Author: bugman
Date: Fri Mar 19 14:48:22 2010
New Revision: 11038
URL: http://svn.gna.org/viewcvs/relax?rev=11038&view=rev
Log:
Created the sphere and spheroid diffusion tensor optimisation system tests.
Added:
1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py
- copied, changed from r11033,
1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py
Removed:
1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py
Modified:
1.3/test_suite/system_tests/diffusion_tensor.py
Modified: 1.3/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/diffusion_tensor.py?rev=11038&r1=11037&r2=11038&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Fri Mar 19 14:48:22 2010
@@ -436,5 +436,34 @@
# Reset the relax data storage object.
ds.__reset__()
+ # The diffusion type (used by the script).
+ ds.diff_type = 'ellipsoid'
+
# Execute the script.
- self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'ellipsoid_opt.py')
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
+
+
+ def test_opt_sphere(self):
+ """Check that the sphere diffusion tensor optimisation functions
correctly."""
+
+ # Reset the relax data storage object.
+ ds.__reset__()
+
+ # The diffusion type (used by the script).
+ ds.diff_type = 'sphere'
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
+
+
+ def test_opt_spheroid(self):
+ """Check that the spheroid diffusion tensor optimisation functions
correctly."""
+
+ # Reset the relax data storage object.
+ ds.__reset__()
+
+ # The diffusion type (used by the script).
+ ds.diff_type = 'spheroid'
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'diff_tensor'+sep+'tensor_opt.py')
Removed: 1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py?rev=11037&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py
(original)
+++ 1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py (removed)
@@ -1,44 +1,0 @@
-"""Script for testing diffusion tensor optimisation."""
-
-# Python module imports.
-import __main__
-from numpy import array, float64
-from os import sep
-import sys
-
-
-# A data pipe.
-pipe.create('diff_opt', 'mf')
-
-# Path of the files.
-path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'ellipsoid'
-
-# Load the sequence.
-sequence.read('NOE.500.out', dir=path, res_num_col=1)
-
-# Load a PDB file.
-structure.read_pdb('uniform.pdb', dir=path)
-
-# Set the spin name and then load the NH vectors.
-spin.name(name='N')
-structure.vectors(spin_id='@N', attached='H*', ave=False)
-
-# Load the relaxation data.
-frq = array([500, 600, 700, 800], float64)
-for i in range(len(frq)):
- relax_data.read('R1', str(int(frq[i])), frq[i] * 1e6,
'R1.%s.out'%str(int(frq[i])), dir=path, res_num_col=1, data_col=2,
error_col=3)
- relax_data.read('R2', str(int(frq[i])), frq[i] * 1e6,
'R2.%s.out'%str(int(frq[i])), dir=path, res_num_col=1, data_col=2,
error_col=3)
- relax_data.read('NOE', str(int(frq[i])), frq[i] * 1e6,
'NOE.%s.out'%str(int(frq[i])), dir=path, res_num_col=1, data_col=2,
error_col=3)
-
-# Setup other values.
-diffusion_tensor.init((8.3333333333333335e-09, 15000000.0,
0.33333333333333331, 1.0, 2.0, 0.5), fixed=False)
-value.set(1.02 * 1e-10, 'bond_length')
-value.set(-172 * 1e-6, 'csa')
-value.set('15N', 'heteronucleus')
-value.set('1H', 'proton')
-
-# Select the model-free model.
-model_free.select_model(model='m0')
-
-# Optimisation.
-minimise('newton')
Copied: 1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py (from
r11033, 1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py?p2=1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py&p1=1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py&r1=11033&r2=11038&rev=11038&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/scripts/diff_tensor/ellipsoid_opt.py
(original)
+++ 1.3/test_suite/system_tests/scripts/diff_tensor/tensor_opt.py Fri Mar 19
14:48:22 2010
@@ -6,12 +6,15 @@
from os import sep
import sys
+# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
+
# A data pipe.
pipe.create('diff_opt', 'mf')
# Path of the files.
-path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+'ellipsoid'
+path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'diffusion_tensor'+sep+ds.diff_type
# Load the sequence.
sequence.read('NOE.500.out', dir=path, res_num_col=1)
@@ -30,8 +33,17 @@
relax_data.read('R2', str(int(frq[i])), frq[i] * 1e6,
'R2.%s.out'%str(int(frq[i])), dir=path, res_num_col=1, data_col=2,
error_col=3)
relax_data.read('NOE', str(int(frq[i])), frq[i] * 1e6,
'NOE.%s.out'%str(int(frq[i])), dir=path, res_num_col=1, data_col=2,
error_col=3)
+# Initialise the diffusion tensors.
+if ds.diff_type == 'sphere':
+ diffusion_tensor.init(1.0/(6.0*2e7), fixed=False)
+elif ds.diff_type == 'spheroid':
+ diffusion_tensor.init((1.0/(6.0*5e7/3.0), -1e7, 2.0, 0.5), fixed=False)
+elif ds.diff_type == 'ellipsoid':
+ diffusion_tensor.init((8.3333333333333335e-09, 15000000.0,
0.33333333333333331, 1.0, 2.0, 0.5), fixed=False)
+else:
+ raise RelaxError, "The diffusion type '%s' is unknown." % ds.diff_type
+
# Setup other values.
-diffusion_tensor.init((8.3333333333333335e-09, 15000000.0,
0.33333333333333331, 1.0, 2.0, 0.5), fixed=False)
value.set(1.02 * 1e-10, 'bond_length')
value.set(-172 * 1e-6, 'csa')
value.set('15N', 'heteronucleus')
r11038 - in /1.3/test_suite/system_tests: ./ scripts/diff_tensor/