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SVN archive Commit Log


Commit Date  
[r23203] by bugman

Eliminated all of the 'line' frame order models, as they are not implemented yet.

This is just frontend code - the backend does not exist.

2014-05-16 12:36:40 Tree
[r23202] by bugman

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.

2014-05-16 12:31:11 Tree
[r23201] by bugman

Alphabetical ordering of functions in the lib.frame_order.pseudo_ellipse module.

2014-05-16 12:20:39 Tree
[r23200] by bugman

Import cleanup for the frame order target functions.

The Scipy quadratic integration functions for the PCS have been removed.

2014-05-16 12:14:48 Tree
[r23199] by bugman

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.

2014-05-16 12:12:07 Tree
[r23198] by bugman

Clean up of the frame order target function code.

This matches the previous changes (r23197), the deletion of the frame_order.average_position user
function. The changes include the removal of the translation optimisation flag as this is now
always performed, and the removal of the flag which causes the average domain rotation pivot point
to match the motional pivot point as these are now permanently decoupled.

2014-05-16 11:44:31 Tree
[r23197] by bugman

Deletion of the frame_order.average_position user function and all of the associated backend code.

This user function allowed the user to specify five different types of displacement to the average
moving domain position:

- A pure rotation, with no translation, about the pivot of the motion in the system.
- A rotation about the pivot of the motion of the system together with a translation.
- A pure translation with no rotation.
- A rotation about the centre of mass of the moving domain with no translation.
- A rotation about the centre of mass of the moving domain together with a translation.

Now the last option will be the default and only option. This option is equivalent to the standard
superimposition algorithm (the Kabsch algorithm) to a hypothetical structure at the real average
position.

The other four are due to the history of the development of the theory. These limit the usefulness
of the theory and will only cause confusion.

2014-05-16 08:45:40 Tree
[r23196] by bugman

Initialized merge tracking via "svnmerge" with revisions "1-23194" from
svn+ssh://bugman@.../svn/relax/trunk

2014-05-16 08:22:37 Tree
[r23195] by bugman

Creation of a branch for cleaning up the frame order analysis.

As this analysis has been in development for many years, a lot of code that was developed for the
theory is no longer needed. Some of this is also a potential source of user confusion. It also
results in many unexpected bugs.

2014-05-16 08:21:23 Tree
[r23194] by bugman

Modified the pivot point PDB representation script to include the shifted pivot.

This is for the 2nd rotor model of CaM frame order in the test suite.

2014-05-15 15:05:36 Tree
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