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."""
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