Author: bugman
Date: Fri Jan 27 11:07:30 2012
New Revision: 15271
URL: http://svn.gna.org/viewcvs/relax?rev=15271&view=rev
Log:
Updated and reactivated all of the CaM frame order system tests.
The scripts are still to be updated.
Modified:
branches/frame_order_testing/test_suite/system_tests/frame_order.py
Modified: branches/frame_order_testing/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/frame_order.py?rev=15271&r1=15270&r2=15271&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/frame_order.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/frame_order.py Fri
Jan 27 11:07:30 2012
@@ -244,193 +244,49 @@
self.check_chi2(5.1)
- def fixme_test_cam_iso_cone_free_rotor(self):
+ def test_cam_iso_cone_free_rotor(self):
"""Test the isotropic cone, free rotor frame order model of CaM."""
- # Execute the script.
+ # The flags, execute the script, and then check the chi2 value.
+ self.flags()
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'iso_cone_free_rotor.py')
-
- # Check the average structure CoM matches that of the original
position (the average structure is not defined along the rotation axis).
- for i in range(3):
- self.assertAlmostEqual(ds['ave pos'].CoM[i], ds['orig
pos'].CoM[i], 0)
-
- # Switch to the correct data pipe.
- self.interpreter.pipe.switch('frame order')
-
- # The base data.
- pivot = array([ 37.254, 0.5, 16.7465])
- com = array([ 26.83678091, -12.37906417, 28.34154128])
- pivot_com_axis = com - pivot
- rot_axis = pivot_com_axis / norm(pivot_com_axis)
-
- # The average position checks.
- ave_pivot_com_axis = ds['ave pos'].CoM - pivot
-
- # The projection of the CoMs onto the rotation axis.
- orig_proj = dot(pivot_com_axis, rot_axis)
- ave_proj = dot(ave_pivot_com_axis, rot_axis)
- print("\nReal projection of the central axis to the pivot-CoM: %s"
% repr(orig_proj))
- print("Fitted projection of the central axis to the pivot-CoM: %s" %
repr(ave_proj))
-
- # Check that the projections are equal.
- self.assertAlmostEqual(orig_proj, ave_proj, 1)
-
- # The rotation axis.
- self.interpreter.pipe.switch('frame order')
- spherical_vect = zeros(3, float64)
- spherical_vect[0] = 1.0
- spherical_vect[1] = cdp.axis_theta
- spherical_vect[2] = cdp.axis_phi
- axis = zeros(3, float64)
- spherical_to_cartesian(spherical_vect, axis)
- print("\nReal rotation axis: %s" % repr(rot_axis))
- print("Fitted rotation axis: %s" % repr(axis))
-
- # Check the angle between the real and fitted rotation axes.
- angle = acos(dot(axis, rot_axis))
- if angle > pi/2:
- angle = acos(dot(axis, -rot_axis))
- self.assertAlmostEqual(angle, 0.0, 2)
-
- # Check the cone angle of 40 deg.
- self.assertAlmostEqual(cdp.cone_theta * 2.0, 40.0 / 360.0 * 2.0 *
pi, 1)
-
-
- def fixme_test_cam_iso_cone_free_rotor2(self):
+ self.check_chi2(0.0)
+
+
+ def test_cam_iso_cone_free_rotor2(self):
"""Test the second isotropic cone, free rotor frame order model of
CaM."""
- # Execute the script.
+ # The flags, execute the script, and then check the chi2 value.
+ self.flags()
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'iso_cone_free_rotor2.py')
-
- # Switch to the correct data pipe.
- self.interpreter.pipe.switch('frame order')
-
- # The base data.
- pivot = array([ 37.254, 0.5, 16.7465])
- com = array([ 26.83678091, -12.37906417, 28.34154128])
- pivot_com_axis = com - pivot
- rot_axis = array([-0.4043088, -0.49985692, 0.76594873])
-
- # The rotation axis.
- self.interpreter.pipe.switch('frame order')
- spherical_vect = zeros(3, float64)
- spherical_vect[0] = 1.0
- spherical_vect[1] = cdp.axis_theta
- spherical_vect[2] = cdp.axis_phi
- axis = zeros(3, float64)
- spherical_to_cartesian(spherical_vect, axis)
- print("\nReal rotation axis: %s" % repr(rot_axis))
- print("Fitted rotation axis: %s" % repr(axis))
-
- # Check the angle between the real and fitted rotation axes.
- angle = acos(dot(axis, rot_axis))
- if angle > pi/2:
- angle = acos(dot(axis, -rot_axis))
- self.assertAlmostEqual(angle, 0.0, 2)
-
- # Check the cone angle of 40 deg.
- self.assertAlmostEqual(cdp.cone_theta * 2.0, 40.0 / 360.0 * 2.0 *
pi, 2)
-
-
- def fixme_test_cam_rigid(self):
+ self.check_chi2(0.0)
+
+
+ def test_cam_rigid(self):
"""Test the rigid frame order model of CaM."""
- # Execute the script.
