Author: bugman Date: Fri Nov 28 12:20:00 2014 New Revision: 26802 URL: http://svn.gna.org/viewcvs/relax?rev=26802&view=rev Log: Created the Frame_order.test_simulate_iso_cone_torsionless_z_axis system test. This is to check the frame_order.simulate user function for the torsionless isotropic cone 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=26802&r1=26801&r2=26802&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 12:20:00 2014 @@ -3354,6 +3354,73 @@ self.assert_(theta <= cone_theta + epsilon) + def test_simulate_iso_cone_torsionless_z_axis(self): + """Check the frame_order.simulate user function PDB file for the torsionless isotropic cone model along the z-axis.""" + + # Init. + cone_theta = 0.5 + pivot = array([1, 0, -2], float64) + l = 24.0 + sim_num = 500 + + # The axis parameters, and printout. + axis_theta = 0.0 + print("Rotor axis: %s" % create_rotor_axis_spherical(axis_theta, 0.0)) + + # Set up. + self.setup_model(pipe_name='PDB model', model='iso cone, torsionless', 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_theta=axis_theta, axis_phi=0.0, cone_theta=cone_theta) + + # 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(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) + self.assert_(theta >= pi/2.0 - cone_theta - epsilon) + self.assert_(theta <= pi/2.0 + cone_theta + epsilon) + self.assert_(phi >= -lateral_slide) + self.assert_(phi <= 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 >= -lateral_slide) + self.assert_(phi-pi/2.0 <= 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_rotor_z_axis(self): """Check the frame_order.simulate user function PDB file for the rotor model along the z-axis."""