relax SVN archive

Merged revisions 23206 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23206 | bugman | 2014-05-16 16:32:03 +0200 (Fri, 16 May 2014) | 5 lines

Added the 'centre_type' argument to the structure.superimpose user function.

This allows the default 'centroid' superimposition to be replaced by a centre of mass (CoM)
superimposition instead. As the CoM and centroid position do not match, the translation vector and
Euler rotation angles will be different.
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Added the 'centre_type' argument to the structure.superimpose user function.

This allows the default 'centroid' superimposition to be replaced by a centre of mass (CoM)
superimposition instead. As the CoM and centroid position do not match, the translation vector and
Euler rotation angles will be different.

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.

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.

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

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

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.

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

Import cleanup for the frame order target functions.

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

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.

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.