Author: bugman
Date: Fri Sep 18 18:19:26 2009
New Revision: 9531
URL: http://svn.gna.org/viewcvs/relax?rev=9531&view=rev
Log:
Created a module for alignment tensor related system tests.
Only the single test test_to_and_from_xml() has been created so far. This
checks the dumping and
reloading of alignment tensors into an XML file.
Added:
1.3/test_suite/system_tests/align_tensor.py
- copied, changed from r9526,
1.3/test_suite/system_tests/diffusion_tensor.py
Modified:
1.3/test_suite/system_tests/__init__.py
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=9531&r1=9530&r2=9531&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Fri Sep 18 18:19:26 2009
@@ -31,6 +31,7 @@
from test_suite.relax_test_runner import RelaxTestRunner
# relax system/functional test module imports.
+from align_tensor import Align_tensor
from angles import Angles
from consistency_tests import Ct
from dasha import Dasha
@@ -56,7 +57,8 @@
from unit_vectors import Unit_vectors
-__all__ = ['angles',
+__all__ = ['align_tensor',
+ 'angles',
'consistency_tests',
'dasha'
'diffusion_tensor',
@@ -99,6 +101,7 @@
# Create an array of test suites (add your new TestCase classes
here).
suite_array = []
+ suite_array.append(TestLoader().loadTestsFromTestCase(Align_tensor))
suite_array.append(TestLoader().loadTestsFromTestCase(Angles))
suite_array.append(TestLoader().loadTestsFromTestCase(Ct))
suite_array.append(TestLoader().loadTestsFromTestCase(Dasha))
Copied: 1.3/test_suite/system_tests/align_tensor.py (from r9526,
1.3/test_suite/system_tests/diffusion_tensor.py)
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/align_tensor.py?p2=1.3/test_suite/system_tests/align_tensor.py&p1=1.3/test_suite/system_tests/diffusion_tensor.py&r1=9526&r2=9531&rev=9531&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/align_tensor.py Fri Sep 18 18:19:26 2009
@@ -21,123 +21,69 @@
###############################################################################
# Python module imports.
-from math import pi
-from os import remove, sep
+from os import remove
+from tempfile import mktemp
from unittest import TestCase
-import sys
# relax module imports.
from data import Relax_data_store; ds = Relax_data_store()
-from data.diff_tensor import DiffTensorSimList
-from generic_fns.pipes import get_pipe
-from tempfile import mktemp
+from relax_io import delete
-class Diffusion_tensor(TestCase):
- """Class for testing various aspects specific to the diffusion tensor."""
+class Align_tensor(TestCase):
+ """Class for testing various aspects specific to the alignment
tensors."""
def setUp(self):
- """Function for initialising a spherical, spheroidal, and
ellipsoidal diffusion tensor."""
+ """Function for initialising a few alignment tensors."""
- # Create three data pipes for spherical, spheroidal, and ellipsoidal
diffusion.
- self.relax.interpreter._Pipe.create('sphere', 'mf')
- self.relax.interpreter._Pipe.create('spheroid', 'mf')
- self.relax.interpreter._Pipe.create('ellipsoid', 'mf')
+ # Create a data pipe.
+ self.relax.interpreter._Pipe.create('test', 'frame order')
- # Sphere tensor initialization.
- self.relax.interpreter._Pipe.switch('sphere')
-
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep+'structures',
read_model=1)
- self.relax.interpreter._Sequence.read(file='Ap4Aase.seq',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep)
- self.relax.interpreter._Diffusion_tensor.init(10e-9, fixed=True)
- self.tmpfile_sphere = mktemp()
+ # Temp file name.
+ self.tmpfile = mktemp()
- # Spheroid tensor initialization.
- self.relax.interpreter._Pipe.switch('spheroid')
-
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep+'structures',
read_model=1)
- self.relax.interpreter._Sequence.read(file='Ap4Aase.seq',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep)
- self.relax.interpreter._Diffusion_tensor.init((5e-09, -10000000.,
1.6, 2.7), angle_units='rad', spheroid_type='oblate', fixed=True)
- self.tmpfile_spheroid = mktemp()
+ # Tensor name lists.
