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 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 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 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 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 Summarize(experiment, choice, IEs, BEs, CEs, mn=None):
"""Summarize the results of a structure refinement"""
# Come up with an appropriate header
if experiment["Type"] == "Mutator":
if mn == 0:
experiment["Summary"] = "\nWildtype Refinement Results\n"
else:
experiment["Summary"] = "\nMutant " + str(
mn) + " Refinement Results\n"
else:
f = open("./Current/iteration.txt", "r")
n = int(f.readline())
f.close()
if n == 0:
experiment["Summary"] = "\nInitial Structures Refinement\n"
else:
experiment["Summary"] = "\nRefinement of Iteration " + str(
n) + "\n"
# Find out when the refinement started
f = open("./Group1/Ensemble1/Ensemble1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Store the information about the calculated energies
for group in experiment:
if experiment["Energy Calculation"] == "Binding" and group.number == \
len(experiment):
continue
# Summarize Complex energy
experiment["Summary"] += "Design Group " + str(group.number) + "\n"
experiment["Summary"] += "Average Complex Energy: " + \
format(CEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(CEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
# IE
experiment["Summary"] += "Average Interaction Energy: " + \
format(IEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(IEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
# BE
if experiment["Energy Calculation"] == "Binding":
experiment["Summary"] += "Average Binding Energy: " + \
format(BEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(BEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
if experiment["Type"] != "Mutator" and n != 0:
if choice:
experiment["Summary"] += "These were the BEST results so far\n"
else:
experiment["Summary"] += "These results were DISCARDED\n"
# Say when the calculations finished
experiment["Summary"] += "Ended" + SHARING.time_stamp()
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 Summarize(experiment, choice, IEs, BEs, CEs, mn = None):
"""Summarize the results of a structure refinement"""
# Come up with an appropriate header
if experiment["Type"] == "Mutator":
if mn == 0:
experiment["Summary"] = "\nWildtype Refinement Results\n"
else:
experiment["Summary"] = "\nMutant " + str(mn)+" Refinement Results\n"
else:
f = open("./Current/iteration.txt", "r")
n = int(f.readline())
f.close()
if n == 0:
experiment["Summary"] = "\nInitial Structures Refinement\n"
else:
experiment["Summary"] = "\nRefinement of Iteration " + str(n) + "\n"
# Find out when the refinement started
f = open("./Group1/Ensemble1/Ensemble1_Summary.txt", "r")
for line in f:
if line.startswith("Started"):
experiment["Summary"] += line
break
f.close()
# Store the information about the calculated energies
for group in experiment:
if experiment["Energy Calculation"] == "Binding" and group.number == \
len(experiment):
continue
# Summarize Complex energy
experiment["Summary"] += "Design Group " + str(group.number) + "\n"
experiment["Summary"] += "Average Complex Energy: " + \
format(CEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(CEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
# IE
experiment["Summary"] += "Average Interaction Energy: " + \
format(IEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(IEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
# BE
if experiment["Energy Calculation"] == "Binding":
experiment["Summary"] += "Average Binding Energy: " + \
format(BEs[group.number]["Average"][0], '.3f') + " +/- " + \
format(BEs[group.number]["Average"][1], '.3f') + " kcal/mol\n"
if experiment["Type"] != "Mutator" and n != 0:
if choice:
experiment["Summary"] += "These were the BEST results so far\n"
else:
experiment["Summary"] += "These results were DISCARDED\n"
# Say when the calculations finished
experiment["Summary"] += "Ended" + SHARING.time_stamp()