Author: bugman
Date: Wed Jan 12 15:39:41 2011
New Revision: 12245
URL: http://svn.gna.org/viewcvs/relax?rev=12245&view=rev
Log:
Created the system test for checking the tm2 grid of model-free parameters.
Added:
1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
- copied, changed from r12243,
1.3/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
Modified:
1.3/test_suite/system_tests/model_free.py
Modified: 1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/model_free.py?rev=12245&r1=12244&r2=12245&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Wed Jan 12 15:39:41 2011
@@ -2070,6 +2070,51 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)
+ def test_tm2_grid(self):
+ """Test the optimisation of the tm2 model-free parameter grid."""
+
+ # Setup the data pipe for optimisation.
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_setup_tm2_grid.py')
+
+ # The model-free parameters.
+ tm = [2e-9, 10e-9, 21e-9]
+ s2 = [0.2, 0.8, 0.95]
+ te = [2e-12, 40e-12, 1e-9]
+
+ # Deselect all spins.
+ self.interpreter.deselect.spin()
+
+ # Residue index.
+ res_index = 0
+
+ # Loop over te.
+ for te_index in range(3):
+ # Loop over s2.
+ for s2_index in range(3):
+ # Loop over tm.
+ for tm_index in range(3):
+ # Alias the relevent spin container.
+ spin = cdp.mol[0].res[res_index].spin[0]
+
+ # Select the spin.
+ spin.select = True
+
+ # Set up the initial model-free parameter values (bypass
the grid search for speed).
+ spin.local_tm = tm[tm_index] - 1e-9
+ spin.s2 = s2[s2_index] - 0.1
+ spin.te = te[te_index] + 10e-12
+
+ # Minimise.
+ self.interpreter.minimise('newton', 'gmw', 'back')
+
+ # Check the values.
+ self.value_test(spin, local_tm=tm[tm_index],
s2=s2[s2_index], te=te[te_index], chi2=0.0)
+
+ # Increment the residue index and deselect the spin.
+ res_index += 1
+ spin.select = False
+
+
def test_tylers_peptide(self):
"""Try a component of model-free analysis on Tyler Reddy's peptide
data (truncated)."""
Copied: 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
(from r12243,
1.3/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py?p2=1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py&p1=1.3/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py&r1=12243&r2=12245&rev=12245&view=diff
==============================================================================
---
1.3/test_suite/system_tests/scripts/model_free/opt_setup_local_tm_10_S2_0_8_te_40.py
(original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py Wed
Jan 12 15:39:41 2011
@@ -1,29 +1,36 @@
-"""Script for setting up the data pipe for testing optimisation.
-
-The data set is:
- S2 = 0.970.
- te = 2048 ps.
- Rex = 0.149 s^-1.
-"""
+"""Script for setting up the data pipe for testing optimisation."""
# Python module imports.
from os import sep
-import sys
# relax module imports.
from status import Status; status = Status()
+# Create a data pipe.
+pipe.create('tm2_grid', 'mf')
+
# Path of the files.
-cdp.path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'local_tm_10_S2_0.8_te_40'
+path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm2_grid'
-# Create the single residue.
-residue.create(res_num=5, res_name='GLU')
+# Create the sequence.
+molecule.create(mol_name='Polycarbonate')
+for i in range(3*3*3):
+ spin.create(spin_num=1, spin_name='C1', res_num=i+1,
res_name='Bisphenol_A', mol_name='Polycarbonate')
+
+# The proton frequencies in MHz.
+frq = ['400', '500', '600', '700', '800', '900', '1000']
+
+# Load the relaxation data.
+for i in range(len(frq)):
+ relax_data.read('NOE', frq[i], float(frq[i])*1e6, 'noe.%s.out' % frq[i],
dir=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('R1', frq[i], float(frq[i])*1e6, 'r1.%s.out' % frq[i],
dir=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('R2', frq[i], float(frq[i])*1e6, 'r2.%s.out' % frq[i],
dir=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)
# Setup other values.
-value.set(1.02 * 1e-10, 'bond_length')
-value.set(-172 * 1e-6, 'csa')
-value.set('15N', 'heteronucleus')
+value.set(1.20 * 1e-10, 'bond_length')
+value.set(200 * 1e-6, 'csa')
+value.set('13C', 'heteronucleus')
value.set('1H', 'proton')
# Select the model-free model.
r12245 - in /1.3/test_suite/system_tests: model_free.py scripts/model_free/opt_setup_tm2_grid.py