Author: bugman
Date: Thu Oct 31 10:55:39 2013
New Revision: 21358
URL: http://svn.gna.org/viewcvs/relax?rev=21358&view=rev
Log:
Fixes and completion of the Relax_disp.test_r2eff_read and
Relax_disp.test_r2eff_read_spin system tests.
These now handle the new user function design and now also check all of the
global and spin data.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=21358&r1=21357&r2=21358&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Oct 31
10:55:39 2013
@@ -1617,10 +1617,115 @@
# Read the sequence data.
self.interpreter.sequence.read(file='66.667.in', dir=data_path,
res_num_col=1)
+ # The ID.
+ id = 'test'
+
+ # Set up the metadata.
+ self.interpreter.spectrometer.frequency(id=id, frq=800e6)
+ self.interpreter.relax_disp.exp_type(spectrum_id=id, exp_type='CPMG')
+
# Try reading the file.
- self.interpreter.relax_disp.r2eff_read(file='66.667.in',
dir=data_path, exp_type='CPMG', frq=800e6, disp_frq=66.667, res_num_col=1,
data_col=2, error_col=3)
-
- # TODO: Data checks.
+ self.interpreter.relax_disp.r2eff_read(id=id, file='66.667.in',
dir=data_path, disp_frq=66.667, res_num_col=1, data_col=2, error_col=3)
+
+ # Check the global data.
+ data = [
+ ['cpmg_frqs', {'test': 66.667}],
+ ['cpmg_frqs_list', [66.667]],
+ ['dispersion_points', 1],
+ ['exp_type', {'test': 'CPMG'}],
+ ['exp_type_list', ['CPMG']],
+ ['spectrometer_frq', {'test': 800000000.0}],
+ ['spectrometer_frq_count', 1],
+ ['spectrometer_frq_list', [800000000.0]],
+ ['spectrum_ids', ['test']]
+ ]
+ for name, value in data:
+ # Does it exist?
+ self.assert_(hasattr(cdp, name))
+
+ # Check the object.
+ obj = getattr(cdp, name)
+ self.assertEqual(obj, value)
+
+ # Check the spin data.
+ data = [
+ [1, 2.3035747e+04, 8.5467725e+01],
+ [2, 9.9629762e+04, 2.8322033e+02],
+ [3, 9.5663137e+04, 2.8632929e+02],
+ [4, 1.7089893e+05, 3.1089428e+02],
+ [5, 4.7323876e+04, 1.0084269e+02],
+ [6, 2.0199122e+04, 1.0135220e+02],
+ [7, 1.6655488e+05, 3.1609061e+02],
+ [8, 9.0061074e+04, 1.9176585e+02],
+ [10, 8.4726204e+04, 2.8898155e+02],
+ [11, 1.5050233e+05, 4.3138029e+02],
+ [12, 9.2998531e+04, 3.0440191e+02],
+ [13, 1.6343507e+05, 3.3144097e+02],
+ [14, 1.0137301e+05, 3.7314642e+02],
+ [15, 8.3407837e+04, 1.6546473e+02],
+ [16, 1.3819126e+05, 3.3388517e+02],
+ [17, 1.1010490e+05, 3.5639222e+02],
+ [18, 9.4324035e+04, 3.2343585e+02],
+ [19, 1.1135179e+05, 3.0706671e+02],
+ [20, 7.6339410e+04, 1.7377460e+02],
+ [21, 6.2008453e+04, 1.7327150e+02],
+ [22, 1.0590404e+05, 2.4814635e+02],
+ [23, 1.0630198e+05, 2.3601100e+02],
+ [24, 7.2996320e+04, 1.4952465e+02],
+ [25, 9.5486742e+04, 2.7080766e+02],
+ [26, 5.8067989e+04, 1.6820462e+02],
+ [27, -1.7168510e+04, 2.2519560e+02],
+ [28, 1.6891473e+05, 2.3497525e+02],
+ [29, 9.4038555e+04, 2.0357593e+02],
+ [30, 2.1386951e+04, 2.2153532e+02],
+ [31, 9.3982899e+04, 2.0937056e+02],
+ [32, 8.6097484e+04, 2.3868467e+02],
