Author: bugman Date: Tue Nov 25 15:32:07 2014 New Revision: 26717 URL: http://svn.gna.org/viewcvs/relax?rev=26717&view=rev Log: Created two new system tests for the free rotor PDB representation file. This is the file from the frame_order.pdb_model user function. The two new unit tests are Frame_order.test_pdb_model_free_rotor_z_axis and Frame_order.test_pdb_model_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=26717&r1=26716&r2=26717&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 15:32:07 2014 @@ -1662,6 +1662,170 @@ self.script_exec(status.install_path + sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opendx_euler_angle_map.py') + def test_pdb_model_free_rotor_xz_plane_tilt(self): + """Check the frame_order.pdb_model user function PDB file for the rotor model with a xz-plane tilt.""" + + # Init. + pivot = array([1, 0, 1], float64) + l = 100.0 + + # 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('free rotor') + + # 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:\n %s" % axis) + print("Rotor apex (100*axis + [1, 0, 1]):\n %s" % (l*axis + pivot)) + + # 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_alpha', val=axis_alpha) + 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=100.0) + + # Create a data pipe for the new structure. + self.interpreter.pipe.create(pipe_name='PDB check', pipe_type='frame order') + self.interpreter.pipe.display() + + # Read the contents of the file. + self.interpreter.structure.read_pdb(file='frame_order.pdb', dir=ds.tmpdir) + + # The data, as it should be with everything along the z-axis, shifted from the origin to the pivot. + data = [ + [ 1, 'PIV', 1, 'Piv', pivot], + [ 1, 'RTX', 2, 'CTR', pivot], + [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0)], + [ 3, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0, neg=True)], + [ 4, 'RTB', 5, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0)], + [ 5, 'RTB', 187, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0)], + [ 6, 'RTB', 369, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0)], + [ 7, 'RTB', 551, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0)], + [ 8, 'RTB', 733, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0, neg=True)], + [ 9, 'RTB', 915, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0, neg=True)], + [10, 'RTB', 1097, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0, neg=True)], + [11, 'RTB', 1279, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=-pi/4.0, neg=True)], + [12, 'RTL', 1461, 'z-ax', self.rotate_from_Z(origin=pivot, length=l+2.0, angle=-pi/4.0)], + [12, 'RTL', 1462, 'z-ax', self.rotate_from_Z(origin=pivot, length=l+2.0, angle=-pi/4.0, neg=True)] + ] + + # 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 (to the 3 places accuracy of a PDB file). + print("Checking residue %s %s, atom %s %s, at position %s." % (data[index][0], data[index][1], data[index][2], data[index][3], data[index][4])) + self.assertEqual(data[index][0], res_num) + self.assertEqual(data[index][1], res_name) + self.assertEqual(data[index][2], atom_num) + self.assertEqual(data[index][3], atom_name) + self.assertAlmostEqual(data[index][4][0], pos[0][0], 3) + self.assertAlmostEqual(data[index][4][1], pos[0][1], 3) + self.assertAlmostEqual(data[index][4][2], pos[0][2], 3) + + # Increment the index. + index += 1 + + + def test_pdb_model_free_rotor_z_axis(self): + """Check the frame_order.pdb_model user function PDB file for the free rotor model along the z-axis.""" + + # Init. + pivot = array([1, 0, 0], float64) + l = 30.0 + + # 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('free rotor') + + # 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 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_alpha', val=axis_alpha) + 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) + + # Create a data pipe for the new structure. + self.interpreter.pipe.create(pipe_name='PDB check', pipe_type='frame order') + self.interpreter.pipe.display() + + # Read the contents of the file. + self.interpreter.structure.read_pdb(file='frame_order.pdb', dir=ds.tmpdir) + + # The data, as it should be with everything along the z-axis, shifted from the origin to the pivot. + data = [ + [ 1, 'PIV', 1, 'Piv', pivot], + [ 1, 'RTX', 2, 'CTR', pivot], + [ 2, 'RTX', 3, 'PRP', self.rotate_from_Z(origin=pivot, length=l, angle=0.0)], + [ 3, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot, length=l, angle=0.0, neg=True)], + [ 4, 'RTB', 5, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0)], + [ 5, 'RTB', 187, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0)], + [ 6, 'RTB', 369, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0)], + [ 7, 'RTB', 551, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0)], + [ 8, 'RTB', 733, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0, neg=True)], + [ 9, 'RTB', 915, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0, neg=True)], + [10, 'RTB', 1097, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0, neg=True)], + [11, 'RTB', 1279, 'BLO', self.rotate_from_Z(origin=pivot, length=l, angle=0.0, neg=True)], + [12, 'RTL', 1461, 'z-ax', self.rotate_from_Z(origin=pivot, length=l+2.0, angle=0.0)], + [12, 'RTL', 1462, 'z-ax', self.rotate_from_Z(origin=pivot, length=l+2.0, angle=0.0, neg=True)] + ] + + # 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[index][0], data[index][1], data[index][2], data[index][3], data[index][4])) + self.assertEqual(data[index][0], res_num) + self.assertEqual(data[index][1], res_name) + self.assertEqual(data[index][2], atom_num) + self.assertEqual(data[index][3], atom_name) + self.assertAlmostEqual(data[index][4][0], pos[0][0], 3) + self.assertAlmostEqual(data[index][4][1], pos[0][1], 3) + self.assertAlmostEqual(data[index][4][2], pos[0][2], 3) + + # Increment the index. + index += 1 + + def test_pdb_model_iso_cone_xz_plane_tilt(self): """Check the frame_order.pdb_model user function PDB file for the isotropic cone model with a xz-plane tilt."""