def End_Iteration(experiment, energies, iteration, gn):
"""End an iteration of IPRO."""
# The standard initial checks
if not isinstance(experiment, EXPERIMENT.Experiment):
text = "The End Iteration function requires an Experiment class object "
text += "as its input."
raise IPRO_Error(text)
refinement = refinement_check(experiment, gn)
if refinement:
return refinement
# Move out of the iteration's folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# Load the appropriate reference energies
if experiment["Activity"] == "Standard":
SHARING.load_reference_Energies(experiment)
else:
SHARING.update_Energies(experiment, "./Best/", gn)
# Determine the last completed iteration
this = SHARING.iteration_counter(SHARING.get_current(), False) + 1
# Determine whether or not keep the iteration results
best, keep = iteration_decision(experiment, energies, this, gn)
# If results should be kept, do so
if best or keep:
store_structures(experiment, gn)
# If these are the best results so far, store the energies
if best:
store_energies(experiment, energies, gn)
# If appropriate, share the results with other processors
SHARING.Results(experiment, this, best, keep, gn)
# Say what happened in the summary
experiment["Summary"] = "\nIteration " + str(this) + "\n" + \
experiment["Summary"] + "The results were "
if best:
experiment["Summary"] += "the BEST so far\n"
elif keep:
experiment["Summary"] += "KEPT by simulated annealing\n"
else:
experiment["Summary"] += "DISCARDED\n"
# Put a time stamp on the summary
experiment["Summary"] += "Ended" + SHARING.time_stamp()
# Get the name of the Summary file
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Delete the iteration
os.system("rm -rf iteration" + str(iteration))
# End sharing
SHARING.End(experiment)
return refinement
def Start_Iteration(experiment, gn = None):
"""Start an iteration of IPRO"""
# Do the standard initial checks
if not isinstance(experiment, EXPERIMENT.Experiment):
text = "The Start Iteration function requires an Experiment class "
text += "object as its input."
raise IPRO_Error(text)
refinement = refinement_check(experiment, gn)
if refinement:
return 0, refinement
# Start sharing so this processor has exclusive access to the shared files
SHARING.Start(experiment)
# Determine what iteration this will be
iteration = SHARING.iteration_counter(SHARING.get_current(), True) + 1
# Determine what the expected maximum number of iterations is
ITERATIONS = max_iterations(experiment)
# Create a folder
while iteration <= ITERATIONS:
folder = "iteration" + str(iteration)
do = SHARING.claim_calculations(folder)
if do:
break
else:
iteration += 1
# If a folder was made
if iteration <= ITERATIONS:
# Start a summary
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Get the last time structures were updated
N = SHARING.identify_last_update("./Current/")
# If necessary, update the structures
if N > experiment["Last Update"]:
SHARING.update_Current(experiment, "./Current/", gn)
experiment["Last Update"] = N
# Say what structures are being used
if experiment["Last Update"] == 0:
experiment["Summary"] += "Using the initial structures\n"
else:
experiment["Summary"] += "Using the structures from iteration "
experiment["Summary"] += str(experiment["Last Update"]) + "\n"
# Move into the appropriate folder
os.chdir(folder)
# Copy in the C++ and force field files
SHARING.copy_standard_files(experiment)
# Update the Experiment's structures
for group in experiment:
if gn not in [None, group.number]:
continue
for molecule in group:
text =format(experiment["Current"][group.number][molecule.name])
molecule.load(text)
# End sharing
SHARING.End(experiment)
return iteration, refinement
def change_iterations(experiment, mn=None):
"""Do 2x the calculations for initial / wildtype calcs"""
# If there is a mutant number that's not 0, don't do this
if mn not in [None, 0]:
return False
# If it is None, check the number of completed iterations
if mn == None:
n = SHARING.iteration_counter(SHARING.get_current(), False)
if n > 0:
return False
# multiply the number by 2
experiment["Refinement Iterations"] *= 2
return True
def change_iterations(experiment, mn = None):
"""Do 2x the calculations for initial / wildtype calcs"""
# If there is a mutant number that's not 0, don't do this
if mn not in [None, 0]:
return False
# If it is None, check the number of completed iterations
if mn == None:
n = SHARING.iteration_counter(SHARING.get_current(), False)
if n > 0:
return False
# multiply the number by 2
experiment["Refinement Iterations"] *= 2
return True
def mutate_DesignGroups(experiment, mn):
"""Make the initial mutants of the Design Groups"""
# Move into the folder to do the initial calculations in
folder = "initial_mutant" + str(mn)
os.chdir(folder)
# Loop through the Design Groups
for group in experiment:
# The calculations will be stored in this folder
folder = "Group" + str(group.number)
# Try to claim the calculations
do = SHARING.claim_calculations(folder)
# If this processor is doing those calculations
if do:
# Time stamp when this started
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Move into the folder
os.chdir(folder)
# Copy in the C++ and force field files
SHARING.copy_standard_files(experiment)
# Use the Current structures
for molecule in experiment[group.number]:
