def _PELEMinimizerLoop(self, general_path, atoms_to_minimize, report_file):
create_directory(general_path)
path = self.path + str(self.PID) + '_' + co.MODELS_FOLDER
for model_id, active in enumerate(report_file.models):
# Set initial variables
file_name = str(model_id) + '-' + report_file.trajectory.name
original_pdb = path + file_name
logfile_name = path + co.LOGFILE_NAME.format(self.PID)
minimized_pdb = general_path + file_name
# Define new PELERunner
runner = PELERunner(self.settings.serial_pele,
number_of_processors=1)
# Write recalculation control file
self._writeRecalculationControlFile(
self.settings.pp_control_file,
original_pdb,
path + co.POST_PROCESSING_CF_NAME.format(self.PID),
logfile_name=logfile_name,
trajectory_name=minimized_pdb,
atoms_to_minimize=atoms_to_minimize)
runner.run(path + co.POST_PROCESSING_CF_NAME.format(self.PID))
self._applyMinimizedDistancesTo(original_pdb, minimized_pdb)
def run(self):
self._start()
create_directory(self.settings.simulation_path)
self._run()
self._finish()
def run(self):
self._start()
create_directory(self.path)
atoms_to_minimize = self._getAtomIdsToMinimize()
for lmb in self.lambdas:
writeLambdaTitle(lmb)
create_directory(self.path + str(self.PID) + '_' +
co.MODELS_FOLDER)
print(" - Splitting PELE models")
simulation = self._getSimulation(lmb)
self._splitModels(simulation)
ctt_lmb = None
if (lmb.index == 2):
if (lmb.type == Lambda.COULOMBIC_LAMBDA):
ctt_lmb = Lambda.Lambda(1.0,
lambda_type=Lambda.STERIC_LAMBDA)
elif (lmb.type == Lambda.STERIC_LAMBDA):
ctt_lmb = Lambda.Lambda(
1.0, lambda_type=Lambda.COULOMBIC_LAMBDA)
self._createAlchemicalTemplate(lmb, ctt_lmb)
self._calculateOriginalEnergies(simulation, lmb)
for shf_lmb in self.sampling_method.getShiftedLambdas(lmb):
print(" - Applying delta lambda " +
str(round(shf_lmb.value - lmb.value, 5)))
self._createAlchemicalTemplate(shf_lmb, ctt_lmb, gap=' ')
general_path = self._getGeneralPath(lmb, shf_lmb)
clear_directory(general_path)
self._minimize(simulation,
lmb.type,
general_path,
atoms_to_minimize,
gap=' ')
self._dECalculation(simulation, lmb, general_path, gap=' ')
remove_directory(self.path + str(self.PID) + '_' +
co.MODELS_FOLDER)
self._finish()
def _parallelPELERecalculatorLoop(self, lambda_, shifted_lambda,
general_path, num, report_file):
create_directory(general_path)
pid = current_process().pid
energies = []
rmsds = []
for model_id, active in enumerate(report_file.models):
# Set initial variables
file_name = str(model_id) + '-' + report_file.trajectory.name
original_pdb = self.path + co.MODELS_FOLDER + file_name
shifted_pdb = general_path + file_name
logfile_name = self.path + co.LOGFILE_NAME.format(pid)
# Define new PELERunner
runner = PELERunner(self.settings.serial_pele,
number_of_processors=1)
# In case bad model was previously removed
"""
if (not active):
print(" - Warning: skipping bad model from path: " +
"\'{}\'".format(shifted_pdb))
continue
"""
# Write recalculation control file
self._writeRecalculationControlFile(
self.settings.sp_control_file,
shifted_pdb,
self.path + co.SINGLE_POINT_CF_NAME.format(pid),
logfile_name=logfile_name)
# Run PELE and extract energy prediction
energies.append(self._getPELEEnergyPrediction(runner, pid))
# Calculate RMSD between original pdb and shifted one
rmsd = self._calculateRMSD(original_pdb, shifted_pdb)
rmsds.append(rmsd)
# Write trajectories and reports
write_energies_report(general_path, report_file, energies, rmsds)
join_splitted_models(general_path, "*-" + report_file.trajectory.name)
# Clean temporal files
remove_splitted_models(general_path,
"*-" + report_file.trajectory.name)
def _PELERecalculatorLoop(self, lmb, general_path, report_file):
create_directory(general_path)
energies = []
rmsds = []
path = self.path + str(self.PID) + '_' + co.MODELS_FOLDER
for model_id, active in enumerate(report_file.models):
# Set initial variables
file_name = str(model_id) + '-' + report_file.trajectory.name
original_pdb = path + file_name
shifted_pdb = general_path + file_name
logfile_name = path + co.LOGFILE_NAME.format(self.PID)
# Define new PELERunner
runner = PELERunner(self.settings.serial_pele,
number_of_processors=1)
# Write recalculation control file
self._writeRecalculationControlFile(
self.settings.sp_control_file,
shifted_pdb,
path + co.SINGLE_POINT_CF_NAME.format(self.PID),
logfile_name=logfile_name)
# Run PELE and extract energy prediction
energies.append(self._getPELEEnergyPrediction(runner))
# Calculate RMSD between original pdb and shifted one
rmsd = self._calculateRMSD(original_pdb, shifted_pdb)
rmsds.append(rmsd)
# Write trajectories and reports
write_energies_report(general_path, report_file, energies, rmsds)
join_splitted_models(general_path, "*-" + report_file.trajectory.name)
# Clean temporal files
remove_splitted_models(general_path,
"*-" + report_file.trajectory.name)