Author: bugman
Date: Wed Dec 3 16:07:24 2014
New Revision: 26918
URL: http://svn.gna.org/viewcvs/relax?rev=26918&view=rev
Log:
Created two system tests for the frame_order.simulate user function for the
double rotor model.
These are Frame_order.test_simulate_double_rotor_mode1_z_axis and
Frame_order.test_simulate_double_rotor_mode2_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=26918&r1=26917&r2=26918&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 Wed
Dec 3 16:07:24 2014
@@ -3178,6 +3178,211 @@
self.assertAlmostEqual(cdp.chi2, 0.011377487066752203, 5)
+ def test_simulate_double_rotor_mode1_z_axis(self):
+ """Check the frame_order.simulate user function PDB file for the
double rotor model along the z-axis for the first rotation mode."""
+
+ # Init.
+ cone_sigma_max = pi / 2.0
+ cone_sigma_max_2 = 0.0
+ pivot = array([20, 20, -20], float64)
+ l = 100.0
+ sim_num = 500
+ pivot_disp = 100.0
+
+ # The eigenframe.
+ eigen_beta = 0.0
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(0.0, eigen_beta, 0.0, R)
+ print("Motional eigenframe:\n%s" % R)
+
+ # Set up.
+ self.setup_model(pipe_name='PDB model', model='double 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=eigen_beta, ave_pos_gamma=0.0,
pivot_disp=pivot_disp, eigen_alpha=0.0, eigen_beta=eigen_beta,
eigen_gamma=0.0, cone_sigma_max=cone_sigma_max,
cone_sigma_max_2=cone_sigma_max_2)
+
+ # 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)
+
+ # X vector maxima.
+ X_theta_min = cartesian_to_spherical([100, 0, 200])[1]
+ X_theta_max = cartesian_to_spherical([-100, 0, 0])[1] + pi
+ print("X vector theta range of [%.5f, %.5f]" % (X_theta_min,
X_theta_max))
+
+ # Check the atomic coordinates.
+ selection = cdp.structure.selection()
+ epsilon = 1e-3
+ 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]))
+
+ # Check the X and nX vectors.
+ if res_name in ['X', 'nX']:
+ self.assert_(theta >= X_theta_min - epsilon)
+ self.assert_(theta <= X_theta_max + epsilon)
+ if phi < 0.1:
+ self.assertAlmostEqual(phi, 0.0, 3)
+ else:
+ self.assertAlmostEqual(phi, pi, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+
+ # Check the Y vector.
+ elif res_name == 'Y':
+ self.assert_(r/100.0 >= 1.0 - epsilon)
+ self.assert_(theta >= pi/4.0 - epsilon)
+ self.assert_(theta <= 2.0*pi - pi/4.0 + epsilon)
+ self.assertAlmostEqual(new_pos[1], 100.0, 3)
+
+ # Check the Z vector (should not move).
+ elif res_name == 'Z':
+ self.assert_(r/100.0 >= 1.0 - epsilon)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 100.0, 3)
+
+ # Check the nY vector.
+ elif res_name == 'nY':
+ self.assert_(r/100.0 >= 1.0 - epsilon)
+ self.assert_(theta >= pi/4.0 - epsilon)
+ self.assert_(theta <= 2.0*pi - pi/4.0 + epsilon)
+ self.assertAlmostEqual(new_pos[1], -100.0, 3)
+
+ # Check the nZ vector (should not move).
+ elif res_name == 'nZ':
+ self.assert_(r/100.0 >= 1.0 - epsilon)
+ self.assert_(theta >= pi/4.0 - epsilon)
+ self.assert_(theta <= 2.0*pi - pi/4.0 + epsilon)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assert_(r/100.0 <= 1.4142135623730951 + epsilon)
+ if not (new_pos[0] == 0.0 and new_pos[1] == 0.0 and
new_pos[2] == 0.0):
+ self.assert_(theta >= pi/4.0 - epsilon)
+ self.assert_(theta <= 2.0*pi - pi/4.0 + epsilon)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == '0':
+ self.assertAlmostEqual(r, 34.641016151377549, 4)
+ self.assertAlmostEqual(pos[0], 0.0, 3)
+ self.assertAlmostEqual(pos[1], 0.0, 3)
+ self.assertAlmostEqual(pos[2], 0.0, 3)
+
+
+ def test_simulate_double_rotor_mode2_z_axis(self):
+ """Check the frame_order.simulate user function PDB file for the
double rotor model along the z-axis for the second rotation mode."""
