added some fixes for lammps running using convert.py
added in some dependencies removed when header_functions.py was removed.
fix for lammps not reading in atomic number

Lammps did not read in atomic number, and may not have it in the file.
temporarily replace it with 0.
modified how constraints and bond order are managed

Now, they are part of the abstract types - constraints
for both, order for bonds

Also changed formatting for some of the "accepts units" directives.

Fixes for angle and bond interpretation by code, with unimplemented angles/bonds/dihedrals
being specifically named.