Author: bugman
Date: Fri Oct 2 14:10:30 2015
New Revision: 27954
URL: http://svn.gna.org/viewcvs/relax?rev=27954&view=rev
Log:
Merged revisions 26015-26016,26019-26042,26047 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
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r26015 | bugman | 2014-09-24 17:01:32 +0200 (Wed, 24 Sep 2014) | 6 lines
Implemented the SciPy quadratic integration target function for the double
rotor frame order model.
This simply follows from what all the other quadratic integration target
functions and
lib.frame_order module functions do.
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r26016 | bugman | 2014-09-24 17:07:40 +0200 (Wed, 24 Sep 2014) | 6 lines
Changed the chi2 value checks in the
Frame_order.test_cam_quad_int_double_rotor* system tests.
These were the values for the quasi-random Sobol' integration and needed
updating for the SciPy
quadratic integration.
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r26019 | bugman | 2014-09-24 17:20:47 +0200 (Wed, 24 Sep 2014) | 6 lines
Removed the skip_tests argument for the Frame_order system tests __init__()
method.
This argument, which was used to manually turn on or off the blacklisted
tests, is no longer needed
due to the new --no-skip relax command line flag which will enable all
blacklisted tests.
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r26020 | bugman | 2014-09-24 17:50:52 +0200 (Wed, 24 Sep 2014) | 7 lines
The frame order auto-analysis Optimisation_settings object now supports the
quad_int flag.
This is for activating the SciPy quadratic integration. It is accepted as
an argument for the
add_grid() and add_min() methods, and it returned by the new
get_grid_quad_int() and
get_min_quad_int() methods.
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r26021 | bugman | 2014-09-24 18:43:46 +0200 (Wed, 24 Sep 2014) | 8 lines
Added the ability to specify a pre-run directory in the frame order
auto-analysis.
This will be used for refinement purposes. If the new pre_run_dir
argument, modelled on the
relaxation dispersion auto-analysis, is supplied then results files will be
loaded from this
directory and the base data pipe copying and PCS subset optimisation steps
will be skipped. The
model nesting algorithm is also deactivated.
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r26022 | bugman | 2014-09-24 18:51:21 +0200 (Wed, 24 Sep 2014) | 8 lines
Activated the SciPy quadratic integration in the frame order auto-analysis.
If the Optimisation_settings object has been set up with the quad_int flag,
then the auto-analysis
will skip the sobol_setup() method and instead directly call the
frame_order.quad_int user function.
Optimisation will then use the SciPy quadratic integration rather than the
quasi-random Sobol'
integration.
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r26023 | bugman | 2014-09-25 09:05:18 +0200 (Thu, 25 Sep 2014) | 7 lines
Improvements for the usage of the frame_order.quad_int user function in the
auto-analysis.
The frame_order.quad_int user function is now called even when the
Optimisation_settings object
quad_int flag is False. This allows for switching between the SciPy
quadratic integration and the
quasi-random Sobol' integration, as the SciPy quadratic integration can now
be turned off.
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r26024 | bugman | 2014-09-25 09:14:30 +0200 (Thu, 25 Sep 2014) | 3 lines
Additions to the frame order auto-analysis documentation.
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r26025 | bugman | 2014-09-25 09:39:41 +0200 (Thu, 25 Sep 2014) | 6 lines
Incorporated the contents of the summarise.py script into the frame order
auto-analysis module.
This has been converted into the summarise() function which will generate a
results summary table as
the analysis is still running.
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r26026 | bugman | 2014-09-25 10:20:42 +0200 (Thu, 25 Sep 2014) | 9 lines
Improved logic in the auto_analyses.frame_order.summarise() function.
The model names, directories and titles are now being auto-generated from
the full list of frame
order models in lib.frame_order.variables.MODEL_LIST.
To create a common mechanism for determining the model directory name, the
Frame_order_analysis.model_directory() method has been converted into a
module function.
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r26027 | bugman | 2014-09-25 10:24:12 +0200 (Thu, 25 Sep 2014) | 3 lines
The frame order auto-analysis now calls the summarise() function at the end
to create a summary table.
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r26028 | bugman | 2014-09-25 10:28:26 +0200 (Thu, 25 Sep 2014) | 3 lines
Shifted the final state saving in the frame order auto-analysis to be
within the safety of the try block.
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r26029 | bugman | 2014-09-25 10:30:28 +0200 (Thu, 25 Sep 2014) | 7 lines
Turned off the final state saving in the Frame_order.test_auto_analysis
system test.
This almost halves the time required for the test. A private class
variable _final_state has been
added to the auto_analyses.frame_order.Frame_order_analysis class which
when False will cause the
state saving step to be skipped.
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r26030 | bugman | 2014-09-25 10:30:57 +0200 (Thu, 25 Sep 2014) | 3 lines
Trailing whitespace cleanup.
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r26031 | bugman | 2014-09-25 10:40:46 +0200 (Thu, 25 Sep 2014) | 7 lines
The summarise() function call is now after saving the final state in the
frame order auto-analysis.
This is needed because the summarise() function will create a new set of
data pipes, loading the
results which already exist under a different pipe name in the relax data
store. Otherwise the
final state file is twice as big as it should be.