+ [33, 1.0194337e+05, 2.7370704e+02],
+ [34, 8.5683111e+04, 2.0838076e+02],
+ [35, 8.6985768e+04, 2.0889310e+02],
+ [36, 8.6011237e+04, 1.7498390e+02],
+ [37, 1.0984097e+05, 2.7622998e+02],
+ [38, 8.7017879e+04, 2.6547994e+02],
+ [39, 9.1682649e+04, 5.2777676e+02],
+ [40, 7.6370440e+04, 1.9873214e+02],
+ [41, 9.1393531e+04, 2.4483824e+02],
+ [42, 1.1017111e+05, 2.8020699e+02],
+ [43, 9.4552366e+04, 3.4394150e+02],
+ [44, 1.2858281e+05, 6.8449252e+02],
+ [45, 7.4583525e+04, 1.9544210e+02],
+ [46, 9.2087490e+04, 2.0491066e+02],
+ [47, 9.7507255e+04, 2.5162839e+02],
+ [48, 1.0033842e+05, 2.7566430e+02],
+ [49, 1.3048305e+05, 2.6797466e+02],
+ [50, 1.0546796e+05, 1.9304384e+02],
+ [51, 9.3099697e+04, 2.0773311e+02],
+ [52, 4.6863758e+04, 1.3169068e+02],
+ [53, 6.1055806e+04, 1.5448477e+02],
+ [55, 6.8629994e+04, 1.6868673e+02],
+ [56, 1.1005552e+05, 2.1940465e+02],
+ [57, 1.0572760e+05, 1.9768486e+02],
+ [58, 1.1176950e+05, 3.0009610e+02],
+ [59, 9.8758603e+04, 3.3803895e+02],
+ [60, 9.9517201e+04, 3.5137994e+02],
+ [61, 5.4357946e+04, 2.5896579e+02],
+ [62, 1.0899978e+05, 2.8720371e+02],
+ [63, 8.4549759e+04, 4.1401837e+02],
+ [64, 5.5014550e+04, 2.1135781e+02],
+ [65, 8.0569666e+04, 2.3249709e+02],
+ [66, 1.2936610e+05, 3.5218725e+02],
+ [67, 3.6438010e+04, 8.7924003e+01],
+ [70, 3.8763157e+04, 1.3325040e+02],
+ [71, 8.5711411e+04, 2.9316183e+02],
+ [72, 3.3211541e+04, 1.2182123e+02],
+ [73, 3.2070576e+04, 1.2305430e+02]
+ ]
+ for res_num, value, error in data:
+ # Get the spin.
+ spin = return_spin(spin_id=":%s"%res_num)
+
+ # Check the values.
+ self.assertEqual(spin.r2eff['800.00000000_66.667'], value)
+ self.assertEqual(spin.r2eff_err['800.00000000_66.667'], error)
def test_r2eff_read_spin(self):
@@ -1635,11 +1740,92 @@
self.interpreter.spin.isotope('1H', spin_id='@H')
self.interpreter.spin.isotope('15N', spin_id='@N')
- # Try reading the file.
- self.interpreter.relax_disp.r2eff_read_spin(file='hs_500.res',
dir=data_path, spin_id=':9@H', exp_type='CPMG', frq=500e6, disp_point_col=1,
data_col=2, error_col=3)
- self.interpreter.relax_disp.r2eff_read_spin(file='ns_500.res',
dir=data_path, spin_id=':9@N', exp_type='CPMG', frq=500e6, disp_point_col=1,
data_col=2, error_col=3)
-
- # TODO: Data checks.
+ # Build the experiment IDs.
+ H_disp_points = [67.0, 133.0, 267.0, 400.0, 533.0, 667.0, 800.0,
933.0, 1067.0, 1600.0, 2133.0, 2667.0]
+ N_disp_points = [50.0, 100.0, 150.0, 200.0, 250.0, 300.0, 350.0,
400.0, 500.0, 600.0, 700.0, 800.0, 900.0, 1000.0]
+ ids = []
+ for value in H_disp_points:
+ ids.append('1H_CPMG_%s' % value)
+ for value in N_disp_points:
+ ids.append('15N_CPMG_%s' % value)
+ print("\n\nThe experiment IDs are %s." % ids)
+
+ # Set up the metadata for the experiments.
+ for id in ids:
+ self.interpreter.spectrometer.frequency(id=id, frq=500e6)
+ self.interpreter.relax_disp.exp_type(spectrum_id=id,
exp_type='CPMG')
+
+ # Loop over the experiments.
