relax SVN archive

Redesign of the geometric representation of the cone structural objects to allow for models.

The old representation was not compatible with the PDB model concept whereby each model must have
the same number of atoms. To handle this situation, the cone objects have been simplified.
Specifically the cone cap.

The old behaviour was to remove all points outside of the cone when creating the cone cap, and then
to stitch the cap to the cone edge in a subsequent step. Now the behaviour is that all points
outside of the distribution are shifted to the cone edge. This avoids the need to stitch the cap to
the edge. This behaviour means that all cones with the same inc value will have the same number of
atoms.

The cones for the pseudo-ellipses are not as nice as the latitudinal lines are not strait at the
cone edge, but at least creating multiple models with different cone sizes is now possible.

Added the geometric module to the specific_analyses.frame_order package __all__ list.

Fixes for the titles in the frame order geometric representation from frame_order.pdb_model.

There were a few bugs for a number of the frame order models preventing this code from working.

Reverted the lines under the table titles for http://www.nmr-relax.com/download.html.

Fixes for the MC simulation rotor objects in the frame order geometric representation.

The axes of the Monte Carlo simulation rotors objects were being set to the original values and not
to the simulation values.

Fix for the internal structural object MolContainer.last_residue() method.

This can now operate when no structural information is present, returning 0 instead of resulting in
an IndeError.

Removed an accidentally committed change to http://www.nmr-relax.com/download.html.

The relax software tables at http://www.nmr-relax.com/download.html are now fixed cell width.

Changes to the rotor object in the frame order geometric representations.

For the isotropic and pseudo-elliptic cone models, the rotor is now halved. Instead of having two
axes radiating from the central pivot and terminating in the propeller blades, now only the positive
axis is shown lying in the centre of the cone.

Changed the alternative representation names for the frame order geometric objects.

The aim is to put both representations on a more equal footing, as they are identical solutions.
Hence the inverted representation might be the correct representation of the domain motions. So
instead of calling these 'positive' and 'negative', the 'A' and 'B' notation will be used.

This affects the names of the files produced by the frame_order.pdb_model user function as well as
the internal titles. Instead of ending the files with "*_pos.*" and ""*_neg.*", these have been
changed to "*_A.*" and ""*_B.*". The atoms used for the titles have also been renamed, and the
pymol.frame_order user function now labels the titles using the 'A' and 'B' notation.