Author: bugman
Date: Thu Oct 1 21:25:47 2015
New Revision: 27931
URL: http://svn.gna.org/viewcvs/relax?rev=27931&view=rev
Log:
Merged revisions 23682-23687,23690-23691,23709 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23682 | bugman | 2014-06-06 10:10:00 +0200 (Fri, 06 Jun 2014) | 8 lines
Fix for a number of the frame order models which do not have parameter
constraints.
This change to the grid_search() API method is similar to the change for
the minimise() method
(r23211). The linear_constraint() function was returning A, b = [], [] for
these models, but these
empty numpy arrays were causing the dot product with A to fail in the
grid_search() API method.
These values are now caught and the constraint algorithm turned off.
........
r23683 | bugman | 2014-06-06 10:26:20 +0200 (Fri, 06 Jun 2014) | 7 lines
Converted the 'free rotor' frame order model to the new axis_alpha
parameter system.
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. The alpha parameter defines the rotor axis angle from the xy-plane.
........
r23684 | bugman | 2014-06-06 10:30:45 +0200 (Fri, 06 Jun 2014) | 6 lines
Parameter conversion for all of the CaM free rotor test data frame_order.py
optimisation scripts.
The rotor axis spherical angles have been replaced by the axis alpha angle
defining the rotor with
respect to the xy-plane.
........
r23685 | bugman | 2014-06-06 10:36:24 +0200 (Fri, 06 Jun 2014) | 8 lines
Modified the CaM frame order base system test script to catch a bug in the
free rotor model.
The axis spherical angles are no longer set for the rotor or free rotor
models, as they use the
alpha angle instead and the lack of the theta and phi parameters triggers
the bug. The PDB
representation of the frame order motions is also now tested for all frame
order models, as it was
turned off for the rigid, rotor and free rotor models and this is where the
bug lies.
........
r23686 | bugman | 2014-06-06 10:37:29 +0200 (Fri, 06 Jun 2014) | 5 lines
Fix for the failure of the frame_order.pdb_model user function for the free
rotor frame order model.
This is due to the recent parameter conversion to the axis alpha angle.
........
r23687 | bugman | 2014-06-06 10:46:02 +0200 (Fri, 06 Jun 2014) | 3 lines
Removed a debugging printout.
........
r23690 | bugman | 2014-06-06 14:08:23 +0200 (Fri, 06 Jun 2014) | 7 lines
Eliminated the average position alpha Euler angle parameter from the
free-rotor pseudo-ellipse model.
As this frame order model is a free-rotor, the average domain position is
therefore undefined and it
can freely rotate about the rotor axis. One of the Euler angles for
rotating to the average
position can therefore be removed, just as in the free rotor and free rotor
isotropic cone models.
........
r23691 | bugman | 2014-06-06 14:11:04 +0200 (Fri, 06 Jun 2014) | 6 lines
Eliminated the free rotor psuedo-ellipse model ave_pos_alpha parameter from
the target function.
The average domain position alpha Euler angle has already been removed from
the specific analyses
code and this change brings the target function into line with these
changes.
........
r23709 | bugman | 2014-06-06 18:00:28 +0200 (Fri, 06 Jun 2014) | 6 lines
Added the full optimisation results for the 2nd rotor frame order model for
the CaM test data.
This is from the new frame_order.py optimisation script and the results
demonstrate the stability of
the rotor model.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/rotor2/ave_pos.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/ave_pos.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor2/ave_pos_fixed_piv.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/ave_pos_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor2/ave_pos_true.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/ave_pos_true.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order_fixed_piv.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order_fixed_piv.pdb.gz
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order_true.pdb.gz
- copied unchanged from r23709,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/rotor2/frame_order_true.pdb.gz
Modified:
trunk/ (props changed)
trunk/specific_analyses/frame_order/api.py
trunk/specific_analyses/frame_order/optimisation.py
trunk/specific_analyses/frame_order/parameters.py
trunk/specific_analyses/frame_order/uf.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/rotor2/frame_order.bz2
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.log.bz2
trunk/test_suite/system_tests/scripts/frame_order/cam/base_script.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: trunk/specific_analyses/frame_order/api.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/frame_order/api.py?rev=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&view=diff
Modified: trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.bz2?rev=27931&r1=27930&r2=27931&view=diff
Modified:
trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.log.bz2
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/frame_order/cam/rotor2/frame_order.log.bz2?rev=27931&r1=27930&r2=27931&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=27931&r1=27930&r2=27931&view=diff
r27931 - in /trunk: ./ specific_analyses/frame_order/ target_functions/ test_suite/shared_data/frame_order/cam/free_rotor/ t...