+ for id, file, spin_id in [['1H_CPMG', 'hs_500.res', ':9@H'],
['15N_CPMG', 'ns_500.res', ':9@N']]:
+ # Try reading the file.
+ self.interpreter.relax_disp.r2eff_read_spin(id=id, file=file,
dir=data_path, spin_id=spin_id, disp_point_col=1, data_col=2, error_col=3)
+
+ # Check the global data.
+ print cdp
+ data = [
+ ['cpmg_frqs', {'1H_CPMG_667.0': 667.0, '1H_CPMG_1067.0': 1067.0,
'15N_CPMG_350.0': 350.0, '1H_CPMG_933.0': 933.0, '15N_CPMG_50.0': 50.0,
'15N_CPMG_100.0': 100.0, '1H_CPMG_400.0': 400.0, '1H_CPMG_533.0': 533.0,
'1H_CPMG_800.0': 800.0, '15N_CPMG_900.0': 900.0, '15N_CPMG_150.0': 150.0,
'15N_CPMG_800.0': 800.0, '1H_CPMG_267.0': 267.0, '1H_CPMG_2667.0': 2667.0,
'15N_CPMG_300.0': 300.0, '1H_CPMG_133.0': 133.0, '15N_CPMG_700.0': 700.0,
'1H_CPMG_67.0': 67.0, '15N_CPMG_400.0': 400.0, '15N_CPMG_250.0': 250.0,
'1H_CPMG_2133.0': 2133.0, '1H_CPMG_1600.0': 1600.0, '15N_CPMG_200.0': 200.0,
'15N_CPMG_1000.0': 1000.0, '15N_CPMG_500.0': 500.0, '15N_CPMG_600.0': 600.0}],
+ ['cpmg_frqs_list', [50.0, 67.0, 100.0, 133.0, 150.0, 200.0,
250.0, 267.0, 300.0, 350.0, 400.0, 500.0, 533.0, 600.0, 667.0, 700.0, 800.0,
900.0, 933.0, 1000.0, 1067.0, 1600.0, 2133.0, 2667.0]],
+ ['dispersion_points', 24],
+ ['exp_type', {'1H_CPMG_667.0': 'CPMG', '1H_CPMG_1067.0': 'CPMG',
'15N_CPMG_350.0': 'CPMG', '1H_CPMG_933.0': 'CPMG', '15N_CPMG_50.0': 'CPMG',
'15N_CPMG_100.0': 'CPMG', '1H_CPMG_400.0': 'CPMG', '1H_CPMG_533.0': 'CPMG',
'1H_CPMG_800.0': 'CPMG', '15N_CPMG_900.0': 'CPMG', '15N_CPMG_150.0': 'CPMG',
'15N_CPMG_800.0': 'CPMG', '1H_CPMG_267.0': 'CPMG', '1H_CPMG_2667.0': 'CPMG',
'15N_CPMG_300.0': 'CPMG', '1H_CPMG_133.0': 'CPMG', '15N_CPMG_700.0': 'CPMG',
'1H_CPMG_67.0': 'CPMG', '15N_CPMG_400.0': 'CPMG', '15N_CPMG_250.0': 'CPMG',
'1H_CPMG_2133.0': 'CPMG', '1H_CPMG_1600.0': 'CPMG', '15N_CPMG_200.0': 'CPMG',
'15N_CPMG_1000.0': 'CPMG', '15N_CPMG_500.0': 'CPMG', '15N_CPMG_600.0':
'CPMG'}],
+ ['exp_type_list', ['CPMG']],
+ ['spectrometer_frq', {'1H_CPMG_667.0': 500000000.0,
'1H_CPMG_1067.0': 500000000.0, '15N_CPMG_350.0': 500000000.0,
'1H_CPMG_933.0': 500000000.0, '15N_CPMG_50.0': 500000000.0, '15N_CPMG_100.0':
500000000.0, '1H_CPMG_400.0': 500000000.0, '1H_CPMG_533.0': 500000000.0,
'1H_CPMG_800.0': 500000000.0, '15N_CPMG_900.0': 500000000.0,
'15N_CPMG_150.0': 500000000.0, '15N_CPMG_800.0': 500000000.0,
'1H_CPMG_267.0': 500000000.0, '1H_CPMG_2667.0': 500000000.0,
'15N_CPMG_300.0': 500000000.0, '1H_CPMG_133.0': 500000000.0,
'15N_CPMG_700.0': 500000000.0, '1H_CPMG_67.0': 500000000.0, '15N_CPMG_400.0':
