relax SVN archive

Changed the CaM frame order test data superimposition values.

Because the domains are now defined via the molecule name rather than the residue numbers, the
centroid of rotation set to the CoM has been shifted as now the Ca2+ ions are included in the CoM
calculation. Therefore the superimpose.py script has been updated to not delete the Ca atoms (this
reverts r23354).

All of the frame order optimisation scripts have been updated with the new rotation Euler angles and
translation vector. To match this, the system test base script for the CaM frame order test data
has also had its rotations and translations updates, and the domain user function call changed to
use molecule names.

The script for representing the frame order dynamics for the CaM test data has been updated.

The domains of the system are now defined.

The CaM frame order test data optimisation scripts now save more state files.

The state of the true dynamics and the fixed pivot optimisation results are now stored as well.
This might be useful for extracting these results without redoing the calculations.

Updates for the frame order system tests for the float32 to float64 change (r24463).

Some chi-squared values have slightly changed.

Updated the chi2 check for the large angle double rotor frame order system tests.

This is needed for the eigenframe fix.

More fixes for the double rotor frame order system tests for the CaM synthetic data.

The eigensystem was inverted.

Fixes for the double rotor frame order system tests for the CaM synthetic data.

The torsion angles needed to be swapped and the pivot point changed from the C terminal domain CoM
to the N domain CoM.

Updated the frame order system test chi-squared values for the fix of r24461.

Converted all frame order target function data structures to float64.

This affects the vector data structures used for the PCS numeric integration. The float32
structures added for speed do not actually increase the speed. For the double rotor model, 10
target function calls took the pcs_pivot_motion_double_rotor() function 44.936 seconds using float32
and 44.105 seconds using all float64. The cumulative time is also longer. This must be because
other parts are float64, and therefore type conversions are happening during target function calls.

Reverted r24332 as this was incorrect - the data input was wrong, not the frame order matrix.

The command used was:
svn merge -r24332:r24331 .

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r24332 | bugman | 2014-06-26 16:29:46 +0200 (Thu, 26 Jun 2014) | 6 lines
Changed paths:
M /branches/frame_order_cleanup/lib/frame_order/double_rotor.py

Fix for the double rotor frame order matrix assembly function.

The rotations where applied in reverse, hence the 2nd degree frame order matrix was the Kronecker
product transpose of the correct form.
.....