+ full_list = ['0 full', '1 full', '2 full', '3 full', '4 full']
+ red_list = ['0 red', '1 red', '2 red', '3 red', '4 red']
- # Ellipsoid tensor initialization.
- self.relax.interpreter._Pipe.switch('ellipsoid')
-
self.relax.interpreter._Structure.read_pdb(file='Ap4Aase_res1-12.pdb',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep+'structures',
read_model=1)
- self.relax.interpreter._Sequence.read(file='Ap4Aase.seq',
dir=sys.path[-1] + sep+'test_suite'+sep+'shared_data'+sep)
- self.relax.interpreter._Diffusion_tensor.init((9e-8, 5e6, 0.3,
60+360, 290, 100), fixed=False)
- self.tmpfile_ellipsoid = mktemp()
+ # Error.
+ error = 1.47411211147e-05
+ # Tensor lists.
+ self.tensors_full = [
+ (0.00014221982216882766, -0.00014454300156652134,
-0.00070779621164871397, -0.00060161949408277324, 0.00020200800707295083),
+ (-0.00014307694949297205, -0.00039671919293883539,
-0.00024724524395487659, 0.00031948292975139144, 0.00018868359624777637),
+ (-0.00022967898444150887, -0.00027171643813494106,
-0.00021961563147411279, 0.00010337393266477703, 0.00029030226175831515),
+ (0.00043690692358615301, -0.00034379559287467062,
-0.00019359695171683388, 0.00030194133983804048, -6.314162250164486e-05),
+ (-0.00026249527958822807, 0.00073561736796410628,
6.3975419225898133e-05, 6.2788017118057252e-05, 0.00020119758245770023)
+ ]
+ self.tensors_red = [
+ (-0.0004037026160192775, 0.00023172423501111316,
-0.00020915186581478394, -0.00028817367472760139, -8.7172337025481604e-05),
+ (0.0003767999506688964, -0.00021492227011444111,
0.00019620694392616774, 0.00027163215478635274, 8.147201253457049e-05),
+ (0.00025970120925482461, -0.00014782823602910519,
0.00013565269563569894, 0.00018741173517420359, 5.6252903270026344e-05),
+ (0.00014574884684542708, -8.3162940224598374e-05,
7.4927100277784987e-05, 0.00010508245294401461, 3.1156238348722986e-05),
+ (-0.00011267453337899962, 6.412308037476237e-05,
-5.7897942333203444e-05, -8.1865863377039068e-05, -2.5273427585025123e-05)
+ ]
- # Some fake MC simulations (for the sphere).
- self.relax.interpreter._Pipe.switch('sphere')
- cdp.diff_tensor.tm_err = 10e-11
- cdp.diff_tensor.tm_sim = DiffTensorSimList('tm', cdp.diff_tensor,
elements=5)
- tm_sim = [8.98e-8, 8.99e-8, 9.00e-7, 9.01e-8, 9.02e-8]
+ # Set up the tensors.
for i in range(5):
- cdp.diff_tensor.tm_sim[i] = tm_sim[i]
+ # Load the tensor.
+ self.relax.interpreter._Align_tensor.init(tensor=full_list[i],
params=self.tensors_full[i], param_types=0)
+ self.relax.interpreter._Align_tensor.init(tensor=red_list[i],
params=self.tensors_red[i], param_types=0)
+
+ # Errors.
+ self.relax.interpreter._Align_tensor.init(tensor=full_list[i],
params=(error, error, error, error, error), param_types=0, errors=True)
+ self.relax.interpreter._Align_tensor.init(tensor=red_list[i],
params=(error, error, error, error, error), param_types=0, errors=True)
+
+ # Domain.
+
self.relax.interpreter._Align_tensor.set_domain(tensor=full_list[i],
domain='full')
+
self.relax.interpreter._Align_tensor.set_domain(tensor=red_list[i],
domain='red')
+
+ # Tensor reductions.
+
self.relax.interpreter._Align_tensor.reduction(full_tensor=full_list[i],
red_tensor=red_list[i])
# Reset some values.
- cdp.diff_tensor.tm_sim[0] = 9.00e-8
-
-
- # Some fake MC simulations (for the spheroid).
- self.relax.interpreter._Pipe.switch('spheroid')
-
- # Initialise the data structures.
