GitLab

Created a public verison of the applyRotationMatrix function so that it can be accessed from outside

Support nucleic acids in AMOEBA 2009

Add CONECT bonds for multi-model pdb files 

Fixed bug in getState() when enforcing periodic boundary conditions

Increased SHAKE iterations when positioning extra particles

Amber switching

 Conflicts:
	wrappers/python/simtk/openmm/app/amberprmtopfile.py

In fixing the merge conflict, I went ahead and fixed up the switchDistance logic
to match what I did in CharmmPsfFile.

Deleted GBVIForce

Fix #1213 addInteractionGroup should accept `set` values as parameters

apparently SWIG typemaps maps Python's list but not set with std::set.
Instead, Python's `set` is mapped with `std::unordered_set`.

The original code of `swigInputBuilder.py` is kindly in a mess. Too much
lines in a single method `writeMethods` which causes debug becomes
difficult. Also there are a lot of warnings about
[PEP8](https://www.python.org/dev/peps/pep-0008/).

A refactoring in the future may be a good idea.

Residue templates can specify atoms by name instead of index

AMD docstring fix