Author: bugman
Date: Tue Dec 3 14:37:09 2013
New Revision: 21743
URL: http://svn.gna.org/viewcvs/relax?rev=21743&view=rev
Log:
Renamed the Relax_disp.test_ns_mmq_3site_branched system test to
Relax_disp.test_ns_mmq_3site.
Added:
trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site.py
- copied unchanged from r21737,
trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py
Removed:
trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py
Modified:
trunk/test_suite/system_tests/relax_disp.py
Modified: trunk/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=21743&r1=21742&r2=21743&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Dec 3 14:37:09 2013
@@ -2420,11 +2420,11 @@
spin_index += 1
- def test_ns_mmq_3site_branched(self):
+ def test_ns_mmq_3site(self):
"""Compare the 'NS MMQ 3-site (branched)' dispersion model to
synthetic data from cpmg_fit."""
# Execute the script.
- self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site_branched.py')
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'ns_mmq_3site.py')
# Check the chi-squared value.
self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.0, 5)
Removed:
trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py?rev=21742&view=auto
==============================================================================
--- trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/ns_mmq_3site_branched.py
(removed)
@@ -1,189 +1,0 @@
-"""Compare the synthetic cpmg_fit data to the relax solution."""
-
-# Python module imports.
-from os import sep
-
-# relax module imports.
-from specific_analyses.relax_disp.disp_data import generate_r20_key
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ,
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ,
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ
-from status import Status; status = Status()
-
-
-# The path to the data files.
-DATA_PATH = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'ns_mmq_3site_branched'
-
-
-# Create a data pipe.
-pipe.create('R2eff', 'relax_disp')
-
-# Create the spin system.
-spin.create(res_name='X', res_num=1, spin_name='H')
-spin.create(res_name='X', res_num=1, spin_name='N')
-spin.element('H', spin_id='@H')
-spin.element('N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
-spin.isotope('15N', spin_id='@N')
-
-# Define the magnetic dipole-dipole relaxation interaction.
-interatom.define(spin_id1=':1@N', spin_id2=':1@H', direct_bond=True)
-
-# The spectral data - experiment ID, R2eff file name, experiment type, spin
ID string, spectrometer frequency in Hertz, relaxation time.
-data = [
- ['1H SQ', '1H_SQ_CPMG_400_MHz', 'HS_400.res',
EXP_TYPE_CPMG_PROTON_SQ, ':1@H', 400e6, 0.03],
- ['1H SQ', '1H_SQ_CPMG_600_MHz', 'HS_600.res',
EXP_TYPE_CPMG_PROTON_SQ, ':1@H', 600e6, 0.03],
- ['1H SQ', '1H_SQ_CPMG_800_MHz', 'HS_800.res',
EXP_TYPE_CPMG_PROTON_SQ, ':1@H', 800e6, 0.03],
