Author: bugman
Date: Fri Nov 21 09:41:51 2014
New Revision: 26678
URL: http://svn.gna.org/viewcvs/relax?rev=26678&view=rev
Log:
Created the Frame_order.test_pdb_model_rotor2 system test to check for an
offset pivot.
The pivot is set to [1, 0, 1] so that the rotor axis is tilted -45 degrees in
the xz-plane. And the
size of the geometric object is set to 100 Angstrom for better testing of the
sizes of the elements.
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=26678&r1=26677&r2=26678&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 09:41:51 2014
@@ -20,7 +20,7 @@
###############################################################################
# Python module imports.
-from math import pi
+from math import pi, sqrt
import platform
import numpy
from numpy import array, float64, transpose
@@ -1686,6 +1686,88 @@
index += 1
+ def test_pdb_model_rotor2(self):
+ """Check the PDB file created by the frame_order.pdb_model user
function for the rotor model with an offset pivot."""
+
+ # 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('rotor')
+
+ # The axis alpha parameter, and printout.
+ axis_alpha = pi / 2.0
+ axis = create_rotor_axis_alpha(pi/2, array([1, 0, 1], float64),
array([0, 0, 0], float64))
+ print("\nRotor axis:\n %s" % axis)
+ print("Rotor apex (100*axis + [1, 0, 1]):\n %s" % (100.0*axis +
[1.0, 0.0, 1.0]))
+
+ # 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_alpha', val=axis_alpha)
+ self.interpreter.value.set(param='cone_sigma_max', val=0.0)
+
+ # Set the pivot.
+ self.interpreter.frame_order.pivot(pivot=[1, 0, 1], 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.
+ l = 100.0
+ proj = sqrt(0.5*l**2)
+ proj2 = sqrt(0.5*(l-2.0)**2)
+ proj3 = sqrt(0.5*(l+2.0)**2)
+ data = [
+ [ 1, 'PIV', 1, 'Piv', [ 1.0, 0.0, 1.0]],
+ [ 1, 'RTX', 2, 'CTR', [ 1.0, 0.0, 1.0]],
+ [ 2, 'RTX', 3, 'PRP', [-proj+1.0, 0.0, proj+1.0]],
+ [ 3, 'RTX', 4, 'PRP', [ proj+1.0, 0.0, -proj+1.0]],
+ [ 4, 'RTB', 5, 'BLO', [-proj+1.0, 0.0, proj+1.0]],
+ [ 5, 'RTB', 187, 'BLO', [-proj2+1.0, 0.0, proj2+1.0]],
+ [ 6, 'RTB', 369, 'BLO', [-proj+1.0, 0.0, proj+1.0]],
+ [ 7, 'RTB', 551, 'BLO', [-proj2+1.0, 0.0, proj2+1.0]],
+ [ 8, 'RTB', 733, 'BLO', [ proj+1.0, 0.0, -proj+1.0]],
+ [ 9, 'RTB', 915, 'BLO', [ proj2+1.0, 0.0, -proj2+1.0]],
+ [10, 'RTB', 1097, 'BLO', [ proj+1.0, 0.0, -proj+1.0]],
+ [11, 'RTB', 1279, 'BLO', [ proj2+1.0, 0.0, -proj2+1.0]],
+ [12, 'RTL', 1461, 'z-ax', [-proj3+1.0, 0.0, proj3+1.0]],
+ [12, 'RTL', 1462, 'z-ax', [ proj3+1.0, 0.0, -proj3+1.0]]
+ ]
+
+ # 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 (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.assertAlmostEqual(data[index][0], res_num, 3)
+ self.assertAlmostEqual(data[index][1], res_name, 3)
+ self.assertAlmostEqual(data[index][2], atom_num, 3)
+ self.assertAlmostEqual(data[index][3], atom_name, 3)
+ 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_pseudo_ellipse_zero_cone_angle(self):
"""Catch for a bug in optimisation when the cone_theta_x is set to
zero in the pseudo-ellipse models."""
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