Author: bugman
Date: Wed Jan 12 17:03:09 2011
New Revision: 12254
URL: http://svn.gna.org/viewcvs/relax?rev=12254&view=rev
Log:
Simplified the 3 system tests based on the model-free tm2 grid by shifting
all the code to the script.
Added:
1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py
- copied, changed from r12252,
1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
Removed:
1.3/test_suite/system_tests/scripts/model_free/opt_setup_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=12254&r1=12253&r2=12254&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/model_free.py (original)
+++ 1.3/test_suite/system_tests/model_free.py Wed Jan 12 17:03:09 2011
@@ -340,105 +340,23 @@
def test_m2_grid(self):
"""Test the optimisation of the m2 model-free model against the tm2
parameter grid."""
+ # Initialise.
+ cdp._model = 'm2'
+ 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_setup_tm2_grid.py')
-
- # Select the model-free model.
- self.interpreter.model_free.select_model(model='m2')
-
- # 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 diffusion tensor.
- if res_index:
- self.interpreter.diffusion_tensor.delete()
- self.interpreter.diffusion_tensor.init(tm[tm_index])
-
- # Set up the initial model-free parameter values (bypass
the grid search for speed).
- spin.s2 = s2[s2_index]
- spin.te = te[te_index]
-
- # Minimise.
- self.interpreter.minimise('newton', 'gmw', 'back')
-
- # Check the values.
- self.value_test(spin, 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
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')
def test_m2_grid_vs_m3(self):
"""Test the optimisation of the m3 model-free model against the tm2
parameter grid."""
+ # Initialise.
+ cdp._model = 'm3'
+ 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_setup_tm2_grid.py')
-
- # Select the model-free model.
- self.interpreter.model_free.select_model(model='m3')
-
- # 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 diffusion tensor.
- if res_index:
- self.interpreter.diffusion_tensor.delete()
- self.interpreter.diffusion_tensor.init(tm[tm_index])
-
- # Set up the initial model-free parameter values (bypass
the grid search for speed).
- spin.s2 = s2[s2_index]
- spin.te = te[te_index]
-
- # Minimise.
- self.interpreter.minimise('newton', 'gmw', 'back')
-
- # Check the values.
- self.value_test(spin, s2=s2[s2_index],
te=te[te_index]*1e12, rex=0.0, chi2=0.0)
-
- # Increment the residue index and deselect the spin.
- res_index += 1
- spin.select = False
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')
def test_omp_analysis(self):
@@ -2176,49 +2094,12 @@
def test_tm2_grid(self):
"""Test the optimisation of the tm2 model-free parameter grid."""
+ # Initialise.
+ cdp._model = 'tm2'
+ 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_setup_tm2_grid.py')
-
- # Select the model-free model.
- self.interpreter.model_free.select_model(model='tm2')
-
- # 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]
- spin.s2 = s2[s2_index]
- spin.te = te[te_index]
-
- # Minimise.
- self.interpreter.minimise('newton', 'gmw', 'back')
-
- # Check the values.
- self.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
+ self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'opt_tm2_grid.py')
def test_tylers_peptide(self):
Removed: 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py?rev=12253&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
(original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
(removed)
@@ -1,34 +1,0 @@
-"""Script for setting up the data pipe for testing optimisation."""
-
-# Python module imports.
-from os import sep
-
-# relax module imports.
-from status import Status; status = Status()
-
-
-# Create a data pipe.
-pipe.create('tm2_grid', 'mf')
-
-# Path of the files.
-path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm2_grid'
-
-# 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(1.20 * 1e-10, 'bond_length')
-value.set(200 * 1e-6, 'csa')
-value.set('13C', 'heteronucleus')
-value.set('1H', 'proton')
Copied: 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py (from
r12252, 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py?p2=1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py&p1=1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py&r1=12252&r2=12254&rev=12254&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/model_free/opt_setup_tm2_grid.py
(original)
+++ 1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py Wed Jan 12
17:03:09 2011
@@ -6,9 +6,6 @@
# relax module imports.
from status import Status; status = Status()
-
-# Create a data pipe.
-pipe.create('tm2_grid', 'mf')
# Path of the files.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'tm2_grid'
@@ -32,3 +29,59 @@
value.set(200 * 1e-6, 'csa')
value.set('13C', '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()
+
+# 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 diffusion tensor.
+ 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]
+ if cdp._model in ['m2', 'm3']:
+ spin.s2 = s2[s2_index]
+ if cdp._model in ['m2', 'm3']:
+ spin.te = te[te_index]
+ if cdp._model in ['m3']:
+ spin.rex = 0.0
+
+ # Minimise.
+ minimise('newton', 'gmw', 'back')
+
+ # 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 == 'm3':
+ 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
r12254 - in /1.3/test_suite/system_tests: ./ scripts/model_free/