def prepare(self): # pragma: no cover
# coverage ignored b/c Travis won't have gmx. However, we do have a
# test that covers this if gmx is present (otherwise it is skipped)
# ensure that the files haven't changed before we run trajectory
_ = ensure_file(self.gro, self.gro_contents, self._gro_hash)
_ = ensure_file(self.mdp, self.mdp_contents, self._mdp_hash)
_ = ensure_file(self.top, self.top_contents, self._top_hash)
# grompp and mdrun
cmd = self.grompp_command
logger.info(cmd)
run_cmd = shlex.split(cmd)
return_code = psutil.Popen(run_cmd, preexec_fn=os.setsid).wait()
return return_code
def __init__(self, gro, mdp, top, options, base_dir="", prefix="gmx"):
self.base_dir = base_dir
self.gro = os.path.join(base_dir, gro)
self.mdp = os.path.join(base_dir, mdp)
self.top = os.path.join(base_dir, top)
self.prefix = os.path.join(base_dir, prefix)
self.gro_contents, self._gro_hash = ensure_file(self.gro)
self.mdp_contents, self._mdp_hash = ensure_file(self.mdp)
self.top_contents, self._top_hash = ensure_file(self.top)
# TODO: move to a later stage, before first traj
dirs = [self.prefix + s for s in ['_trr', '_log', '_edr']]
for d in dirs:
try:
os.mkdir(d)
except OSError:
pass # the directory already exists
self._file = None # file open/close efficiency
self._last_filename = None
# TODO: add snapshot_timestep; first via options, later read mdp
template = snapshot_from_gro(self.gro)
self.topology = template.topology
descriptor = template.engine.descriptor # descriptor from gro file
# initial placeholders
self.input_file = "INITIAL.trr"
self.output_file = self.prefix + "_trr/OUTPUT_NAME.trr"
self.edr_file = self.prefix + "_edr/OUTPUT_NAME.edr"
self.log_file = self.prefix + "_log/OUTPUT_NAME.log"
self.tpr_file = "topol.tpr"
self.mdout_file = "mdout.mdp"
self._mdtraj_topology = None
super(GromacsEngine, self).__init__(options,
descriptor,
template,
first_frame_in_file=True)
def from_dict(cls, dct):
dct = dict(dct) # make a copy
for ftype in ['gro', 'top', 'mdp']:
contents = dct.pop(ftype + "_contents")
_ = ensure_file(filename=dct[ftype], old_contents=contents)
return super(GromacsEngine, cls).from_dict(dct)