Author: bugman
Date: Fri Oct 2 12:31:21 2015
New Revision: 27947
URL: http://svn.gna.org/viewcvs/relax?rev=27947&view=rev
Log:
Merged revisions 24778,24783-24784,24787,24798-24810,24814-24817 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24778 | bugman | 2014-07-27 10:40:21 +0200 (Sun, 27 Jul 2014) | 7 lines
Fixes for the CaM free-rotor pseudo-ellipse frame order model test data set.
This is for the constraint 0 <= theta_x <= theta_y <= pi, as the old data
was created with theta_x
> theta_y. The new data is also of high quality using 20 million
structures and numpy.float128 data
averaging.
........
r24783 | bugman | 2014-07-28 14:21:04 +0200 (Mon, 28 Jul 2014) | 5 lines
Created the lib.frame_order.rotor_axis.convert_axis_alpha_to_spherical()
function.
This will convert the axis alpha angle to the equivalent spherical angles
theta and phi.
........
r24784 | bugman | 2014-07-28 15:48:50 +0200 (Mon, 28 Jul 2014) | 5 lines
Renamed the lib.frame_order.rotor_axis module to
lib.frame_order.conversions.
This module will be used for all sorts of frame order parameter conversions.
........
r24787 | bugman | 2014-07-28 16:29:59 +0200 (Mon, 28 Jul 2014) | 5 lines
Added the pipe_name argument to the
specific_analyses.frame_order.data.generate_pivot() function.
This allows the pivot from data pipes other than the current one to be
assembled and returned.
........
r24798 | bugman | 2014-07-29 11:39:10 +0200 (Tue, 29 Jul 2014) | 8 lines
Updated the frame order optimisation results for the CaM free rotor,
pseudo-ellipse test data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository, as well
as the intermediate
state files.
........
r24799 | bugman | 2014-07-29 11:40:25 +0200 (Tue, 29 Jul 2014) | 8 lines
Updated the frame order optimisation results for the CaM torsionless,
pseudo-ellipse test data.
The optimisation in the frame_order.py is now of higher precision with the
number of Sobol' numeric
integration points significantly increased, especially for the Monte Carlo
simulations. The new
frame order representation files have been added to the repository, as well
as the intermediate
state files.
........
r24800 | bugman | 2014-07-29 11:58:19 +0200 (Tue, 29 Jul 2014) | 5 lines
Fix for the Frame_order.test_cam_pseudo_ellipse_free_rotor system test.
This is for the change of the X and Y cone opening angles.
........
r24801 | bugman | 2014-07-29 13:11:20 +0200 (Tue, 29 Jul 2014) | 14 lines
Redesign and expansion of the nested model parameter copying in the frame
order auto-analysis.
The nested parameter protocol used to allow the analysis to complete in
under 1,000,000 years was no
longer functional due to the switching to the axis alpha parameter to
decrease parameter number and
redundancy. The copying of the average domain position for the free rotor
models was also incorrect
as the dropping of the alpha Euler angle cause the translation parameters
and beta and gamma angles
to change drastically.
The new protocol has been split into four methods for the average domain
position, the pivot point,
the motional eigenframe and the parameters of ordering. These use the fact
that the free rotor and
torsionless models are the two extrema of the models where the torsion
angle is restricted. The
pivot copying is a new addition.
........
r24802 | bugman | 2014-07-29 13:58:14 +0200 (Tue, 29 Jul 2014) | 7 lines
Created the Frame_order.test_auto_analysis system test.
This will be an extremely quick run through of the frame order
auto-analysis as this is not
currently tested. 1 Sobol' quasi-random integration point will be used for
all models for speed.
The system test uses the rigid CaM test data to perform a full analysis.
........
r24803 | bugman | 2014-07-29 13:59:39 +0200 (Tue, 29 Jul 2014) | 3 lines
Import fix for the frame order auto-analysis.
........
r24804 | bugman | 2014-07-29 14:01:04 +0200 (Tue, 29 Jul 2014) | 3 lines
Alphabetical ordering of the imports in the frame order auto-analysis
module.
........
r24805 | bugman | 2014-07-29 14:06:14 +0200 (Tue, 29 Jul 2014) | 5 lines
Fixes for the backend script of the Frame_order.test_auto_analysis system
test.
This includes a missing import and the removal of a long ago deleted user
function.
........
r24806 | bugman | 2014-07-29 14:08:11 +0200 (Tue, 29 Jul 2014) | 6 lines
Fix for the frame order auto-analysis for the call to the grid search user
function.
This user function has been renamed to minimise.grid_search, however not
all parts of the analysis
had been converted to the new name.
