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This doesn't lead to incorrect results, but it does erroneously flag some radii
as being illegal when they aren't (making it impossible to run some suggested
systems).

The parameters need to be compared to the table limits *before* subtracting off
the offset, whereas it's currently being done after.

See https://simtk.org/forums/viewtopic.php?f=161&t=6512&p=16820#p16820 for more
information

See http://docs.openmm.org/development/api-python/generated/simtk.openmm.mtsintegrator.MTSIntegrator.html#
for the rendered results that are less than ideal.

Also changes a bunch of old-style Python classes to new-style (Py3 only has the
latter)

factors.

Add test for parameterizing system using templates built with the help of getUniqueUnmatchedResidues()