Author: bugman
Date: Mon Dec 9 11:13:17 2013
New Revision: 21885
URL: http://svn.gna.org/viewcvs/relax?rev=21885&view=rev
Log:
Created the Relax_disp.test_ns_r1rho_3site_linear system test.
This is for the 'NS R1rho 3-site' and 'NS R1rho 3-site linear' dispersion
models.
This follows the tutorial for adding relaxation dispersion models at:
http://wiki.nmr-relax.com/Tutorial_for_adding_relaxation_dispersion_models_to_relax#The_test_suite
Added:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
- copied, changed from r21883,
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.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=21885&r1=21884&r2=21885&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Dec 9 11:13:17 2013
@@ -2440,6 +2440,16 @@
self.assertAlmostEqual(cdp.mol[0].res[0].spin[1].chi2, 0.0, 3)
+ def test_ns_r1rho_3site_linear(self):
+ """Compare the 'NS R1rho 3-site linear' 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_r1rho_3site_linear.py')
+
+ # Check the chi-squared value.
+ self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 0.0, 3)
+
+
def test_r2eff_read(self):
"""Test the operation of the relax_disp.r2eff_read user function."""
Copied:
trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
(from r21883,
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py?p2=trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py&p1=trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py&r1=21883&r2=21885&rev=21885&view=diff
==============================================================================
---
trunk/test_suite/shared_data/dispersion/ns_r1rho_3site_linear/relax_results/solution.py
(original)
+++ trunk/test_suite/system_tests/scripts/relax_disp/ns_r1rho_3site_linear.py
Mon Dec 9 11:13:17 2013
@@ -1,14 +1,18 @@
-"""Compare the synthetic cpmg_fit data to the relax solution.
+"""Compare the synthetic cpmg_fit data to the relax solution."""
-To run this, type:
-
-$ rm -f solution.log; ../../../../../relax --tee solution.log solution.py
-"""
+# Python module imports.
+from os import sep
# relax module imports.
+from data_store import Relax_data_store; ds = Relax_data_store()
from lib.nmr import frequency_to_ppm
from specific_analyses.relax_disp.disp_data import generate_r20_key
from specific_analyses.relax_disp.variables import EXP_TYPE_R1RHO
+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_r1rho_3site_linear'
# Create a data pipe.
@@ -85,11 +89,11 @@
relax_disp.spin_lock_offset(spectrum_id=new_id,
offset=-frequency_to_ppm(frq=offset, B0=H_frq, isotope='15N'))
# Read the R2eff data.
- relax_disp.r2eff_read_spin(id=id, file=file, dir='..', spin_id=':1',
offset_col=6, data_col=10, error_col=9)
+ relax_disp.r2eff_read_spin(id=id, file=file, dir=DATA_PATH,
spin_id=':1', offset_col=6, data_col=10, error_col=9)
# Load the R1 data.
-relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6,
file='R1_600MHz.out', dir='..', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
-relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6,
file='R1_800MHz.out', dir='..', mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='600MHz', ri_type='R1', frq=600e6,
file='R1_600MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
+relax_data.read(ri_id='800MHz', ri_type='R1', frq=800e6,
file='R1_800MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
# Change the model.
relax_disp.select_model('NS R1rho 3-site')
@@ -117,12 +121,8 @@
# Calculate.
calc()
-# Minimisation.
-grid_search(inc=7)
-minimise('simplex', constraints=True)
-
# Plot the dispersion curves.
-relax_disp.plot_disp_curves(dir='.', num_points=100, extend=0, force=True)
+relax_disp.plot_disp_curves(dir=ds.tmpdir, num_points=100, extend=0,
force=True)
# Save the results.
-state.save('state', dir='.', compress_type=1, force=True)
+state.save('state', dir=ds.tmpdir, compress_type=1, force=True)
r21885 - in /trunk/test_suite/system_tests: relax_disp.py scripts/relax_disp/ns_r1rho_3site_linear.py