........
r24807 | bugman | 2014-07-29 15:13:46 +0200 (Tue, 29 Jul 2014) | 6 lines
Created a method in the frame order auto-analysis to reorder the models.
This is needed as the nested model parameter copying protocol requires the
simpler models to be
optimised first.
........
r24808 | bugman | 2014-07-29 15:17:02 +0200 (Tue, 29 Jul 2014) | 5 lines
The Frame_order.test_auto_analysis system test now writes all files to the
directory of ds.tmpdir.
This is to prevent the system test from dumping files in the current
directory.
........
r24809 | bugman | 2014-07-29 15:38:41 +0200 (Tue, 29 Jul 2014) | 5 lines
Modified the specific_analyses.frame_order.parameters.update_model()
function.
This will no longer set all parameters to 0.0, excluding the pivot point.
........
r24810 | bugman | 2014-07-29 16:07:28 +0200 (Tue, 29 Jul 2014) | 6 lines
Modified the
specific_analyses.frame_order.parameters.assemble_param_vector() function.
This can now handle the case of no parameters being present. The
corresponding elements of the
numpy array will consist of NaN values.
........
r24814 | bugman | 2014-07-29 16:41:17 +0200 (Tue, 29 Jul 2014) | 10 lines
Better handling of unset parameters in the frame order optimisation
functions.
The specific_analyses.frame_order.optimisation.target_fn_data_setup() and
specific_analyses.frame_order.parameters.assemble_param_vector() function
both now accept the
unset_fail argument. This is set in both the calculate() and minimise()
API methods. When set, a
RelaxError will be raised in the assemble_param_vector() function when a
parameter has not been set
yet. This together with previous changes will prevent the frame order
analysis from using 0.0 as a
starting value for unset parameters.
........
r24815 | bugman | 2014-07-29 17:01:55 +0200 (Tue, 29 Jul 2014) | 7 lines
Fixes for all of the Frame_order.test_rigid_data_to_*_model system tests.
The base script now sets all parameter values so that the
minimise.calculate user function can
operate. The two free rotor model chi-squared values have been updated as
these are sensitive to
the motional eigenframe parameter values - these models can never
approximate a rigid state.
........
r24816 | bugman | 2014-07-29 17:38:31 +0200 (Tue, 29 Jul 2014) | 5 lines
Modified the optimisation of the rigid model in the frame order
auto-analysis.
The grid search is now implemented as a zooming grid search.
........
r24817 | bugman | 2014-07-29 18:03:37 +0200 (Tue, 29 Jul 2014) | 5 lines
Missing import in the lib.frame_order.rotor module.
This was identified by the new Frame_order.test_auto_analysis system test.
........
Added:
trunk/lib/frame_order/conversions.py
- copied unchanged from r24817,
branches/frame_order_cleanup/lib/frame_order/conversions.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_sim.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.bz2
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_sim_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.bz2
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_sim.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_sim_B.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_A.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true_B.pdb.gz
trunk/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
- copied unchanged from r24817,
branches/frame_order_cleanup/test_suite/system_tests/scripts/frame_order/cam/auto_analysis_to_rigid.py
Removed:
trunk/lib/frame_order/rotor_axis.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order_true.pdb.gz
Modified:
trunk/ (props changed)
trunk/auto_analyses/frame_order.py
trunk/lib/frame_order/__init__.py
trunk/lib/frame_order/rotor.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/data.py
trunk/specific_analyses/frame_order/geometric.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/rdc_tm.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
trunk/test_suite/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/rigid_test.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=27947&r1=27946&r2=27947&view=diff
Modified: trunk/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/__init__.py?rev=27947&r1=27946&r2=27947&view=diff
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27947&r1=27946&r2=27947&view=diff
Removed: trunk/lib/frame_order/rotor_axis.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor_axis.py?rev=27946&view=auto
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27947&r1=27946&r2=27947&view=diff
Modified: trunk/specific_analyses/frame_order/data.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/data.py?rev=27947&r1=27946&r2=27947&view=diff
Modified: trunk/specific_analyses/frame_order/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/geometric.py?rev=27947&r1=27946&r2=27947&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=27947&r1=27946&r2=27947&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=27947&r1=27946&r2=27947&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27947&r1=27946&r2=27947&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos.pdb.gz?rev=27947&r1=27946&r2=27947&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/ave_pos_fixed_piv.pdb.gz?rev=27947&r1=27946&r2=27947&view=diff
[... 108 lines stripped ...]
r27947 - in /trunk: ./ auto_analyses/ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_da...