allow skipping of frames where PROPKA fails

[orbeckst]

If PROPKA fails for mysterious reasons then we want to have the option to move on and skip frames.

requirements

• keyword argument that allows ignoring failing frames (skip_failing = True)
• use try/except to skip
• log frames that fail
• log error message at end if any frames were skipped and summarize the percentage of skipped frames

design notes

Put a try/except around https://github.com/Becksteinlab/propkatraj/blob/master/propkatraj/propkatraj.py#L74 together with the logging.

• If skip_failing = False then raise the exception.
• If skip_failing = True then log error and continue

Something like

try:
        mol = pk.single(pstream, optargs=['--quiet'])
except IndexError as err:
        if not skip_failing:
            raise
        else:
            # log ...
            # continue the loop at the next frame, not sure if this
            # is working....
            continue
finally:
       pstream.close(force=True) # deallocate

(IndexError is the PROPKA error that @rsexton2 encounters.)

[orbeckst]

@rsexton2 please attach a zip file with structure and trajectory that fail together with the code you used for testing. Thanks!

[rsexton2]

Script used where failing frame is isolated (ts = 1414ns).

import MDAnalysis as mda
import propkatraj

traj = 'test_traj.xtc'
topology = 'test_top.gro'
u = mda.Universe(topology, traj)

pkas = propkatraj.get_propka(u, sel='protein', skip_failure=True, start=10, stop=19)

[rsexton2]

Zip file containing the topology and trajectory where propka fails.

test_traj_top.zip