GitLab

clang is tested everywhere else, and it's not as routinely up-to-date on
my Jenkins machine.

PythonInstall failed on Linux machines where the build/install
directories had paths with spaces in them.

- Test system is translated to the origin
- Energy is computed again after updating Gromacs input to reflect no-cutoff option (rcoulomb = rlist = rvdw = 0.0)

The pickle round trip for the Bond object does not preserve the `type` and `order` parameters in Python 2.7.

Near as I can tell, its because the parent `namedtuple` already has a __getstate__ method, so the default
of returning the `__dict__` is never given, so `__setstate__` is not called (as default). This leads to pickle
 restoring the state, but never invoking the `__new__` statement, resulting in `type` and `order` being
 lost.

 This PR fixes this problem in python 2.7, without breaking python 3.x versions.

 Related mdtraj/mdtraj#1308

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