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."""
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