Author: bugman
Date: Fri Nov 28 08:55:30 2014
New Revision: 26797
URL: http://svn.gna.org/viewcvs/relax?rev=26797&view=rev
Log:
Created the Frame_order.test_simulate_free_rotor_z_axis system test.
This is to check the frame_order.simulate user function for the free rotor
model along the z-axis.
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=26797&r1=26796&r2=26797&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 Fri Nov
28 08:55:30 2014
@@ -3172,6 +3172,64 @@
self.assertAlmostEqual(cdp.chi2, 0.011377487066752203, 5)
+ def test_simulate_free_rotor_z_axis(self):
+ """Check the frame_order.simulate user function PDB file for the free
rotor model along the z-axis."""
+
+ # Init.
+ pivot = array([1, 0, 0], float64)
+ l = 10.0
+ sim_num = 500
+
+ # The axis alpha parameter, and printout.
+ axis_alpha = pi / 2.0
+ axis = create_rotor_axis_alpha(pi/2, pivot, array([0, 0, 0], float64))
+ print("\nRotor axis: %s" % axis)
+ print("Rotor apex (100*axis + [1, 0, 0]):\n %s" % (l*axis + pivot))
+
+ # Set up.
+ self.setup_model(pipe_name='PDB model', model='free rotor',
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=0.0, ave_pos_gamma=0.0, axis_alpha=axis_alpha)
+
+ # 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()
+ 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(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':
+ self.assertAlmostEqual(theta, pi/2.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the Y vector.
+ elif res_name == 'Y':
+ self.assertAlmostEqual(theta, pi/2.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the Z vector (should not move).
+ elif res_name == 'Z':
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 100.0, 3)
+
+
def test_simulate_rotor_z_axis(self):
"""Check the frame_order.simulate user function PDB file for the rotor
model along the z-axis."""
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