- cdp.diff_tensor.tm_sim = DiffTensorSimList('tm', cdp.diff_tensor,
elements=5)
- cdp.diff_tensor.Da_sim = DiffTensorSimList('Da', cdp.diff_tensor,
elements=5)
- cdp.diff_tensor.theta_sim = DiffTensorSimList('theta',
cdp.diff_tensor, elements=5)
- cdp.diff_tensor.phi_sim = DiffTensorSimList('phi', cdp.diff_tensor,
elements=5)
-
- # Set some errors.
- cdp.diff_tensor.Da_err = 1000000
- cdp.diff_tensor.theta_err = 0.01
- cdp.diff_tensor.tm_err = 1e-11
- cdp.diff_tensor.phi_err = 0.01
-
- # The sim data.
- Da_sim = [-12000000., -11000000., -10000000., -9000000., -8000000.]
- theta_sim = [1.70, 1.65, 1.6, 1.55, 1.50]
- tm_sim = [5.4e-09, 4.8e-09, 5e-09, 5.4e-09, 5.8e-09]
- phi_sim = [2.5, 2.6, 2.7, 2.8, 100]
- for i in range(5):
- cdp.diff_tensor.Da_sim[i] = Da_sim[i]
- cdp.diff_tensor.theta_sim[i] = theta_sim[i]
- cdp.diff_tensor.tm_sim[i] = tm_sim[i]
- cdp.diff_tensor.phi_sim[i] = phi_sim[i]
-
- # Reset some values.
- cdp.diff_tensor.tm_sim[0] = 4.4e-9
- cdp.diff_tensor.phi_sim[4] = 2.9
-
-
- # Some fake MC simulations (for the ellipsoid).
- self.relax.interpreter._Pipe.switch('ellipsoid')
-
- # Initialise the data structures.
- cdp.diff_tensor.tm_sim = DiffTensorSimList('tm', cdp.diff_tensor,
elements=5)
- cdp.diff_tensor.Da_sim = DiffTensorSimList('Da', cdp.diff_tensor,
elements=5)
- cdp.diff_tensor.Dr_sim = DiffTensorSimList('Dr', cdp.diff_tensor,
elements=5)
- cdp.diff_tensor.alpha_sim = DiffTensorSimList('alpha',
cdp.diff_tensor, elements=5)
- cdp.diff_tensor.beta_sim = DiffTensorSimList('beta',
cdp.diff_tensor, elements=5)
- cdp.diff_tensor.gamma_sim = DiffTensorSimList('gamma',
cdp.diff_tensor, elements=5)
-
- # The sim data.
- Dr_sim = [0.28, 0.29, 0.3, 0.31, 0.32]
- tm_sim = [8.97e-8, 8.99e-8, 9.00e-8, 9.01e-8, 9.02e-8]
- Da_sim = [5.02e6, 5.01e6, 5.00e6, 4.99e6, 4.98e6]
- alpha_sim = [80.0/360*2*pi, 70.0/360*2*pi, 60.0/360*2*pi,
50.0/360*2*pi, 40.0/360*2*pi]
- beta_sim = [295.0/360*2*pi, 292.5/360*2*pi, 290.0/360*2*pi,
289.5/360*2*pi, 288.0/360*2*pi]
- gamma_sim = [102.0/360*2*pi, 101.0/360*2*pi, 0, 99.0/360*2*pi,
98.0/360*2*pi]
- for i in range(5):
- cdp.diff_tensor.Dr_sim[i] = Dr_sim[i]
- cdp.diff_tensor.tm_sim[i] = tm_sim[i]
- cdp.diff_tensor.Da_sim[i] = Da_sim[i]
- cdp.diff_tensor.alpha_sim[i] = alpha_sim[i]
- cdp.diff_tensor.beta_sim[i] = beta_sim[i]
- cdp.diff_tensor.gamma_sim[i] = gamma_sim[i]
-
- # Reset some values.
