Author: bugman
Date: Thu Oct 1 19:17:15 2015
New Revision: 27916
URL: http://svn.gna.org/viewcvs/relax?rev=27916&view=rev
Log:
Merged revisions 23199-23205 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/frame_order_cleanup
........
r23199 | bugman | 2014-05-16 14:12:07 +0200 (Fri, 16 May 2014) | 7 lines
Deletion of half of the frame order target functions.
All of the target functions using Scipy quadratic integration (which cause
a frame order analysis to
take over 1,000,000 years to complete) have been deleted. The quasi-random
target functions that
replace these have been renamed to remove the '_qrint' ending.
........
r23200 | bugman | 2014-05-16 14:14:48 +0200 (Fri, 16 May 2014) | 5 lines
Import cleanup for the frame order target functions.
The Scipy quadratic integration functions for the PCS have been removed.
........
r23201 | bugman | 2014-05-16 14:20:39 +0200 (Fri, 16 May 2014) | 3 lines
Alphabetical ordering of functions in the lib.frame_order.pseudo_ellipse
module.
........
r23202 | bugman | 2014-05-16 14:31:11 +0200 (Fri, 16 May 2014) | 6 lines
Deletion of all of the Scipy quadratic integration functions for the PCS in
the relax library.
These are no longer used, as they are far too slow. The quasi-random
functions have long replaced
these.
........
r23203 | bugman | 2014-05-16 14:36:40 +0200 (Fri, 16 May 2014) | 5 lines
Eliminated all of the 'line' frame order models, as they are not
implemented yet.
This is just frontend code - the backend does not exist.
........
r23204 | bugman | 2014-05-16 15:39:36 +0200 (Fri, 16 May 2014) | 5 lines
Updated the isotropic cone CaM frame order test model optimisation script.
Due to all of the changes in the frame order analysis, the old script was
no longer functional.
........
r23205 | bugman | 2014-05-16 15:55:40 +0200 (Fri, 16 May 2014) | 9 lines
Created a script for the CaM frame order test models for finding the
average domain position.
As the rotation about a fixed pivot has been eliminated, the shift from
1J7P_1st_NH_rot.pdb to
1J7P_1st_NH.pdb has to be converted into a translation and rotation about
the CoM. This script will
be used to replace the pivot rotation Euler angles with the translation
vector and CoM rotation
Euler angles. However the structure.superimpose user function will need to
be modified to handle
both the standard centroid superimposition as well as a CoM superimposition.
........
Added:
trunk/test_suite/shared_data/frame_order/cam/superimpose.py
- copied unchanged from r23205,
branches/frame_order_cleanup/test_suite/shared_data/frame_order/cam/superimpose.py
Modified:
trunk/ (props changed)
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/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/iso_cone/frame_order.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/iso_cone.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/iso_cone.py?rev=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&view=diff
Modified: trunk/lib/frame_order/pseudo_ellipse_torsionless.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/pseudo_ellipse_torsionless.py?rev=27916&r1=27915&r2=27916&view=diff
Modified: trunk/lib/frame_order/rotor.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/frame_order/rotor.py?rev=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&view=diff
Modified: trunk/target_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order.py?rev=27916&r1=27915&r2=27916&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=27916&r1=27915&r2=27916&view=diff
Modified: trunk/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/frame_order.py?rev=27916&r1=27915&r2=27916&view=diff
r27916 - in /trunk: ./ lib/frame_order/ specific_analyses/frame_order/ target_functions/ test_suite/shared_data/frame_order/...