def DO(experiment, mn):
"""Make a particular Mutant"""
# Determine if the mutant should be made
do = initial_check(experiment, mn)
# If it should be, do so
if do:
# Mutate the Design Groups
mutate_DesignGroups(experiment, mn)
# Check to see if everything is finished
finished = check_finish(experiment)
# If everything is done, start the refinement calculations for the
# mutant
if finished:
Finish(experiment, mn)
else:
# Otherwise, go back to the Experiment's folder, end sharing, and
# wait for the initial folder to be deleted
os.chdir(experiment["Folder"])
SHARING.End(experiment)
SHARING.Wait("initial_mutant" + str(mn))
def DO(experiment, mn=None):
"""Do a Refinement"""
# Only do a refinement when there is a refinement folder to do the
# refinement IN
if experiment["Type"] == "Mutator":
if mn in [None, 0]:
name = "wildtype"
else:
name = "mutant" + str(mn)
else:
name = "refinement"
# If the folder doesn't exist, don't do anything
if name in os.listdir("./"):
# Initialize the experiment for the refinement
modify = initialize(experiment, mn)
# do the first set of refinement calculations - which exist to try and
# keep the processors working on separate jobs as much as possible
first_group_refinement(experiment)
# And the second, which exists to get everything finished ASAP
second_group_refinement(experiment)
# Determine if the calculations are finished yet
finished = finish_check(experiment, mn)
# If the refinement is not finished, move out of the refinement's folder
# and wait for it to be deleted
if not finished:
os.chdir(experiment["Folder"])
SHARING.End(experiment)
# There's no need to wait during mutator experiments, except for the
# Wildtype values to finish
if experiment["Type"] != "Mutator" or mn in [None, 0]:
SHARING.Wait(name)
# If the refinement is finished, store the information
else:
Finish(experiment, mn)
# The refinement folder is gone, the structures and energies are stored,
# so we can be done with the refinement after a few more things
delete_extra_group(experiment)
if modify:
experiment["Refinement Iterations"] = int(
experiment["Refinement Iterations"] / 2)
experiment["Activity"] = "Standard"
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)