relax SVN archive

cone_pdb() now handles the AXE residue.

Changed the scaling arg to a direct size arg.

Bug fix for the pymol.cartoon() user function.

This was failing when multiple proteins were loaded.

Added a test for a loaded structure to the pymol.cartoon() user function.

Bug fixes for the generate_vector_dist() function.

The protons were not being correctly stitched together!

Fixes for the cone_pdb() method.

Bug fixes for the write_pdb() method.

The Hetrogen section was failing with MC simulations.

Renaming and fixes for stitch_cone_to_edge().

This was stitch_cap_to_cone().

Wrote the cone_pdb() and pivot() methods.

Bug fix for generate_vector_residues() when the neg flag is False.

The atoms were incorrectly numbered.