Author: bugman
Date: Thu Nov 18 14:03:01 2010
New Revision: 11677
URL: http://svn.gna.org/viewcvs/relax?rev=11677&view=rev
Log:
Added 6 system tests for the initialisation of the prolate spheroid diffusion
tensor.
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=11677&r1=11676&r2=11677&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/diffusion_tensor.py (original)
+++ 1.3/test_suite/system_tests/diffusion_tensor.py Thu Nov 18 14:03:01 2010
@@ -273,10 +273,12 @@
Dratio = Dpar / Dper
# The eigenvalues and unique axis in the eigenframe.
- Dx = Dpar
- Dy = Dper
- Dz = Dper
- axis = array([1, 0, 0], float64)
+ if Dpar > Dper:
+ Dx, Dy, Dz = Dper, Dper, Dpar
+ axis = array([0, 0, 1], float64)
+ else:
+ Dx, Dy, Dz = Dpar, Dper, Dper
+ axis = array([1, 0, 0], float64)
# The actual tensor in the PDB frame.
R = zeros((3, 3), float64)
@@ -295,8 +297,9 @@
D = dot(transpose(R), dot(D_prime, R))
# Rotate a little about the unique axis!
- axis_angle_to_R(diff_axis, 0.3, R)
- D = dot(transpose(R), dot(D, R))
+ twist = zeros((3, 3), float64)
+ axis_angle_to_R(diff_axis, 0.3, twist)
+ D = dot(transpose(twist), dot(D, twist))
# Return the data.
return tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R
@@ -629,8 +632,8 @@
self.assertAlmostEqual(proj1, proj2)
- def test_init_spheroid_param_types_0(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 0."""
+ def test_init_oblate_spheroid_param_types_0(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 0."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
@@ -646,8 +649,8 @@
self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
- def test_init_spheroid_param_types_1(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 1."""
+ def test_init_oblate_spheroid_param_types_1(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
@@ -663,8 +666,8 @@
self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
- def test_init_spheroid_param_types_1_deg(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 1, and angles in deg."""
+ def test_init_oblate_spheroid_param_types_1_deg(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 1, and angles in deg."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
@@ -680,8 +683,8 @@
self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
- def test_init_spheroid_param_types_2(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 2."""
+ def test_init_oblate_spheroid_param_types_2(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 2."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
@@ -697,8 +700,8 @@
self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
- def test_init_spheroid_param_types_3(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 3."""
+ def test_init_oblate_spheroid_param_types_3(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 3."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
@@ -714,11 +717,113 @@
self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
- def test_init_spheroid_param_types_4(self):
- """Test the initialisation of the spheroid diffusion tensor using
parameter set 4."""
+ def test_init_oblate_spheroid_param_types_4(self):
+ """Test the initialisation of the oblate spheroid diffusion tensor
using parameter set 4."""
# Get the spheroid data.
Dpar, Dper, theta, phi = 1e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Diso, Dratio, theta, phi),
param_types=4, angle_units='rad')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_0(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 0."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((tm, Da, theta, phi),
param_types=0, angle_units='rad')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_1(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 1."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Diso, Da, theta, phi),
param_types=1, angle_units='rad')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_1_deg(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 1, and angles in deg."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Diso, Da,
theta/2.0/pi*360.0, phi/2.0/pi*360.0), param_types=1, angle_units='deg')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_2(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 2."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((tm, Dratio, theta, phi),
param_types=2, angle_units='rad')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_3(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 3."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
+ tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
+
+ # Create a new data pipe.
+ self.interpreter.pipe.create('spheroid2', 'mf')
+
+ # Tensor initialization.
+ self.interpreter.diffusion_tensor.init((Dpar, Dper, theta, phi),
param_types=3, angle_units='rad')
+
+ # Check the spheroid.
+ self.check_spheroid(tm, Dpar, Dper, Diso, Da, Dratio, theta, phi, D,
D_prime, R)
+
+
+ def test_init_prolate_spheroid_param_types_4(self):
+ """Test the initialisation of the prolate spheroid diffusion tensor
using parameter set 4."""
+
+ # Get the spheroid data.
+ Dpar, Dper, theta, phi = 8e7, 4e7, 0.5, 1.0
tm, Dx, Dy, Dz, Diso, Da, Dratio, D, D_prime, R =
self.get_spheroid(Dpar=Dpar, Dper=Dper, theta=theta, phi=phi)
# Create a new data pipe.
r11677 - /1.3/test_suite/system_tests/diffusion_tensor.py