relax SVN archive

Created a frame order rotor test model whereby the rotation axis is perpendicular to the domain.

The rotation is a total of 60 degrees about an axis perpendicular to the pivot-CoM vector. The
'rotor' test model directory is reserved for a model whereby the rotation axis is the pivot-CoM
vector.

Properly added the add_atom() and connect_atom() methods to the structural API.

Fixes and speed up for the 2nd frame order free rotor model system test.

The grid search has been replaced by the setting of values to that after a high resolution grid
search, decreasing the test time from ~39 seconds to ~0.8 seconds.

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.