relax SVN archive

Fixes for all system tests failing due to the expanded and improved PDB REMARK section.

The system tests now remove all REMARK records prior to comparing file contents. The special
strip_remarks() system test method has been created to simplify the stripping process.

Fixes for the Diffusion_tensor system tests due to the recent PDB file changes.

Prior to the comparison of the generated PDB files, all REMARK PDB lines are now stripped out.

Expansion of the REMARK section of the PDB file created for the internal structural object.

This is visible when using the structure.write_pdb user function, as well as the many other user
functions which create PDB files. The relax version as well as the file creation date are now
recorded in the PDB file. This extra information should be very useful. Empty lines in the REMARK
section improve the formatting.

Empty lines are now handled by the lib.structure.pdb_write.record() function.

By supplying the remark as None, empty lines can now be created in the REMARK section of a PDB file.
This can be used for nicer formatting.

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.