GitLab

to support triclinic cells.

Also extend unitcell.computePeriodicBoxVectors to take Quantity inputs rather
than *just* scalars assumed to be nanometers.

now that triclinics are supported this is important).

Update the Python application layer to use both force constants when building
the AmoebaStretchBendForce.

between 1 and 2 Angstroms, or they fall outside the bounds of the neck lookup
tables.

At least on my Mac, this results in a C++ exception that does not get translated
into a Python exception (i.e., it is not catchable and crashes the application)

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()