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Prints out a more helpful error message than a weird regex-based missing
"groups" attribute on NoneType.

This also removes assert statements, since those can't be relied upon to *not*
be optimized away -- they should never be used to check user input sanity.

Masses do not increase monotonically with atomic number

Also fixes the test case.  Everything should pass now.

Reduces time taken from 15.7 seconds (last commit) to 2.2 seconds by avoiding
Quantity comparisons altogether.

The old approach iterated through the entire periodic table by atomic number and
subtracted the provided mass by the element's mass and kept track of the
smallest difference. The new approach steps through the elements in order of
atomic number and bails once it hits an element with a higher mass than the
target mass (assuming masses are monotonically increasing).

On my desktop, processing 4TVP-dmj_wat-ion.psf dropped from 297 s to 15.4 s. But
15.4 s is still a bit too long...

See swig/swig#387 for a discussion.  It would actually be nice to *not* set the
"compactdefaultargs" feature globally, since that would allow us to actually see
the real API at the Python level the same as you would see by looking at the C++
header files. But this is the only way to support both SWIG 2 and SWIG 3 easily
and avoid a lot of retooling for the SWIG input code generator.

Apparently CHARMM PSF files (particularly those printed by VMD's psfgen) can
have an insertion code tacked on to the end of the residue number, meaning that
casting to an integer will invariably fail.  We can't just ignore the insertion
code, though, since it will differentiate from the residues that came before and
after (which will likely have the same number -- same general idea as insertion
codes from PDB files). So instead we pull the insertion code off of the residue
number and extend the Residue object to accommodate that.

This is the port of the fix from ParmEd: ParmEd/ParmEd#98

I added a test for this case.

Adds a test for it as well.

files.

Some topology files have some of the nonbonded pairs in the Lennard-Jones matrix
pointing to a 0 entry in the HBOND_ACOEF and HBOND_BCOEF arrays. This commit
simply skips over those entries, having previously checked that all entries in
the 10-12 sections are 0.  There is actually an example of this already in the
test suite (see ff14ipq.parm7), but this fortuitously did not cause any
difference in those test results.

The reason this bug is not evident in that test case is because the A- and
B-coefficients pulled when the index was -1 (later decremented to -2) was also
coincidentally 0. However, if this was not the case (as it does not *have* to
be), then who knows what could happen.

This also adds more of a check against 10-12 topology files. ParmEd actually
supports using the 10-12 potential in OpenMM when specified in the Amber prmtop,
but it is sufficiently rare that it is not worth porting to OpenMM, IMO.

flags. This can cause a KeyError when trying to look up the format of the
current section when it's reading the %COMMENT line (before any Format has been
assigned).

mdtraj) does *not* fully reduce the vectors.

Also adds a test for this.

Also added a test suite for them.

truncated octahedron inpcrd and prmtop file.

to support triclinic cells.

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