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SyntaxWarning otherwise). So move those imports back to the module level and
save any error messages for when the tests are actually run (if ever).

python -m simtk.testInstallation

runs the tests, whereas

python -c "import simtk.testInstallation"

does not.

Also copy the test PDB file to the data/ directory, since we rather need it...

most important and we don't want false positives.

At some point, at least, TP4 was the residue label for water (I think tleap
currently translates most of the water residue labels to WAT, but there are at
least some -- like $AMBERHOME/test/tip4p/prmtop -- that use older labels).

Make sure files are appropriately closed by PDBFile()

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.

underlying numpy array. This function would be used in instances where, for
instance, a certain API would send a flattened array of coordinates or
velocities with units attached, and you wanted to reshape the array into
(natom, 3) to be consistent with OpenMM's Context object.

arguments and pass them to the numpy function if applicable. That way, users get
the full flexibility of the numpy API on those particular methods AND get the
added benefit that the result has the correct units (and it all runs fast).

it.  Not only that, I got this FutureWarning:

/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simtk/unit/quantity.py:170:
FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
  if value == None:

sqrt of the variance), and average, returning a Quantity with the proper units.

This should be reasonably efficient, as it takes advantage of numpy-accelerated
methods if they're present.

parameter set.

 Changes to be committed:
	modified:   checkpointreporter.py

there is a small typo in checkpointreporter.py in openmm. line 81 has:
self._own_handle = true
instead of True.

terms of supporting PSF files that don't really conform to the "standard" way
that CHARMM prints them.

The downside is that it relies on ! comment tags which I think are comments for
CHARMM.  However, the use of !NATOM and !NBOND and other tags seem to be _much_
more conserved than the general format of the PSF file across different dialects
of PSFs.  So the current approach should be more flexible.