GitLab

* In CharmmPsfFile, add lonepair exceptions even when no Drude particles
  are present

* In ForceField, correctly update the indices of virtual site exclusion
  reference particles in a residue when applying a patch to it

* Atom types in CHARMM FF are non-case-sensitive

* Atom type name in CHARMM RTF

* Make atom section in CHARMM PSF file to be uppercase

* Update charmmparameterset.py

* Update charmmpsffile.py

* Top level Python module is now "openmm"

* Updated module names in examples

* Updated module names in documentation

* Updated module in CI scripts

* Added deprecation warning

* Do not alter mass of hydrogens in rigid water

* Do not alter mass of hydrogens in rigid water

* nbthole

* Update charmmpsffile.py

* Update charmmpsffile.py

* Update charmmparameterset.py

fix multiple dihedral with the same periodicity and add a warning reminder for improper dihedral

* add test example for NBTHole

add system files of CYT-GUA-CYT DNA segment for testing NBThole

* Update TestCharmmFiles.py

Make CharmmPsfFile ignore H-H water bond that is required for rigid water with original CHARMM implementation of constrains.

* Use list-comprehension in Python code

A minor change, but slighly easier to understand the initialization of
`parent_exclude_list` in my opinion.

* Implement __ne__ in Python classes that has __eq__

In Python 3, `__ne__` is automatically implemented as `not __eq__`.

However, in Python 2 it seems to be implemented as `not is` (so based on object
identity).

Based on setup.py [0] which says that "OpenMM requires Python 2.7 or better", it
should be useful to have better support for Python 2 :)

This was already done in 4 of the 12 classes that implements `__eq__`

```
>>> class WildCard(object):
...     def __eq__(self, other): return True

>>> w = WildCard()

>>> w == 42
True

>>> w != 42
True

>>> w != w
False
```

[0]: https://github.com/openmm/openmm/blob/5cef29ce8d4e17b6d0f9fd8a3c6cc1669ca0ba2b/wrappers/python/setup.py#L237

* Use umambiguous floor division for index calculations in Python

This makes the code work as intended if run as Python 3

```
$ python2 -c 'print(3/2, 3//2)'
(1, 1)
$ python3 -c 'print(3/2, 3//2)'
1.5 1
```

* Use `with` for file handling in Python

* Use `is None` instead of `== None` in Python

This is recommended in PEP8:

> Comparisons to singletons like None should always be done with is or is not, never the equality operators.
> - https://www.python.org/dev/peps/pep-0008/#programming-recommendations

when the number of molecules does not agree
with the number of holders.

createSystem for both Amber and CHARMM files.