relax SVN archive

Replaced 'Q-factor' with 'Q factor' throughout the relax codebase.

This change to the correct notation covers code, comments, and docstrings.

Docstring improvements for the stereochem_analysis.py N-state model sample script.

The paragraphs are now all on one line and 'Q-factor' has been changed to 'Q factor'.

Spacing improvements in the stereochem_analysis.py N-state mode sample script.

Started to create a chapter for the N-state model or ensemble analysis in the manual.

This simply consists of a few introductory sections and the phathalic acid graphic.

Fixed the description of the N-state model in the pipe.create user function.

This has nothing to do with domain motions - it is the treatment of ensembles of structures.

Big bug fix for the relax installation path determination.

This is to fix bug #22037 (http://gna.org/bugs/?22037), the failure to load graphics in the GUI due
to the relax installation path not being set up correctly.

The problem is that the status module was looking for the compat.py file to determine where the base
directory is, but this file has been moved into the lib/ package. Now the dep_check.py file is
being searched for.

Created the Status_object.test_install_path system verification test.

This is to catch bug #22037 (http://gna.org/bugs/?22037), the failure to load graphics in the GUI
due to the relax installation path not being set up correctly.

Removed the domain rotation code from the pymol.cone_pdb user function backend.

This should only display the cone PDB object. The domain rotation is now performed by the far more
powerful frame_order.pdb_model user function.

Modified the rotor2 CaM frame order test data optimisation script to compare the rotor axes.

The optimised rotor axis is recreated with the lib.frame_order.rotor_axis.create_rotor_axis_alpha()
function, and then the original and optimsed axes are compared. The state.save user function has
been shifted forwards in the script to avoid a later RelaxError.

The log file, average position PDB file, and state file from running the script have been added to
the repository or updated.

Modified the rotor2 CaM frame order test data optimisation script to optimise the pivot.

Print statements has been added for comparing the optimised to the original pivot. The rotation
axis is now also only created once, as it is now used in three places in the script, hence the two
functions for converting parameters to the new parameterisation have been updated.