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Swigged python docstrings now include documented return values and type
information or their arguments. They are generated in numpydoc format.
Furthermore, all of the Python app layer docstrings have been changed
to numpydoc format. The filterPythonFiles.py script which helps to
generate the Doxygen Python API docs has been updated to reflect these
changes.

This was actually fully supported already, since it parsed pairtypes and
assigned the exception parameters correctly from there. All this does is throw
an exception when pair parameters are not defined and gen-pairs=no.

Virtual sites are never created by the OpenMM system, and their information is
not parsed from the Gromacs topology file. For now just throw an exception
rather than let them run, since TIP4Pew behaves *very* strangely...

Gromacs uses the preprocessor to replace previously #define'd tokens in strings.
This is used, for instance, to override certain parameters without having to
introduce new file types.  This is how Gromacs implemented ff99SB-ILDN (i.e., by
simply replacing the chi torsion for isoleucine, leucine, aspartate, and
asparagine with a define token).  So OpenMM *was* missing some in-line
parameters that were defined.

The immediate consequence I see is that whenever someone tried to run
ff99SB-ILDN with OpenMM, what they were *really* getting was ff99SB. Not sure
where else, if anywhere, this kind of thing was happening.

This reverts commit 4572d2e3.