text =format(experiment["Current"][group.number][molecule.name])
molecule.load(text)
# Set the permissions for the Molecules
permission_setter(experiment, group.number, mn)
# Mutate the Residues
refinement = IPRO_FUNCTIONS.Optimal_Rotamers(experiment, \
group.number)
refinement = IPRO_FUNCTIONS.Relaxation(experiment, group.number, \
True)
energies, refinement = IPRO_FUNCTIONS.Calculate_Energy(experiment, \
group.number)
# Start sharing
SHARING.Start(experiment)
# Write a brief summary file
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Move up a folder
os.chdir("../")
# Store the structures in the Current dictionary
IPRO_FUNCTIONS.store_structures(experiment, group.number)
IPRO_FUNCTIONS.store_energies(experiment, energies, group.number)
# Write the structures to the Current folder
SHARING.output_Current(experiment, "./Current/", group.number)
SHARING.output_Energies(experiment, "./Current/", group.number)
# End sharing
SHARING.End(experiment)
def mutate_DesignGroups(experiment, mn):
"""Make the initial mutants of the Design Groups"""
# Move into the folder to do the initial calculations in
folder = "initial_mutant" + str(mn)
os.chdir(folder)
# Loop through the Design Groups
for group in experiment:
# The calculations will be stored in this folder
folder = "Group" + str(group.number)
# Try to claim the calculations
do = SHARING.claim_calculations(folder)
# If this processor is doing those calculations
if do:
# Time stamp when this started
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Move into the folder
os.chdir(folder)
# Copy in the C++ and force field files
SHARING.copy_standard_files(experiment)
# Use the Current structures
for molecule in experiment[group.number]:
text =format(experiment["Current"][group.number][molecule.name])
molecule.load(text)
# Set the permissions for the Molecules
permission_setter(experiment, group.number, mn)
# Mutate the Residues
refinement = IPRO_FUNCTIONS.Optimal_Rotamers(experiment, \
group.number)
refinement = IPRO_FUNCTIONS.Relaxation(experiment, group.number, \
True)
energies, refinement = IPRO_FUNCTIONS.Calculate_Energy(experiment, \
group.number)
# Start sharing
SHARING.Start(experiment)
# Write a brief summary file
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Move up a folder
os.chdir("../")
# Store the structures in the Current dictionary
IPRO_FUNCTIONS.store_structures(experiment, group.number)
IPRO_FUNCTIONS.store_energies(experiment, energies, group.number)
# Write the structures to the Current folder
SHARING.output_Current(experiment, "./Current/", group.number)
SHARING.output_Energies(experiment, "./Current/", group.number)
# End sharing
SHARING.End(experiment)
def initialize_molecule(experiment, mn):
"""Initialize a Molecule"""
# Create the folder's name
folder = "Molecule" + mn
do = SHARING.claim_calculations(folder)
# If this processor is doing the calculations
if do:
# Make a summary
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Move into the folder
os.chdir(folder)
SHARING.copy_standard_files(experiment)
# Get a unique copy of the Molecule
molecule = experiment[0][mn].duplicate()
for residue in molecule:
residue.freedom = "FREE"
# Store the calculated energies here
energies = {}
# Do a relaxation and energy calculation
if experiment["Force Field"] == "CHARMM":
CHARMM.Relaxation(molecule, experiment)
energies["Complex"] = CHARMM.Energy(molecule, experiment)
else:
text = "The initialize molecule function does not support the "
text += str(experiment["Force Field"]) + " force field."
raise IPRO_Error(text)
# Format the energy
text = SHARING.format_energies(energies)
experiment["Summary"] += text
# Create the summary file for the Molecule
experiment["Summary"] += "Ended" + SHARING.time_stamp()
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Leave this folder, then start sharing
os.chdir('../')
SHARING.Start(experiment)
# Output the Molecule's structure
name = "./Current/" + molecule.generate_name()
molecule.output(name, molecule.fileFormat, experiment["User"])
# Output the Complex energy
f = open("./Current/Molecule" + mn + "_Energy.txt", "w")
f.write(text)
f.close()
# End sharing
SHARING.End(experiment)
def Wait(experiment):
"""Wait for an IPRO Experiment to be entirely completed"""
# Keep track using this variable
finished = False
while not finished:
# Periodically check the last completed iteration
SHARING.Start(experiment)
n = SHARING.iteration_counter(SHARING.get_current(), False)
SHARING.End(experiment)
# If all iterations are complete, the program doesn't need to wait any
# more
if n == experiment["IPRO Iterations"]:
finished = True
# If another processor has called for a refinement, do it
REFINEMENT.DO(experiment)
# If the experiment isn't done yet, take a 15 second break before
# continuing the while loop
if not finished:
time.sleep(15)
def initialize_group(experiment, gn):
"""Initialize a Design Group"""
# Create the folder's name
folder = "Group" + str(gn)
# Try to claim it for calculations
do = SHARING.claim_calculations(folder)
# If this processor is doing the calculations
if do:
# Make a summary
experiment["Summary"] = "Started" + SHARING.time_stamp()
# Move into the folder and copy in files
os.chdir(folder)
SHARING.copy_standard_files(experiment)
