Author: bugman
Date: Thu Oct 1 20:33:47 2015
New Revision: 27920
URL: http://svn.gna.org/viewcvs/relax?rev=27920&view=rev
Log:
Merged revisions 23394-23407,23411,23421-23424 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23394 | bugman | 2014-05-24 09:11:48 +0200 (Sat, 24 May 2014) | 5 lines
Improved the value setting in the optimisation() method of the CaM frame
order system tests.
This is in the base script used by all scripts in
test_suite/system_tests/scripts/frame_order/cam/.
........
r23395 | bugman | 2014-05-24 09:14:53 +0200 (Sat, 24 May 2014) | 9 lines
Changed the average domain position parameter values in the CaM frame order
system tests.
This is in the base script used by all scripts in
test_suite/system_tests/scripts/frame_order/cam/.
The translation vector coordinates are now set, as well as the CoM Euler
angle rotations. These
come from the log file of the
test_suite/shared_data/frame_order/cam/superimpose.py script, and are
needed due to the simplification of the average domain position mechanics
now mimicking the Kabsch
superimposition algorithm.
........
r23396 | bugman | 2014-05-24 09:16:28 +0200 (Sat, 24 May 2014) | 6 lines
The CaM frame order system test mesg_opt_debug() method not prints out the
translation vector.
This is printed out at the end of all CaM frame order system tests to help
with debugging when the
test fails.
........
r23397 | bugman | 2014-05-24 09:32:21 +0200 (Sat, 24 May 2014) | 16 lines
Change for how the CaM frame order system test scripts handle the average
domain position rotation.
The trick of pre-rotating the 3D coordinates was used to solve the {a, b,
g} -> {0, b', g'} angle
conversion problem in the rotor models no longer works now that the average
domain position
mechanics has been simplified. Instead, high precision optimised b' and g'
values are now set, and
the ave_pos_alpha value set to None.
The high precision parameters were obtained with the frame_order.py script
located in the directory
test_suite/shared_data/frame_order/cam/free_rotor. The free rotor target
function was modified so
that the translation vector is hard-coded to [-20.859750185691549,
-2.450606987447843,
-2.191854570352916] and the axis theta and phi angles to
0.96007997859534299767 and
4.0322755062196229403. These parameters were then commented out for the
model in the module
specific_analyses.frame_order.parameters so only b' and g' were optimised.
Iterative optimisation
was used with increasing precision, ending up with high precision using
10,000 Sobol' points.
........
r23398 | bugman | 2014-05-24 10:03:22 +0200 (Sat, 24 May 2014) | 5 lines
Updated a number of the CaM frame order system tests for the higher
precision data.
The new data results in chi-squared values at the real solution to be much
closer to zero.
........
r23399 | bugman | 2014-05-24 10:09:39 +0200 (Sat, 24 May 2014) | 5 lines
Change for how the CaM frame order free-rotor pseudo-ellipse test script
handle the average position.
This should have been updated earlier (r23397).
........
r23400 | bugman | 2014-05-24 10:10:46 +0200 (Sat, 24 May 2014) | 6 lines
Added FIXME comments to the 2nd free-rotor CaM frame order model system
test scripts.
These explain the steps required to obtain the correct b' and g' average
domain position rotation
angles.
........
r23401 | bugman | 2014-05-24 11:47:05 +0200 (Sat, 24 May 2014) | 4 lines
Large increase in precision for the CaM frame order isotropic cone model
test data set.
The higher precision is because the number structures in the distribution
is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
........
r23402 | bugman | 2014-05-25 08:49:33 +0200 (Sun, 25 May 2014) | 4 lines
Large increase in precision for the CaM frame order free-rotor, isotropic
cone model test data set.
The higher precision is because the number structures in the distribution
is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
........
r23403 | bugman | 2014-05-25 09:39:39 +0200 (Sun, 25 May 2014) | 7 lines
Updated the CaM frame order free-rotor model test data set for testing for
missing data.
This is the data in
test_suite/shared_data/frame_order/cam/free_rotor_missing_data. To simplify
the
copying of data from test_suite/shared_data/frame_order/cam/free_rotor and
then the deletion of
data, the missing.py script was created to automate the process. The
generate_distribution.py
script and some of the files it creates were removed from the repository so
it is clearer how the
data has been created.
........
r23404 | bugman | 2014-05-26 09:05:05 +0200 (Mon, 26 May 2014) | 4 lines
Large increase in precision for the 2nd CaM frame order free-rotor,
isotropic cone model test data set.
