Author: bugman
Date: Fri Oct 2 12:39:07 2015
New Revision: 27948
URL: http://svn.gna.org/viewcvs/relax?rev=27948&view=rev
Log:
Merged revisions 24819-24823,24832-24836 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24819 | bugman | 2014-07-29 18:43:34 +0200 (Tue, 29 Jul 2014) | 5 lines
Missing import in the lib.frame_order.double_rotor module.
This was identified by the new Frame_order.test_auto_analysis system test.
........
r24820 | bugman | 2014-07-30 08:46:03 +0200 (Wed, 30 Jul 2014) | 7 lines
Updates and fixes for the frame order auto-analysis.
The custom grid setup now works for the new reduced parameter set models
and the double rotor model
is now also included. The cone axis alpha angle to spherical angle
conversion has had a bug
removed. And some of the printouts are now more detailed.
........
r24821 | bugman | 2014-07-30 09:34:22 +0200 (Wed, 30 Jul 2014) | 8 lines
Redesigned the Frame_order.test_auto_analysis system test.
This now uses a hypothetical new Optimisation_settings object from the
frame order auto-analysis
module for holding all of the grid search, zooming grid search and
minimisation settings. This will
allow for far greater user control of the settings and hugely simplify the
auto-analysis interface
by decreasing the number of input arguments. It should also be less
confusing.
........
r24822 | bugman | 2014-07-30 11:07:47 +0200 (Wed, 30 Jul 2014) | 16 lines
Implementation of the Optimisation_settings object in the frame order
auto-analysis.
This object holds all of the grid search, zooming grid search, and
minimisation settings. It
provides the add_grid() and add_min() methods to allow the user to add
successive iterations of
optimisation and settings to the object. The loop_grid() and loop_min()
methods are used to loop
over each iteration of each method. And the get_grid_inc(),
get_grid_num_int_pts(),
get_grid_zoom_level(), get_min_algor(), get_min_func_tol() and
get_min_num_int_pts() methods are
used to access the user defined settings.
The auto-analysis has been redesigned around this new concept. All of the
optimisation arguments
have been replaced. Instead there are the opt_rigid, opt_subset, opt_full,
and opt_mc arguments
which are expected to be instances of the Optimisation_settings object.
The optimisation in the
auto-analysis is now more advanced in that more user optimisation settings
are now available and
active.
........
r24823 | bugman | 2014-07-30 12:22:43 +0200 (Wed, 30 Jul 2014) | 9 lines
Added linear constraints for the pivot and average domain translation frame
order parameters.
The pivot coordinates are constrained between -999 and 999 Angstrom and the
translation between -500
and 500 Angstrom. This allows the frame_order.pdb_model user function to
operate in the case of
failed models - often the free rotors fitting to torsionally restricted
data - by preventing the PDB
coordinates from being out of the PDB format range. It should also speed
up optimisation by
stopping the optimisation of failed models earlier.
........
r24832 | bugman | 2014-07-30 14:26:15 +0200 (Wed, 30 Jul 2014) | 8 lines
The frame order auto-analysis Optimisation_settings object now handles the
maximum iterations.
The new max_iter argument has been added to the add_min() method, and the
new get_min_max_iter()
method added to fetch the value. This is used in the auto-analysis to set
the maximum number of
optimisation iterations in the minimise.execute user function calls.
Limiting this will be of
greatest benefit for the test suite.
........
r24833 | bugman | 2014-07-30 14:27:47 +0200 (Wed, 30 Jul 2014) | 7 lines
Speed up of the Frame_order.test_auto_analysis system test.
This involves limiting the maximum number of optimisation steps to 20 for
most parts (the rigid
model excluded so the average domain position is correctly found), and
using the PCS subset data for
the full data set.
........
r24834 | bugman | 2014-07-30 14:36:03 +0200 (Wed, 30 Jul 2014) | 6 lines
Updated the full_analysis.py script for the CaM frame order test data.
This is for the recent changes to the auto-analysis with the
Optimisation_settings object and for
the changes of this branch.
........
r24835 | bugman | 2014-07-30 14:38:21 +0200 (Wed, 30 Jul 2014) | 5 lines
Fix for the previous commit (r24834).
The results directory was incorrectly set.
........
r24836 | bugman | 2014-07-30 15:31:09 +0200 (Wed, 30 Jul 2014) | 10 lines
Removed the RDC data checks from the frame order optimisation.
This is in the minimise_setup_rdcs() and store_bc_data() functions of the
specific_analyses.frame_order.optimisation module, called before and after
all optimisation. The
reason was identified by profiling - this check was adding significant
amounts of time to the setup
and results unpacking parts of the optimisation. Specifically the
interatomic_loop() function was
identified via profiling as the function requiring the most amount of
cumulative time in the
Frame_order.test_auto_analysis system test (17 seconds out of a total of
~60 seconds).
........
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/lib/frame_order/double_rotor.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.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=27948&r1=27947&r2=27948&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=27948&r1=27947&r2=27948&view=diff
Modified: trunk/specific_analyses/frame_order/optimisation.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/optimisation.py?rev=27948&r1=27947&r2=27948&view=diff
Modified: trunk/specific_analyses/frame_order/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/parameters.py?rev=27948&r1=27947&r2=27948&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/full_analysis.py?rev=27948&r1=27947&r2=27948&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=27948&r1=27947&r2=27948&view=diff
r27948 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam...