/grace.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/jw_mapping.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/minimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/minimisation.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/model_free.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/model_selection.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/molecule.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/molmol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/molmol.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/monte_carlo.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/monte_carlo.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/n_state_model.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/noe.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/palmer.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/pcs.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/pipe.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/pymol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/pymol.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/rdc.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/relax_data.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/relax_fit.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/residue.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/results.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/select.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/select.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/sequence.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/spectrum.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/spin.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/state.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/structure.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/temperature.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/temperature.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/value.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/prompt/vmd.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/prompt/vmd.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/__init__.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/specific_fns/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/api_base.py?rev=10036&r1=10035&r2=10036&view=diff
Modified: branches/multi_processor_merge/specific_fns/consistency_tests.py
[... 32 lines stripped ...]
r10036 - in /branches/multi_processor_merge: ./ generic_fns/ generic_fns/structure/ prompt/ specific_fns/ specific_fns/model...