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 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 input_validation(experiment):
"""Make sure that the force field and rotamer calculations will work"""
# Clear the screen
os.system("clear")
# Tell the user what is happening
message = """
The inputs you have provided are now being validated. This should only take a
moment, so please be patient."""
print screen_formatting(message[1:])
# Make the Experiment's folder
os.mkdir(experiment["Folder"])
# Get the current folder, so we can move back to it when finished
current = os.getcwd()
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# copy in the force field and solvation files
SHARING.copy_standard_files(experiment, current + "/input_files/", False, \
True, True)
# Check the appropriateness of the Molecules, force field, and non-bonded
# energy parameters
molecules = appropriateness(experiment, True)
# If everything worked correctly, the folder can be prepped for the
# experiment
# Delete all files, as they're not needed anymore
names = os.listdir("./")
for name in names:
i = os.remove(name)
# Make an input files folder
os.mkdir("input_files")
# Move into that folder
os.chdir("input_files")
# Copy in the force field and solvation files
SHARING.copy_standard_files(experiment, current + "/input_files/", False, \
True, True)
# Move back to the Experiment's folder
os.chdir(experiment["Folder"])
# Create a results folder
os.mkdir("results")
# Create a structures folder
os.mkdir("structures")
# Move into that folder
os.chdir("structures")
# Output each Molecule in the structures folder
for molecule in molecules:
molecule.output(None, experiment["File Format"], experiment["User"])
# Move back to the starting folder
os.chdir(current)
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 input_validation(experiment):
"""Make sure that the force field and rotamer calculations will work"""
# Clear the screen
os.system("clear")
# Tell the user what is happening
message = """
The inputs you have provided are now being validated. This should only take a
moment, so please be patient."""
print screen_formatting(message[1:])
# Make the Experiment's folder
os.mkdir(experiment["Folder"])
# Get the current folder, so we can move back to it when finished
current = os.getcwd()
# Move to the Experiment's folder
os.chdir(experiment["Folder"])
# copy in the force field and solvation files
SHARING.copy_standard_files(experiment, current + "/input_files/", False, \
True, True)
# Check the appropriateness of the Molecules, force field, and non-bonded
# energy parameters
molecules = appropriateness(experiment, True)
# If everything worked correctly, the folder can be prepped for the
# experiment
# Delete all files, as they're not needed anymore
names = os.listdir("./")
for name in names:
i = os.remove(name)
# Make an input files folder
os.mkdir("input_files")
# Move into that folder
os.chdir("input_files")
# Copy in the force field and solvation files
SHARING.copy_standard_files(experiment, current + "/input_files/", False, \
True, True)
# Move back to the Experiment's folder
os.chdir(experiment["Folder"])
# Create a results folder
os.mkdir("results")
# Create a structures folder
os.mkdir("structures")
# Move into that folder
os.chdir("structures")
# Output each Molecule in the structures folder
for molecule in molecules:
molecule.output(None, experiment["File Format"], experiment["User"])
# Move back to the starting folder
os.chdir(current)
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 make_extra_group(experiment):
"""Create an extra Design Group with no Target Molecules"""
# Only do this if Binding energy calculations are being done
if experiment["Energy Calculation"] == "Binding":
# Get all of the Design Molecules from Design Group 1
molecules = []
for molecule in experiment[1]:
if molecule.design:
molecules.append(molecule)
# Make and store a new Design Group (which duplicates these Molecules
# for run independence reasons)
N = len(experiment) + 1
group = MOLECULES.DesignGroup(N, molecules, experiment["Force Field"], \
experiment["File Format"])
experiment._groupOrder.append(N)
experiment._groups[N] = group
n = len(experiment)
# Update the Current dictionary, too
experiment["Current"][n] = {}
for molecule in experiment[n]:
new = molecule.duplicate()
experiment["Current"][n][new.name] = new
# Those structures are essentially place holders at this point. However,
# we do need to run an energy minimization and calculate an initial
# energy for that group
name = "Group" + str(n) + "_Energies.txt"
SHARING.Start(experiment)
# If another processor already did the calculation, we're fine
if name not in os.listdir("./Current/"):
# Try to make a temp directory to do the calculations in
if "temp" not in os.listdir("./"):
# Make the directory and move into it
os.mkdir("temp")
os.chdir("temp")
# Stop sharing
SHARING.End(experiment)
# Copy in the relevant files
SHARING.copy_standard_files(experiment, False)
# Relax the Design Group
refinement = IPRO_FUNCTIONS.Relaxation(experiment, n, True)
# And calculate the energies
energies, refinement = \
IPRO_FUNCTIONS.Calculate_Energy(experiment, n)
# Move back up a folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# Store the energy
text = SHARING.format_energies(energies[n])
f = open("./Current/" + name, "w")
f.write(text)
f.close()
SHARING.output_Current(experiment, "./Current/", n)
# Delete the temp folder
os.system("rm -rf temp")
# Otherwise, just wait
else:
SHARING.End(experiment)
SHARING.Wait("temp", "./")
SHARING.Start(experiment)
# Store that complex energy
f = open("./Current/" + name, "r")
experiment["Energies"][n] = {"Complex": float(f.readline().split()[2])}
f.close()
SHARING.End(experiment)
def make_extra_group(experiment):
"""Create an extra Design Group with no Target Molecules"""
# Only do this if Binding energy calculations are being done
if experiment["Energy Calculation"] == "Binding":
# Get all of the Design Molecules from Design Group 1
molecules = []
for molecule in experiment[1]:
if molecule.design:
molecules.append(molecule)
# Make and store a new Design Group (which duplicates these Molecules
# for run independence reasons)
N = len(experiment) + 1
group = MOLECULES.DesignGroup(N, molecules, experiment["Force Field"], \
experiment["File Format"])
experiment._groupOrder.append(N)
experiment._groups[N] = group
n = len(experiment)
# Update the Current dictionary, too
experiment["Current"][n] = {}
for molecule in experiment[n]:
new = molecule.duplicate()
experiment["Current"][n][new.name] = new
# Those structures are essentially place holders at this point. However,
# we do need to run an energy minimization and calculate an initial
# energy for that group
name = "Group" + str(n) + "_Energies.txt"
SHARING.Start(experiment)
# If another processor already did the calculation, we're fine
if name not in os.listdir("./Current/"):
# Try to make a temp directory to do the calculations in
if "temp" not in os.listdir("./"):
# Make the directory and move into it
os.mkdir("temp")
os.chdir("temp")
# Stop sharing
SHARING.End(experiment)
# Copy in the relevant files
SHARING.copy_standard_files(experiment, False)
# Relax the Design Group
refinement = IPRO_FUNCTIONS.Relaxation(experiment, n, True)
# And calculate the energies
energies, refinement = \
IPRO_FUNCTIONS.Calculate_Energy(experiment, n)
# Move back up a folder
os.chdir("../")
# Start sharing
SHARING.Start(experiment)
# Store the energy
text = SHARING.format_energies(energies[n])
f = open("./Current/" + name, "w")
f.write(text)
f.close()
SHARING.output_Current(experiment, "./Current/", n)
# Delete the temp folder
os.system("rm -rf temp")
# Otherwise, just wait
else:
SHARING.End(experiment)
SHARING.Wait("temp", "./")
SHARING.Start(experiment)
# Store that complex energy
f = open("./Current/" + name, "r")
experiment["Energies"][n] = {"Complex":float(f.readline().split()[2])}
f.close()
SHARING.End(experiment)