relax SVN archive

Merged revisions 23208-23211 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23208 | bugman | 2014-05-16 16:36:45 +0200 (Fri, 16 May 2014) | 7 lines

Updated the CaM frame order test model superimposition script.

The structure.superimpose user function is now correctly called. The output log file has been added
to the repository as it contains the correct translation and Euler rotation information needed for
the test models.
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r23209 | bugman | 2014-05-16 16:55:55 +0200 (Fri, 16 May 2014) | 6 lines

Parameter update for the isotropic cone CaM frame order test model optimisation script.

The Euler angles for the rotation about the motional pivot have been replaced by the translation
vector and Euler angle CoM rotation parameters.
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r23210 | bugman | 2014-05-17 18:03:44 +0200 (Sat, 17 May 2014) | 1 line

Removed an unused import and an extra blank line.
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r23211 | bugman | 2014-05-17 18:03:46 +0200 (Sat, 17 May 2014) | 5 lines

Fix for a number of the frame order models which do not have parameter constraints.

The linear_constraint() function was returning A, b = [], [] for these models, but these empty numpy
arrays were causing the minfx library (https://gna.org/projects/minfx/) to fail. These values are
now caught and the constraint algorithm turned off in the minimise() specific API method.
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Merged revisions 23199-23205 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Merged revisions 23198 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23198 | bugman | 2014-05-16 13:44:31 +0200 (Fri, 16 May 2014) | 8 lines

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.
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Merged revisions 23197 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

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r23197 | bugman | 2014-05-16 10:45:40 +0200 (Fri, 16 May 2014) | 19 lines

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.
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Initialized merge tracking via "svnmerge" with revisions "1-23195" from
svn+ssh://bugman@.../svn/relax/branches/frame_order_cleanup

Indentation fix for allowing the API documentation to be properly compiled.

Merged revisions 27904,27906-27907,27910 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27904 | bugman | 2015-09-30 12:08:12 +0200 (Wed, 30 Sep 2015) | 6 lines

Backported the relax 3.3.9 CHANGES file changes to trunk.

The command used was:
svn merge -r27902:27903 svn+ssh://bugman@.../svn/relax/tags/3.3.9 .
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r27906 | bugman | 2015-09-30 14:42:40 +0200 (Wed, 30 Sep 2015) | 6 lines

Added a patch file for fixing Epydoc version 3.0.1.

This is needed to allow the dot graph files names to be unique (by no longer truncating to 30
characters), and to allow epydoc to handle newer Graphvis versions.
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r27907 | bugman | 2015-09-30 14:43:40 +0200 (Wed, 30 Sep 2015) | 6 lines

Improvements for the release checklist document.

The backporting of the CHANGES file to trunk is now more obvious, and instructions for fixing Epydoc
have been added.
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r27910 | bugman | 2015-10-01 14:55:29 +0200 (Thu, 01 Oct 2015) | 3 lines

Clean up of some of the release instructions (for using vim).
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Clean up of some of the release instructions (for using vim).

Updated the http://www.nmr-relax.com/download.html webpage for the relax 3.3.9 release.

Updated the relax API documentation at http://www.nmr-relax.com/api/3.3/ to version 3.3.9.