Author: bugman
Date: Fri Oct 2 13:41:38 2015
New Revision: 27949
URL: http://svn.gna.org/viewcvs/relax?rev=27949&view=rev
Log:
Merged revisions 24839-24840,25299-25301,25402,25416,25536-25537,25710-25711
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24839 | bugman | 2014-07-30 17:27:07 +0200 (Wed, 30 Jul 2014) | 8 lines
Fixes for the removal of the RDC data checks from the frame order
optimisation functions.
The specific analysis API method overfit_deselect() has now been created to
deselect spins which do
not have PCS data or interatomic data containers missing RDC data. The
handling of deselected spins
and interatomic data containers is now also correctly handled throughout
the frame order specific
code.
........
r24840 | bugman | 2014-07-30 17:27:48 +0200 (Wed, 30 Jul 2014) | 3 lines
Enabled pivot optimisation in the full_analysis.py script for the CaM frame
order test data.
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r25299 | bugman | 2014-08-26 17:31:19 +0200 (Tue, 26 Aug 2014) | 6 lines
The frame order auto-analysis now calls the time() user function.
This is used at the start of each model section, as well as at the very
start and very end of the
analysis. This feedback is needed for the user to be able to optimise the
optimisation settings.
........
r25300 | bugman | 2014-08-26 17:49:16 +0200 (Tue, 26 Aug 2014) | 8 lines
Major bugfix for the frame order auto-analysis.
The algorithm of using a PCS data subset of a few selected residues to find
an initial parameter
estimate followed by using all PCS data was badly implemented. The use of
the PCS subset caused
most spin systems to be deselected, however they remained deselected once
all data was being used.
So the result was that only the spin subset was ever being used in the
analysis.
........
r25301 | bugman | 2014-08-26 17:52:19 +0200 (Tue, 26 Aug 2014) | 3 lines
Removed some printouts accidentally committed in the previous revision.
........
r25402 | bugman | 2014-08-28 18:45:24 +0200 (Thu, 28 Aug 2014) | 3 lines
Fix for the recent lib.period_table and lib.physical_constant module
changes.
........
r25416 | bugman | 2014-08-29 10:11:58 +0200 (Fri, 29 Aug 2014) | 7 lines
Created the model_directory() method for the frame order auto-analysis.
This is used to create the full path for saving model specific files. It
replaces spaces with
underscores in the path and removes all commas. The commas in the path
appear to be fatal for
certain PyMOL versions when viewing the frame order representation.
........
r25536 | bugman | 2014-09-02 11:35:22 +0200 (Tue, 02 Sep 2014) | 3 lines
The frame order auto-analysis results printout has been extended to include
the pivot point.
........
r25537 | bugman | 2014-09-02 11:39:40 +0200 (Tue, 02 Sep 2014) | 7 lines
Change to the parameter nesting in the frame order auto-analysis.
The pivot is now taken from the rotor model for all other models. Taking
the pivot point from the
isotropic cone model is not a good idea as there are situations where the
pivot point optimisation
catastrophically fails, sending the point many tens or hundreds of Angstrom
away from the molecule.
........
r25710 | bugman | 2014-09-09 09:18:49 +0200 (Tue, 09 Sep 2014) | 10 lines
Copied a frame order results file for testing axis permutations.
The command used was:
svn cp
test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.bz2@r23644
test_suite/shared_data/frame_order/axis_permutations/cam_pseudo_ellipse.bz2
This is from the test_suite/shared_data/frame_order/cam/pseudo_ellipse/
directory. The optimisation
results back at r23644 were identified to have failed, in that it found the
alternative minimum.
The pseudo-ellipse model as two minima in the space, and in this case the
global minimum was missed.
........
r25711 | bugman | 2014-09-09 10:55:41 +0200 (Tue, 09 Sep 2014) | 5 lines
Created the Frame_order.test_axis_permutation system test.
This is to test the operation of the yet-to-be implemented
frame_order.permute_axes user function.
........
Added:
trunk/test_suite/shared_data/frame_order/axis_permutations/
- copied from r25711,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/axis_permutations/
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/test_suite/shared_data/frame_order/cam/full_analysis.py
trunk/test_suite/shared_data/frame_order/cam/generate_base.py
trunk/test_suite/system_tests/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=27949&r1=27948&r2=27949&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=27949&r1=27948&r2=27949&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=27949&r1=27948&r2=27949&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=27949&r1=27948&r2=27949&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/generate_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/generate_base.py?rev=27949&r1=27948&r2=27949&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=27949&r1=27948&r2=27949&view=diff
r27949 - in /trunk: ./ auto_analyses/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/axis_permutations/ t...