GitLab

Remove optimization to ForceField LennardJonesGenerator that was causing issues with CHARMM conversion

Changed format to 'pdbx' for consistency within the test framework. Added 'cif' to CMakeLists.txt for correctness for the future

There are times when it is helpful to have the energy terms actually
added to the System even if that degree of freedom is constrained. Other
parsers (notably the Amber parsers) already support this keyword, so add
that support to ForceField as well

This also replaces some string-based element detection algorithms with
whatever the PDB parser does (by comparing directly to atom.element)

createSystem for both Amber and CHARMM files.

take everything out to a function, RBTorsion and CustomTorsion now use ordering=charmm as their default