relax SVN archive

Speed up of the PCS component of the rigid frame order model.

The lanthanide to atom vectors are now being calculated outside of the alignment tensor and spin
loops, as well as the inverse vector lengths to the 5th power. This increases the speed by a factor
of 1.216 (from 38.133 to 31.368 seconds for 23329 calls of the func_rigid() target function).

Changed the grid search pivot displacement frame order parameter.

Instead of searching from 0 to 50 Angstroms, the search is now from 10 to 50. This is to avoid the
edge case of pivot_disp = 0.0 from which the optimisation cannot escape.

Added model support for the rotor geometric object.

This is the structural object used in the frame order analysis to create PDB representations of
rotor motions. The number of atoms created for the rotor is now constant, allowing for models
whereby the atom number and connectivity must be preserved between all models.

Removal of some accidentally committed debugging code.

Added the full optimisation results for the large angle double rotor frame order model.

This is for the CaM test data using the new frame_order.py optimisation script.

Simplified the PyMOL visualisation relax script created by the frame order auto-analysis.

This now consists of a single pymol.frame_order user function call. The other pymol user function
calls were unnecessary.

Changed some of the default values for the frame order auto-analysis.

The number of Sobol' quasi-random integration points were far too low to obtain any reasonable
results.

Added support for the 'pivot_disp' frame order parameter to the grid search.

This is required for the double rotor model.

Updated all of the CaM frame order system test chi-squared values.

These have changed slightly due to the rotation and translation changes (r24471).

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.