The higher precision is because the number structures in the distribution
is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
........
r23405 | bugman | 2014-05-26 09:05:09 +0200 (Mon, 26 May 2014) | 4 lines
Large increase in precision for the CaM frame order free-rotor,
pseudo-ellipse model test data set.
The higher precision is because the number structures in the distribution
is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
........
r23406 | bugman | 2014-05-26 09:05:12 +0200 (Mon, 26 May 2014) | 4 lines
Large increase in precision for the CaM frame order pseudo-ellipse model
test data set.
The higher precision is because the number structures in the distribution
is now 20 million rather
than 1 million and the numpy.float128 data averaging has been used.
........
r23407 | bugman | 2014-05-26 09:48:42 +0200 (Mon, 26 May 2014) | 5 lines
Updated a number of the CaM frame order system tests for the higher
precision data.
The new data results in chi-squared values at the real solution to be much
closer to zero. The
free-rotor pseudo-ellipse models might need investigation however as the
chi-squared values have
increased.
........
r23411 | bugman | 2014-05-26 11:43:18 +0200 (Mon, 26 May 2014) | 6 lines
Elimination of the error_flag variable from the frame order analysis.
This flag is used to activate some old code paths which have now been
deleted as they are never
used.
........
r23421 | bugman | 2014-05-26 15:20:04 +0200 (Mon, 26 May 2014) | 10 lines
Optimisation of the average domain position for the CaM frame order
free-rotor models.
The log file that shows the optimisation of the average domain position for
the free-rotor models
has been added to the repository for reference. This is for the simple
free-rotor model, but the
optimised position holds for the isotropic cone and pseudo-ellipse model
data too.
To perform the optimisation, the axis_theta and axis_phi parameters were
removed from the model and
hardcoded into the target function. As the rotor axis is know, this allows
the average domain
position to be optimised in isolation. Visual inspection of the results
confirmed the position to
be correct.
........
r23422 | bugman | 2014-05-26 15:23:37 +0200 (Mon, 26 May 2014) | 6 lines
Fixes for the 2nd frame order free-rotor system tests.
The average domain position parameters are now set to the correct values,
matching those in the
relax log file frame_order_ave_pos_opt.log in
test_suite/shared_data/frame_order/cam/free_rotor2.
........
r23423 | bugman | 2014-05-26 15:37:55 +0200 (Mon, 26 May 2014) | 3 lines
Updated the 2nd CaM free-rotor frame order system tests for the correct
average domain position.
The chi-squared values are now significantly lower.
........
r23424 | bugman | 2014-05-26 16:24:42 +0200 (Mon, 26 May 2014) | 5 lines
Increased the precision of the chi-squared value testing in the CaM frame
order system tests.
The check_chi2 method has been modified so that the chi-squared value is no
longer scaled, and the
precision has been increased from 1 significant figure to 4. All of the
tests have been updated to
match.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_ave_pos_opt.log
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order_ave_pos_opt.log
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/missing.log
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/missing.log
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/missing.py
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/missing.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.bz2
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.bz2
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.bz2
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.bz2
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.bz2
- copied unchanged from r23424,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/generate_distribution.bz2
Removed:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/subset_pcs.py
Modified:
trunk/ (props changed)
trunk/lib/frame_order/double_rotor.py
trunk/lib/frame_order/iso_cone.py
trunk/lib/frame_order/iso_cone_torsionless.py
trunk/lib/frame_order/matrix_ops.py
trunk/lib/frame_order/pseudo_ellipse.py
trunk/lib/frame_order/pseudo_ellipse_torsionless.py
trunk/lib/frame_order/rotor.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/rdc_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone/rdc_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/rdc_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/rdc_tm.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/axis.pdb
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/rdc_tm.txt
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_matrix
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/system_tests/frame_order.py
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/free_rotor_missing_data.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/iso_cone_free_rotor2.py
trunk/test_suite/system_tests/scripts/frame_order/cam/pseudo_ellipse_free_rotor.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/frame_order/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/double_rotor.py?rev=27920&r1=27919&r2=27920&view=diff
Modified: trunk/lib/frame_order/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone.py?rev=27920&r1=27919&r2=27920&view=diff
Modified: trunk/lib/frame_order/iso_cone_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone_torsionless.py?rev=27920&r1=27919&r2=27920&view=diff
Modified: trunk/lib/frame_order/matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/matrix_ops.py?rev=27920&r1=27919&r2=27920&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse.py?rev=27920&r1=27919&r2=27920&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse_torsionless.py
[... 311 lines stripped ...]
r27920 - in /trunk: ./ lib/frame_order/ target_functions/ test_suite/shared_data/frame_order/cam/free_rotor2/ test_suite/sha...