Author: bugman
Date: Fri Oct 2 11:18:36 2015
New Revision: 27937
URL: http://svn.gna.org/viewcvs/relax?rev=27937&view=rev
Log:
Merged revisions 24327-24334,24344-24346 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r24327 | bugman | 2014-06-26 13:42:33 +0200 (Thu, 26 Jun 2014) | 7 lines
Small fix for the large angle CaM double rotor frame order model synthetic
test data.
The way the rotation angle was calculated was slightly out due to integer
truncation. The integers
are now converted to floats in the generate_distribution.py script and all
of the PCS and RDC data
averaged over ~20 million states has been recalculated.
........
r24328 | bugman | 2014-06-26 14:21:15 +0200 (Thu, 26 Jun 2014) | 8 lines
Added proper support for the double rotor frame order models to the system
test scripts.
This is for the CaM synthetic data. The base script can now handle the
current parameterisation of
the double rotor model with a single pivot, an eigenframe, and the second
pivot defined by a
displacement along the z-axis. The scripts for the double_rotor and
double_rotor_large_angle data
sets have been changed to use this parameterisation as well.
........
r24329 | bugman | 2014-06-26 14:27:55 +0200 (Thu, 26 Jun 2014) | 5 lines
Attempt at implementing the 2nd degree frame order matrix for the double
rotor model.
This is required for the RDC.
........
r24330 | bugman | 2014-06-26 14:31:30 +0200 (Thu, 26 Jun 2014) | 6 lines
The second torsion angle is now printed out for the frame order system
tests.
This is in the system test class mesg_opt_debug() method and allows for
better debugging of the
double rotor models.
........
r24331 | bugman | 2014-06-26 14:46:43 +0200 (Thu, 26 Jun 2014) | 5 lines
Fix for the Frame_order.test_cam_double_rotor_large_angle* system tests.
The system test script was pointing to the wrong data directory.
........
r24332 | bugman | 2014-06-26 16:29:46 +0200 (Thu, 26 Jun 2014) | 6 lines
Fix for the double rotor frame order matrix assembly function.
The rotations where applied in reverse, hence the 2nd degree frame order
matrix was the Kronecker
product transpose of the correct form.
........
r24333 | bugman | 2014-06-26 16:32:23 +0200 (Thu, 26 Jun 2014) | 3 lines
The double rotor frame order system tests are no longer blacklisted.
........
r24334 | bugman | 2014-06-26 16:40:02 +0200 (Thu, 26 Jun 2014) | 3 lines
Updated the chi-squared values being checked for the double rotor frame
order system tests.
........
r24344 | bugman | 2014-06-27 15:57:39 +0200 (Fri, 27 Jun 2014) | 5 lines
Shifted the frame order geometric representation functions into their own
module.
This is the new specific_analyses.frame_order.geometric module.
........
r24345 | bugman | 2014-06-27 16:07:16 +0200 (Fri, 27 Jun 2014) | 7 lines
The frame order geometric representation functions are no longer PDB
specific.
Instead the format argument is accepted. This will allow different formats
to be supported in the
future. Because of this change, all
specific_analyses.frame_order.geometric.pdb_*() functions has
been renamed to create_*().
........
r24346 | bugman | 2014-06-27 16:31:45 +0200 (Fri, 27 Jun 2014) | 7 lines
Created an auxiliary function for automatically generating the pivots of
the frame order analysis.
This is the new specific_analyses.frame_order.data.generate_pivot()
function. It will generate the
1st or 2nd pivot, hence supporting both the single motion models and the
double motion double rotor
model.
........
Added:
trunk/specific_analyses/frame_order/geometric.py
- copied unchanged from r24346,
branches/frame_order_cleanup/specific_analyses/frame_order/geometric.py
Modified:
trunk/ (props changed)
trunk/lib/frame_order/double_rotor.py
trunk/specific_analyses/frame_order/data.py
trunk/specific_analyses/frame_order/uf.py
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_matrix
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.log.bz2
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy_subset.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er_subset.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb_subset.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm_subset.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_dy.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_er.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_tb.txt
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/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/double_rotor.py
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.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=27937&r1=27936&r2=27937&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=27937&r1=27936&r2=27937&view=diff
Modified: trunk/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/uf.py?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_matrix
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/frame_order_matrix?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.log.bz2?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/generate_distribution.py?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_dy_subset.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_er_subset.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tb_subset.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm_subset.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/pcs_tm_subset.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_dy.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_dy.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_er.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_er.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_tb.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_tb.txt?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_tm.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/double_rotor_large_angle/rdc_tm.txt?rev=27937&r1=27936&r2=27937&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=27937&r1=27936&r2=27937&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor.py?rev=27937&r1=27936&r2=27937&view=diff
Modified:
trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/double_rotor_large_angle.py?rev=27937&r1=27936&r2=27937&view=diff
r27937 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ test_suite/shared_data/frame_order/cam/double_rotor_l...