Author: bugman
Date: Tue Nov 25 19:39:46 2014
New Revision: 26722
URL: http://svn.gna.org/viewcvs/relax?rev=26722&view=rev
Log:
Created two new frame order system tests for the double rotor 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_double_rotor_z_axis and
Frame_order.test_pdb_model_double_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=26722&r1=26721&r2=26722&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 19:39:46 2014
@@ -1662,6 +1662,236 @@
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_double_rotor_xz_plane_tilt(self):
+ """Check the frame_order.pdb_model user function PDB file for the
rotor model along the z-axis."""
+
+ # Init.
+ pivot2 = array([1, 0, 0], float64)
+ pivot_disp = 100
+ pivot1 = pivot2 + (z_axis-x_axis)/sqrt(2.0)*pivot_disp
+ l = 20.0
+
+ # 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('double rotor')
+
+ # The axis parameters, and printout.
+ eigen_alpha = 0.0
+ eigen_beta = -pi/4.0
+ eigen_gamma = 0.0
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
+ print("Motional eigenframe:\n%s" % R)
+
+ # 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='pivot_disp', val=pivot_disp)
+ self.interpreter.value.set(param='eigen_alpha', val=eigen_alpha)
+ self.interpreter.value.set(param='eigen_beta', val=eigen_beta)
+ self.interpreter.value.set(param='eigen_gamma', val=eigen_gamma)
+ self.interpreter.value.set(param='cone_sigma_max', val=0.0)
+ self.interpreter.value.set(param='cone_sigma_max_2', val=0.0)
+
+ # Set the pivot.
+ self.interpreter.frame_order.pivot(pivot=pivot2, 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 = [
+ # The pivots.
+ [ 1, 'PIV', 1, 'Piv1', pivot1],
+ [ 1, 'PIV', 2, 'Piv2', pivot2],
+
+ # The x-axis rotor.
+ [ 1, 'RTX', 3, 'CTR', pivot2],
+ [ 2, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta)],
+ [ 3, 'RTX', 5, 'PRP', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta, neg=True)],
+ [ 4, 'RTB', 6, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta)],
+ [ 5, 'RTB', 188, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0+eigen_beta)],
+ [ 6, 'RTB', 370, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta)],
+ [ 7, 'RTB', 552, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0+eigen_beta)],
+ [ 8, 'RTB', 734, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta, neg=True)],
+ [ 9, 'RTB', 916, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0+eigen_beta, neg=True)],
+ [10, 'RTB', 1098, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0+eigen_beta, neg=True)],
+ [11, 'RTB', 1280, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0+eigen_beta, neg=True)],
+ [12, 'RTL', 1462, 'x-ax', self.rotate_from_Z(origin=pivot2,
length=l+2.0, angle=pi/2.0+eigen_beta)],
+ [12, 'RTL', 1463, 'x-ax', self.rotate_from_Z(origin=pivot2,
length=l+2.0, angle=pi/2.0+eigen_beta, neg=True)],
+
+ # The y-axis rotor.
+ [ 1, 'RTX', 1464, 'CTR', pivot1],
+ [ 2, 'RTX', 1465, 'PRP', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 3, 'RTX', 1466, 'PRP', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [ 4, 'RTB', 1467, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 5, 'RTB', 1649, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis)],
+ [ 6, 'RTB', 1831, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 7, 'RTB', 2013, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis)],
+ [ 8, 'RTB', 2195, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [ 9, 'RTB', 2377, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+ [10, 'RTB', 2559, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [11, 'RTB', 2741, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+ [12, 'RTL', 2923, 'y-ax', self.rotate_from_Z(origin=pivot1,
length=l+2.0, angle=pi/2.0, axis=y_axis)],
+ [12, 'RTL', 2924, 'y-ax', self.rotate_from_Z(origin=pivot1,
length=l+2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+
+ # The z-axis.
+ [ 1, 'AXE', 2925, 'R', pivot2],
+ [ 1, 'AXE', 2926, 'z-ax', pivot1],
+ [ 1, 'AXE', 2927, 'z-ax', (pivot1-pivot2)*1.1+pivot2],
+ ]
+
+ # 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]))
+ print(" to residue %s %s, atom %s %s, at position %s." %
(res_num, res_name, atom_num, atom_name, pos[0]))
+ 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_double_rotor_z_axis(self):
+ """Check the frame_order.pdb_model user function PDB file for the
rotor model along the z-axis."""
