def _setup(self):
"""Setup the input files and working directory ready for simulation."""
# Create the input files...
# First create a copy of the system.
system = self._system.copy()
# If the we are performing a free energy simulation, then check that
# the system contains a single perturbable molecule. If so, then create
# and write a perturbation file to the work directory.
if type(self._protocol) is _Protocol.FreeEnergy:
if system.nPerturbableMolecules() == 1:
# Extract the perturbable molecule.
pert_mol = system.getPerturbableMolecules()[0]
# Write the perturbation file and get the molecule corresponding
# to the lambda = 0 state.
pert_mol = pert_mol._toPertFile(
self._pert_file, property_map=self._property_map)
self._input_files.append(self._pert_file)
# Remove the perturbable molecule.
system._sire_object.remove(pert_mol.number())
# Recreate the system, putting the perturbable molecule with
# renamed properties first.
updated_system = _System(pert_mol) + _System(system)
# Copy across all of the properties from the orginal system.
for prop in system._sire_object.propertyKeys():
updated_system._sire_object.setProperty(
prop, system._sire_object.property(prop))
# Copy the updated system object across.
system = updated_system
else:
raise ValueError("'BioSimSpace.Protocol.FreeEnergy' requires a single "
"perturbable molecule. The system has %d" \
% system.nPerturbableMolecules())
# If this is a different protocol and the system still contains a
# perturbable molecule, then we'll warn the user and simulate the
# lambda = 0 state.
else:
if system.nPerturbableMolecules() > 0:
if not "is_lambda1" in self._property_map:
is_lambda1 = False
_warnings.warn(
"The system contains a perturbable molecule but "
"this isn't a 'FreeEnergy' protocol. We will assume "
"that you intend to simulate the lambda = 0 state. "
"If you want to simulate the lambda = 1 state, then "
"pass {'is_lambda1' : True} in the 'property_map' "
"argument.")
else:
is_lambda1 = self._property_map["is_lambda1"]
self._property_map.pop("is_lambda1")
# Loop over all perturbable molecules in the system and replace them
# with a regular molecule and the chosen end state.
for mol in system.getPerturbableMolecules():
system.updateMolecules(
mol._toRegularMolecule(property_map=self._property_map,
is_lambda1=is_lambda1))
# Copy across the properties from the original system.
for prop in self._system._sire_object.propertyKeys():
system._sire_object.setProperty(
prop, self._system._sire_object.property(prop))
# RST file (coordinates).
try:
rst = _SireIO.AmberRst7(system._sire_object, self._property_map)
rst.writeToFile(self._rst_file)
except Exception as e:
msg = "Failed to write system to 'RST7' format."
if _isVerbose():
raise IOError(msg) from e
else:
raise IOError(msg) from None
# PRM file (topology).
try:
prm = _SireIO.AmberPrm(system._sire_object, self._property_map)
prm.writeToFile(self._top_file)
except Exception as e:
msg = "Failed to write system to 'PRM7' format."
if _isVerbose():
raise IOError(msg) from e
else:
raise IOError(msg) from None
# Generate the SOMD configuration file.
# Skip if the user has passed a custom config.
if type(self._protocol) is _Protocol.Custom:
self.setConfig(self._protocol.getConfig())
else:
self._generate_config()
self.writeConfig(self._config_file)
# Generate the dictionary of command-line arguments.
self._generate_args()
# Return the list of input files.
return self._input_files
def _setup(self):
"""Setup the input files and working directory ready for simulation."""
# Create the input files...
# First create a copy of the system.
system = _System(self._system)
# If the we are performing a free energy simulation, then check that
# the system contains a single perturbable molecule. If so, then create
# and write a perturbation file to the work directory.
if type(self._protocol) is _Protocol.FreeEnergy:
if system.nPerturbableMolecules() == 1:
# Extract the perturbable molecule.
pert_mol = system.getPerturbableMolecules()[0]
# Write the perturbation file and get the molecule corresponding
# to the lambda = 0 state.
pert_mol = pert_mol._toPertFile(
self._pert_file, property_map=self._property_map)
self._input_files.append(self._pert_file)
# Remove the perturbable molecule.
system._sire_system.remove(pert_mol.number())
# Recreate the system, putting the perturbable molecule with
# renamed properties first.
updated_system = _System(pert_mol) + _System(system)
# Copy across all of the properties from the orginal system.
for prop in system._sire_system.propertyKeys():
updated_system._sire_system.setProperty(
prop, system._sire_system.property(prop))
# Copy the updated system object across.
system = updated_system
else:
raise ValueError("'BioSimSpace.Protocol.FreeEnergy' requires a single "
"perturbable molecule. The system has %d" \
% system.nPerturbableMolecules())
# Extract the updated Sire system.
system = system._sire_system
# RST file (coordinates).
try:
rst = _SireIO.AmberRst7(system, self._property_map)
rst.writeToFile(self._rst_file)
except:
raise IOError("Failed to write system to 'RST7' format.") from None
# PRM file (topology).
try:
prm = _SireIO.AmberPrm(system, self._property_map)
prm.writeToFile(self._top_file)
except:
raise IOError("Failed to write system to 'PRM7' format.") from None
# Generate the SOMD configuration file.
# Skip if the user has passed a custom config.
if type(self._protocol) is _Protocol.Custom:
self.setConfig(self._protocol.getConfig())
else:
self._generate_config()
self.writeConfig(self._config_file)
# Generate the dictionary of command-line arguments.
self._generate_args()
# Return the list of input files.
return self._input_files