relax SVN archive

Fixes for the free rotor frame order 2nd test model data.

The rotation axes were not normalised, so the data was not correct!

The generation script for the free rotor frame order test model 2 creates a PDB for the axis system.

The generate_distribution.py now creates the axis.pdb file which encoded the rotation axis of the
domain distribution. The animate.py will also display this rotation axis.

The internal structural reader can now create PDB files if atom numbers are missing.

This fixes the structure.write_pdb user function in certain edge cases.

Created the structure.connect_atom user function to expose the back-end functionality.

This works with atom indices, so is not ideal for a user function. In the future this should be
modified to handle atom ID strings instead.

Slight changes to the pivot-CoM PDB representation for the frame order test data.

The internal structural object no longer requires the 'ATOM' PDB record for creating PDB files.

This affects the structure.write_pdb user function.

Created the structure.add_atom user function.

This simply exposes some of the functionality of the structural API to the user. The get_molecule()
API method has also been added to return molecule containers.

Created the Frame_order.test_cam_free_rotor2 system test.

This tests the free rotor frame order CaM test model where the axis is tilted from the pivot-CoM
axis.

Created a second test model for the free rotor frame order model.

In this case, the C-domain does not rotate about the pivot-CoM axis, but an axis tilted 30 degrees
from the pivot-CoM axis.

Fix for the structure.displacement user function.

The kabsch() function now returns the pivot of the rotation as well.