Author: bugman
Date: Wed Jan 12 21:55:48 2011
New Revision: 12268
URL: http://svn.gna.org/viewcvs/relax?rev=12268&view=rev
Log:
Added a system test for the optimisation of the tm0 model-free parameter grid.
Added:
1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py
- copied, changed from r12261,
1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.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=12268&r1=12267&r2=12268&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Wed Jan 12 21:55:48 2011
@@ -2091,6 +2091,17 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].r, NH_BOND_LENGTH)
+ def test_tm0_grid(self):
+ """Test the optimisation of the tm0 model-free parameter grid."""
+
+ # Initialise.
+ cdp._model = 'tm0'
+ cdp._value_test = self.value_test
+
+ # 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_tm0_grid.py')
+
+
def test_tm2_grid(self):
"""Test the optimisation of the tm2 model-free parameter grid."""
Copied: 1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py (from
r12261, 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py?p2=1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py&p1=1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py&r1=12261&r2=12268&rev=12268&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py (original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_tm0_grid.py Wed Jan 12
21:55:48 2011
@@ -2,17 +2,21 @@
# Python module imports.
from os import sep
+from re import search
# relax module imports.
from status import Status; status = Status()
+# The model-free parameters.
+tm = [2e-9, 10e-9, 80e-9]
+
# Path of the files.
-path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm2_grid'
+path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm0_grid'
# Create the sequence.
molecule.create(mol_name='Polycarbonate')
-for i in range(3*3*3):
+for i in range(len(tm)):
spin.create(spin_num=1, spin_name='C1', res_num=i+1,
res_name='Bisphenol_A', mol_name='Polycarbonate')
# The proton frequencies in MHz.
@@ -25,18 +29,13 @@
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(1.20 * 1e-10, 'bond_length')
-value.set(200 * 1e-6, 'csa')
-value.set('13C', 'heteronucleus')
+value.set(1.04 * 1e-10, 'bond_length')
+value.set(-160 * 1e-6, 'csa')
+value.set('15N', 'heteronucleus')
value.set('1H', 'proton')
# Select the model-free model.
model_free.select_model(model=cdp._model)
-
-# 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.
deselect.spin()
@@ -44,45 +43,41 @@
# 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]
+# Loop over tm.
+for tm_index in range(len(tm)):
+ # Alias the relevent spin container.
+ spin = cdp.mol[0].res[res_index].spin[0]
- # Select the spin.
- spin.select = True
+ # Select the spin.
+ spin.select = True
- # Set up the diffusion tensor.
- if cdp._model in ['m2', 'm4']:
- if res_index:
- diffusion_tensor.delete()
- diffusion_tensor.init(tm[tm_index])
+ # Set up the diffusion tensor.
+ if search('^m', cdp._model):
+ if res_index:
+ diffusion_tensor.delete()
+ diffusion_tensor.init(tm[tm_index])
- # Set up the initial model-free parameter values (bypass the
grid search for speed).
- if cdp._model in ['tm2']:
- spin.local_tm = tm[tm_index] + 1e-11
- if cdp._model in ['tm2', 'm2', 'm4']:
- spin.s2 = s2[s2_index] - 0.01
- if cdp._model in ['tm2', 'm2', 'm4']:
- spin.te = te[te_index] + 1e-12
- if cdp._model in ['m4']:
- spin.rex = 0.1 / (2.0 * pi * spin.frq[0])**2
+ # Set up the initial model-free parameter values (bypass the grid search
for speed).
+ if search('^t', cdp._model):
+ spin.local_tm = tm[tm_index] + 1e-11
+ if cdp._model in ['tm2', 'm2']:
+ spin.s2 = 0.98
+ if cdp._model in ['tm2', 'm2']:
+ spin.te = 1e-12
+ if cdp._model in ['m3']:
+ spin.rex = 0.1 / (2.0 * pi * spin.frq[0])**2
- # Minimise.
- minimise('newton', 'gmw', 'back', constraints=False)
+ # Minimise.
+ minimise('newton', 'gmw', 'back', constraints=False)
- # Check the values.
- if cdp._model == 'm2':
- cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
chi2=0.0)
- elif cdp._model == 'm4':
- cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
rex=0.0, chi2=0.0)
- elif cdp._model == 'tm2':
- cdp._value_test(spin, local_tm=tm[tm_index]*1e9,
s2=s2[s2_index], te=te[te_index]*1e12, chi2=0.0)
+ # Check the values.
+ if cdp._model == 'm2':
+ cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
chi2=0.0)
+ elif cdp._model == 'm4':
+ cdp._value_test(spin, s2=s2[s2_index], te=te[te_index]*1e12,
rex=0.0, chi2=0.0)
+ elif cdp._model == 'tm2':
+ cdp._value_test(spin, local_tm=tm[tm_index]*1e9, s2=s2[s2_index],
te=te[te_index]*1e12, chi2=0.0)
- # Increment the residue index and deselect the spin.
- res_index += 1
- spin.select = False
+ # Increment the residue index and deselect the spin.
+ res_index += 1
+ spin.select = False
r12268 - in /1.3/test_suite/system_tests: model_free.py scripts/model_free/opt_tm0_grid.py