Author: bugman
Date: Thu Apr 3 20:07:28 2014
New Revision: 22644
URL: http://svn.gna.org/viewcvs/relax?rev=22644&view=rev
Log:
Merged revisions 22511,22514-22515,22522-22529,22612,22614-22617,22622-22625
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/double_rotor
........
r22511 | bugman | 2014-03-19 10:45:46 +0100 (Wed, 19 Mar 2014) | 6 lines
The AXIS_ALPHA parameter is now initialised in the CaM frame order system
test base script.
The base script was broken a while back (r22192) due to AXIS_ALPHA not
being defined but being
checked for.
........
r22514 | bugman | 2014-03-21 09:17:23 +0100 (Fri, 21 Mar 2014) | 5 lines
Improvements for the centre of mass calculation for the frame order model
optimisation.
This is now only calculated for the rotor models. The CoM is also printed
out for better user feedback.
........
r22515 | bugman | 2014-03-21 09:39:33 +0100 (Fri, 21 Mar 2014) | 7 lines
The CaM frame order system tests for the rotor models are converted to the
new axis_alpha parameter.
The axis_theta and axis_phi spherical coordinates are converted to the new
reduced parameter set
defined by a random point in space (the CoM of all atoms), the pivot point,
and a single angle
alpha.
........
r22522 | bugman | 2014-03-24 17:15:10 +0100 (Mon, 24 Mar 2014) | 5 lines
The CaM frame order system test base script is now using
lib.geometry.vectors.vector_angle().
This is for correctly calculating the alpha axis angle for the rotor models.
........
r22523 | bugman | 2014-03-25 08:51:56 +0100 (Tue, 25 Mar 2014) | 7 lines
Fixes for the rotor axis alpha angle conversion in the CaM frame order
system test base script.
The pivot point is not the point on the rotor axis closest to the reference
point (the CoM).
Therefore the closest point is now calculated from the pivot point on the
axis and the axis vector.
This closest point is needed for defining the new minimal parameter set for
the rotor models.
........
r22524 | bugman | 2014-03-25 10:00:04 +0100 (Tue, 25 Mar 2014) | 6 lines
Changes for the convert_rotor() method of the CaM frame order system test
base script.
The method now sets the alpha angle rather than returning it. The method
now also resets the pivot
point to the point on the rotation axis closest to the CoM.
........
r22525 | bugman | 2014-03-25 10:08:00 +0100 (Tue, 25 Mar 2014) | 6 lines
Fixes for the rotor axis reconstruction in the func_rotor_qrint() frame
order target function.
This is for the rotor model. The axis alpha angle is now correctly
converted into the rotor axis
using the CoM and pivot point.
........
r22526 | bugman | 2014-03-25 10:26:03 +0100 (Tue, 25 Mar 2014) | 5 lines
Optimisation is now turned on for the Frame_order.test_cam_rotor2 system
test.
This is to reveal deficiencies in the handling of the new axis alpha
parameter.
........
r22527 | bugman | 2014-03-25 10:37:49 +0100 (Tue, 25 Mar 2014) | 5 lines
The frame order optimisation results unpacking function now supports the
axis alpha parameter.
This is in the function
specific_analyses.frame_order.optimisation.unpack_opt_results().
........
r22528 | bugman | 2014-03-25 11:33:22 +0100 (Tue, 25 Mar 2014) | 6 lines
Updated the chi2 value check in some of the CaM frame order system tests
for the rotor model.
The chi2 value is slightly different due to truncation and conversion
artifacts of the parameter set
reduction.
........
r22529 | bugman | 2014-03-25 17:36:10 +0100 (Tue, 25 Mar 2014) | 6 lines
Shifted all of the code for calculating the frame order rotor axis into
lib.frame_order.rotor_axis.
The new frame_order.rotor_axis module consists of three function for
creating a unit vector or the
rotor axis using either the axis alpha angle, the two spherical angles or
the three Euler angles.
........
r22612 | bugman | 2014-03-31 08:36:59 +0200 (Mon, 31 Mar 2014) | 3 lines
Import fix.
