def open_with_pygmx(topology, trajectory, cached=False, reindex=False,
ignore_index_timestamps=False, index_file=None):
"""Open a topology and trajectory with pygmx."""
try:
rd = pygmx.open(trajectory, ignore_index_timestamps=ignore_index_timestamps)
except InvalidMagicException:
raise InvalidIndexException('This is not a valid index file: {}'.format(trajectory))
except InvalidIndexException:
if reindex:
try:
os.remove(pygmx.index_filename_for_xtc(trajectory))
except FileNotFoundError:
pass
rd = pygmx.open(trajectory)
else:
raise InvalidIndexException('Index file is invalid, us reindex=True to regenerate.')
if cached is not False:
if isinstance(cached, bool):
maxsize = 128
else:
maxsize = cached
reader = CachedReader(rd, maxsize)
else:
reader = BaseReader(rd)
if topology.endswith('.tpr'):
atms = atoms.from_tprfile(topology, index_file=index_file)
elif topology.endswith('.gro'):
atms = atoms.from_grofile(topology, index_file=index_file)
return atms, reader
def __init__(self, edrfile):
"""
Args:
edrfile: Filename of the energy file
topology (opt.): Filename of the topology, speeds up file io since the length of the energy file is known
"""
edr = pygmx.open(edrfile)
self.time, data = edr.read()
self.types, self.units = zip(*edr.types)
self.data = data.T