# Relax everything
refinement = Relaxation(experiment, gn, True)
# Assign closest rotamers
Closest_Rotamers(experiment, gn)
# Do another relaxation
refinement = Relaxation(experiment, gn, True)
# Calculate the initial energies
energies, refinement = Calculate_Energy(experiment, gn)
# Store the structures and energies
store_structures(experiment, gn)
store_energies(experiment, energies, gn)
# Create a summary file
experiment["Summary"] += "Ended" + SHARING.time_stamp()
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Move up a folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# output the structures and energies to the Current folder
SHARING.output_Current(experiment, "./Current/", gn)
SHARING.output_Energies(experiment, "./Current/", gn)
# End sharing
SHARING.End(experiment)
return do
def Finish(experiment, mn):
"""Finish the initial creation of a mutant"""
# Sharing was started in check finish
# Load the structures and energies
SHARING.update_Current(experiment, "./Current/")
SHARING.update_Energies(experiment, "./Current/")
# Create a brief summary of the information
experiment["Summary"] = '\nMutant ' + str(mn) + " Creation\n"
f = open("Group1/Group1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include information about the energies
for group in experiment:
experiment["Summary"] += \
SHARING.format_energies(experiment["Energies"][group.number], \
group.number, False)
# Put this in the overall summary
os.chdir(experiment["Folder"])
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Make a folder to do the structure refinements in
folder = "mutant" + str(mn)
os.mkdir(folder)
folder += "/Current/"
os.mkdir(folder)
SHARING.output_Current(experiment, folder)
SHARING.output_Energies(experiment, folder)
f = open(folder + "iteration.txt", "w")
f.write(str(mn))
f.close()
# Delete the current folder
name = "initial_mutant" + str(mn)
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
def Finish(experiment, mn):
"""Finish the initial creation of a mutant"""
# Sharing was started in check finish
# Load the structures and energies
SHARING.update_Current(experiment, "./Current/")
SHARING.update_Energies(experiment, "./Current/")
# Create a brief summary of the information
experiment["Summary"] = '\nMutant ' + str(mn) + " Creation\n"
f = open("Group1/Group1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include information about the energies
for group in experiment:
experiment["Summary"] += \
SHARING.format_energies(experiment["Energies"][group.number], \
group.number, False)
# Put this in the overall summary
os.chdir(experiment["Folder"])
name = SHARING.summary_name(SHARING.get_current())
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Make a folder to do the structure refinements in
folder = "mutant" + str(mn)
os.mkdir(folder)
folder += "/Current/"
os.mkdir(folder)
SHARING.output_Current(experiment, folder)
SHARING.output_Energies(experiment, folder)
f = open(folder + "iteration.txt", "w")
f.write(str(mn))
f.close()
# Delete the current folder
name = "initial_mutant" + str(mn)
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
def finish_check(experiment, mn):
"""Check that all ensembles are entirely finished"""
# NOTE THAT THIS DOES NOT END SHARING
SHARING.Start(experiment)
# Figure out what folder we should be looking for
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
folder = "wildtype"
else:
folder = "mutant" + str(mn)
else:
folder = "refinement"
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# If the appropriate folder no longer exists, be done but return False so
# the Finish function isn't called
if folder not in os.listdir("./"):
return False
os.chdir(folder)
finished = True
# Loop through the groups
for group in experiment:
os.chdir("Group" + str(group.number))
# and the ensembles
for en in range(1, experiment["Ensemble Number"] + 1):
os.chdir("Ensemble" + str(en))
# Get the number of the last completed iteration
I = SHARING.iteration_counter(SHARING.get_current(), False)
# If they aren't all done yet
if I < experiment["Refinement Iterations"]:
finished = False
os.chdir("../../")
break
os.chdir("../")
if not finished:
break
os.chdir("../")
return finished
def finish_check(experiment, mn):
"""Check that all ensembles are entirely finished"""
# NOTE THAT THIS DOES NOT END SHARING
SHARING.Start(experiment)
# Figure out what folder we should be looking for
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
folder = "wildtype"
else:
folder = "mutant" + str(mn)
else:
folder = "refinement"
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# If the appropriate folder no longer exists, be done but return False so
# the Finish function isn't called
if folder not in os.listdir("./"):
return False
os.chdir(folder)
finished = True
# Loop through the groups
for group in experiment:
os.chdir("Group" + str(group.number))
# and the ensembles
for en in range(1, experiment["Ensemble Number"] + 1):
os.chdir("Ensemble" + str(en))
# Get the number of the last completed iteration
I = SHARING.iteration_counter(SHARING.get_current(), False)
# If they aren't all done yet
if I < experiment["Refinement Iterations"]:
finished = False
os.chdir("../../")
break
os.chdir("../")
if not finished:
break
os.chdir("../")
return finished