Author: bugman Date: Fri Nov 21 19:32:37 2014 New Revision: 26697 URL: http://svn.gna.org/viewcvs/relax?rev=26697&view=rev Log: Modified the Frame_order.test_pdb_model_iso_cone_xz_plane_tilt system test to have a cone angle. The cone opening half-angle was previously 0.0. The test now checks the geometric object in the PDB file for a cone opening half-angle of 2.0. 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=26697&r1=26696&r2=26697&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 21 19:32:37 2014 @@ -32,7 +32,7 @@ import dep_check from lib.frame_order.conversions import create_rotor_axis_alpha, create_rotor_axis_spherical from lib.frame_order.variables import MODEL_DOUBLE_ROTOR, MODEL_FREE_ROTOR, MODEL_ISO_CONE, MODEL_ISO_CONE_FREE_ROTOR, MODEL_ISO_CONE_TORSIONLESS, MODEL_PSEUDO_ELLIPSE, MODEL_PSEUDO_ELLIPSE_TORSIONLESS, MODEL_RIGID, MODEL_ROTOR -from lib.geometry.rotations import euler_to_R_zyz, R_to_euler_zyz +from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz, R_to_euler_zyz from status import Status; status = Status() from test_suite.system_tests.base_classes import SystemTestCase @@ -1679,6 +1679,135 @@ # The axis parameters, and printout. axis_theta = -pi/4.0 axis_phi = 0.0 + axis = create_rotor_axis_spherical(axis_theta, axis_phi) + print("Rotor axis: %s" % axis) + + # Rotation matrix. + R = zeros((3, 3), float64) + axis_angle_to_R([0, 1, 0], axis_theta, R) + + # Cone parameters. + theta = 2.0 + + # Set the average domain position translation parameters. + self.interpreter.value.set(param='ave_pos_x', val=0.0) + self.interpreter.value.set(param='ave_pos_y', val=0.0) + self.interpreter.value.set(param='ave_pos_z', val=0.0) + self.interpreter.value.set(param='ave_pos_alpha', val=0.0) + self.interpreter.value.set(param='ave_pos_beta', val=0.0) + self.interpreter.value.set(param='ave_pos_gamma', val=0.0) + self.interpreter.value.set(param='axis_theta', val=axis_theta) + self.interpreter.value.set(param='axis_phi', val=axis_phi) + self.interpreter.value.set(param='cone_theta', val=theta) + self.interpreter.value.set(param='cone_sigma_max', val=0.0) + + # Set the pivot. + self.interpreter.frame_order.pivot(pivot=pivot, fix=True) + + # Create the PDB. + self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=10, size=l) + + # The files. + files = ['frame_order_A.pdb', 'frame_order_B.pdb'] + + # The xy-plane vectors. + inc = 2.0 * pi / 10.0 + vectors = zeros((10, 3), float64) + for i in range(10): + # The angle phi. + phi = inc * i + + # The xy-plane, starting along the x-axis. + vectors[i, 0] = cos(phi) + vectors[i, 1] = sin(phi) + + # The data, as it should be with everything along the z-axis, shifted from the origin to the pivot. + neg = [False, True] + tle = ['a', 'b'] + data = [] + for i in range(2): + data.append([ + # The pivot. + [ 1, 'PIV', 1, 'Piv', pivot], + + # The rotor. + [ 1, 'RTX', 2, 'CTR', pivot], + [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], + [ 3, 'RTB', 4, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], + [ 4, 'RTB', 186, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor-2.0, angle=axis_theta, neg=neg[i])], + [ 5, 'RTB', 368, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], + [ 6, 'RTB', 550, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor-2.0, angle=axis_theta, neg=neg[i])], + [ 7, 'RTL', 732, 'z-ax', self.rotate_from_Z(origin=pivot, length=l_rotor+2.0, angle=axis_theta, neg=neg[i])], + + # The cone edge. + [ 3, 'CNE', 733, 'APX', pivot], + [ 3, 'CNE', 734, 'H2', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[0], R=R, neg=neg[i])], + [ 3, 'CNE', 735, 'H3', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[1], R=R, neg=neg[i])], + [ 3, 'CNE', 736, 'H4', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[2], R=R, neg=neg[i])], + [ 3, 'CNE', 737, 'H5', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[3], R=R, neg=neg[i])], + [ 3, 'CNE', 738, 'H6', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[4], R=R, neg=neg[i])], + [ 3, 'CNE', 739, 'H7', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[5], R=R, neg=neg[i])], + [ 3, 'CNE', 740, 'H8', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[6], R=R, neg=neg[i])], + [ 3, 'CNE', 741, 'H9', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[7], R=R, neg=neg[i])], + [ 3, 'CNE', 742, 'H10', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[8], R=R, neg=neg[i])], + [ 3, 'CNE', 743, 'H11', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[9], R=R, neg=neg[i])], + + # Titles. + [ 1, 'TLE', 804, tle[i], self.rotate_from_Z(origin=pivot, length=l+10, angle=axis_theta, neg=neg[i])] + ]) + + # Loop over the representations. + for i in range(2): + # Delete all structural data. + self.interpreter.structure.delete() + + # Read the contents of the file. + self.interpreter.structure.read_pdb(file=files[i], dir=ds.tmpdir) + + # Check the atomic coordinates. + selection = cdp.structure.selection() + index = 0 + 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): + # Skip the propeller blades. + if atom_name == 'BLD': + continue + + # Skip the cone interior (checking the edge will be sufficient). + if res_name == 'CON': + continue + + # Checks. + print("Checking