for time in times:
# The file names.
file1 = 'nu_1kHz_relaxT_%.2f' % time
file2 = 'nu_2kHz_relaxT_%.2f' % time
# Calculate the peak intensities.
heights1 = []
heights2 = []
for i in range(len(res_data)):
# Append the intensities.
heights1.append(res_data[i][4] * exp(-res_data[i][2] * time))
heights2.append(res_data[i][5] * exp(-res_data[i][3] * time))
# Write out the file.
write_list(file_prefix=file1,
res_names=res_names,
res_nums=res_nums,
atom1_names=atom1_names,
atom2_names=atom2_names,
w1=w1,
w2=w2,
data_height=heights1)
write_list(file_prefix=file2,
res_names=res_names,
res_nums=res_nums,
atom1_names=atom1_names,
atom2_names=atom2_names,
w1=w1,
w2=w2,
data_height=heights2)
for time_index in range(len(times)):
# Loop over the spins.
intensities = []
for spin_index in range(len(r1rho_prime)):
# The rate.
nomen = pA**2 * (1.0 - pA) * (delta_omega[spin_index] * frq * 2 *
pi)**2 * kex
denom = kex**2 + pA**2 * (delta_omega[spin_index] * frq * 2 *
pi)**2 + (2 * pi *
spin_lock[spin_lock_index])**2
rx = r1rho_prime[spin_index] + nomen / denom
# The peak intensity.
intensities.append(i0[spin_index] * exp(-rx * times[time_index]))
# Create a Sparky .list file.
name = 'nu_%s' % spin_lock[spin_lock_index]
if time_index == 0:
name += '_ref'
else:
name += '_time_%s' % times[time_index]
write_list(file_prefix=name,
dir=None,
res_names=res_names,
res_nums=res_nums,
atom1_names=atom1_names,
atom2_names=atom2_names,
w1=w1,
w2=w2,
data_height=intensities)
atom1_names = []
atom2_names = []
w1 = []
w2 = []
for i in range(len(res_data)):
res_names.append(res_data[i][0])
res_nums.append(res_data[i][1])
atom1_names.append('N')
atom2_names.append('H')
w1.append(0.0)
w2.append(0.0)
# The relaxation times to use (seconds).
times = [0.01, 0.02, 0.04, 0.06, 0.08, 0.10, 0.12]
for time in times:
# The file names.
file1 = 'nu_1kHz_relaxT_%.2f' % time
file2 = 'nu_2kHz_relaxT_%.2f' % time
# Calculate the peak intensities.
heights1 = []
heights2 = []
for i in range(len(res_data)):
# Append the intensities.
heights1.append(res_data[i][4] * exp(-res_data[i][2] * time))
heights2.append(res_data[i][5] * exp(-res_data[i][3] * time))
# Write out the file.
write_list(file_prefix=file1, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=heights1)
write_list(file_prefix=file2, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=heights2)
# Setup for the Sparky peak list.
res_names = ['Trp', 'Trp']
res_nums = [1, 1]
atom1_names = ['N', 'NE1']
atom2_names = ['HN', 'HE1']
w1 = [122.454, 111.978]
w2 = [8.397, 8.720]
# Loop over the spin-lock fields.
for spin_lock_index in range(len(spin_lock)):
# Loop over the relaxation times.
for time_index in range(len(times)):
# Loop over the spins.
intensities = []
for spin_index in range(len(r1rho_prime)):
# The rate.
nomen = pA**2 * (1.0 - pA) * (delta_omega[spin_index]*frq*2*pi)**2 * kex
denom = kex**2 + pA**2 * (delta_omega[spin_index]*frq*2*pi)**2 + (2*pi*spin_lock[spin_lock_index])**2
rx = r1rho_prime[spin_index] + nomen / denom
# The peak intensity.
intensities.append(i0[spin_index] * exp(-rx*times[time_index]))
# Create a Sparky .list file.
name = 'nu_%s' % spin_lock[spin_lock_index]
if time_index == 0:
name += '_ref'
else:
name += '_time_%s' % times[time_index]
write_list(file_prefix=name, dir=None, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=intensities)