- ['1H SQ', '1H_SQ_CPMG_1000_MHz', 'HS_1000.res',
EXP_TYPE_CPMG_PROTON_SQ, ':1@H', 1000e6, 0.03],
- ['SQ', '15N_SQ_CPMG_400_MHz', 'NS_400.res', EXP_TYPE_CPMG_SQ,
':1@N', 400e6, 0.04],
- ['SQ', '15N_SQ_CPMG_600_MHz', 'NS_600.res', EXP_TYPE_CPMG_SQ,
':1@N', 600e6, 0.04],
- ['SQ', '15N_SQ_CPMG_800_MHz', 'NS_800.res', EXP_TYPE_CPMG_SQ,
':1@N', 800e6, 0.04],
- ['SQ', '15N_SQ_CPMG_1000_MHz', 'NS_1000.res', EXP_TYPE_CPMG_SQ,
':1@N', 1000e6, 0.04],
- ['ZQ', '15N_ZQ_CPMG_400_MHz', 'ZQ_400.res', EXP_TYPE_CPMG_ZQ,
':1@N', 400e6, 0.03],
- ['ZQ', '15N_ZQ_CPMG_600_MHz', 'ZQ_600.res', EXP_TYPE_CPMG_ZQ,
':1@N', 600e6, 0.03],
- ['ZQ', '15N_ZQ_CPMG_800_MHz', 'ZQ_800.res', EXP_TYPE_CPMG_ZQ,
':1@N', 800e6, 0.03],
- ['ZQ', '15N_ZQ_CPMG_1000_MHz', 'ZQ_1000.res', EXP_TYPE_CPMG_ZQ,
':1@N', 1000e6, 0.03],
- ['DQ', '15N_DQ_CPMG_400_MHz', 'DQ_400.res', EXP_TYPE_CPMG_DQ,
':1@N', 400e6, 0.03],
- ['DQ', '15N_DQ_CPMG_600_MHz', 'DQ_600.res', EXP_TYPE_CPMG_DQ,
':1@N', 600e6, 0.03],
- ['DQ', '15N_DQ_CPMG_800_MHz', 'DQ_800.res', EXP_TYPE_CPMG_DQ,
':1@N', 800e6, 0.03],
- ['DQ', '15N_DQ_CPMG_1000_MHz', 'DQ_1000.res', EXP_TYPE_CPMG_DQ,
':1@N', 1000e6, 0.03],
- ['1H MQ', '1H_MQ_CPMG_400_MHz', 'HM_400.res',
EXP_TYPE_CPMG_PROTON_MQ, ':1@H', 400e6, 0.02],
- ['1H MQ', '1H_MQ_CPMG_600_MHz', 'HM_600.res',
EXP_TYPE_CPMG_PROTON_MQ, ':1@H', 600e6, 0.02],
- ['1H MQ', '1H_MQ_CPMG_800_MHz', 'HM_800.res',
EXP_TYPE_CPMG_PROTON_MQ, ':1@H', 800e6, 0.02],
- ['1H MQ', '1H_MQ_CPMG_1000_MHz', 'HM_1000.res',
EXP_TYPE_CPMG_PROTON_MQ, ':1@H', 1000e6, 0.02],
- ['MQ', '15N_MQ_CPMG_400_MHz', 'NM_400.res', EXP_TYPE_CPMG_MQ,
':1@N', 400e6, 0.02],
- ['MQ', '15N_MQ_CPMG_600_MHz', 'NM_600.res', EXP_TYPE_CPMG_MQ,
':1@N', 600e6, 0.02],
- ['MQ', '15N_MQ_CPMG_800_MHz', 'NM_800.res', EXP_TYPE_CPMG_MQ,
':1@N', 800e6, 0.02],
- ['MQ', '15N_MQ_CPMG_1000_MHz', 'NM_1000.res', EXP_TYPE_CPMG_MQ,
':1@N', 1000e6, 0.02]
-]
-cpmg_frqs_1h_sq = []
-for i in range(80):
- cpmg_frqs_1h_sq.append(100/3.0 * (i + 1))
-cpmg_frqs_sq = []
-for i in range(40):
- cpmg_frqs_sq.append(25.0 * (i + 1))
-cpmg_frqs_dq = []
-for i in range(32):
- cpmg_frqs_dq.append(100/3.0 * (i + 1))
-cpmg_frqs_zq = []
-for i in range(32):
- cpmg_frqs_zq.append(100/3.0 * (i + 1))
-cpmg_frqs_1h_mq = []
-for i in range(50):
- cpmg_frqs_1h_mq.append(50.0 * (i + 1))
-cpmg_frqs_mq = []
-for i in range(20):
- cpmg_frqs_mq.append(50.0 * (i + 1))
-
-# Loop over the files, reading in the data.
-for data_type, id, file, exp_type, spin_id, H_frq, relax_time in data:
- # Alias the CPMG frequencies.
- if data_type == 'SQ':
- cpmg_frqs = cpmg_frqs_sq
- elif data_type == '1H SQ':
- cpmg_frqs = cpmg_frqs_1h_sq
- elif data_type == 'DQ':
- cpmg_frqs = cpmg_frqs_dq
- elif data_type == 'ZQ':
- cpmg_frqs = cpmg_frqs_zq
- elif data_type == '1H MQ':
- cpmg_frqs = cpmg_frqs_1h_mq
- elif data_type == 'MQ':
- cpmg_frqs = cpmg_frqs_mq
-
- # Loop over each CPMG frequency.
