GitLab

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.

Add relevant tests (that used to fail). This also fixes a subtle bug where
switching functions were not applied when NBFIXes were specified.

Also fixes the test case.  Everything should pass now.

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.

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).

terms of supporting PSF files that don't really conform to the "standard" way
that CHARMM prints them.

The downside is that it relies on ! comment tags which I think are comments for
CHARMM.  However, the use of !NATOM and !NBOND and other tags seem to be _much_
more conserved than the general format of the PSF file across different dialects
of PSFs.  So the current approach should be more flexible.

single parameter.

the switchDistance argument to CharmmPsfFile.createSystem().

Also add a check to protect against negative switching distances.

    - Adjust CharmmPsfFile parser to accept multiple blank lines before the
      NATOM record (I saw 1 PSF file like this... not sure how common it really
      is)
    - Removed the shebang line from element.py and removed execute permissions--
      it should never be executed directly (evidenced by the fact that the
      original shebang line was wrong and would never work, anyway).
    - Fix a test to determine if a Bond is part of an Angle in the PSF data
      structures.

former has a single entry for all unique dihedrals. The latter has a separate
entry for every _term_ of every dihedral (and the latter is the one with the
parameters loaded into it). This way, parameter sets can be reloaded at will
without relying on the hack that createSystem previously employed (i.e., backing
up the dihedral array, clobbering it, then putting it back). This way is cleaner
and safer (although functionally equivalent for typical OpenMM use).

boxVectors, so they should be a property computed from the vectors). Also make
sure that any attempts to change the boxVectors correspondingly deletes the
cached copies of the box lengths so they are recomputed if necessary.

correction maps in their calculations.

boxVectors directly (which is how you would do it if you set up a PDB with a
CRYST1 record, for instance).

My test with a periodic system now works, but the interface to adding box
vectors should be improved.

Traceback (most recent call last):
  File "/path/to/python/tests/TestCharmmFiles.py", line 91, in test_HydrogenMass
    topology = self.psf_v.topology
  File "/path/to/lib/python2.7/site-packages/simtk/openmm/app/charmmpsffile.py", line 782, in topology
    topology.addAtom(atom.name, elem, residue)
UnboundLocalError: local variable 'elem' referenced before assignment

ERROR: Test that altering the mass of hydrogens works correctly.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/SimTk/openmm/python/tests/TestCharmmFiles.py", line 91, in test_HydrogenMass
    topology = self.psf_v.topology
  File "/usr/local/lib/python2.7/dist-packages/simtk/openmm/app/charmmpsffile.py", line 777, in topology
    masselem = Element.getByMass(mass)
NameError: global name 'Element' is not defined

- Add a docstring to element.Element.getByMass describing what it does
- Add a new element virtualsite with atomic number 0 (and alias it to extrapoint
  and lonepair)

parameters to a ProteinStructure before calling createSystem.