+ # The flags, execute the script, and then check the chi2 value.
+ self.flags()
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rigid.py')
-
- # Check the average structure atomic positions (to only one decimal
point as the PDB file accuracy isn't great).
- ave_pos = ds['ave pos'].structure.structural_data[0].mol[0]
- orig_pos = ds['orig pos'].structure.structural_data[0].mol[0]
- for i in range(len(ave_pos.atom_name)):
- self.assertAlmostEqual(ave_pos.x[i], orig_pos.x[i], 1)
- self.assertAlmostEqual(ave_pos.y[i], orig_pos.y[i], 1)
- self.assertAlmostEqual(ave_pos.z[i], orig_pos.z[i], 1)
-
-
- def fixme_test_cam_rotor(self):
+ self.check_chi2(0.0)
+
+
+ def test_cam_rotor(self):
"""Test the rotor frame order model of CaM."""
- # Execute the script.
+ # The flags, execute the script, and then check the chi2 value.
+ self.flags()
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rotor.py')
-
- # Switch to the correct data pipe.
- self.interpreter.pipe.switch('frame order')
-
- # The base data.
- pivot = array([ 37.254, 0.5, 16.7465])
- com = array([ 26.83678091, -12.37906417, 28.34154128])
- pivot_com_axis = com - pivot
- rot_axis = pivot_com_axis / norm(pivot_com_axis)
-
- # The average position checks.
- real_pos = array([[-0.31334613, -0.88922808, -0.33329811],
- [ 0.93737972, -0.23341205, -0.2585306 ],
- [ 0.15209688, -0.39343645, 0.90668313]], float64)
- ave_pos = zeros((3, 3), float64)
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, ave_pos)
- print("\nReal domain position:\n%s" % repr(real_pos))
- print("Fitted domain position:\n%s" % repr(ave_pos))
- for i in range(3):
- for j in range(3):
- self.assertAlmostEqual(ave_pos[i, j], real_pos[i, j], 3)
-
- # The axis system.
- axis = zeros(3, float64)
- spherical_to_cartesian(array([1, cdp.axis_theta, cdp.axis_phi]),
axis)
- print("\nReal rotation axis: %s" % repr(rot_axis))
- print("Fitted rotation axis: %s" % repr(axis))
-
- # Check the angle between the real and fitted rotation axes.
- angle = acos(dot(axis, rot_axis))
- if angle > pi/2:
- angle = acos(dot(axis, -rot_axis))
- self.assertAlmostEqual(angle, 0.0, 2)
-
- # Check the cone angle of 60 deg.
- self.assertAlmostEqual(cdp.cone_sigma_max * 2.0, 60.0 / 360.0 * 2.0
* pi, 1)
-
-
- def fixme_test_cam_rotor2(self):
+ self.check_chi2(0.0)
+
+
+ def test_cam_rotor2(self):
"""Test the second rotor frame order model of CaM."""
- # Execute the script.
+ # The flags, execute the script, and then check the chi2 value.
+ self.flags()
self.interpreter.run(script_file=status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'cam'+sep+'rotor2.py')
-
- # Switch to the correct data pipe.
- self.interpreter.pipe.switch('frame order')
-
- # The base data.
- pivot = array([ 37.254, 0.5, 16.7465])
- com = array([ 26.83678091, -12.37906417, 28.34154128])
- pivot_com_axis = com - pivot
- rot_axis = array([ 0.40416535, 0.49967956, 0.76614014])
-
- # The average position checks.
- real_pos = array([[-0.31334613, -0.88922808, -0.33329811],
- [ 0.93737972, -0.23341205, -0.2585306 ],
- [ 0.15209688, -0.39343645, 0.90668313]], float64)
- ave_pos = zeros((3, 3), float64)
- euler_to_R_zyz(cdp.ave_pos_alpha, cdp.ave_pos_beta,
cdp.ave_pos_gamma, ave_pos)
- print("\nReal domain position:\n%s" % repr(real_pos))
- print("Fitted domain position:\n%s" % repr(ave_pos))
- for i in range(3):
- for j in range(3):
- self.assertAlmostEqual(ave_pos[i, j], real_pos[i, j], 1)
-
- # The axis system.
- axis = zeros(3, float64)
- spherical_to_cartesian(array([1, cdp.axis_theta, cdp.axis_phi]),
axis)
- print("\nReal rotation axis: %s" % repr(rot_axis))
- print("Fitted rotation axis: %s" % repr(axis))
-
- # Check the angle between the real and fitted rotation axes.
- angle = acos(dot(axis, rot_axis))
- if angle > pi/2:
- angle = acos(dot(axis, -rot_axis))
- self.assertAlmostEqual(angle, 0.0, 2)
-
- # Check the cone angle of 60 deg.
- self.assertAlmostEqual(cdp.cone_sigma_max * 2.0, 60.0 / 360.0 * 2.0
* pi, 1)
+ self.check_chi2(0.0)
def fixme_test_model_free_rotor(self):
r15271 - /branches/frame_order_testing/test_suite/system_tests/frame_order.py