def process_parameters(self, initial_settings, _saved_settings=None):
"""
Process information to properly set the initial settings
"""
if initial_settings.R_value_used:
R_str = "R"
else:
R_str = ""
num_binding_sites = initial_settings.num_binding_sites.get()
solutes, charges = self.get_settings(initial_settings)
print 'making script with num binding sties= ', num_binding_sites
QR_str = "single Q" + R_str
# make the script for the Eyring rate model
print 'mpmath used = ', initial_settings.mpmath_used
if initial_settings.mpmath_used:
math_package = 'mpmath'
else:
math_package = 'numpy'
print 'math package: ', math_package
_eyring_rate_script = script_maker.make_template(math_package, num_binding_sites,
solutes, charges, QR_str)
with open("eyring_rate_script.py", "w") as _file:
_file.write(_eyring_rate_script)
_file.close()
reload(eyring_rate_script)
self.set_parameters(solutes, initial_settings.charges,
initial_settings.num_binding_sites.get(), _saved_settings)
'GCa': [8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8],
'GMg': [8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8],
'GFe': [8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8],
'GBa': [8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8],
'GCd': [8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8, -12, 8]}
Qs = 30*[5]
Rs = 30*[0.5]
total_results_eig = []
total_results_svd = []
for num_binding_sites in range(1, 5):
for num_ions in range(1, 5):
print 'num barriers: ', num_binding_sites
print 'num ions: ', num_ions
# make the script make an eyring rate model and save it to test_script.py
eyring_rate_script = tm.make_template('numpy', num_binding_sites, ions[:num_ions], charges, 'full QR')
with open("test_script.py", "w") as file:
file.write(eyring_rate_script)
file.close()
# make a list of the electrical distances to update the energy_barriers dict with
distance_buffer = 2 * (num_binding_sites + 1)
distance = []
for i in range(1, distance_buffer):
distance.append(float(i)/distance_buffer)
energy_barriers['distance'] = distance
# call the erying rate model script made earlier
results_eig, results_svd = test_script.eyring_rate_algo(voltages,
ion_conc,
energy_barriers,
