def runDielec(arg):
"""
Runs UHBD calculation with a set of dielectric constants in dielc_file.
"""
# Parse the command line arguments
dielec = ArgParser.modeClass("dielec",["pdb_file","dielec_file"],
["inpfile","inpfile"],["ionic_strength","pHtitr","out_dir"])
dielec.parseArg(arg)
filename = dielec.required["pdb_file"]
dielec_file = dielec.required["dielec_file"]
output_path = dielec.optional.out_dir
pH_start = dielec.optional.pHtitr[0]
pH_stop = dielec.optional.pHtitr[1]
pH_interval = dielec.optional.pHtitr[2]
salt = dielec.optional.ionic_strength
f = open(dielec_file)
dielectric_constants = [float(d) for d in f.readlines()]
f.close()
base_path = os.path.join(__init__.invocation_path,output_path)
for dielectric in dielectric_constants:
print "dielectric constant: %4.2F" % dielectric
dielec_path = os.path.join(base_path,"D%.1F" % dielectric)
FileOps.makeDir(dielec_path)
dielec_output = os.path.join(dielec_path,"%.1F" % salt)
FileOps.makeDir(dielec_output)
indivRun(filename,dielec_output,pH_start,pH_stop,pH_interval,salt,
dielectric)
def runSingle(arg):
"""
Runs UHBD calculation on a single file.
"""
single = ArgParser.modeClass("single",["pdb_file"],["inpfile"],
["dielectric", "ionic_strength","pHtitr","out_dir"])
single.parseArg(arg)
indivRun(single.required["pdb_file"],single.optional.out_dir,
single.optional.pHtitr[0],single.optional.pHtitr[1],
single.optional.pHtitr[2],single.optional.ionic_strength,
single.optional.dielectric)
def runSalts(arg):
"""
Runs UHBD calculation on set of salts in salts_file.
"""
# Parse the command line arguments
salts = ArgParser.modeClass("salts",["pdb_file","salt_file"],
["inpfile","inpfile"],["dielectric","pHtitr","out_dir"])
salts.parseArg(arg)
filename = salts.required["pdb_file"]
salts_file = salts.required["salt_file"]
output_path = salts.optional.out_dir
pH_start = salts.optional.pHtitr[0]
pH_stop = salts.optional.pHtitr[1]
pH_interval = salts.optional.pHtitr[2]
dielectric = salts.optional.dielectric
# Execute the indivRun function for every salt in salts_file
f = open(salts_file)
salts = [float(salt) for salt in f.readlines()]
f.close()
for salt in salts:
print "Ionic strength: %4.2F" % salt
salt_output = os.path.join(output_path,"%.1F" % salt)
# Create output directory
try:
os.mkdir(os.path.join(__init__.invocation_path,salt_output))
except OSError, value:
# Don't stop if we are only overwriting existing directory
if value[0] != 17:
print 'File error.'
print value[0], os.path.join(__init__.invocation_path,
salt_output), value[1]
sys.exit()
# Run UHBD at this specific salt concentration
indivRun(filename,salt_output,pH_start,pH_stop,pH_interval,salt,
dielectric)
def runDielec(arg):
"""
Runs UHBD calculation with a set of dielectric constants in dielc_file.
"""
# Parse the command line arguments
dielec = ArgParser.modeClass("dielec",["pdb_file","dielec_file"],
["inpfile","inpfile"],["ionic_strength","pHtitr","out_dir"])
dielec.parseArg(arg)
filename = dielec.required["pdb_file"]
dielec_file = dielec.required["dielec_file"]
output_path = dielec.optional.out_dir
pH_start = dielec.optional.pHtitr[0]
pH_stop = dielec.optional.pHtitr[1]
pH_interval = dielec.optional.pHtitr[2]
salt = dielec.optional.ionic_strength
f = open(dielec_file)
dielectric_constants = [float(d) for d in f.readlines()]
f.close()
for dielectric in dielectric_constants:
print "dielectric constant: %4.2F" % dielectric
dielec_output = os.path.join(output_path,"%.1F" % dielectric)
# Create output directory
try:
os.mkdir(os.path.join(__init__.invocation_path,dielec_output))
except OSError, value:
# Don't stop if we are only overwriting existing directory
if value[0] != 17:
print 'File error.'
print value[0], os.path.join(__init__.invocation_path,
dielec_output), value[1]
sys.exit()
indivRun(filename,dielec_output,pH_start,pH_stop,pH_interval,salt,
dielectric)
def runSalts(arg):
"""
Runs UHBD calculation on set of salts in salts_file.
"""
# Parse the command line arguments
salts = ArgParser.modeClass("salts",["pdb_file","salt_file"],
["inpfile","inpfile"],["dielectric","pHtitr","out_dir"])
salts.parseArg(arg)
filename = salts.required["pdb_file"]
salts_file = salts.required["salt_file"]
output_path = salts.optional.out_dir
pH_start = salts.optional.pHtitr[0]
pH_stop = salts.optional.pHtitr[1]
pH_interval = salts.optional.pHtitr[2]
dielectric = salts.optional.dielectric
# Execute the indivRun function for every salt in salts_file
f = open(salts_file)
salts = [float(salt) for salt in f.readlines()]
f.close()
base_path = os.path.join(__init__.invocation_path,output_path)
dielec_path = os.path.join(base_path,"D%.1F" % dielectric)
FileOps.makeDir(dielec_path)
for salt in salts:
print "Ionic strength: %4.2F" % salt
salt_output = os.path.join(dielec_path,"%.1F" % salt)
# Create output directory
FileOps.makeDir(salt_output)
# Run UHBD at this specific salt concentration
indivRun(filename,salt_output,pH_start,pH_stop,pH_interval,salt,
dielectric)
