def _initialise_runner(self, system0, system1):
"""Internal helper function to initialise the process runner.
Parameters
----------
system0 : :class:`System <BioSimSpace._SireWrappers.System>`
The system for the first free energy leg.
system1 : :class:`System <BioSimSpace._SireWrappers.System>`
The system for the second free energy leg.
"""
if type(system0) is not _System:
raise TypeError(
"'system0' must be of type 'BioSimSpace._SireWrappers.System'")
if type(system1) is not _System:
raise TypeError(
"'system1' must be of type 'BioSimSpace._SireWrappers.System'")
# Initialise lists to store the processes for each leg.
leg0 = []
leg1 = []
# Get the simulation type.
sim_type = self.__class__.__name__
# Store the working directories for the legs.
if sim_type == "Solvation":
self._dir0 = "%s/free" % self._work_dir
if self._is_dual:
self._dir1 = "%s/vacuum" % self._work_dir
elif sim_type == "Binding":
self._dir0 = "%s/bound" % self._work_dir
if self._is_dual:
self._dir1 = "%s/free" % self._work_dir
else:
raise TypeError("Unsupported FreeEnergy simulation: '%s'" %
sim_type)
# Convert to an appropriate AMBER topology. (Required by SOMD.)
if self._engine == "SOMD":
# Try to get the water model used to solvate the system.
try:
water_model = system0._sire_object.property(
"water_model").toString()
waters0 = _SireIO.setAmberWater(
system0._sire_object.search("water"), water_model)
if self._is_dual:
waters1 = _SireIO.setAmberWater(
system1._sire_object.search("water"), water_model)
# If the system wasn't solvated by BioSimSpace, e.g. read from file, then try
# to guess the water model from the topology.
except:
num_point = system0.getWaterMolecules()[0].nAtoms()
if num_point == 3:
# TODO: Assume TIP3P. Not sure how to detect SPC/E.
waters0 = _SireIO.setAmberWater(
system0._sire_object.search("water"), "TIP3P")
if self._is_dual:
waters1 = _SireIO.setAmberWater(
system1._sire_object.search("water"), "TIP3P")
water_model = "tip3p"
elif num_point == 4:
waters0 = _SireIO.setAmberWater(
system0._sire_object.search("water"), "TIP4P")
if self._is_dual:
waters1 = _SireIO.setAmberWater(
system1._sire_object.search("water"), "TIP4P")
water_model = "tip4p"
elif num_point == 5:
waters0 = _SireIO.setAmberWater(
system0._sire_object.search("water"), "TIP5P")
if self._is_dual:
waters1 = _SireIO.setAmberWater(
system1._sire_object.search("water"), "TIP5P")
water_model = "tip5p"
else:
raise RuntimeError("Unsupported %d-point water model!" %
num_point)
# Warn the user that we've guessed the water topology.
_warnings.warn("Guessed water topology: %r" % water_model)
# Remove the existing water molecules from the systems.
system0.removeWaterMolecules()
if self._is_dual:
system1.removeWaterMolecules()
# Convert the waters to BioSimSpace molecule containers.
waters0 = _Molecules(waters0.toMolecules())
if self._is_dual:
waters1 = _Molecules(waters1.toMolecules())
# Add the updated water topology back into the systems.
system0.addMolecules(waters0)
if self._is_dual:
system1.addMolecules(waters1)
# Get the lambda values from the protocol.
lam_vals = self._protocol.getLambdaValues()
# Loop over all of the lambda values.
for lam in lam_vals:
# Update the protocol lambda values.
self._protocol.setLambdaValues(lam=lam, lam_vals=lam_vals)
