Author: bugman
Date: Fri Nov 21 10:51:43 2014
New Revision: 26683
URL: http://svn.gna.org/viewcvs/relax?rev=26683&view=rev
Log:
Created the Frame_order.test_pdb_model_iso_cone system test.
This is for checking the PDB representation of the isotropic cone frame order
model created by the
frame_order.pdb_model user function. It checks both A and B representations.
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=26683&r1=26682&r2=26683&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 Fri Nov
21 10:51:43 2014
@@ -1610,6 +1610,107 @@
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_iso_cone(self):
+ """Check the PDB file from frame_order.pdb_model for the isotropic
cone model."""
+
+ # Lengths.
+ l = 25.0
+ l_rotor = l + 5.0
+ l_in = l_rotor - 2.0
+ l_out = l_rotor + 2.0
+ label = l + 10.0
+
+ # 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')
+
+ # The axis parameters, and printout.
+ axis_theta = 0.0
+ axis_phi = 0.0
+ print("Rotor axis: %s" % create_rotor_axis_alpha(pi/2, array([1, 0,
0], float64), array([0, 0, 0], float64)))
+
+ # 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=0.0)
+ self.interpreter.value.set(param='cone_sigma_max', val=0.0)
+
+ # Set the pivot.
+ self.interpreter.frame_order.pivot(pivot=[1, 0, 0], fix=True)
+
+ # Create the PDB.
+ self.interpreter.frame_order.pdb_model(dir=ds.tmpdir, inc=1, size=l)
+
+ # The files.
+ files = ['frame_order_A.pdb', 'frame_order_B.pdb']
+
+ # The data, as it should be with everything along the z-axis, shifted
from the origin to the pivot.
+ data = [[
+ [ 1, 'PIV', 1, 'Piv', [1.0, 0.0, 0.0]],
+ [ 1, 'RTX', 2, 'CTR', [1.0, 0.0, 0.0]],
+ [ 2, 'RTX', 3, 'PRP', [1.0, 0.0, l_rotor]],
+ [ 3, 'RTB', 4, 'BLO', [1.0, 0.0, l_rotor]],
+ [ 4, 'RTB', 186, 'BLO', [1.0, 0.0, l_in]],
+ [ 5, 'RTB', 368, 'BLO', [1.0, 0.0, l_rotor]],
+ [ 6, 'RTB', 550, 'BLO', [1.0, 0.0, l_in]],
+ [ 7, 'RTL', 732, 'z-ax', [1.0, 0.0, l_out]],
+ [ 3, 'CNE', 733, 'APX', [1.0, 0.0, 0.0]],
+ [ 3, 'CNE', 734, 'H2', [1.0, 0.0, l]],
+ [ 4, 'CON', 735, 'H3', [1.0, 0.0, l]],
+ [ 1, 'TLE', 736, 'a', [1.0, 0.0, label]],
+ ], [
+ [ 1, 'PIV', 1, 'Piv', [1.0, 0.0, 0.0]],
+ [ 1, 'RTX', 2, 'CTR', [1.0, 0.0, 0.0]],
+ [ 2, 'RTX', 3, 'PRP', [1.0, 0.0, -l_rotor]],
+ [ 3, 'RTB', 4, 'BLO', [1.0, 0.0, -l_rotor]],
+ [ 4, 'RTB', 186, 'BLO', [1.0, 0.0, -l_in]],
+ [ 5, 'RTB', 368, 'BLO', [1.0, 0.0, -l_rotor]],
+ [ 6, 'RTB', 550, 'BLO', [1.0, 0.0, -l_in]],
+ [ 7, 'RTL', 732, 'z-ax', [1.0, 0.0, -l_out]],
+ [ 3, 'CNE', 733, 'APX', [1.0, 0.0, 0.0]],
+ [ 3, 'CNE', 734, 'H2', [1.0, 0.0, -l]],
+ [ 4, 'CON', 735, 'H3', [1.0, 0.0, -l]],
+ [ 1, 'TLE', 736, 'a', [1.0, 0.0, -label]],
+ ]]
+
+ # 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
+
+ # 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]))
+ 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.assertEqual(data[i][index][4][0], pos[0][0])
+ self.assertEqual(data[i][index][4][1], pos[0][1])
+ self.assertEqual(data[i][index][4][2], pos[0][2])
+
+ # Increment the index.
+ index += 1
+
+
def test_pdb_model_rotor(self):
"""Check the PDB file created by the frame_order.pdb_model user
function for the rotor model."""
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