def initialize(experiment, mn):
"""Set up an Experiment to work in a refinement"""
# Start sharing
SHARING.Start(experiment)
# Modify the number of iterations
modify = change_iterations(experiment, mn)
# Identify the proper folder for the refinement
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
folder = "./wildtype/"
else:
folder = "./mutant" + str(mn) + "/"
else:
folder = "./refinement/"
# Move into the refinement folder
os.chdir(folder)
# Load the current structures and energies
SHARING.update_Current(experiment, "./Current/")
SHARING.update_Energies(experiment, "./Current/")
# Stop sharing
SHARING.End(experiment)
# Make the extra Design Group
make_extra_group(experiment)
# Modify the 'Activity' of the Experiment
experiment['Activity'] = "Refinement"
return modify
def initial_check(experiment, mn):
"""Do an initial check about doing calculations for a mutant"""
# Start sharing
SHARING.Start(experiment)
# This is the name of the folder we're looking for
folder = "mutant" + str(mn)
# If the results are already completed
if folder in os.listdir(experiment["Folder"] + "results/"):
SHARING.End(experiment)
return False
# Or if the refinement is ongoing
elif folder in os.listdir(experiment["Folder"]):
SHARING.End(experiment)
return False
# If the initial folder for that mutant does not yet exist, make it
folder = "initial_" + folder
if folder not in os.listdir(experiment["Folder"]):
os.mkdir(folder)
os.mkdir(folder + "/Current")
# Load the wildtype structures
SHARING.update_Current(experiment, experiment["Folder"] + \
"results/wildtype/")
SHARING.update_Energies(experiment, experiment["Folder"] + \
"results/wildtype/")
# End sharing
SHARING.End(experiment)
return True
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 check_finish(experiment):
"""Check to see if the initial structures for a mutant have been made yet"""
# Start sharing
SHARING.Start(experiment)
# Keep track of whether everything is finished
finished = True
# Check every Design Group for a summary file
for group in experiment:
label = "Group" + str(group.number)
if label + "_Summary.txt" not in os.listdir(label):
finished = False
break
return finished
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 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 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)