relax SVN archive

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.

Renamed the residues of the rotor geometric object representation.

The rotor axis atoms now belong to the RTX residue and the propeller blades to the RTB residue. The
'RT' at the start represents the rotor and this will allow all the geometric objects to be better
isolated.

Refactored the frame order geometric motional representation code.

The code of the specific_analyses.frame_order.geometric.create_geometric_rep() function has been
spun out into 3 new functions: add_rotors(), add_axes(), and add_cones(). This is to better isolate
the various elements to allow for better control. Each function now adds the atoms for its
geometric representation to a separate molecule called 'axes' or 'cones'. The add_rotors() does not
create a molecule as the lib.structure.represent.rotor.rotor_pdb() function creates its own. As
part of the rafactorisation, the neg_cone flag has been eliminated.

Fixes for the cone geometric representation in the internal structural object.

The representation can now be created if the given MoleculeContainer object is empty.

Fix for the pivots created by the specific_analyses.frame_order.data.generate_pivot() function.

This is for the double rotor model where the 1st mode of motion is about the 2nd pivot, and the 2nd
mode of motion about the 1st pivot.

Created the very basic structure.com user function for calculating the centre of mass.

This is to simply allow an easy interface to the pipe_control.structure.mass.pipe_centre_of_mass()
function.