relax SVN archive

Wrote the __minimise_bc_data() method to extract the back calculated data after minimisation.

Removed some debugging print statements.

Fixed the generation of the diffusion in a cone geometric object.

Fixed the cone_edge() function.

Fixed the call to and the execution of the stitch_cap_to_cone() function.

Fixed calls to the atom_connect() structural API method.

Atom number fixes for the cone_edge() function.

First try at fixing the generate_vector_dist() function.

Removed some useless code in generate_vector_residues().

Removed some debugging code.