500000000.0, '15N_CPMG_250.0': 500000000.0, '1H_CPMG_2133.0': 500000000.0,
'1H_CPMG_1600.0': 500000000.0, '15N_CPMG_200.0': 500000000.0,
'15N_CPMG_1000.0': 500000000.0, '15N_CPMG_500.0': 500000000.0,
'15N_CPMG_600.0': 500000000.0}],
+ ['spectrometer_frq_count', 1],
+ ['spectrometer_frq_list', [500000000.0]],
+ ['spectrum_ids', ['1H_CPMG_67.0', '1H_CPMG_133.0',
'1H_CPMG_267.0', '1H_CPMG_400.0', '1H_CPMG_533.0', '1H_CPMG_667.0',
'1H_CPMG_800.0', '1H_CPMG_933.0', '1H_CPMG_1067.0', '1H_CPMG_1600.0',
'1H_CPMG_2133.0', '1H_CPMG_2667.0', '15N_CPMG_50.0', '15N_CPMG_100.0',
'15N_CPMG_150.0', '15N_CPMG_200.0', '15N_CPMG_250.0', '15N_CPMG_300.0',
'15N_CPMG_350.0', '15N_CPMG_400.0', '15N_CPMG_500.0', '15N_CPMG_600.0',
'15N_CPMG_700.0', '15N_CPMG_800.0', '15N_CPMG_900.0', '15N_CPMG_1000.0']]
+ ]
+ for name, value in data:
+ # Does it exist?
+ self.assert_(hasattr(cdp, name))
+
+ # Check the object.
+ obj = getattr(cdp, name)
+ if not isinstance(data, dict):
+ self.assertEqual(obj, value)
+
+ # Check the global dictionary data.
+ else:
+ for id in ids:
+ self.assertEqual(obj[id], value[id])
+
+ # Check the spin data.
+ h_data = [
+ [ 67.0, 21.47924, 0.42958],
+ [ 133.0, 16.73898, 0.33478],
+ [ 267.0, 9.97357, 0.19947],
+ [ 400.0, 8.23877, 0.24737],
+ [ 533.0, 7.59290, 0.24263],
+ [ 667.0, 7.45843, 0.24165],
+ [ 800.0, 7.11222, 0.23915],
+ [ 933.0, 7.40880, 0.24129],
+ [1067.0, 6.55191, 0.16629],
+ [1600.0, 6.72177, 0.23637],
+ [2133.0, 7.09629, 0.23904],
+ [2667.0, 7.14675, 0.23940]
+ ]
+ for disp_point, value, error in h_data:
+ id = '500.00000000_%.3f' % disp_point
+ self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff[id], value)
+ self.assertEqual(cdp.mol[0].res[0].spin[0].r2eff_err[id], error)
+ n_data = [
+ [ 50.0, 27.15767, 0.54315],
+ [ 100.0, 26.55781, 0.53116],
+ [ 150.0, 24.73462, 0.49469],
+ [ 200.0, 20.98617, 0.41972],
+ [ 250.0, 17.82442, 0.35649],
+ [ 300.0, 15.55352, 0.31107],
+ [ 350.0, 13.78958, 0.27579],
+ [ 400.0, 12.48334, 0.24967],
+ [ 500.0, 11.55724, 0.23114],
+ [ 600.0, 10.53874, 0.21077],
+ [ 700.0, 10.07395, 0.20148],
+ [ 800.0, 9.62952, 0.19259],
+ [ 900.0, 9.49994, 0.19000],
+ [1000.0, 8.71350, 0.17427]
+ ]
+ for disp_point, value, error in n_data:
+ id = '500.00000000_%.3f' % disp_point
+ self.assertEqual(cdp.mol[0].res[0].spin[1].r2eff[id], value)
+ self.assertEqual(cdp.mol[0].res[0].spin[1].r2eff_err[id], error)
def test_r2eff_fit_fixed_time(self):
r21358 - /branches/relax_disp/test_suite/system_tests/relax_disp.py