+
+ # Init.
+ cone_sigma_max = 0.0
+ cone_sigma_max_2 = pi / 2.0
+ pivot = array([20, 20, -20], float64)
+ l = 100.0
+ sim_num = 500
+ pivot_disp = 100.0
+
+ # The eigenframe.
+ eigen_beta = 0.0
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(0.0, eigen_beta, 0.0, R)
+ print("Motional eigenframe:\n%s" % R)
+
+ # Set up.
+ self.setup_model(pipe_name='PDB model', model='double 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=eigen_beta, ave_pos_gamma=0.0,
pivot_disp=pivot_disp, eigen_alpha=0.0, eigen_beta=eigen_beta,
eigen_gamma=0.0, cone_sigma_max=cone_sigma_max,
cone_sigma_max_2=cone_sigma_max_2)
+
+ # 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
+ 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]))
+
+ # Check the X and nX vectors.
+ if res_name == 'X':
+ self.assertAlmostEqual(new_pos[0], 100.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the Y vector.
+ elif res_name == 'Y':
+ self.assertAlmostEqual(r/100.0, 1.0, 3)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assert_(new_pos[1] >= 0.0 - epsilon)
+ self.assert_(new_pos[1] <= 100.0 + epsilon)
+ self.assert_(new_pos[2] >= -100.0 - epsilon)
+ self.assert_(new_pos[2] <= 100.0 + epsilon)
+
+ # Check the Z vector (should not move).
+ elif res_name == 'Z':
+ self.assertAlmostEqual(r/100.0, 1.0, 3)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assert_(new_pos[1] >= -100.0 - epsilon)
+ self.assert_(new_pos[1] <= 100.0 + epsilon)
+ self.assert_(new_pos[2] >= 0.0 - epsilon)
+ self.assert_(new_pos[2] <= 100.0 + epsilon)
+
+ # Check the X and nX vectors.
+ elif res_name == 'nX':
+ self.assertAlmostEqual(new_pos[0], -100.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the nY vector.
+ elif res_name == 'nY':
+ self.assertAlmostEqual(r/100.0, 1.0, 3)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assert_(new_pos[1] >= -100.0 - epsilon)
+ self.assert_(new_pos[1] <= 0.0 + epsilon)
+ self.assert_(new_pos[2] >= -100.0 - epsilon)
+ self.assert_(new_pos[2] <= 100.0 + epsilon)
+
+ # Check the nZ vector (should not move).
+ elif res_name == 'nZ':
+ self.assertAlmostEqual(r/100.0, 1.0, 3)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assert_(new_pos[1] >= -100.0 - epsilon)
+ self.assert_(new_pos[1] <= 100.0 + epsilon)
+ self.assert_(new_pos[2] >= -100.0 - epsilon)
+ self.assert_(new_pos[2] <= 0.0 + epsilon)
+
+ # Check the centre.
+ elif res_name == 'C':
+ self.assertAlmostEqual(r, 0.0, 3)
+ self.assertAlmostEqual(new_pos[0], 0.0, 3)
+ self.assertAlmostEqual(new_pos[1], 0.0, 3)
+ self.assertAlmostEqual(new_pos[2], 0.0, 3)
+
+ # Check the origin.
+ elif res_name == '0':
+ self.assertAlmostEqual(pos[0], 20.0, 3)
+ self.assertAlmostEqual(pos[1], 20.0, 3)
+ self.assertAlmostEqual(pos[2], -20.0, 3)
+
+
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."""
r26918 - /branches/frame_order_cleanup/test_suite/system_tests/frame_order.py