+
+ # Init.
+ pivot2 = array([1, 0, 0], float64)
+ pivot_disp = 100
+ pivot1 = pivot2 + z_axis*pivot_disp
+ 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('double rotor')
+
+ # The axis parameters, and printout.
+ eigen_alpha = 0.0
+ eigen_beta = 0.0
+ eigen_gamma = 0.0
+ R = zeros((3, 3), float64)
+ euler_to_R_zyz(eigen_alpha, eigen_beta, eigen_gamma, R)
+ print("Motional eigenframe:\n%s" % R)
+
+ # 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='pivot_disp', val=pivot_disp)
+ self.interpreter.value.set(param='eigen_alpha', val=eigen_alpha)
+ self.interpreter.value.set(param='eigen_beta', val=eigen_beta)
+ self.interpreter.value.set(param='eigen_gamma', val=eigen_gamma)
+ self.interpreter.value.set(param='cone_sigma_max', val=0.0)
+ self.interpreter.value.set(param='cone_sigma_max_2', val=0.0)
+
+ # Set the pivot.
+ self.interpreter.frame_order.pivot(pivot=pivot2, 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 = [
+ # The pivots.
+ [ 1, 'PIV', 1, 'Piv1', pivot1],
+ [ 1, 'PIV', 2, 'Piv2', pivot2],
+
+ # The x-axis rotor.
+ [ 1, 'RTX', 3, 'CTR', pivot2],
+ [ 2, 'RTX', 4, 'PRP', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0)],
+ [ 3, 'RTX', 5, 'PRP', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0, neg=True)],
+ [ 4, 'RTB', 6, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0)],
+ [ 5, 'RTB', 188, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0)],
+ [ 6, 'RTB', 370, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0)],
+ [ 7, 'RTB', 552, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0)],
+ [ 8, 'RTB', 734, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0, neg=True)],
+ [ 9, 'RTB', 916, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0, neg=True)],
+ [10, 'RTB', 1098, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l, angle=pi/2.0, neg=True)],
+ [11, 'RTB', 1280, 'BLO', self.rotate_from_Z(origin=pivot2,
length=l-2.0, angle=pi/2.0, neg=True)],
+ [12, 'RTL', 1462, 'x-ax', self.rotate_from_Z(origin=pivot2,
length=l+2.0, angle=pi/2.0)],
+ [12, 'RTL', 1463, 'x-ax', self.rotate_from_Z(origin=pivot2,
length=l+2.0, angle=pi/2.0, neg=True)],
+
+ # The y-axis rotor.
+ [ 1, 'RTX', 1464, 'CTR', pivot1],
+ [ 2, 'RTX', 1465, 'PRP', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 3, 'RTX', 1466, 'PRP', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [ 4, 'RTB', 1467, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 5, 'RTB', 1649, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis)],
+ [ 6, 'RTB', 1831, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis)],
+ [ 7, 'RTB', 2013, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis)],
+ [ 8, 'RTB', 2195, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [ 9, 'RTB', 2377, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+ [10, 'RTB', 2559, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l, angle=pi/2.0, axis=y_axis, neg=True)],
+ [11, 'RTB', 2741, 'BLO', self.rotate_from_Z(origin=pivot1,
length=l-2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+ [12, 'RTL', 2923, 'y-ax', self.rotate_from_Z(origin=pivot1,
length=l+2.0, angle=pi/2.0, axis=y_axis)],
+ [12, 'RTL', 2924, 'y-ax', self.rotate_from_Z(origin=pivot1,
length=l+2.0, angle=pi/2.0, axis=y_axis, neg=True)],
+
+ # The z-axis.
+ [ 1, 'AXE', 2925, 'R', pivot2],
+ [ 1, 'AXE', 2926, 'z-ax', pivot1],
+ [ 1, 'AXE', 2927, 'z-ax', self.rotate_from_Z(origin=pivot2,
length=pivot_disp*1.1, angle=0.0)],
+ ]
+
+ # 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]))
+ print(" to residue %s %s, atom %s %s, at position %s." %
(res_num, res_name, atom_num, atom_name, pos[0]))
+ 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_xz_plane_tilt(self):
"""Check the frame_order.pdb_model user function PDB file for the
rotor model with a xz-plane tilt."""
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