- for cpmg_frq in cpmg_frqs:
- # The id.
- new_id = "%s_%.3f" % (id, cpmg_frq)
-
- # Set the NMR field strength.
- spectrometer.frequency(id=new_id, frq=H_frq)
-
- # Set the relaxation dispersion experiment type.
- relax_disp.exp_type(spectrum_id=new_id, exp_type=exp_type)
-
- # Relaxation dispersion CPMG constant time delay T (in s).
- relax_disp.relax_time(spectrum_id=new_id, time=relax_time)
-
- # Set the CPMG frequency.
- relax_disp.cpmg_frq(spectrum_id=new_id, cpmg_frq=cpmg_frq)
-
- # Read the R2eff data.
- relax_disp.r2eff_read_spin(id=id, file=file, dir=DATA_PATH,
spin_id=spin_id, disp_point_col=7, data_col=10, error_col=9)
-
-# Change the model.
-relax_disp.select_model('NS MMQ 3-site')
-
-# The R20 keys.
-r20_1h_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=400e6)
-r20_1h_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=600e6)
-r20_1h_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=800e6)
-r20_1h_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ,
frq=1000e6)
-r20_sq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=400e6)
-r20_sq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
-r20_sq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
-r20_sq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=1000e6)
-r20_zq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=400e6)
-r20_zq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
-r20_zq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
-r20_zq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=1000e6)
-r20_dq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=400e6)
-r20_dq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
-r20_dq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
-r20_dq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=1000e6)
-r20_1h_mq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=400e6)
-r20_1h_mq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=600e6)
-r20_1h_mq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=800e6)
-r20_1h_mq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ,
frq=1000e6)
-r20_mq_400_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=400e6)
-r20_mq_600_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
-r20_mq_800_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
-r20_mq_1000_key = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=1000e6)
-
-# Manually set the parameter values.
-spin_N = cdp.mol[0].res[0].spin[1]
-spin_N.r2 = {
- r20_1h_sq_400_key: 6.5,
- r20_1h_sq_600_key: 7.0,
- r20_1h_sq_800_key: 5.5,
- r20_1h_sq_1000_key: 5.0,
- r20_sq_400_key: 8.0,
- r20_sq_600_key: 9.0,
- r20_sq_800_key: 10.5,
- r20_sq_1000_key: 11.5,
- r20_zq_400_key: 6.0,
- r20_zq_600_key: 7.5,
- r20_zq_800_key: 7.0,
- r20_zq_1000_key: 6.5,
- r20_dq_400_key: 8.5,
- r20_dq_600_key: 10.5,
- r20_dq_800_key: 12.5,
- r20_dq_1000_key: 14.5,
- r20_1h_mq_400_key: 7.5,
- r20_1h_mq_600_key: 8.5,
- r20_1h_mq_800_key: 11.5,
- r20_1h_mq_1000_key: 13.5,
- r20_mq_400_key: 9.0,
- r20_mq_600_key: 10.0,
- r20_mq_800_key: 12.0,
- r20_mq_1000_key: 13.0
-}
-spin_N.pA = 0.85
-spin_N.pB = 0.05
-spin_N.pC = 0.10
-spin_N.kAB = 500.0
-spin_N.kAC = 0.0
-spin_N.kBC = 2000.0
-spin_N.dw_AB = -3.0
-spin_N.dw_AC = 8.0
-spin_N.dw_BC = 11.0
-spin_N.dwH_AB = 0.5
-spin_N.dwH_AC = -1.5
-spin_N.dwH_BC = -2.0
-
-# Calculate.
-calc()
-
-# Plot the dispersion curves.
-relax_disp.plot_disp_curves(dir=ds.tmpdir, num_points=100, extend=0,
force=True)
-
-# Save the results.
-state.save('state', dir=ds.tmpdir, compress_type=1, force=True)
r21743 - in /trunk/test_suite/system_tests: ./ scripts/relax_disp/