- cdp.diff_tensor.tm_sim[0] = 8.98e-8
- cdp.diff_tensor.gamma_sim[2] = 100.0/360*2*pi
+ cdp.align_tensors[2].Axx = 1
def tearDown(self):
@@ -147,157 +93,34 @@
ds.__reset__()
# Delete the temporary files.
- try:
- remove(self.tmpfile_sphere)
- remove(self.tmpfile_spheroid)
- remove(self.tmpfile_ellipsoid)
- except OSError:
- pass
+ delete(self.tmpfile, fail=False)
- def test_copy(self):
- """The user function diffusion_tensor.copy()."""
+ def test_to_and_from_xml(self):
+ """Test the conversion to and from XML."""
- # Create three additional data pipes for copying the spherical,
spheroidal, and ellipsoidal diffusion data.
- self.relax.interpreter._Pipe.create('sphere2', 'mf')
- self.relax.interpreter._Pipe.create('spheroid2', 'mf')
- self.relax.interpreter._Pipe.create('ellipsoid2', 'mf')
+ # Save the data pipe.
+ self.relax.interpreter._Results.write(self.tmpfile, dir=None)
- # Copy the data.
- self.relax.interpreter._Diffusion_tensor.copy('sphere', 'sphere2')
- self.relax.interpreter._Diffusion_tensor.copy('spheroid',
'spheroid2')
- self.relax.interpreter._Diffusion_tensor.copy('ellipsoid',
'ellipsoid2')
+ # Create a new data pipe.
+ self.relax.interpreter._Pipe.create('new', 'frame order')
- # Get the data pipes.
- sphere_pipe = get_pipe('sphere')
- sphere2_pipe = get_pipe('sphere2')
+ # Load the data.
+ self.relax.interpreter._Results.read(self.tmpfile, dir=None)
- # Check that this is indeed a copy.
- self.assertEqual(sphere2_pipe.diff_tensor.tm_sim[4], 9.02e-8)
- self.assertEqual(sphere2_pipe.diff_tensor.Diso_sim[4], 1/(6*9.02e-8))
- sphere_pipe.diff_tensor.tm_sim[4] = 8.88e-8
- self.assertEqual(sphere_pipe.diff_tensor.tm_sim[4], 8.88e-8)
- self.assertEqual(sphere_pipe.diff_tensor.Diso_sim[4], 1/(6*8.88e-8))
- self.assertEqual(sphere2_pipe.diff_tensor.tm_sim[4], 9.02e-8)
- self.assertEqual(sphere2_pipe.diff_tensor.Diso_sim[4], 1/(6*9.02e-8))
+ # Checks.
+ self.assertEqual(len(cdp.align_tensors), 5)
+ for i in range(5):
+ # Full tensors.
+ self.assertEqual(cdp.align_tensors[i*2].Axx,
self.tensors_full[i][0])
+ self.assertEqual(cdp.align_tensors[i*2].Ayy,
self.tensors_full[i][1])
+ self.assertEqual(cdp.align_tensors[i*2].Axy,
self.tensors_full[i][2])
+ self.assertEqual(cdp.align_tensors[i*2].Axz,
self.tensors_full[i][3])
+ self.assertEqual(cdp.align_tensors[i*2].Ayz,
self.tensors_full[i][4])
-
- def test_delete(self):
- """The user function diffusion_tensor.delete()."""
-
- # Delete the data.
- self.relax.interpreter._Pipe.switch('sphere')
- self.relax.interpreter._Diffusion_tensor.delete()
- self.relax.interpreter._Pipe.switch('spheroid')
- self.relax.interpreter._Diffusion_tensor.delete()
- self.relax.interpreter._Pipe.switch('ellipsoid')
- self.relax.interpreter._Diffusion_tensor.delete()
-
-
- def test_display(self):
- """The user function diffusion_tensor.display()."""
-
- # Display the data.
- self.relax.interpreter._Pipe.switch('sphere')
- self.relax.interpreter._Diffusion_tensor.display()
- self.relax.interpreter._Pipe.switch('spheroid')
- self.relax.interpreter._Diffusion_tensor.display()
- self.relax.interpreter._Pipe.switch('ellipsoid')
- self.relax.interpreter._Diffusion_tensor.display()
-
-
- def test_create_diff_tensor_pdb_sphere(self):
- """Test the user function structure.create_diff_tensor_pdb() for the
sphere."""
-
- # First copy the data (a more vigorous copy test!).
