relax SVN archive

Fix for the pymol.frame_order user function.

The representation function for the rotor objects was hiding all parts of the representation, hence
the pivot labels where being hidden. To fix this, the hiding of the geometric object now occurs in
the base frame_order_geometric() function prior to setting up the representations for the various
objects.

Fixes for the cone geometric object created by the frame_order.pdb_model user function.

This was broken by the code refactoring and now works again for the pseudo-ellipse models.

Redesign of the axis geometric representation for the frame order motions.

This is now much more model dependent to avoid clashes with the rotor objects and other
representations:

- For the torsionless isotropic cone, a single z-axis is created.

- For the double rotor, a single z-axis is produced connecting the two pivots, from pivot2 to pivot1.

- For the pseudo-ellipse and free rotor pseudo-ellipse, the x and y-axes are created.

- For the torsionless pseudo-ellipse, all three x, y and z-axes are created.

- For all other models, no axis system is produced as this has been made redundant by the rotor
objects.

Modified the rotor representation generated by the pymol.frame_order user function.

This is to make the object less bulky.

Added support for labels in the rotor geometric object for the internal structural object.

The labels are created by the frame_order.pdb_model user function backend. For the double rotor
model, these are 'x-ax' and 'y-ax'. For all other models, the label is 'z-ax'.

The labels are then sent into the lib.structure.represent.rotor.rotor() function via the new label
argument. This function adds two new atoms to the rotor molecule which are 2 Angstrom outside of
the rotor span and lying on the rotor axis. These then have their atom name set to the label. The
residue name is set to the new RTL name which has been added to the internal structural object
_get_chemical_name() method to describe the residue in the PDB file for the user.

Finally the pymol.frame_order user function selects these atoms, hides them and then labels them
using the atom name (x-ax, y-ax, or z-ax).

Renamed the lib.structure.represent.rotor.rotor_pdb() function to rotor().

This function is not PDB specific and it just creates a 3D structural representation of a rotor
object.

The motional pivots for the frame order models are now labelled in the geometric representation.

The pivot points are now added as a new molecule called 'pivots' in the frame_order.pdb_model user
function. The atoms all belong to the PIV residue. The pymol.frame_order user function now selects
this residue, hides its atoms, and then shows the atom name 'Piv' as the label. For the double
rotor model, the atom names 'Piv1' and 'Piv2' are used to differentiate the pivots.

Renaming of the residues of the cone geometric representation.

The cone apex or centre is now the CNC residue, the cone axis is now CNX and the cone edge is now
CNE. These used to be APX, AXE, and EDG respectively. The aim is to make these names 100% specific
to the cone object so that they can be more easily selected for manipulating the representation and
so that they are more easily identifiable. The internal structural object _get_chemical_name()
function now returns a description for each of these. Note that the main cone object is still named
CON.

Typo fix for r24368, the 'cones' molecule was mistyped.

Improvements to the internal structural object _get_chemical_name() method.

This now uses a translation table to convert the hetID or residue name into a description, for
example as used in the PDB HETNAM records to give a human readable description of the residue inside
the PDB file itself. The new rotor RTX and RTB residue names have been added to the table as well.