Author: bugman
Date: Tue Dec 2 16:02:05 2014
New Revision: 26896
URL: http://svn.gna.org/viewcvs/relax?rev=26896&view=rev
Log:
Created the Frame_order.test_simulate_iso_cone_xz_plane_tilt system test.
This is to check the frame_order.simulate user function for the torsionless
isotropic cone model
with a xz-plane tilt.
Modified:
branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
Modified: branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/frame_order.py?rev=26896&r1=26895&r2=26896&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/frame_order.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/frame_order.py Tue
Dec 2 16:02:05 2014
@@ -3298,6 +3298,78 @@
print("Maximum phi for X and Y: %s" % max_phi)
+ def test_simulate_iso_cone_xz_plane_tilt(self):
+ """Check the frame_order.simulate user function PDB file for the
isotropic cone model with a xz-plane tilt."""
+
+ # Init.
+ cone_theta = 0.5
+ cone_sigma_max = 0.3
+ pivot = array([1, 0, -2], float64)
+ l = 24.0
+ sim_num = 500
+
+ # The axis parameters, and printout.
+ axis_theta = -pi/4.0
+ axis = create_rotor_axis_spherical(axis_theta, 0.0)
+ print("Rotor axis: %s" % axis)
+ R = zeros((3, 3), float64)
+ axis_angle_to_R([0, 1, 0], axis_theta, R)
+
+ # Set up.
+ self.setup_model(pipe_name='PDB model', model='iso cone',
pivot=pivot, ave_pos_x=pivot[0], ave_pos_y=pivot[1], ave_pos_z=pivot[2],
ave_pos_alpha=0.0, ave_pos_beta=axis_theta, ave_pos_gamma=0.0,
axis_theta=axis_theta, axis_phi=0.0, cone_theta=cone_theta,
cone_sigma_max=cone_sigma_max)
+
+ # Create the PDB.
+ self.interpreter.frame_order.simulate(file='simulation.pdb',
dir=ds.tmpdir, step_size=10.0, snapshot=10, total=sim_num)
+
+ # Delete all structural data.
+ self.interpreter.structure.delete()
+
+ # Read the contents of the file.
+ self.interpreter.structure.read_pdb(file='simulation.pdb',
dir=ds.tmpdir)
+
+ # Check the atomic coordinates.
+ selection = cdp.structure.selection()
+ epsilon = 1e-3
+ max_phi = 0.0
+ lateral_slide = 0.07
+ for res_num, res_name, atom_num, atom_name, pos in
cdp.structure.atom_loop(selection=selection, res_num_flag=True,
res_name_flag=True, atom_num_flag=True, atom_name_flag=True, pos_flag=True):
+ # Loop over all positions.
+ for i in range(sim_num):
+ # Shift the position back to the origin, and decompose into
spherical coordinates.
+ new_pos = pos[i] - pivot
+ r, theta, phi = cartesian_to_spherical(dot(transpose(R),
new_pos))
+
+ # Printout.
+ print("Checking residue %s %s, atom %s %s, at shifted
position %s, with spherical coordinates %s." % (res_num, res_name, atom_num,
atom_name, new_pos, [r, theta, phi]))
+
+ # The vector length.
+ self.assertAlmostEqual(r/100.0, 1.0, 4)
+
+ # Check the X vector.
+ if res_name == 'X':
+ if abs(phi) > max_phi:
+ max_phi = abs(phi)
+ print pi/2.0 - cone_theta - epsilon
+ self.assert_(theta >= pi/2.0 - cone_theta - epsilon)
+ self.assert_(theta <= pi/2.0 + cone_theta + epsilon)
+ self.assert_(phi >= -cone_sigma_max - lateral_slide)
+ self.assert_(phi <= cone_sigma_max + lateral_slide)
+
+ # Check the Y vector.
+ elif res_name == 'Y':
+ self.assert_(theta >= pi/2.0 - cone_theta - epsilon)
+ self.assert_(theta <= pi/2.0 + cone_theta + epsilon)
+ self.assert_(phi-pi/2.0 >= -cone_sigma_max -
lateral_slide)
+ self.assert_(phi-pi/2.0 <= cone_sigma_max +
lateral_slide)
+
+ # Check the Z vector (should be in the cone defined by
theta).
+ elif res_name == 'Z':
+ self.assert_(theta <= cone_theta + epsilon)
+
+ # Print out the maximum phi value.
+ print("Maximum phi for X and Y: %s" % max_phi)
+
+
def test_simulate_iso_cone_free_rotor_z_axis(self):
"""Check the frame_order.simulate user function PDB file for the
free rotor isotropic cone model along the z-axis."""
r26896 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py