- self.relax.interpreter._Pipe.copy('sphere', 'sphere2')
- self.relax.interpreter._Pipe.switch('sphere2')
- self.relax.interpreter._Diffusion_tensor.delete()
- self.relax.interpreter._Diffusion_tensor.copy('sphere', 'sphere2')
-
- # Create the diffusion tensor objects.
-
self.relax.interpreter._Structure.create_diff_tensor_pdb(file=self.tmpfile_sphere)
-
- # Open the temp file.
- file = open(self.tmpfile_sphere)
- new_data = file.readlines()
- file.close()
-
- # Open the real file.
- file = open(sys.path[-1] +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'diff_tensors'+sep+'sphere.pdb')
- real_data = file.readlines()
- file.close()
-
- # Check the data.
- self.assertEqual(len(real_data), len(new_data))
- for i in range(len(real_data)):
- # Print the PDB line, for debugging.
- print((real_data[i][0:-1]))
-
- # Check the line.
- self.assertEqual(real_data[i], new_data[i])
-
-
- def test_create_diff_tensor_pdb_spheroid(self):
- """Test the user function structure.create_diff_tensor_pdb() for the
spheroid."""
-
- # First copy the data (a more vigorous copy test!).
- self.relax.interpreter._Pipe.copy('spheroid', 'spheroid2')
- self.relax.interpreter._Pipe.switch('spheroid2')
- self.relax.interpreter._Diffusion_tensor.delete()
- self.relax.interpreter._Diffusion_tensor.copy('spheroid',
'spheroid2')
-
- # Create the diffusion tensor objects.
-
self.relax.interpreter._Structure.create_diff_tensor_pdb(file=self.tmpfile_spheroid)
-
- # Open the temp file.
- file = open(self.tmpfile_spheroid)
- new_data = file.readlines()
- file.close()
-
- # Open the real file.
- file = open(sys.path[-1] +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'diff_tensors'+sep+'spheroid.pdb')
- real_data = file.readlines()
- file.close()
-
- # Check the data.
- self.assertEqual(len(real_data), len(new_data))
- for i in range(len(real_data)):
- # Print the PDB line, for debugging.
- print((real_data[i][0:-1]))
-
- # Check the line.
- self.assertEqual(real_data[i], new_data[i])
-
-
- def test_create_diff_tensor_pdb_ellipsoid(self):
- """Test the user function structure.create_diff_tensor_pdb() for the
ellipsoid."""
-
- # First copy the data (a more vigorous copy test!).
- self.relax.interpreter._Pipe.copy('ellipsoid', 'ellipsoid2')
- self.relax.interpreter._Pipe.switch('ellipsoid2')
- self.relax.interpreter._Diffusion_tensor.delete()
- self.relax.interpreter._Diffusion_tensor.copy('ellipsoid',
'ellipsoid2')
-
- # Create the diffusion tensor objects.
-
self.relax.interpreter._Structure.create_diff_tensor_pdb(file=self.tmpfile_ellipsoid,
scale=1e-05)
-
- # Open the temp file.
- file = open(self.tmpfile_ellipsoid)
- new_data = file.readlines()
- file.close()
-
- # Open the real file.
- file = open(sys.path[-1] +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'diff_tensors'+sep+'ellipsoid.pdb')
- real_data = file.readlines()
- file.close()
-
- # Check the data.
- self.assertEqual(len(real_data), len(new_data))
- for i in range(len(real_data)):
- # Print the PDB line, for debugging.
- print((real_data[i][0:-1]))
-
- # Check the line.
- self.assertEqual(real_data[i], new_data[i])
-
+ # Reduced tensors.
+ self.assertEqual(cdp.align_tensors[i*2+1].Axx,
self.tensors_red[i][0])
+ self.assertEqual(cdp.align_tensors[i*2+1].Ayy,
self.tensors_red[i][1])
+ self.assertEqual(cdp.align_tensors[i*2+1].Axy,
self.tensors_red[i][2])
+ self.assertEqual(cdp.align_tensors[i*2+1].Axz,
self.tensors_red[i][3])
+ self.assertEqual(cdp.align_tensors[i*2+1].Ayz,
self.tensors_red[i][4])
r9531 - in /1.3/test_suite/system_tests: __init__.py align_tensor.py