def Finish(experiment, mn=None):
"""Finish a Refinement"""
# Sharing will have been started elsewhere (in finish_check)
# Collect the calculated energies
energies = gather_energies(experiment)
# Get interaction, complex, and binding energies
IEs = calculate_IEs(energies)
CEs = calculate_CEs(energies)
BEs = calculate_BEs(experiment, energies)
# Evaluate the results
choice = make_refinement_choice(experiment, IEs, BEs)
# If the choice is to keep the results, make a permanent copy
if choice:
store_results(experiment, IEs, BEs, CEs, mn)
# Summarize the results
Summarize(experiment, choice, IEs, BEs, CEs, mn)
# Move out of the refinement's folder
os.chdir(experiment["Folder"])
# Store the refinement summary
name = SHARING.summary_name(experiment["Folder"])
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Delete the folder the refinement happened in
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
name = "wildtype"
else:
name = "mutant" + str(mn)
else:
name = "refinement"
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
def finish_initialization(experiment):
"""Finish an initialization"""
# Sharing is already started and the structures and energies have already
# been loaded into the Experiment
# Make the initial experiment summary
experiment["Summary"] = "Initial Calculations\n"
# Determine when they started
f = open(experiment["Folder"]+"initialize/Group1/Group1_Summary.txt","r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Include the energies of each Design Group
for group in experiment:
experiment["Summary"] += SHARING.format_energies(\
experiment["Energies"][group.number], group.number, False)
# Create the initial folder in results
SHARING.output_best(experiment, 0, None)
# Figure out the name of the output file
if experiment["Type"] == "Mutator":
folder = experiment["Folder"] + "results/wildtype/"
else:
folder = experiment["Folder"] + "results/initial/"
# List the energies of each Target Molecule, too
if experiment["Energy Calculation"] == "Binding":
for molecule in experiment[0]:
if not molecule.design:
name = experiment["Folder"] + "initialize/Current/Molecule"
name += molecule.name + "_Energy.txt"
f = open(name, "r")
energy = f.readline().split()[2]
f.close()
experiment["Summary"] += "The energy of Target Molecule "
experiment["Summary"] += molecule.name + " is " + energy
experiment["Summary"] += " kcal / mol\n"
# Copy the file to the output folder
os.system("cp " + name + " " + folder)
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# Try to make the current folder
try:
os.mkdir("Current")
except OSError:
pass
# Write the Structures to the Current folder
SHARING.output_Current(experiment, "./Current/", None, 0)
experiment["Last Update"] = 0
# Start a refinment
REFINEMENT.Start(experiment, 0, None)
# Create the initial summary file
experiment["Summary"] += "Ended" + SHARING.time_stamp()
name = SHARING.summary_name(experiment["Folder"])
f = open(name, "w")
f.write(experiment["Summary"])
f.close()
# Remove the initialization folder
os.system("rm -rf initialize")
# End the sharing that was started elsewhere
SHARING.End(experiment)
def Finish(experiment, mn = None):
"""Finish a Refinement"""
# Sharing will have been started elsewhere (in finish_check)
# Collect the calculated energies
energies = gather_energies(experiment)
# Get interaction, complex, and binding energies
IEs = calculate_IEs(energies)
CEs = calculate_CEs(energies)
BEs = calculate_BEs(experiment, energies)
# Evaluate the results
choice = make_refinement_choice(experiment, IEs, BEs)
# If the choice is to keep the results, make a permanent copy
if choice:
store_results(experiment, IEs, BEs, CEs, mn)
# Summarize the results
Summarize(experiment, choice, IEs, BEs, CEs, mn)
# Move out of the refinement's folder
os.chdir(experiment["Folder"])
# Store the refinement summary
name = SHARING.summary_name(experiment["Folder"])
f = open(name, "a")
f.write(experiment["Summary"])
f.close()
# Delete the folder the refinement happened in
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
name = "wildtype"
else:
name = "mutant" + str(mn)
else:
name = "refinement"
os.system("rm -rf " + name)
# End sharing
SHARING.End(experiment)
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 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 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)