........
r22614 | bugman | 2014-03-31 10:07:25 +0200 (Mon, 31 Mar 2014) | 5 lines
Renamed the specific_analyses.frame_order.user_functions module to uf.
This is to match the changes in trunk.
........
r22615 | bugman | 2014-03-31 10:52:12 +0200 (Mon, 31 Mar 2014) | 9 lines
Reverted r22192 as the parameter conversion is now performed by the base
script.
This is only for the rotor CaM frame order system test script. The changes
to the base script have
already been rewritten.
The command used was:
svn merge -r22192:22191
test_suite/system_tests/scripts/frame_order/cam/rotor.py
........
r22616 | bugman | 2014-03-31 15:53:03 +0200 (Mon, 31 Mar 2014) | 5 lines
Fix for the optimised chi-squared value check in the
Frame_order.test_cam_rotor system test.
The reduced parameter set results in a slightly different chi2 value.
........
r22617 | bugman | 2014-03-31 16:23:19 +0200 (Mon, 31 Mar 2014) | 3 lines
Shifted the frame order average domain position info check from the
'optimisation' to 'checks' module.
........
r22622 | bugman | 2014-04-03 13:26:47 +0200 (Thu, 03 Apr 2014) | 7 lines
Fix for the CaM frame order system tests.
The axis alpha angle and pivot shifting to the closest point to the CoM in
the base system test
script now only happens for the 'rotor' and 'free rotor' models. This
allows the tests for the
isotropic cone models to pass again.
........
r22623 | bugman | 2014-04-03 18:24:17 +0200 (Thu, 03 Apr 2014) | 3 lines
Fixed a missing import.
........
r22624 | bugman | 2014-04-03 18:30:35 +0200 (Thu, 03 Apr 2014) | 5 lines
Fixes for all of the CaM frame order optimisation scripts in the test data
directories.
The frame_order.average_position user function is now essential.
........
r22625 | bugman | 2014-04-03 19:13:43 +0200 (Thu, 03 Apr 2014) | 5 lines
The centre of mass printout in the frame order target function setup now
uses the verbosity argument.
This means that the printout is not shown for the Monte Carlo simulation
optimisation.
........
Added:
trunk/lib/frame_order/rotor_axis.py
- copied unchanged from r22529,
branches/double_rotor/lib/frame_order/rotor_axis.py
trunk/specific_analyses/frame_order/uf.py
- copied unchanged from r22617,
branches/double_rotor/specific_analyses/frame_order/uf.py
Removed:
trunk/specific_analyses/frame_order/user_functions.py
Modified:
trunk/ (props changed)
trunk/lib/frame_order/__init__.py
trunk/specific_analyses/frame_order/__init__.py
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/checks.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/target_functions/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
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_torsionless/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rigid/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
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/rotor.py
trunk/user_functions/frame_order.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/lib/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/__init__.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/specific_analyses/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/__init__.py?rev=22644&r1=22643&r2=22644&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=22644&r1=22643&r2=22644&view=diff
Modified: trunk/specific_analyses/frame_order/checks.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/checks.py?rev=22644&r1=22643&r2=22644&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=22644&r1=22643&r2=22644&view=diff
Removed: trunk/specific_analyses/frame_order/user_functions.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/user_functions.py?rev=22643&view=auto
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor2/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/free_rotor_missing_data/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_free_rotor2/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/iso_cone_torsionless/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse2/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_free_rotor/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/pseudo_ellipse_torsionless/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/rigid/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rigid/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor_2_state/frame_order.py?rev=22644&r1=22643&r2=22644&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=22644&r1=22643&r2=22644&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=22644&r1=22643&r2=22644&view=diff
Modified: trunk/test_suite/system_tests/scripts/frame_order/cam/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/frame_order/cam/rotor.py?rev=22644&r1=22643&r2=22644&view=diff
Modified: trunk/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/frame_order.py?rev=22644&r1=22643&r2=22644&view=diff
r22644 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_data/frame_order/...