residue %s %s, atom %s %s, at position %s." % (data[i][index][0], data[i][index][1], data[i][index][2], data[i][index][3], data[i][index][4])) + print(" to residue %s %s, atom %s %s, at position %s." % (res_num, res_name, atom_num, atom_name, pos[0])) + self.assertEqual(data[i][index][0], res_num) + self.assertEqual(data[i][index][1], res_name) + self.assertEqual(data[i][index][2], atom_num) + self.assertEqual(data[i][index][3], atom_name) + self.assertAlmostEqual(data[i][index][4][0], pos[0][0], 3) + self.assertAlmostEqual(data[i][index][4][1], pos[0][1], 3) + self.assertAlmostEqual(data[i][index][4][2], pos[0][2], 3) + + # Increment the index. + index += 1 + + + def test_pdb_model_iso_cone_z_axis(self): + """Check the frame_order.pdb_model user function PDB file for the isotropic cone model along the z-axis.""" + + # Init. + pivot = array([1, 0, -2], float64) + l = 25.0 + l_rotor = l + 5.0 + + # Create a data pipe. + self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame order') + + # Select the model. + self.interpreter.frame_order.select_model('iso cone') + + # The axis parameters, and printout. + axis_theta = 0.0 + axis_phi = 0.0 print("Rotor axis: %s" % create_rotor_axis_spherical(axis_theta, axis_phi)) # Set the average domain position translation parameters. @@ -1752,96 +1881,6 @@ index += 1 - def test_pdb_model_iso_cone_z_axis(self): - """Check the frame_order.pdb_model user function PDB file for the isotropic cone model along the z-axis.""" - - # Init. - pivot = array([1, 0, -2], float64) - l = 25.0 - l_rotor = l + 5.0 - - # Create a data pipe. - self.interpreter.pipe.create(pipe_name='PDB model', pipe_type='frame order') - - # Select the model. - self.interpreter.frame_order.select_model('iso cone') - - # The axis parameters, and printout. - axis_theta = 0.0 - axis_phi = 0.0 - print("Rotor axis: %s" % create_rotor_axis_spherical(axis_theta, axis_phi)) - - # Set the average domain position translation parameters. - self.interpreter.value.set(param='ave_pos_x', val=0.0) - self.interpreter.value.set(param='ave_pos_y', val=0.0) - self.interpreter.value.set(param='ave_pos_z', val=0.0) - self.interpreter.value.set(param='ave_pos_alpha', val=0.0) - self.interpreter.value.set(param='ave_pos_beta', val=0.0) - self.interpreter.value.set(param='ave_pos_gamma', val=0.0) - self.interpreter.value.set(param='axis_theta', val=axis_theta) - self.interpreter.value.set(param='axis_phi', val=axis_phi) - self.interpreter.value.set(param='cone_theta', val=0.0) - self.interpreter.value.set(param='cone_sigma_max', val=0.0) - - # Set the pivot. - self.interpreter.frame_order.pivot(pivot=pivot, fix=True) - - # Create the PDB. - self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=1, size=l) - - # The files. - files = ['frame_order_A.pdb', 'frame_order_B.pdb'] - - # The data, as it should be with everything along the z-axis, shifted from the origin to the pivot. - neg = [False, True] - tle = ['a', 'b'] - data = [] - for i in range(2): - data.append([ - [ 1, 'PIV', 1, 'Piv', pivot], - [ 1, 'RTX', 2, 'CTR', pivot], - [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], - [ 3, 'RTB', 4, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], - [ 4, 'RTB', 186, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor-2.0, angle=axis_theta, neg=neg[i])], - [ 5, 'RTB', 368, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor, angle=axis_theta, neg=neg[i])], - [ 6, 'RTB', 550, 'BLO', self.rotate_from_Z(origin=pivot, length=l_rotor-2.0, angle=axis_theta, neg=neg[i])], - [ 7, 'RTL', 732, 'z-ax', self.rotate_from_Z(origin=pivot, length=l_rotor+2.0, angle=axis_theta, neg=neg[i])], - [ 3, 'CNE', 733, 'APX', pivot], - [ 3, 'CNE', 734, 'H2', self.rotate_from_Z(origin=pivot, length=l, angle=axis_theta, neg=neg[i])], - [ 4, 'CON', 735, 'H3', self.rotate_from_Z(origin=pivot, length=l, angle=axis_theta, neg=neg[i])], - [ 1, 'TLE', 736, tle[i], self.rotate_from_Z(origin=pivot, length=l+10, angle=axis_theta, neg=neg[i])] - ]) - - # Loop over the representations. - for i in range(2): - # Delete all structural data. - self.interpreter.structure.delete() - - # Read the contents of the file. - self.interpreter.structure.read_pdb(file=files[i], dir=ds.tmpdir) - - # Check the atomic coordinates. - selection = cdp.structure.selection() - index = 0 - 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): - # Skip the propeller blades. - if atom_name == 'BLD': - continue - - # Checks. - print("Checking residue %s %s, atom %s %s, at position %s." % (data[i][index][0], data[i][index][1], data[i][index][2], data[i][index][3], data[i][index][4])) - self.assertEqual(data[i][index][0], res_num) - self.assertEqual(data[i][index][1], res_name) - self.assertEqual(data[i][index][2], atom_num) - self.assertEqual(data[i][index][3], atom_name) - self.assertAlmostEqual(data[i][index][4][0], pos[0][0], 3) - self.assertAlmostEqual(data[i][index][4][1], pos[0][1], 3) - self.assertAlmostEqual(data[i][index][4][2], pos[0][2], 3) - - # Increment the index. - index += 1 - - def test_pdb_model_pseudo_ellipse_xz_plane_tilt(self): """Check the frame_order.pdb_model user function PDB file for the pseudo-ellipse model with a xz-plane tilt."""