# Create and append the required processes for each leg.
# Nest the working directories inside self._work_dir.
# SOMD.
if self._engine == "SOMD":
# Check for GPU support.
if "CUDA_VISIBLE_DEVICES" in _os.environ:
platform = "CUDA"
else:
platform = "CPU"
leg0.append(
_Process.Somd(system0,
self._protocol,
platform=platform,
work_dir="%s/lambda_%5.4f" %
(self._dir0, lam)))
if self._is_dual:
leg1.append(
_Process.Somd(system1,
self._protocol,
platform=platform,
work_dir="%s/lambda_%5.4f" %
(self._dir1, lam)))
# GROMACS.
elif self._engine == "GROMACS":
leg0.append(
_Process.Gromacs(system0,
self._protocol,
work_dir="%s/lambda_%5.4f" %
(self._dir0, lam)))
if self._is_dual:
leg1.append(
_Process.Gromacs(system1,
self._protocol,
work_dir="%s/lambda_%5.4f" %
(self._dir1, lam)))
# Initialise the process runner. All processes have already been nested
# inside the working directory so no need to re-nest.
self._runner = _Process.ProcessRunner(leg0 + leg1,
work_dir=self._work_dir,
nest_dirs=False)
def _initialise_runner(self, system0, system1):
"""Internral helper function to initialise the process runner.
Parameters
----------
system0 : :class:`System <BioSimSpace._SireWrappers.System>`
The system for the first free energy leg.
system1 : :class:`System <BioSimSpace._SireWrappers.System>`
The system for the second free energy leg.
"""
if type(system0) is not _System:
raise TypeError(
"'system0' must be of type 'BioSimSpace._SireWrappers.System'")
if type(system1) is not _System:
raise TypeError(
"'system1' must be of type 'BioSimSpace._SireWrappers.System'")
# Initialise lists to store the processes for each leg.
leg0 = []
leg1 = []
# Get the simulation type.
sim_type = self.__class__.__name__
# Store the working directories for the legs.
if sim_type == "Solvation":
self._dir0 = "%s/free" % self._work_dir
self._dir1 = "%s/vacuum" % self._work_dir
elif sim_type == "Binding":
self._dir0 = "%s/bound" % self._work_dir
self._dir1 = "%s/free" % self._work_dir
else:
raise TypeError("Unsupported FreeEnergy simulation: '%s'" %
sim_type)
# Try to get the water model property of the system.
try:
water_model = system0._sire_system.property(
"water_model").toString()
# Default to TIP3P.
except:
water_model = "tip3p"
if self._engine == "SOMD":
# Reformat all of the water molecules so that they match the expected
# AMBER topology template. (Required by SOMD.)
waters0 = _SireIO.setAmberWater(
system0._sire_system.search("water"), water_model)
waters1 = _SireIO.setAmberWater(
system1._sire_system.search("water"), water_model)
# Loop over all of the renamed water molecules, delete the old one
# from the system, then add the renamed one back in.
# TODO: This is a hack since the "update" method of Sire.System
# doesn't work properly at present.
system0.removeWaterMolecules()
system1.removeWaterMolecules()
for wat in waters0:
system0._sire_system.add(wat, _SireMol.MGName("all"))
for wat in waters1:
system1._sire_system.add(wat, _SireMol.MGName("all"))
# Get the lambda values from the protocol.
lam_vals = self._protocol.getLambdaValues()
# Loop over all of the lambda values.
for lam in lam_vals:
# Update the protocol lambda values.
self._protocol.setLambdaValues(lam=lam, lam_vals=lam_vals)
# Create and append the required processes for each leg.
# Nest the working directories inside self._work_dir.
# SOMD.
if self._engine == "SOMD":
# TODO: This is currently hard-coded to use SOMD with the CUDA platform.
leg0.append(
_Process.Somd(system0,
self._protocol,
platform="CUDA",
work_dir="%s/lambda_%5.4f" %
(self._dir0, lam)))
leg1.append(
_Process.Somd(system1,
self._protocol,
platform="CUDA",
work_dir="%s/lambda_%5.4f" %
(self._dir1, lam)))
# GROMACS.
elif self._engine == "GROMACS":
# TODO: This is currently hard-coded to use SOMD with the CUDA platform.
leg0.append(
_Process.Gromacs(system0,
self._protocol,
work_dir="%s/lambda_%5.4f" %
(self._dir0, lam)))
leg1.append(
_Process.Gromacs(system1,
self._protocol,
work_dir="%s/lambda_%5.4f" %
(self._dir1, lam)))
# Initialise the process runner. All processes have already been nested
# inside the working directory so no need to re-nest.
self._runner = _Process.ProcessRunner(leg0 + leg1,
work_dir=self._work_dir,
nest_dirs=False)