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r26032 | bugman | 2014-09-25 11:14:31 +0200 (Thu, 25 Sep 2014) | 6 lines
Incorporated the contents of count_sobol_points.py into the frame order
auto-analysis module.
The analysis script has been converted into the count_sobol_points()
function which will generate a
summary table of the number of quasi-random Sobol' points used for the PCS
numerical integration.
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r26033 | bugman | 2014-09-25 11:16:29 +0200 (Thu, 25 Sep 2014) | 5 lines
The frame order auto-analysis now calls the count_sobol_points() function
at the end.
This is to automatically create the Sobol' point summary table.
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r26034 | bugman | 2014-09-25 11:20:25 +0200 (Thu, 25 Sep 2014) | 7 lines
Fixes for the auto_analyses.frame_order.summerise() function.
If the count_sobol_points() function is called followed by summerise(), a
RelaxError will be raised
as the data pipe already exists. The summerise() function has been
modified to switch to the data
pipe if it already exists.
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r26035 | bugman | 2014-09-25 11:26:31 +0200 (Thu, 25 Sep 2014) | 5 lines
Expanded the frame order auto-analysis documentation.
This adds a description for the summarise() and count_sobol_points()
functions.
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r26036 | bugman | 2014-09-25 11:49:05 +0200 (Thu, 25 Sep 2014) | 9 lines
Elimination of most of the Frame_order.fixme_test_* system tests and
associated data.
These tests are from a very early stage of the development of the frame
order theory back when the
base data was the full and reduced alignment tensors for the each domain
calculated from the RDC
data. They do not fit into the current analysis where the base data is the
RDCs and PCSs for the
moving domain. There is no point upgrading the tests as it will be far too
much effort and it will
only duplicate the coverage of the Frame_order.test_cam_* system tests.
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r26037 | bugman | 2014-09-25 11:49:34 +0200 (Thu, 25 Sep 2014) | 3 lines
Updated the test_suite.system_tests.scripts.frame_order package __all__
list.
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r26038 | bugman | 2014-09-25 12:09:56 +0200 (Thu, 25 Sep 2014) | 3 lines
Renamed the Frame_order.fixme_test_opendx_map system test to
Frame_order.test_opendx_map to activate it.
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r26039 | bugman | 2014-09-25 13:19:59 +0200 (Thu, 25 Sep 2014) | 7 lines
Upgraded the Frame_order.test_opendx_map system test.
To upgrade from the ancient design to the current design so that the test
is functional and
relevant, this now uses the same setup as the
Frame_order.test_cam_qr_int_rigid user function.
Instead of performing optimisation, the test calls the dx.map user function.
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r26040 | bugman | 2014-09-25 13:26:16 +0200 (Thu, 25 Sep 2014) | 8 lines
Fix for the frame order specific API calculate() method.
This was caught by the Frame_order.test_opendx_map system test. The
scaling matrix was not being
specified by the dx.map user function backend and this was causing the
method to fail. Instead of
passing the non-existent scaling matrix into the target function, the
argument is simply ignored.
The scaling matrix has no effect on the minimise.calculate user function so
it is not necessary.
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r26041 | bugman | 2014-09-25 13:28:30 +0200 (Thu, 25 Sep 2014) | 7 lines
The verbosity flag is now being respected by the frame order specific API
calculate() method.
This silences the method when executing the dx.map user function. The chi2
value printout is
suppressed and the verbosity argument is being sent into the frame order
count_sobol_points()
function.
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r26042 | bugman | 2014-09-25 13:58:18 +0200 (Thu, 25 Sep 2014) | 3 lines
Added a section printout to the frame order auto-analysis when summary
tables are created.
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r26047 | bugman | 2014-09-26 10:02:47 +0200 (Fri, 26 Sep 2014) | 5 lines
The frame_order.simulate user function now defaults to creating a gzipped
PDB file.
This is to save room, and because most molecular viewers will automatically
read gzipped PDB files.
........
Removed:
trunk/test_suite/shared_data/frame_order/synth_tensors/
trunk/test_suite/system_tests/scripts/frame_order/model_calcs/
trunk/test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py
trunk/test_suite/system_tests/scripts/frame_order/parametric_restriction/
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/lib/frame_order/double_rotor.py
trunk/specific_analyses/frame_order/api.py
trunk/target_functions/frame_order.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/__init__.py
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
trunk/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py
trunk/user_functions/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/auto_analyses/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/frame_order.py?rev=27954&r1=27953&r2=27954&view=diff
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27954&r1=27953&r2=27954&view=diff
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27954&r1=27953&r2=27954&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27954&r1=27953&r2=27954&view=diff
Modified: trunk/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/frame_order.py?rev=27954&r1=27953&r2=27954&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/__init__.py?rev=27954&r1=27953&r2=27954&view=diff
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py?rev=27954&r1=27953&r2=27954&view=diff
Modified:
trunk/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py?rev=27954&r1=27953&r2=27954&view=diff
Removed:
trunk/test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py?rev=27953&view=auto
Modified: trunk/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/frame_order.py?rev=27954&r1=27953&r2=27954&view=diff
r27954 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_da...