Author: bugman Date: Tue Nov 25 16:14:06 2014 New Revision: 26718 URL: http://svn.gna.org/viewcvs/relax?rev=26718&view=rev Log: Created two new frame order system tests for the free rotor isotropic cone PDB representation file. This is the two PDB files from the frame_order.pdb_model user function. The two new system tests are Frame_order.test_pdb_model_iso_cone_free_rotor_z_axis and Frame_order.test_pdb_model_iso_cone_free_rotor_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=26718&r1=26717&r2=26718&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 Nov 25 16:14:06 2014 @@ -2079,6 +2079,257 @@ index += 1 + def test_pdb_model_iso_cone_free_rotor_xz_plane_tilt(self): + """Check the frame_order.pdb_model user function PDB file for the free rotor isotropic cone model with a xz-plane tilt.""" + + # Init. + pivot = array([1, 1, 1], float64) + l = 40.0 + 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, free rotor') + + # 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) + + # 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, 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, 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_free_rotor_z_axis(self): + """Check the frame_order.pdb_model user function PDB file for the free rotor 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, free rotor') + + # 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)) + + # 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) + + # 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, 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, 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], neg=neg[i])], + [ 3, 'CNE', 735, 'H3', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[1], neg=neg[i])], + [ 3, 'CNE', 736, 'H4', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[2], neg=neg[i])], + [ 3, 'CNE', 737, 'H5', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[3], neg=neg[i])], + [ 3, 'CNE', 738, 'H6', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[4], neg=neg[i])], + [ 3, 'CNE', 739, 'H7', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[5], neg=neg[i])], + [ 3, 'CNE', 740, 'H8', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[6], neg=neg[i])], + [ 3, 'CNE', 741, 'H9', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[7], neg=neg[i])], + [ 3, 'CNE', 742, 'H10', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[8], neg=neg[i])], + [ 3, 'CNE', 743, 'H11', self.rotate_from_Z(origin=pivot, length=l, angle=theta, axis=vectors[9], 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_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."""