GitLab

    - existence of velocities and box vectors is auto-detected, so
      loadVelocities and loadBoxVectors are unnecessary
    - recognizes NetCDF-format Amber restart files (which can be written by
      tleap, sander, pmemd, and cpptraj).
    - Restart files coordinate/velocity/box fields have a hard width of 12
      characters and does not ensure that fields are whitespace delimited. This
      commit will correctly parse (valid) Amber restart files in which a
      particular coordinate is <= -100 A or >= 1000 A (not uncommon for restart
      files from sander/pmemd).
    - File format (ASCII vs. NetCDF) is auto-detected.

I deprecated the loadVelocities and loadBoxVectors arguments, since the behavior
does not change (and is correct) whether these variables are set or not. A
DeprecationWarning is emitted if users specify these variables.

the file name (not the path) for "top" and "par" to determine file type.  Often
enough, these files are stored in a "toppar" directory, so all of them will be
interpreted as RTF files.

correction maps in their calculations.

patched up by me).

boxVectors directly (which is how you would do it if you set up a PDB with a
CRYST1 record, for instance).

My test with a periodic system now works, but the interface to adding box
vectors should be improved.

Traceback (most recent call last):
  File "/path/to/python/tests/TestCharmmFiles.py", line 91, in test_HydrogenMass
    topology = self.psf_v.topology
  File "/path/to/lib/python2.7/site-packages/simtk/openmm/app/charmmpsffile.py", line 782, in topology
    topology.addAtom(atom.name, elem, residue)
UnboundLocalError: local variable 'elem' referenced before assignment

ERROR: Test that altering the mass of hydrogens works correctly.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/SimTk/openmm/python/tests/TestCharmmFiles.py", line 91, in test_HydrogenMass
    topology = self.psf_v.topology
  File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/app/charmmpsffile.py", line 777, in topology
    masselem = Element.getByMass(mass)
NameError: global name 'Element' is not defined

pickleability.

- Add a docstring to element.Element.getByMass describing what it does
- Add a new element virtualsite with atomic number 0 (and alias it to extrapoint
  and lonepair)

constructor _should_ be able to take all of files in the CHARMM parameter set
distribution and correctly determine file type from just the name and/or
filename extension.

parameters to a ProteinStructure before calling createSystem.