First try at fixing the generate_vector_dist() function.
Removed some useless code in generate_vector_residues().
Removed some debugging code.
Fixes for the cone_edge() function for the structural API changes.
Fixed the creation of the PIV and AVE residues for the cone models.
The structural data structure for the cone is now properly initialised.
Fixed a call to the structural PDB writer.
Fixed some more calls to the structural method atom_add().
Typo bug fix for another call to the structural method atom_add().
Fixed a call to atom_add().