def _clear_output(self):
"""Reset stdout and stderr."""
# Call the base class method.
super()._clear_output()
# Delete any restart and trajectory files in the working directory.
file = "%s/sim_restart.s3" % self._work_dir
if _os.path.isfile(file):
_os.remove(file)
file = "%s/SYSTEM.s3" % self._work_dir
if _os.path.isfile(file):
_os.remove(file)
files = _IO.glob("%s/traj*.dcd" % self._work_dir)
for file in files:
if _os.path.isfile(file):
_os.remove(file)
# Additional files for free energy simulations.
if type(self._protocol) is _Protocol.FreeEnergy:
file = "%s/gradients.dat" % self._work_dir
if _os.path.isfile(file):
_os.remove(file)
file = "%s/simfile.dat" % self._work_dir
if _os.path.isfile(file):
_os.remove(file)
def _find_force_field(forcefield):
"""Internal function to search LEaP compatible force field files.
Parameters
----------
forcefield : str
The name of the force field.
Returns
-------
file : str
The full path of the matching force field file.
"""
# Whether the force field is old.
is_old = False
# Search for a compatible force field file.
ff = _IO.glob("%s/*.%s" % (_cmd_dir, forcefield))
# Search the old force fields. First try a specific match.
if len(ff) == 0:
ff = _IO.glob("%s/oldff/leaprc.%s" % (_cmd_dir, forcefield))
is_old = True
# No matches, try globbing all files with matching extension.
if len(ff) == 0:
ff = _IO.glob("%s/oldff/*.%s" % (_cmd_dir, forcefield))
# No force field found!
if len(ff) == 0:
raise ValueError("No force field file found for '%s'" % forcefield)
# Multiple force fields found.
elif len(ff) > 1:
raise ValueError("Multiple force fields found for '%s': %s" %
(forcefield, ff))
# Create the force field name.
ff = _os.path.basename(ff[0])
if is_old:
ff = "oldff/" + ff
# Return the force field.
return ff