def test_write_list(self):
"""Test the lib.software.sparky.write_list() function."""
# The data.
res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
res_nums = [3, 4, 5, 6, 40, 40, 55]
atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]
# The result.
file_data = [
' Assignment w1 w2 Data Height\n',
'\n',
' LEU3N-HN 122.454 8.397 2535\n',
' GLY4N-HN 111.978 8.720 5050\n',
' SER5N-HN 115.069 8.177 51643\n',
' MET6N-HN 120.910 8.813 53663\n',
' TRP40N-HN 123.335 8.005 -65111\n',
' TRP40NE1-HE1 130.204 10.294 -181131\n',
' ASN55N-HN 116.896 7.468 -105322\n'
]
# Write the data out.
file = DummyFileObject()
write_list(file_prefix=file, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=heights)
# Check the file data.
lines = file.readlines()
self.assertEqual(len(lines), len(file_data))
for i in range(len(lines)):
self.assertEqual(lines[i], file_data[i])
def test_write_list(self):
"""Test the lib.software.sparky.write_list() function."""
# The data.
res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
res_nums = [3, 4, 5, 6, 40, 40, 55]
atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]
# The result.
file_data = [
' Assignment w1 w2 Data Height\n', '\n',
' LEU3N-HN 122.454 8.397 2535\n',
' GLY4N-HN 111.978 8.720 5050\n',
' SER5N-HN 115.069 8.177 51643\n',
' MET6N-HN 120.910 8.813 53663\n',
' TRP40N-HN 123.335 8.005 -65111\n',
' TRP40NE1-HE1 130.204 10.294 -181131\n',
' ASN55N-HN 116.896 7.468 -105322\n'
]
# Write the data out.
file = DummyFileObject()
write_list(file_prefix=file,
res_names=res_names,
res_nums=res_nums,
atom1_names=atom1_names,
atom2_names=atom2_names,
w1=w1,
w2=w2,
data_height=heights)
# Check the file data.
lines = file.readlines()
self.assertEqual(len(lines), len(file_data))
for i in range(len(lines)):
self.assertEqual(lines[i], file_data[i])
# The rate.
nomen = pA * pB * dw[spin_index]**2 * kex
denom = omega_aeff2[spin_index] * omega_beff2[
spin_index] / omega_eff2[spin_index] + kex**2
rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 * (
r1rho_prime[spin_index, frq_index] + nomen / denom)
# The peak intensity.
intensities.append(i0[spin_index, frq_index] *
exp(-rx * times[time_index]))
# Create a Sparky .list file.
if time_index == 0 and spin_lock_index == 0:
name = 'ref_%s' % frq_label[frq_index]
elif time_index == 0:
name = None
else:
name = 'nu_%s_%s' % (spin_lock[spin_lock_index],
frq_label[frq_index])
if name:
write_list(file_prefix=name,
dir=None,
res_names=res_names,
res_nums=res_nums,
atom1_names=atomN_names,
atom2_names=atomH_names,
w1=wN,
w2=wH,
data_height=intensities)
omega_beff2 = omega1**2 + delta_b**2
omega_eff2 = omega1**2 + delta_ave**2
# 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)):
# Spin dependent parameters.
theta = atan(omega1 / delta_ave[spin_index])
sin_theta2 = sin(theta)**2
cos_theta2 = cos(theta)**2
# The rate.
nomen = pA * pB * dw[spin_index]**2 * kex
denom = omega_aeff2[spin_index] * omega_beff2[spin_index] / omega_eff2[spin_index] + kex**2
rx = r1[spin_index, frq_index] * cos_theta2 + sin_theta2 * (r1rho_prime[spin_index, frq_index] + nomen / denom)
# The peak intensity.
intensities.append(i0[spin_index, frq_index] * exp(-rx*times[time_index]))
# Create a Sparky .list file.
if time_index == 0 and spin_lock_index == 0:
name = 'ref_%s' % frq_label[frq_index]
elif time_index == 0:
name = None
else:
name = 'nu_%s_%s' % (spin_lock[spin_lock_index], frq_label[frq_index])
if name:
write_list(file_prefix=name, dir=None, res_names=res_names, res_nums=res_nums, atom1_names=atomN_names, atom2_names=atomH_names, w1=wN, w2=wH, data_height=intensities)