Author: bugman
Date: Thu Jun 6 19:47:57 2013
New Revision: 19906
URL: http://svn.gna.org/viewcvs/relax?rev=19906&view=rev
Log:
Created the Relax_disp.test_r1rho_on_res_fixed_time_m61 system test.
This checks the R1rho-type experiment with a fixed relaxation time period
using the 'R2eff' and
'M61' models. It uses the auto-analysis for this, and the 'r1rho_on_res'
synthetic relaxation data.
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
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=19906&r1=19905&r2=19906&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Jun 6
19:47:57 2013
@@ -28,6 +28,7 @@
# relax module imports.
from auto_analyses import relax_disp
from data_store import Relax_data_store; ds = Relax_data_store()
+from pipe_control.mol_res_spin import spin_loop
from specific_analyses.relax_disp.variables import MODEL_LIST_CPMG
from status import Status; status = Status()
from test_suite.system_tests.base_classes import SystemTestCase
@@ -460,3 +461,51 @@
self.assertEqual(cdp.mol[0].res[0].spin[0].ri_data['R2eff.600'],
15.000)
self.assertEqual(cdp.mol[0].res[1].spin[0].ri_data['R2eff.600'],
4.2003)
self.assertEqual(cdp.mol[0].res[2].spin[0].ri_data['R2eff.600'],
7.2385)
+
+
+ def test_r1rho_on_res_fixed_time_m61(self):
+ """Test the relaxation dispersion 'M61' model curve fitting to fixed
time synthetic data."""
+
+ # Fixed time variable.
+ ds.fixed = True
+
+ # Execute the script.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_disp'+sep+'r1rho_on_res_m61.py')
+
+ # The original parameters.
+ i0 = [100000.0, 20000.0]
+ r1rho_prime = [2.25, 24.0]
+ pA = 0.7
+ kex = 1000.0
+ delta_omega = [1.0, 2.0]
+ keys = ['1000.0', '1500.0', '2000.0', '2500.0', '3000.0', '3500.0',
'4000.0', '4500.0', '5000.0', '5500.0', '6000.0']
+
+ # Switch to the 'R2eff' model data pipe, then check for each spin.
+ self.interpreter.pipe.switch('R2eff')
+ spin_index = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Printout.
+ print("\nSpin %s." % spin_id)
+ print spin
+
+ # Check the fitted parameters.
+ for key in keys:
+ self.assertAlmostEqual(spin.r2eff[key],
r1rho_prime[spin_index])
+
+ # Increment the spin index.
+ spin_index += 1
+
+ # Switch to the 'M61' model data pipe, then check for each spin.
+ self.interpreter.pipe.switch('M61')
+ spin_index = 0
+ for spin, spin_id in spin_loop(return_id=True):
+ # Printout.
+ print("\nSpin %s." % spin_id)
+
+ # Check the fitted parameters.
+ self.assertAlmostEqual(spin.pA, pA)
+ self.assertAlmostEqual(spin.kex, kex)
+ self.assertAlmostEqual(spin.delta_omega, delta_omega[spin_index])
+
+ # Increment the spin index.
+ spin_index += 1
Added:
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py?rev=19906&view=auto
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
(added)
+++
branches/relax_disp/test_suite/system_tests/scripts/relax_disp/r1rho_on_res_m61.py
Thu Jun 6 19:47:57 2013
@@ -1,0 +1,105 @@
+# Optimise the R1rho on-resonance synthetic data using the M61 model.
+
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from auto_analyses.relax_disp import Relax_disp
+from data_store import Relax_data_store; ds = Relax_data_store()
+from status import Status; status = Status()
+
+
+# Analysis variables.
+#####################
+
+# The dispersion models.
+MODELS = ['R2eff', 'No Rex', 'M61']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 3
+
+# The number of Monte Carlo simulations to be used for error analysis at the
end of the analysis.
+MC_NUM = 3
+
+# Fixed relaxation time period flag.
+if not hasattr(ds, 'fixed'):
+ ds.fixed = True
+
+
+# Set up the data pipe.
+#######################
+
+# The results directory.
+if not hasattr(ds, 'tmpdir'):
+ ds.tmpdir = None
+
+# Create the data pipe.
+pipe_name = 'base pipe'
+pipe_bundle = 'relax_disp'
+pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_disp')
+
+# The path to the data files.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'r1rho_on_res'
+
+# Create the sequence data.
+spin.create(res_name='Trp', res_num=1, spin_name='N')
+spin.create(res_name='Trp', res_num=1, spin_name='NE1')
+
+# Set the isotope information.
+spin.isotope(isotope='15N')
+
+# Set the relaxation dispersion experiment type.
+if ds.fixed:
+ relax_disp.exp_type('r1rho fixed')
+else:
+ relax_disp.exp_type('r1rho exponential')
+
+# The spectral data - spectrum ID, peak lists, offset frequency (Hz),
relaxation time period (s), baseplane RMSD estimate.
+data = []
+times = [0.00, 0.01, 0.02, 0.04, 0.06, 0.08, 0.1, 0.12, 0.15]
+ncyc = [1, 2, 3, 4, 5, 6, 7, 8, 9]
+if ds.fixed:
+ times = [0.15]
+ ncyc = [9]
+spin_lock = [1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500,
6000]
+for spin_lock_index in range(len(spin_lock)):
+ for time_index in range(len(times)):
+ data.append(["nu_%s_ncyc%s" % (spin_lock[spin_lock_index],
ncyc[time_index]), "nu_%s_ncyc%s.list" % (spin_lock[spin_lock_index],
ncyc[time_index]), spin_lock[spin_lock_index], times[time_index], 200.0])
+
+# Load the reference spectrum.
+if ds.fixed:
+ # Load the peak intensities and set the errors.
+ spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='N',
proton='HN')
+ spectrum.read_intensities(file="nu_%s_ncyc1.list" % spin_lock[0],
dir=data_path, spectrum_id='ref', int_method='height', heteronuc='NE1',
proton='HE1')
+ spectrum.baseplane_rmsd(spectrum_id='ref', error=data[0][4])
+
+ # Set as the reference.
+ relax_disp.spin_lock_field(spectrum_id='ref', field=None)
+
+# Loop over the spectral data, loading it and setting the metadata.
+for i in range(len(data)):
+ # Load the peak intensities and set the errors.
+ spectrum.read_intensities(file=data[i][1], dir=data_path,
spectrum_id=data[i][0], int_method='height', heteronuc='N', proton='HN')
+ spectrum.read_intensities(file=data[i][1], dir=data_path,
spectrum_id=data[i][0], int_method='height', heteronuc='NE1', proton='HE1')
+ spectrum.baseplane_rmsd(spectrum_id=data[i][0], error=data[i][4])
+
+ # Set the relaxation dispersion spin-lock field strength (nu1).
+ relax_disp.spin_lock_field(spectrum_id=data[i][0], field=data[i][2])
+
+ # Set the relaxation times.
+ relax_disp.relax_time(spectrum_id=data[i][0], time=data[i][3])
+
+# Clustering.
+relax_disp.cluster(cluster_id='cluster', spin_id='@N,NE1')
+
+
+
+# Auto-analysis execution.
+##########################
+
+# Do not change!
+Relax_disp(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=ds.tmpdir, models=MODELS, grid_inc=GRID_INC, mc_sim_num=MC_NUM)
+
+# Save the program state.
+state.save('devnull', force=True)
r19906 - in /branches/relax_disp/test_suite/system_tests: relax_disp.py scripts/relax_disp/r1rho_on_res_m61.py