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This also removes assert statements, since those can't be relied upon to *not*
be optimized away -- they should never be used to check user input sanity.

Also fixes the test case.  Everything should pass now.

Apparently CHARMM PSF files (particularly those printed by VMD's psfgen) can
have an insertion code tacked on to the end of the residue number, meaning that
casting to an integer will invariably fail.  We can't just ignore the insertion
code, though, since it will differentiate from the residues that came before and
after (which will likely have the same number -- same general idea as insertion
codes from PDB files). So instead we pull the insertion code off of the residue
number and extend the Residue object to accommodate that.

This is the port of the fix from ParmEd: ParmEd/ParmEd#98

I added a test for this case.

Adds a test for it as well.

mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.

Also added a test suite for them.

truncated octahedron inpcrd and prmtop file.

cutoff GB.

found in doctests.py (and quite a bit more, too)

Make sure files are appropriately closed by PDBFile()

can't validate the that this object does anything more than simply write without
exceptions (i.e., we can't tell if the DCD file is actually _valid_)

Add a test for the various numpy attributes (and the arguments they take) for
the unit module.

Traceback (most recent call last):
  File ".../python/tests/TestNumpyCompatibility.py", line 87, in testNumpyAttributes
    d = self.data.reshape((100, 3))
  File ".../simtk/unit/quantity.py", line 575, in reshape
    return Quantity(self._value.reshape(shape, order=order))
  File ".../simtk/unit/quantity.py", line 142, in __init__
    if value == first_item:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

Also add a test for new unit numpy capabilities.