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 first_group_refinement(experiment):
"""Start all ensembles for the Design Groups"""
# Start sharing (for file creation reasons)
SHARING.Start(experiment)
# Loop through the design groups
print "Check1"
for group in experiment:
gn = group.number
# Generate the name for the Design Group's calculations
folder = "Group" + str(gn)
try:
os.mkdir(folder)
except OSError:
pass
os.chdir(folder)
# Start each ensemble
for en in range(1, experiment["Ensemble Number"] + 1):
eFolder = "Ensemble" + str(en)
do = SHARING.claim_calculations(eFolder)
# If this processor has started the calculations for this ensemble
print en, do
if do:
# Make sure the experiment has the right structures and energies
SHARING.update_Current(experiment, "../Current/", gn)
SHARING.update_Energies(experiment, "../Current/", gn)
# Move into the folder
os.chdir(eFolder)
# Make a copy of the best structures and energies for the group
os.mkdir("Current")
SHARING.output_Current(experiment, "./Current/", gn, 0)
os.mkdir("Best")
SHARING.output_Current(experiment, "./Best/", gn)
SHARING.output_Energies(experiment, "./Best/", gn)
# Move out of the e Folder
os.chdir("../")
SHARING.End(experiment)
# Do the ensemble refinement
ensemble_refinement(experiment, gn, en)
SHARING.Start(experiment)
# Move out of the folder
os.chdir("../")
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)
def first_group_refinement(experiment):
"""Start all ensembles for the Design Groups"""
# Start sharing (for file creation reasons)
SHARING.Start(experiment)
# Loop through the design groups
for group in experiment:
gn = group.number
# Generate the name for the Design Group's calculations
folder = "Group" + str(gn)
try:
os.mkdir(folder)
except OSError:
pass
os.chdir(folder)
# Start each ensemble
for en in range(1, experiment["Ensemble Number"] + 1):
eFolder = "Ensemble" + str(en)
do = SHARING.claim_calculations(eFolder)
# If this processor has started the calculations for this ensemble
if do:
# Make sure the experiment has the right structures and energies
SHARING.update_Current(experiment, "../Current/", gn)
SHARING.update_Energies(experiment, "../Current/", gn)
# Move into the folder
os.chdir(eFolder)
# Make a copy of the best structures and energies for the group
os.mkdir("Current")
SHARING.output_Current(experiment, "./Current/", gn, 0)
os.mkdir("Best")
SHARING.output_Current(experiment, "./Best/", gn)
SHARING.output_Energies(experiment, "./Best/", gn)
# Move out of the e Folder
os.chdir("../")
SHARING.End(experiment)
# Do the ensemble refinement
ensemble_refinement(experiment, gn, en)
SHARING.Start(experiment)
# Move out of the folder
os.chdir("../")
SHARING.End(experiment)
def Start(experiment, iteration, gn=None):
"""Create a folder to run a refinement in."""
# Only do this when appropriate
if not experiment["Do Refinement"] or gn != None or experiment["Activity"] \
!= "Standard":
return False
# Try to make the directory
if experiment["Type"] == "Mutator":
folder = "wildtype"
else:
folder = "refinement"
try:
os.mkdir(folder)
except OSError:
return False
# Assuming that was successful, prep that 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(iteration))
f.close()
return True
def Start(experiment, iteration, gn = None):
"""Create a folder to run a refinement in."""
# Only do this when appropriate
if not experiment["Do Refinement"] or gn != None or experiment["Activity"] \
!= "Standard":
return False
# Try to make the directory
if experiment["Type"] == "Mutator":
folder = "wildtype"
else:
folder = "refinement"
try:
os.mkdir(folder)
except OSError:
return False
# Assuming that was successful, prep that 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(iteration))
f.close()
return True