GitLab

cutoff GB.

topology file with the Amber file parsers. These do *not* currently work for
creating a system.

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

are NOT numpy arrays.

run_tests to TestingError so users only ever have one exception to catch.

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()

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_)