Do CHARMM parameter/topology/stream file type detection based on file names
WITHOUT any directory names.
Add the "charmm" package to setup.py
Fix setBox to work with the OpenMM class
Update dates and a few other small fixes.
Improved error checking.
Fix chamber action.
Add a function to clear cmaps.
Fix mbondi radii specification.
Add 2 examples (explicit solvent an GB implicit solvent) for CHARMM files.
Add 2 examples using Amber files.
1) Do not add duplicate dihedral types in addDihedral.
2) Allow the "chamber" action to take CHARMM crd and restart files.
Update version ID.
Merge branch 'master' into sphinx